Difference: CemComputerAdmin (1 vs. 25)

Revision 2507 Dec 2016 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
- DONE 04-27-11

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

April 20 2011
- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

April 21 2011
- Checked Tecnai F20 computer (Win 2000)
  - 19 GB used out of 34 GB
  - deleted ~3 GB of images from old tests
  - deleted empty folders for several users who are no longer here
  - deleted serialem links for users who are no longer here
  - shortcut to feispy and teispy found in trash; restored to desktop
  - Current disk usage =~ 16 GB, just under 50% capacity
  - TODO -- install internal drive temporarily for backup. Do on maintenance day

April 27 2011
- updated hostname of cem100 to athena
- remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
- ensured that hosts file is updated
- updated hosts file on jeol1230 computer -- cem100 is now athena
- updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
- todo -- fix mounting of cem100 as athena on j1230 -- ckim is using

May 2011

May 24 2011
- updated imod on /cryoem to IMOD 4.1.10
- installed SerialEM 3 on Tecnai F20

May 26 2011
testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work
- divctf-working-2006 (ELF class 64 shared library)
- hlxavg (ELF class 64 shared library)
- hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
- maskparam (ELF class 64 shared library)
- plotphase (ELF class 64 shared library)

July 2011

update priam to CENTOS5
- repalced root drive with 500GB drive
- root partition 100GB
- hector partition 350 GB
- memory upgraded to 12GB
- new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
Zeiss Windows 2000PC -- removed Norton antivirus
- disk nearly 100% full -- this saved 1 GB of space
- computer is isolated from web, so viruses should not be a problem

August 2011

Aug 17-19 --
update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
now uses BeautifulSoup^? to do most searching
- need to update twiki script to do the same
Aug 24 -- set up backup server tartarus:
- running CENTOS 6
- partitioned backup partiton 23.9 TB (RAID5) with GPT (parted)
  - "mkpart ext4 1 -1" --> makes a single partiton using all of disk space, named it ext4
- xfs format (ext4 currently has 16TB maximum size)
- mount as /pithos/
- installed rdiff-backup:
  - needed to enable rpmforge repository
  - installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  - no repository for rdiff backup: installation required manually installing
    - pylibacl-0.5.0-1.el6.x86_64.rpm
    - pyxattr-0.5.0-1.el6.x86_64.rpm
    - gcc using yum
    - python-devel using yum
    - librsync-devel using yum
    - then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
    - installed in /usr/local/

Aug 23
- installed gromus on agamemnon
  - required installation of fftw3 libraries in /usr/local

December 2011

Agamemnon: menelaus drive moved from /dev/sda5 to /cem03_bigdata_backup
- menelaus now has lots of space, and root partition can be expanded to take over all of /dev/sda
Nicolas, Mariena,Ralph PC's are backed up to /hector

January 2012

Jan 3
- New PC set up: rhea (one of the old Win2000 Dell PC's)
- purpose is to
  1. act as a spare workstation
  2. drive added - hades, which is exported onto windows drives using samba.
  3. EM users who want to copy onto USB flash disks the same day can do safely so via this PC
Jan 16
- Priam: mounted former /cemo2_bigdatabackup as /paris (1.4 TB drive)
- /paris exported and mounted on eurydice, agamemnon, minotaur,cem11
- /paris set up to be backed up daily on tartarus
- Agamemnon : root partiton resized to 230 GB, from 30
  - root was very full (2Gb free), so expanded ino space formerly used by menelaus

March 2012

March 14
- Set up Ed's PC - Centos5
- install php mrc tools:
  - copied source from cronus (/usr/include/php/ext/mrc) and unzipped in identical location
  - downloaded FFTW2 library source (NOT FFTW3 as is mention in docs) and installed:

      ./configure --enable-float --enable-type-prefix --enable-shared
      make
      make install

- - libs were put in /usr/local/lib, however, they are 64-bit libraries so made links in /usr/local/lib64/
  - compiled without error however fft power spectrum was invisible

November 2012

Setting up new Hp 620z workstation

system
- two six-core Xeon processors (12 cores total)
- 32 GB RAM (4* 8 GB; system came with 6*2 GB but this is incompatible; there are 8 slots still free for a max of 96 GB RAM)
- 500 GB HD with Windows 7-64 pro installed; 3 extra disks Western Digital 2GB Black 7200rpm
- NVidia Quadro 2000 GPU (192 CUDA cores)
hardware setup
- Installed RAM and GPU; boots windows
- only 2 bays left for the 3 drives; need to convert one 5.25" bay to 3.5"; adapter on order (Nov 20)
- Attempted to install all RAM simultaneously -- no boot. Removing origina RAM allowed boot.
linux install
- Choosing CentOS^? 6.3 as a modern system
- system could not boot from DVD: has EFI instead of old-style BIOS
- therefore had to choose install from Centos6.3-64 EFI minimal CD

linux install details

minimal is truly minimal: no graphics, no make, almost nothing but a shell
set up networking to work according to http://www.convirture.com/ee_wiki/index.php?title=RedHat_6_Networking
- plug in ethernet to bottom port (with sticker) -- this is eth0
- /etc/sysconfig/network-scripts/ifcfg-eth0

       DEVICE="eth0"
      HWADDR=specifc mac address
      NM_CONTROLLED="no"
      ONBOOT="yes"
      BOOTPROTO="static"
      IPADDR=ip address here.
      NETMASK=netmask here.

- /etc/sysconfig/network and /etc/resolv.conf left unchanged (resol.conf was a 0 length file)
- restart network

      /etc/init.d/network restart

install some packages
- yum install kdebase.x86_64 -- get some graphics at least
- yum install firefox -- get a browser
- yum install xorg-x11-server-xorg.X86_64 - - get startx to work
- yum install xorg-x11-xinit-session-1.09-13.el6.x86-64 --
- sudo nano vim wget system-config-network-tui kernel-headers make gcc ntp tcsh emacs kernel-devel
- install Nvidia driver NVIDIA-Linux-x86_64-310.19.run
  - problem: complains about Nouveau kernel driver. Alllowed it to disable this.
  - to undo this, need to delete /etd/modprobe.d/nvidia-installer-disable-nouveu.conf
  - reboot and try again
  - still enabled!
  - yum update -y
  - edit /boot/efi/EFI/redhat/grub.conf anmd append rdblacklist=nouveau to kernal boot command to disable
  - reboot. /sbin/lsmod | grep nouveau indicates that it was not loaded
  - install NVIDIA module and run startx. success!
  - edit /sbin/inittab to make level 5 the default boot
    - konsole terminal seems messed up a bit
  - yum groupinstall "Graphical Administration Tools" -- gui to admin tasks
  - now can use gpk-application to install required software

desktop details

switchdesk, used to switch between gnome, kde, and others is no longer available
attempts to make this available by making /etc/sysconfig/desktop did not work
in home directory, make the file ~/.dmrc as follows:


[Desktop]
Session=kde
Language=en_US.utf8

needed to install 32-bit libraries to get web to work:
- libXmu-1.0.5-1.el6.i686
- libXt-1.0.7-1.el6.i686
- libXtst-1.0.99.2-3.el6.i686
- libXp-1.0.0-15.1.el6.i686

November 26 2012

yum update -y on orpheus, installed latest Nvidia driver, and rebooted

January 2 2013

Setup Styx /computer for storage

Put together Intel Core i3 CPU + motherboard + 8 GB RAM + 450W power supply
- Motherboard: ASUS P8H61-MLE/CSM
- RAM: 2x 4GB
Install one boot drive: 500 GB from Kakoli's old RAID system
Install 5X 2TB drives for storage (configure as RAID5; see below)
No CD/DVD/floppy

details of system install

Install CENTOS 6.3 Minimal from external USB DVD drive
network configured manually as described above
yum update -y
reboot
install other essential packages as detailed above

preparation of hades RAID5 disk

hades: RAID 5 using 5x 2 TB Western Digital drives
instructions on making these drives a RAID (hdb,hdc,hdd,hde,hdf)

   > sudo mdadm --create /dev/md0 --level=5 --raid-devices=5 /dev/sd[bcdef]1
   > watch cat /proc/mdstat  (wait until done, about 450 minutes)

mdadm.conf file:

DEVICE /dev/sdf1 /dev/sde1 /dev/sdd1 /dev/sdc1 /dev/sdb1
ARRAY /dev/md0 level=raid5 num-devices=5 metadata=1.2 name=styx.nysbc.org:0 UUID=2d2b02fa:a1970439:77152d3a:7d64280e
   devices=/dev/sdb1,/dev/sdc1,/dev/sdd1,/dev/sde1,/dev/sdf1
MAILADDR rice@nysbc.org

set up monitoring:

   > sudo chkconfig mdmonitor on

make a logical volume, format it and mount it

   > sudo pvcreate /dev/md0     -- creates a physical volume
   > sudo vgvreate HADES /dev/md0   -- creates a volume group on that physical volume
   > sudo lvcreate -L 7.27T -n hades HADES  -- creates a logical volume in that volume group
   > sudo mkfs.ext4 /dev/HADES/hades   -- makes the filesystem on the logical volume
   > sudo mkdir /hades
   > sudo mount /dev/HADES/hades /hades

nfs configured to export /hades

Setup new workstation fir rice Dec 2014

* Configuration:

- AMD FX-6350 six core processor
- 16 GB RAM
- 650 W power supply
- ATI graphics card
- Crucial MX100 512 GB SSD for OS
- 4X 3 TB WD Red drives for storage
- originally bought as dataserver; found performacs = 2X that of current CEM11 (Fabiana's old workstation)
- Will repurpose cem11 as data server (with Nvidia card) and use new system as my desktop
- keep paris,cem11data in cem11 computer, keep runnina as headless server
- to do later: upgrade to CentOS^? 6

Standard Linux Mint 17.1 install with cinnamon
set up 3 TB drives as RAID 1 0
- format using parted:

   > sudo parted /dev/sdb
   > mklabel gpt
   > mkpart primary ext4 0% 100%
   > quit

repat for /dev/sdc,/dev/sdd/, /dev/sde

Install Linux Mint 17.1 onto 512 GB SDD
Netowrking not working -- ifcofig seems ok but ping does not work
after MUCH strugging, solution was
- go to BIOS
- enable IOMMU
- restart
- edit /etc/default grub: change empty quotes in line to:

GRUB_CMDLINE_LINUX="iommu=soft"

- then run

   sudo update-grub

Now networking, USB2 and USB3 all work

install new drive : 2 TB spare drive
this renumbered disks:
boot is /dev/sdc
spare is /dev/sdb

make RAID on sda,sdd,sde,sdf
re-format sda1,sdd1,sde1,sdf1 as ext4
sudp apt-get install mdadm

 sudo mdadm -v --create /dev/md0 --level=raid10 --raid-devices=4 /dev/sda1 /dev/sdd1 /dev/sde1 /dev/sdf1
mdadm: layout defaults to n2
mdadm: layout defaults to n2
mdadm: chunk size defaults to 512K
mdadm: /dev/sda1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sdd1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sde1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sdf1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: size set to 2930133504K
Continue creating array? y
mdadm: Defaulting to version 1.2 metadata
mdadm: array /dev/md0 started.

Format as follows:

sudo pvcreate /dev/md0
sudo vgcreate PARKING /dev/md0
sudo lvcreate -l100%FREE -n parking PARKING
sudo mkfs.ext4 /dev/PARKING/parking
sudo mkdir /parking
sudo mount /dev/PARKING/parking /parking

mounted OK
for debian-type, need to manually edit mdadm.conf as follows (as root)

 mdadm --examine --scan --config=mdadm.conf >> /etc/mdadm/mdadm.conf

NOTE
tried flag "amd_iommu=on" : USB2 and ethernet still work but no USB3
left as iommu=soft

Failing Disk on hades April 13 2015

April 11: /var/log/messages showed that /dev/sdd1 was failing
error was as follows:

Apr 11 00:23:38 styx smartd[2136]: Device: /dev/sdd [SAT], 3 Currently unreadable (pending) sectors 
Apr 11 00:53:38 styx smartd[2136]: Device: /dev/sdd [SAT], 3 Currently unreadable (pending) sectors
Apr 11 01:23:39 styx smartd[2136]: Device: /dev/sdd [SAT], 3 Currently unreadable (pending) sectors 
...

errors indicate that this disk is failing, but not yet dead
Replace with new 2 TB disk as follows:

Replacement of failing disk in RAID 5 array

Step 1: Identify which disk it is
Each disk is labelled with a serial number on the front

Get serial number in linux to figure out which is which:

[rice@styx ~]$ sudo hdparm -i /dev/sda | grep Serial
 Model=WDC, FwRev=02.03B03, SerialNo=WD-WCASY7050076
[rice@styx ~]$ sudo hdparm -i /dev/sdb | grep Serial
 Model=WDC, FwRev=05.01D05, SerialNo=WD-WMAWP0561880
[rice@styx ~]$ sudo hdparm -i /dev/sdc | grep Serial
 Model=WDC, FwRev=80.00A80, SerialNo=WD-WMC1T0928093
[rice@styx ~]$ sudo hdparm -i /dev/sdd | grep Serial
 Model=WDC, FwRev=80.00A80, SerialNo=WD-WMC1T1328932
[rice@styx ~]$ sudo hdparm -i /dev/sde | grep Serial
 Model=WDC, FwRev=80.00A80, SerialNo=WD-WMC1T0906133

Therefore replace disk with serial number WMC1T1328932

Step 2: remove failing disk from array
- first unmount from exported computers
following commands label disk as failed then remove it from array

  499  sudo mdadm --manage /dev/md0 --fail /dev/sdd1
  500  sudo mdadm --manage /dev/md0 --remove /dev/sdd1

- Note: Get email from system that diks has failed:

This is an automatically generated mail message from mdadm
running on styx.nysbc.org

A DegradedArray event had been detected on md device /dev/md0.

Faithfully yours, etc.

P.S. The /proc/mdstat file currently contains the following:

Personalities : [raid6] [raid5] [raid4]
md0 : active raid5 sdc1[6] sdf1[5] sdb1[0] sde1[3]
     7814047744 blocks super 1.2 level 5, 512k chunk, algorithm 2 [5/4] [UU_UU]

Step 3: Shut dwon computer and physically replace the disk
Step 4: Boot up
Step 5: add replaced disk to array and rebuild

    sudo mdadm --manage /dev/md0 --add /dev/sdd1

Step 6: Array rebuilds automatically -- 12h
to watch:

   cat /proc/mdstat

New IP addresses for orpheus and zeus

computers moved to control room may 19 2015
zeus: 192.168.4.202
orpheus: 192.168.4.201

Added:

>
>

Dec 6 2016: Zeus reformatted

Carl Negro installed CENTOS6.7 on 500 GB drive on zeus (formerly Win7 Pro, and unused)
system set up with LDAP, etc so it is part of the new system
hera disks not yet mounted, but backed up on tartarus and on external drive
perhaps set these up as RAID1 local array, or even RAID0 fast local scratch
installed NVIDIA Quadro card will work for frame alignment, GCTF once NVIDIA drivers and CUDA are installed

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Revision 2420 May 2015 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
- DONE 04-27-11

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

April 20 2011
- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

April 21 2011
- Checked Tecnai F20 computer (Win 2000)
  - 19 GB used out of 34 GB
  - deleted ~3 GB of images from old tests
  - deleted empty folders for several users who are no longer here
  - deleted serialem links for users who are no longer here
  - shortcut to feispy and teispy found in trash; restored to desktop
  - Current disk usage =~ 16 GB, just under 50% capacity
  - TODO -- install internal drive temporarily for backup. Do on maintenance day

April 27 2011
- updated hostname of cem100 to athena
- remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
- ensured that hosts file is updated
- updated hosts file on jeol1230 computer -- cem100 is now athena
- updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
- todo -- fix mounting of cem100 as athena on j1230 -- ckim is using

May 2011

May 24 2011
- updated imod on /cryoem to IMOD 4.1.10
- installed SerialEM 3 on Tecnai F20

May 26 2011
testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work
- divctf-working-2006 (ELF class 64 shared library)
- hlxavg (ELF class 64 shared library)
- hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
- maskparam (ELF class 64 shared library)
- plotphase (ELF class 64 shared library)

July 2011

update priam to CENTOS5
- repalced root drive with 500GB drive
- root partition 100GB
- hector partition 350 GB
- memory upgraded to 12GB
- new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
Zeiss Windows 2000PC -- removed Norton antivirus
- disk nearly 100% full -- this saved 1 GB of space
- computer is isolated from web, so viruses should not be a problem

August 2011

Aug 17-19 --
update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
now uses BeautifulSoup^? to do most searching
- need to update twiki script to do the same
Aug 24 -- set up backup server tartarus:
- running CENTOS 6
- partitioned backup partiton 23.9 TB (RAID5) with GPT (parted)
  - "mkpart ext4 1 -1" --> makes a single partiton using all of disk space, named it ext4
- xfs format (ext4 currently has 16TB maximum size)
- mount as /pithos/
- installed rdiff-backup:
  - needed to enable rpmforge repository
  - installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  - no repository for rdiff backup: installation required manually installing
    - pylibacl-0.5.0-1.el6.x86_64.rpm
    - pyxattr-0.5.0-1.el6.x86_64.rpm
    - gcc using yum
    - python-devel using yum
    - librsync-devel using yum
    - then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
    - installed in /usr/local/

Aug 23
- installed gromus on agamemnon
  - required installation of fftw3 libraries in /usr/local

December 2011

Agamemnon: menelaus drive moved from /dev/sda5 to /cem03_bigdata_backup
- menelaus now has lots of space, and root partition can be expanded to take over all of /dev/sda
Nicolas, Mariena,Ralph PC's are backed up to /hector

January 2012

Jan 3
- New PC set up: rhea (one of the old Win2000 Dell PC's)
- purpose is to
  1. act as a spare workstation
  2. drive added - hades, which is exported onto windows drives using samba.
  3. EM users who want to copy onto USB flash disks the same day can do safely so via this PC
Jan 16
- Priam: mounted former /cemo2_bigdatabackup as /paris (1.4 TB drive)
- /paris exported and mounted on eurydice, agamemnon, minotaur,cem11
- /paris set up to be backed up daily on tartarus
- Agamemnon : root partiton resized to 230 GB, from 30
  - root was very full (2Gb free), so expanded ino space formerly used by menelaus

March 2012

March 14
- Set up Ed's PC - Centos5
- install php mrc tools:
  - copied source from cronus (/usr/include/php/ext/mrc) and unzipped in identical location
  - downloaded FFTW2 library source (NOT FFTW3 as is mention in docs) and installed:

      ./configure --enable-float --enable-type-prefix --enable-shared
      make
      make install

- - libs were put in /usr/local/lib, however, they are 64-bit libraries so made links in /usr/local/lib64/
  - compiled without error however fft power spectrum was invisible

November 2012

Setting up new Hp 620z workstation

system
- two six-core Xeon processors (12 cores total)
- 32 GB RAM (4* 8 GB; system came with 6*2 GB but this is incompatible; there are 8 slots still free for a max of 96 GB RAM)
- 500 GB HD with Windows 7-64 pro installed; 3 extra disks Western Digital 2GB Black 7200rpm
- NVidia Quadro 2000 GPU (192 CUDA cores)
hardware setup
- Installed RAM and GPU; boots windows
- only 2 bays left for the 3 drives; need to convert one 5.25" bay to 3.5"; adapter on order (Nov 20)
- Attempted to install all RAM simultaneously -- no boot. Removing origina RAM allowed boot.
linux install
- Choosing CentOS^? 6.3 as a modern system
- system could not boot from DVD: has EFI instead of old-style BIOS
- therefore had to choose install from Centos6.3-64 EFI minimal CD

linux install details

minimal is truly minimal: no graphics, no make, almost nothing but a shell
set up networking to work according to http://www.convirture.com/ee_wiki/index.php?title=RedHat_6_Networking
- plug in ethernet to bottom port (with sticker) -- this is eth0
- /etc/sysconfig/network-scripts/ifcfg-eth0

       DEVICE="eth0"
      HWADDR=specifc mac address
      NM_CONTROLLED="no"
      ONBOOT="yes"
      BOOTPROTO="static"
      IPADDR=ip address here.
      NETMASK=netmask here.

- /etc/sysconfig/network and /etc/resolv.conf left unchanged (resol.conf was a 0 length file)
- restart network

      /etc/init.d/network restart

install some packages
- yum install kdebase.x86_64 -- get some graphics at least
- yum install firefox -- get a browser
- yum install xorg-x11-server-xorg.X86_64 - - get startx to work
- yum install xorg-x11-xinit-session-1.09-13.el6.x86-64 --
- sudo nano vim wget system-config-network-tui kernel-headers make gcc ntp tcsh emacs kernel-devel
- install Nvidia driver NVIDIA-Linux-x86_64-310.19.run
  - problem: complains about Nouveau kernel driver. Alllowed it to disable this.
  - to undo this, need to delete /etd/modprobe.d/nvidia-installer-disable-nouveu.conf
  - reboot and try again
  - still enabled!
  - yum update -y
  - edit /boot/efi/EFI/redhat/grub.conf anmd append rdblacklist=nouveau to kernal boot command to disable
  - reboot. /sbin/lsmod | grep nouveau indicates that it was not loaded
  - install NVIDIA module and run startx. success!
  - edit /sbin/inittab to make level 5 the default boot
    - konsole terminal seems messed up a bit
  - yum groupinstall "Graphical Administration Tools" -- gui to admin tasks
  - now can use gpk-application to install required software

desktop details

switchdesk, used to switch between gnome, kde, and others is no longer available
attempts to make this available by making /etc/sysconfig/desktop did not work
in home directory, make the file ~/.dmrc as follows:


[Desktop]
Session=kde
Language=en_US.utf8

needed to install 32-bit libraries to get web to work:
- libXmu-1.0.5-1.el6.i686
- libXt-1.0.7-1.el6.i686
- libXtst-1.0.99.2-3.el6.i686
- libXp-1.0.0-15.1.el6.i686

November 26 2012

yum update -y on orpheus, installed latest Nvidia driver, and rebooted

January 2 2013

Setup Styx /computer for storage

Put together Intel Core i3 CPU + motherboard + 8 GB RAM + 450W power supply
- Motherboard: ASUS P8H61-MLE/CSM
- RAM: 2x 4GB
Install one boot drive: 500 GB from Kakoli's old RAID system
Install 5X 2TB drives for storage (configure as RAID5; see below)
No CD/DVD/floppy

details of system install

Install CENTOS 6.3 Minimal from external USB DVD drive
network configured manually as described above
yum update -y
reboot
install other essential packages as detailed above

preparation of hades RAID5 disk

hades: RAID 5 using 5x 2 TB Western Digital drives
instructions on making these drives a RAID (hdb,hdc,hdd,hde,hdf)

   > sudo mdadm --create /dev/md0 --level=5 --raid-devices=5 /dev/sd[bcdef]1
   > watch cat /proc/mdstat  (wait until done, about 450 minutes)

mdadm.conf file:

DEVICE /dev/sdf1 /dev/sde1 /dev/sdd1 /dev/sdc1 /dev/sdb1
ARRAY /dev/md0 level=raid5 num-devices=5 metadata=1.2 name=styx.nysbc.org:0 UUID=2d2b02fa:a1970439:77152d3a:7d64280e
   devices=/dev/sdb1,/dev/sdc1,/dev/sdd1,/dev/sde1,/dev/sdf1
MAILADDR rice@nysbc.org

set up monitoring:

   > sudo chkconfig mdmonitor on

make a logical volume, format it and mount it

   > sudo pvcreate /dev/md0     -- creates a physical volume
   > sudo vgvreate HADES /dev/md0   -- creates a volume group on that physical volume
   > sudo lvcreate -L 7.27T -n hades HADES  -- creates a logical volume in that volume group
   > sudo mkfs.ext4 /dev/HADES/hades   -- makes the filesystem on the logical volume
   > sudo mkdir /hades
   > sudo mount /dev/HADES/hades /hades

nfs configured to export /hades

Setup new workstation fir rice Dec 2014

* Configuration:

- AMD FX-6350 six core processor
- 16 GB RAM
- 650 W power supply
- ATI graphics card
- Crucial MX100 512 GB SSD for OS
- 4X 3 TB WD Red drives for storage
- originally bought as dataserver; found performacs = 2X that of current CEM11 (Fabiana's old workstation)
- Will repurpose cem11 as data server (with Nvidia card) and use new system as my desktop
- keep paris,cem11data in cem11 computer, keep runnina as headless server
- to do later: upgrade to CentOS^? 6

Standard Linux Mint 17.1 install with cinnamon
set up 3 TB drives as RAID 1 0
- format using parted:

   > sudo parted /dev/sdb
   > mklabel gpt
   > mkpart primary ext4 0% 100%
   > quit

repat for /dev/sdc,/dev/sdd/, /dev/sde

Install Linux Mint 17.1 onto 512 GB SDD
Netowrking not working -- ifcofig seems ok but ping does not work
after MUCH strugging, solution was
- go to BIOS
- enable IOMMU
- restart
- edit /etc/default grub: change empty quotes in line to:

GRUB_CMDLINE_LINUX="iommu=soft"

- then run

   sudo update-grub

Now networking, USB2 and USB3 all work

install new drive : 2 TB spare drive
this renumbered disks:
boot is /dev/sdc
spare is /dev/sdb

make RAID on sda,sdd,sde,sdf
re-format sda1,sdd1,sde1,sdf1 as ext4
sudp apt-get install mdadm

 sudo mdadm -v --create /dev/md0 --level=raid10 --raid-devices=4 /dev/sda1 /dev/sdd1 /dev/sde1 /dev/sdf1
mdadm: layout defaults to n2
mdadm: layout defaults to n2
mdadm: chunk size defaults to 512K
mdadm: /dev/sda1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sdd1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sde1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sdf1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: size set to 2930133504K
Continue creating array? y
mdadm: Defaulting to version 1.2 metadata
mdadm: array /dev/md0 started.

Format as follows:

sudo pvcreate /dev/md0
sudo vgcreate PARKING /dev/md0
sudo lvcreate -l100%FREE -n parking PARKING
sudo mkfs.ext4 /dev/PARKING/parking
sudo mkdir /parking
sudo mount /dev/PARKING/parking /parking

mounted OK
for debian-type, need to manually edit mdadm.conf as follows (as root)

 mdadm --examine --scan --config=mdadm.conf >> /etc/mdadm/mdadm.conf

NOTE
tried flag "amd_iommu=on" : USB2 and ethernet still work but no USB3
left as iommu=soft

Failing Disk on hades April 13 2015

April 11: /var/log/messages showed that /dev/sdd1 was failing
error was as follows:

Apr 11 00:23:38 styx smartd[2136]: Device: /dev/sdd [SAT], 3 Currently unreadable (pending) sectors 
Apr 11 00:53:38 styx smartd[2136]: Device: /dev/sdd [SAT], 3 Currently unreadable (pending) sectors
Apr 11 01:23:39 styx smartd[2136]: Device: /dev/sdd [SAT], 3 Currently unreadable (pending) sectors 
...

errors indicate that this disk is failing, but not yet dead
Replace with new 2 TB disk as follows:

Replacement of failing disk in RAID 5 array

Step 1: Identify which disk it is
Each disk is labelled with a serial number on the front

Get serial number in linux to figure out which is which:

[rice@styx ~]$ sudo hdparm -i /dev/sda | grep Serial
 Model=WDC, FwRev=02.03B03, SerialNo=WD-WCASY7050076
[rice@styx ~]$ sudo hdparm -i /dev/sdb | grep Serial
 Model=WDC, FwRev=05.01D05, SerialNo=WD-WMAWP0561880
[rice@styx ~]$ sudo hdparm -i /dev/sdc | grep Serial
 Model=WDC, FwRev=80.00A80, SerialNo=WD-WMC1T0928093
[rice@styx ~]$ sudo hdparm -i /dev/sdd | grep Serial
 Model=WDC, FwRev=80.00A80, SerialNo=WD-WMC1T1328932
[rice@styx ~]$ sudo hdparm -i /dev/sde | grep Serial
 Model=WDC, FwRev=80.00A80, SerialNo=WD-WMC1T0906133

Therefore replace disk with serial number WMC1T1328932

Step 2: remove failing disk from array
- first unmount from exported computers
following commands label disk as failed then remove it from array

  499  sudo mdadm --manage /dev/md0 --fail /dev/sdd1
  500  sudo mdadm --manage /dev/md0 --remove /dev/sdd1

- Note: Get email from system that diks has failed:

This is an automatically generated mail message from mdadm
running on styx.nysbc.org

A DegradedArray event had been detected on md device /dev/md0.

Faithfully yours, etc.

P.S. The /proc/mdstat file currently contains the following:

Personalities : [raid6] [raid5] [raid4]
md0 : active raid5 sdc1[6] sdf1[5] sdb1[0] sde1[3]
     7814047744 blocks super 1.2 level 5, 512k chunk, algorithm 2 [5/4] [UU_UU]

Step 3: Shut dwon computer and physically replace the disk
Step 4: Boot up
Step 5: add replaced disk to array and rebuild

    sudo mdadm --manage /dev/md0 --add /dev/sdd1

Step 6: Array rebuilds automatically -- 12h
to watch:

   cat /proc/mdstat

Added:

>
>

New IP addresses for orpheus and zeus

computers moved to control room may 19 2015
zeus: 192.168.4.202
orpheus: 192.168.4.201

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Revision 2313 Apr 2015 - Main.BillRice

   META TOPICPARENT   name="CemITSystem" 

Contents
 
 Administration logs 
  Jan 2011
   April 2011
   May 2011 
  July 2011
  August 2011
   December 2011
   January 2012
   March 2012
  November 2012 
 Setting up new Hp 620z workstation
   linux install details
   desktop details
 
 
   November 26 2012
   January 2 2013 
  Setup Styx /computer for storage 
  details of system install
   preparation of hades RAID5 disk
 
 
   Setup new workstation fir rice Dec 2014
 
 


 Administration logs 

 Jan 2011 
 
 Set up and installed new computer, cem15
  CentOS^? 5.5, RAID5, 5.2 TB disk
  All standard EM software installed
  cem15data drive is nfs shared and exported 
  users added on ad hoc basis
 

 April 2011 
 
 April 7 2011 
 back up svn server from cem100 and move to cem01
  cem01 now running svn server (current revision=48) and apache server
  made very basic web page for cem01 which links to svn repos as well as sesame
 
 
 

 April 8 2011 -- rename computers as follows 
 cem15 --> orpheus
  cem01 -->cronus
  cem02 --> priam
  cem03 --> agamemnon
  cem11 --> tlaloc
  cem12 --> minotaur
 
  made new hosts file listing these changes, and uploaded to svn server
 
 

 TO DO 
 rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
  DONE 04-27-11
 
 
 

 April 10 2011 
 copy all of Kens' data from Tecnai to external hard drive
  delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps
 
 
 

 April 11 2011 -- rename drives as follows: 
 cem02bigdata --> helen
  cem02data --> hector
  cem02data2 --> hecuba
  cem03bigdata --> achilles
  cem03data --> menelaus
  cem03data2 --> iphigenia
  cem11data --> tonatiu
  cem12data --> theseus
  cem15data --> eurydice
 
  exported and mounted all newly named drives
  updated hosts file on jeol1230 pc to reflect these changes
  change backup scripts to reflect these changes
  found problem with leginon not talking to jerol1230 from minotaur (cem12) after change 
 fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
  verified that leginon is still working directly on jeol1230 and remotely from minotaur
 
 
 

 links made to old drive names
  cronus (cem01) now viewable from outside as cronus.nysbc.org 
 verified by browsing cronus.nysbc.org from public network
 
  TO DO 
 rename dl380 to arachne, and make link
  finish renaming, after backup server installed and running 
 rename cem02bigdata_backup to paris
  rename cem03bigdata_backup to odysseus
  find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???
 
 
 
 

 April 20 2011 
 updated IMOD to IMOD 4.1.9 (current version) on /cryoem 
 /cryoem/IMOD now refers to this version
  /cryoem/IMOD3 referes to imod 3.13
  updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  note that priam (centos4) will likely not run this version 
 
 
 
 

 April 21 2011 
 Checked Tecnai F20 computer (Win 2000) 
 19 GB used out of 34 GB
  deleted ~3 GB of images from old tests
  deleted empty folders for several users who are no longer here
  deleted serialem links for users who are no longer here
  shortcut to feispy and teispy found in trash; restored to desktop
  Current disk usage =~ 16 GB, just under 50% capacity
  TODO -- install internal drive temporarily for backup. Do on maintenance day
 
 
 
 

 April 27 2011 
 updated hostname of cem100 to athena
  remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
  ensured that hosts file is updated
  updated hosts file on jeol1230 computer -- cem100 is now athena
  updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
  todo -- fix mounting of cem100 as athena on j1230 -- ckim is using
 
 

 May 2011 
 
 May 24 2011 
 updated imod on /cryoem to IMOD 4.1.10
  installed SerialEM 3 on Tecnai F20
 
 
 

 May 26 2011
  testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work 
 divctf-working-2006 (ELF class 64 shared library)
  hlxavg (ELF class 64 shared library)
  hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
  maskparam (ELF class 64 shared library)
  plotphase (ELF class 64 shared library)
 
 

 July 2011 
 
 update priam to CENTOS5 
 repalced root drive with 500GB drive
  root partition 100GB
  hector partition 350 GB
  memory upgraded to 12GB
  new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
 
  Zeiss Windows 2000PC -- removed Norton antivirus 
 disk nearly 100% full -- this saved 1 GB of space
  computer is isolated from web, so viruses should not be a problem
 
 

 August 2011 
 
 Aug 17-19 -- 
  update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
  now uses BeautifulSoup^? to do most searching 
 need to update  twiki script to do the same
 
  Aug 24 -- set up backup server tartarus: 
 running CENTOS 6
  partitioned backup partiton 23.9 TB (RAID5) with GPT (parted) 
 "mkpart ext4 1 -1"  --> makes a single partiton using all of disk space, named it ext4
 
  xfs format (ext4 currently has 16TB maximum size)
  mount as /pithos/
  installed rdiff-backup: 
 needed to enable rpmforge repository
  installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  no repository for rdiff backup: installation required manually installing  
 pylibacl-0.5.0-1.el6.x86_64.rpm
  pyxattr-0.5.0-1.el6.x86_64.rpm
  gcc using yum
  python-devel using yum
  librsync-devel using yum
  then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
  installed in /usr/local/
 
 
 
 
 

 Aug 23 
 installed gromus on agamemnon 
 required installation of fftw3 libraries in /usr/local
 
 
 

 December 2011 
 
 Agamemnon: menelaus drive moved from /dev/sda5 to /cem03_bigdata_backup 
 menelaus now has lots of space, and root partition can be expanded to take over all of /dev/sda  
 
  Nicolas, Mariena,Ralph PC's are backed up to /hector
 

 January 2012 
 
 Jan 3 
 New PC set up: rhea (one of the old Win2000 Dell PC's)
  purpose is to  
 act as a spare workstation
  drive added - hades, which is exported onto windows drives using samba. 
  EM users who want to copy onto USB flash disks the same day can do safely so via this PC 
 
 
  Jan 16 
 Priam: mounted former /cemo2_bigdatabackup as /paris (1.4 TB drive)
  /paris exported and mounted on eurydice, agamemnon, minotaur,cem11
  /paris set up to be backed up daily on tartarus
  Agamemnon : root partiton resized to 230 GB, from 30 
 root was very full (2Gb free), so expanded ino space formerly used by menelaus
 
 
 

 March 2012 
 
 March 14 
 Set up Ed's PC - Centos5
  install php mrc tools: 
 copied source from cronus (/usr/include/php/ext/mrc) and unzipped in identical location
  downloaded FFTW2 library source (NOT FFTW3 as is mention in docs) and installed:
 
 
 
      ./configure --enable-float --enable-type-prefix --enable-shared
      make
      make install
 
 
 
 
 
 libs were put in /usr/local/lib, however, they are 64-bit libraries so made links in /usr/local/lib64/
  compiled without error however fft power spectrum was invisible
 
 
 


 November 2012 
 Setting up new Hp 620z workstation 
 
 system  
 two six-core Xeon processors (12 cores total)
  32 GB RAM (4* 8 GB; system came with 6*2 GB but this is incompatible; there are 8 slots still free for a max of 96 GB RAM)
  500 GB HD with Windows 7-64 pro installed; 3 extra disks Western Digital 2GB Black 7200rpm
  NVidia Quadro 2000 GPU (192 CUDA cores)
 
  hardware setup 
 Installed RAM and GPU; boots windows
  only 2 bays left for the 3 drives; need to convert one 5.25" bay to 3.5"; adapter on order (Nov 20)
  Attempted to install all RAM simultaneously -- no boot. Removing origina RAM allowed boot.
 
  linux install 
 Choosing CentOS^? 6.3 as a modern system
  system could not boot from DVD: has EFI instead of old-style BIOS
  therefore had to choose install from Centos6.3-64 EFI minimal CD
 
 
 linux install details 
 
 minimal is truly minimal: no graphics, no make, almost nothing but a shell
  set up networking to work  according to http://www.convirture.com/ee_wiki/index.php?title=RedHat_6_Networking 
 plug in ethernet to bottom port (with sticker) -- this is eth0
  /etc/sysconfig/network-scripts/ifcfg-eth0
 
 
       DEVICE="eth0"
      HWADDR=specifc mac address
      NM_CONTROLLED="no"
      ONBOOT="yes"
      BOOTPROTO="static"
      IPADDR=ip address here.
      NETMASK=netmask here.
 
 
 
 /etc/sysconfig/network and /etc/resolv.conf left unchanged (resol.conf was a 0 length file) 
  restart network
 
 
      /etc/init.d/network restart
 
 install some packages 
 yum install kdebase.x86_64   -- get some graphics at least
  yum install firefox -- get a browser
  yum install xorg-x11-server-xorg.X86_64   - - get startx to work
  yum install xorg-x11-xinit-session-1.09-13.el6.x86-64  -- 
  sudo nano vim wget system-config-network-tui kernel-headers make gcc ntp tcsh emacs kernel-devel
  install Nvidia driver NVIDIA-Linux-x86_64-310.19.run 
 problem: complains about Nouveau kernel driver. Alllowed it to disable this. 
  to undo this, need to delete /etd/modprobe.d/nvidia-installer-disable-nouveu.conf
  reboot and try again
  still enabled!
  yum update -y
  edit /boot/efi/EFI/redhat/grub.conf anmd append rdblacklist=nouveau to kernal boot command to disable
  reboot. /sbin/lsmod | grep nouveau indicates that it was not loaded
  install NVIDIA module and run startx. success!
  edit /sbin/inittab to make level 5 the default boot 
 konsole terminal seems messed up a bit
 
  yum groupinstall "Graphical Administration Tools"  -- gui to admin tasks
  now can use gpk-application to install required software
 
 
 
 desktop details 
 
 switchdesk, used to switch between gnome, kde, and others is no longer available
  attempts to make this available by making /etc/sysconfig/desktop did not work
  in home directory, make the file ~/.dmrc as follows:
 

[Desktop]
Session=kde
Language=en_US.utf8

 

 needed to install 32-bit libraries to get web to work: 
 libXmu-1.0.5-1.el6.i686
  libXt-1.0.7-1.el6.i686
  libXtst-1.0.99.2-3.el6.i686
  libXp-1.0.0-15.1.el6.i686
 
 

 November 26 2012 
 
 yum update -y on orpheus, installed latest Nvidia driver, and rebooted
 

 January 2 2013 
 Setup Styx /computer for storage 
 
 Put together Intel Core i3 CPU + motherboard + 8 GB RAM + 450W power supply 
 Motherboard: ASUS P8H61-MLE/CSM
  RAM: 2x 4GB 
 
  Install one boot drive: 500 GB from Kakoli's old RAID system
  Install 5X 2TB drives for storage (configure as RAID5; see below)
  No CD/DVD/floppy
 
 details of system install 
 
 Install CENTOS 6.3 Minimal from external USB DVD drive
  network configured manually as described above
  yum update -y 
  reboot 
  install other essential packages as detailed above
 
 preparation of hades RAID5 disk 
 
 hades: RAID 5 using 5x 2 TB Western Digital drives
  instructions on making these drives a RAID (hdb,hdc,hdd,hde,hdf)
 
   > sudo mdadm --create /dev/md0 --level=5 --raid-devices=5 /dev/sd[bcdef]1
   > watch cat /proc/mdstat  (wait until done, about 450 minutes)
 
 mdadm.conf file:
 
DEVICE /dev/sdf1 /dev/sde1 /dev/sdd1 /dev/sdc1 /dev/sdb1
ARRAY /dev/md0 level=raid5 num-devices=5 metadata=1.2 name=styx.nysbc.org:0 UUID=2d2b02fa:a1970439:77152d3a:7d64280e
   devices=/dev/sdb1,/dev/sdc1,/dev/sdd1,/dev/sde1,/dev/sdf1
MAILADDR rice@nysbc.org
 
 set up monitoring:
 
   > sudo chkconfig mdmonitor on
 
 make a logical volume, format it and mount it
 
   > sudo pvcreate /dev/md0     -- creates a physical volume
   > sudo vgvreate HADES /dev/md0   -- creates a volume group on that physical volume
   > sudo lvcreate -L 7.27T -n hades HADES  -- creates a logical volume in that volume group
   > sudo mkfs.ext4 /dev/HADES/hades   -- makes the filesystem on the logical volume
   > sudo mkdir /hades
   > sudo mount /dev/HADES/hades /hades
 
 nfs configured to export /hades
 

 Setup new workstation fir rice Dec 2014 

    * Configuration:  

 
 
 AMD FX-6350 six core processor
  16 GB RAM
  650 W power supply
  ATI graphics card
  Crucial MX100 512 GB SSD for OS
  4X 3 TB WD Red drives for storage
  originally bought as dataserver; found performacs = 2X that of current CEM11 (Fabiana's old workstation)
  Will repurpose cem11 as data server (with Nvidia card) and use new system as  my desktop
  keep paris,cem11data in cem11 computer, keep runnina as headless server
  to do later: upgrade to CentOS^? 6
 
 
 

 Standard Linux Mint 17.1 install with cinnamon
  set up 3 TB drives as RAID 1 0  
 format using parted:
 
 
   > sudo parted /dev/sdb
   > mklabel gpt
   > mkpart primary ext4 0% 100%
   > quit
 
 repat for /dev/sdc,/dev/sdd/, /dev/sde
 
 

 Install Linux Mint 17.1 onto 512 GB SDD
  Netowrking not working -- ifcofig seems ok but ping does not work
  after MUCH strugging, solution was 
 go to BIOS
  enable IOMMU
  restart
  edit /etc/default grub: change empty quotes in line to:
 
 
GRUB_CMDLINE_LINUX="iommu=soft"
 
 
 
 then run
 
 
   sudo update-grub

 

 Now networking, USB2 and USB3 all work
 
 

 install new drive : 2 TB spare drive
  this renumbered disks:
  boot is /dev/sdc
  spare is /dev/sdb
 
 

 make RAID on sda,sdd,sde,sdf
  re-format sda1,sdd1,sde1,sdf1 as ext4
  sudp apt-get install mdadm
 
 sudo mdadm -v --create /dev/md0 --level=raid10 --raid-devices=4 /dev/sda1 /dev/sdd1 /dev/sde1 /dev/sdf1
mdadm: layout defaults to n2
mdadm: layout defaults to n2
mdadm: chunk size defaults to 512K
mdadm: /dev/sda1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sdd1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sde1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sdf1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: size set to 2930133504K
Continue creating array? y
mdadm: Defaulting to version 1.2 metadata
mdadm: array /dev/md0 started.
 
 Format as follows:
 
sudo pvcreate /dev/md0
sudo vgcreate PARKING /dev/md0
sudo lvcreate -l100%FREE -n parking PARKING
sudo mkfs.ext4 /dev/PARKING/parking
sudo mkdir /parking
sudo mount /dev/PARKING/parking /parking
 
 mounted OK
  for debian-type, need to manually edit mdadm.conf as follows (as root)
 
 mdadm --examine --scan --config=mdadm.conf >> /etc/mdadm/mdadm.conf

 

 NOTE
  tried flag "amd_iommu=on" : USB2 and ethernet still work but no USB3
  left as iommu=soft
-  META TOPICPARENT
+ name="CemITSystem"
-<
<
+ Failing Disk on hades
->
>
+ Failing Disk on hades  April 13 2015
->
>
+ April 11: /var/log/messages showed that /dev/sdd1 was failing
  error was as follows:
 
Apr 11 00:23:38 styx smartd[2136]: Device: /dev/sdd [SAT], 3 Currently unreadable (pending) sectors 
Apr 11 00:53:38 styx smartd[2136]: Device: /dev/sdd [SAT], 3 Currently unreadable (pending) sectors
Apr 11 01:23:39 styx smartd[2136]: Device: /dev/sdd [SAT], 3 Currently unreadable (pending) sectors 
...
 
 errors indicate that this disk is failing, but not yet dead
  Replace with new 2 TB disk as follows:
 
 Replacement of failing disk in RAID 5 array 
 
 Step 1: Identify which disk it is
  Each disk is labelled with a serial number on the front
  Get serial number in linux to figure out which is which:
  [rice@styx ~]$ sudo hdparm -i /dev/sda | grep Serial
 Model=WDC, FwRev=02.03B03, SerialNo=WD-WCASY7050076
[rice@styx ~]$ sudo hdparm -i /dev/sdb | grep Serial
 Model=WDC, FwRev=05.01D05, SerialNo=WD-WMAWP0561880
[rice@styx ~]$ sudo hdparm -i /dev/sdc | grep Serial
 Model=WDC, FwRev=80.00A80, SerialNo=WD-WMC1T0928093
[rice@styx ~]$ sudo hdparm -i /dev/sdd | grep Serial
 Model=WDC, FwRev=80.00A80, SerialNo=WD-WMC1T1328932
[rice@styx ~]$ sudo hdparm -i /dev/sde | grep Serial
 Model=WDC, FwRev=80.00A80, SerialNo=WD-WMC1T0906133
->
>
->
>
+ Therefore replace disk with serial number WMC1T1328932
 
 

 Step 2: remove failing disk from array 
 first unmount from exported computers
 
  following commands label disk as failed then remove it from array
 
  499  sudo mdadm --manage /dev/md0 --fail /dev/sdd1
  500  sudo mdadm --manage /dev/md0 --remove /dev/sdd1
->
>
+ Note: Get email from system that diks has failed:
 
 
This is an automatically generated mail message from mdadm
running on styx.nysbc.org

A DegradedArray event had been detected on md device /dev/md0.

Faithfully yours, etc.

P.S. The /proc/mdstat file currently contains the following:

Personalities : [raid6] [raid5] [raid4]
md0 : active raid5 sdc1[6] sdf1[5] sdb1[0] sde1[3]
     7814047744 blocks super 1.2 level 5, 512k chunk, algorithm 2 [5/4] [UU_UU] 

 

 Step 3: Shut dwon computer and physically replace the disk
  Step 4: Boot up
  Step 5: add replaced disk to array and rebuild
 
    sudo mdadm --manage /dev/md0 --add /dev/sdd1
 
 Step 6: Array rebuilds automatically -- 12h
  to watch:
 
   cat /proc/mdstat
  Set ALLOWTOPICVIEW = 
 

-- BillRice - 12 Apr 2011

Revision 2213 Apr 2015 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
- DONE 04-27-11

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

April 20 2011
- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

April 21 2011
- Checked Tecnai F20 computer (Win 2000)
  - 19 GB used out of 34 GB
  - deleted ~3 GB of images from old tests
  - deleted empty folders for several users who are no longer here
  - deleted serialem links for users who are no longer here
  - shortcut to feispy and teispy found in trash; restored to desktop
  - Current disk usage =~ 16 GB, just under 50% capacity
  - TODO -- install internal drive temporarily for backup. Do on maintenance day

April 27 2011
- updated hostname of cem100 to athena
- remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
- ensured that hosts file is updated
- updated hosts file on jeol1230 computer -- cem100 is now athena
- updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
- todo -- fix mounting of cem100 as athena on j1230 -- ckim is using

May 2011

May 24 2011
- updated imod on /cryoem to IMOD 4.1.10
- installed SerialEM 3 on Tecnai F20

May 26 2011
testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work
- divctf-working-2006 (ELF class 64 shared library)
- hlxavg (ELF class 64 shared library)
- hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
- maskparam (ELF class 64 shared library)
- plotphase (ELF class 64 shared library)

July 2011

update priam to CENTOS5
- repalced root drive with 500GB drive
- root partition 100GB
- hector partition 350 GB
- memory upgraded to 12GB
- new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
Zeiss Windows 2000PC -- removed Norton antivirus
- disk nearly 100% full -- this saved 1 GB of space
- computer is isolated from web, so viruses should not be a problem

August 2011

Aug 17-19 --
update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
now uses BeautifulSoup^? to do most searching
- need to update twiki script to do the same
Aug 24 -- set up backup server tartarus:
- running CENTOS 6
- partitioned backup partiton 23.9 TB (RAID5) with GPT (parted)
  - "mkpart ext4 1 -1" --> makes a single partiton using all of disk space, named it ext4
- xfs format (ext4 currently has 16TB maximum size)
- mount as /pithos/
- installed rdiff-backup:
  - needed to enable rpmforge repository
  - installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  - no repository for rdiff backup: installation required manually installing
    - pylibacl-0.5.0-1.el6.x86_64.rpm
    - pyxattr-0.5.0-1.el6.x86_64.rpm
    - gcc using yum
    - python-devel using yum
    - librsync-devel using yum
    - then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
    - installed in /usr/local/

Aug 23
- installed gromus on agamemnon
  - required installation of fftw3 libraries in /usr/local

December 2011

Agamemnon: menelaus drive moved from /dev/sda5 to /cem03_bigdata_backup
- menelaus now has lots of space, and root partition can be expanded to take over all of /dev/sda
Nicolas, Mariena,Ralph PC's are backed up to /hector

January 2012

Jan 3
- New PC set up: rhea (one of the old Win2000 Dell PC's)
- purpose is to
  1. act as a spare workstation
  2. drive added - hades, which is exported onto windows drives using samba.
  3. EM users who want to copy onto USB flash disks the same day can do safely so via this PC
Jan 16
- Priam: mounted former /cemo2_bigdatabackup as /paris (1.4 TB drive)
- /paris exported and mounted on eurydice, agamemnon, minotaur,cem11
- /paris set up to be backed up daily on tartarus
- Agamemnon : root partiton resized to 230 GB, from 30
  - root was very full (2Gb free), so expanded ino space formerly used by menelaus

March 2012

March 14
- Set up Ed's PC - Centos5
- install php mrc tools:
  - copied source from cronus (/usr/include/php/ext/mrc) and unzipped in identical location
  - downloaded FFTW2 library source (NOT FFTW3 as is mention in docs) and installed:

      ./configure --enable-float --enable-type-prefix --enable-shared
      make
      make install

- - libs were put in /usr/local/lib, however, they are 64-bit libraries so made links in /usr/local/lib64/
  - compiled without error however fft power spectrum was invisible

November 2012

Setting up new Hp 620z workstation

system
- two six-core Xeon processors (12 cores total)
- 32 GB RAM (4* 8 GB; system came with 6*2 GB but this is incompatible; there are 8 slots still free for a max of 96 GB RAM)
- 500 GB HD with Windows 7-64 pro installed; 3 extra disks Western Digital 2GB Black 7200rpm
- NVidia Quadro 2000 GPU (192 CUDA cores)
hardware setup
- Installed RAM and GPU; boots windows
- only 2 bays left for the 3 drives; need to convert one 5.25" bay to 3.5"; adapter on order (Nov 20)
- Attempted to install all RAM simultaneously -- no boot. Removing origina RAM allowed boot.
linux install
- Choosing CentOS^? 6.3 as a modern system
- system could not boot from DVD: has EFI instead of old-style BIOS
- therefore had to choose install from Centos6.3-64 EFI minimal CD

linux install details

minimal is truly minimal: no graphics, no make, almost nothing but a shell
set up networking to work according to http://www.convirture.com/ee_wiki/index.php?title=RedHat_6_Networking
- plug in ethernet to bottom port (with sticker) -- this is eth0
- /etc/sysconfig/network-scripts/ifcfg-eth0

       DEVICE="eth0"
      HWADDR=specifc mac address
      NM_CONTROLLED="no"
      ONBOOT="yes"
      BOOTPROTO="static"
      IPADDR=ip address here.
      NETMASK=netmask here.

- /etc/sysconfig/network and /etc/resolv.conf left unchanged (resol.conf was a 0 length file)
- restart network

      /etc/init.d/network restart

install some packages
- yum install kdebase.x86_64 -- get some graphics at least
- yum install firefox -- get a browser
- yum install xorg-x11-server-xorg.X86_64 - - get startx to work
- yum install xorg-x11-xinit-session-1.09-13.el6.x86-64 --
- sudo nano vim wget system-config-network-tui kernel-headers make gcc ntp tcsh emacs kernel-devel
- install Nvidia driver NVIDIA-Linux-x86_64-310.19.run
  - problem: complains about Nouveau kernel driver. Alllowed it to disable this.
  - to undo this, need to delete /etd/modprobe.d/nvidia-installer-disable-nouveu.conf
  - reboot and try again
  - still enabled!
  - yum update -y
  - edit /boot/efi/EFI/redhat/grub.conf anmd append rdblacklist=nouveau to kernal boot command to disable
  - reboot. /sbin/lsmod | grep nouveau indicates that it was not loaded
  - install NVIDIA module and run startx. success!
  - edit /sbin/inittab to make level 5 the default boot
    - konsole terminal seems messed up a bit
  - yum groupinstall "Graphical Administration Tools" -- gui to admin tasks
  - now can use gpk-application to install required software

desktop details

switchdesk, used to switch between gnome, kde, and others is no longer available
attempts to make this available by making /etc/sysconfig/desktop did not work
in home directory, make the file ~/.dmrc as follows:


[Desktop]
Session=kde
Language=en_US.utf8

needed to install 32-bit libraries to get web to work:
- libXmu-1.0.5-1.el6.i686
- libXt-1.0.7-1.el6.i686
- libXtst-1.0.99.2-3.el6.i686
- libXp-1.0.0-15.1.el6.i686

November 26 2012

yum update -y on orpheus, installed latest Nvidia driver, and rebooted

January 2 2013

Setup Styx /computer for storage

Put together Intel Core i3 CPU + motherboard + 8 GB RAM + 450W power supply
- Motherboard: ASUS P8H61-MLE/CSM
- RAM: 2x 4GB
Install one boot drive: 500 GB from Kakoli's old RAID system
Install 5X 2TB drives for storage (configure as RAID5; see below)
No CD/DVD/floppy

details of system install

Install CENTOS 6.3 Minimal from external USB DVD drive
network configured manually as described above
yum update -y
reboot
install other essential packages as detailed above

preparation of hades RAID5 disk

hades: RAID 5 using 5x 2 TB Western Digital drives
instructions on making these drives a RAID (hdb,hdc,hdd,hde,hdf)

   > sudo mdadm --create /dev/md0 --level=5 --raid-devices=5 /dev/sd[bcdef]1
   > watch cat /proc/mdstat  (wait until done, about 450 minutes)

mdadm.conf file:

DEVICE /dev/sdf1 /dev/sde1 /dev/sdd1 /dev/sdc1 /dev/sdb1
ARRAY /dev/md0 level=raid5 num-devices=5 metadata=1.2 name=styx.nysbc.org:0 UUID=2d2b02fa:a1970439:77152d3a:7d64280e
   devices=/dev/sdb1,/dev/sdc1,/dev/sdd1,/dev/sde1,/dev/sdf1
MAILADDR rice@nysbc.org

set up monitoring:

   > sudo chkconfig mdmonitor on

make a logical volume, format it and mount it

   > sudo pvcreate /dev/md0     -- creates a physical volume
   > sudo vgvreate HADES /dev/md0   -- creates a volume group on that physical volume
   > sudo lvcreate -L 7.27T -n hades HADES  -- creates a logical volume in that volume group
   > sudo mkfs.ext4 /dev/HADES/hades   -- makes the filesystem on the logical volume
   > sudo mkdir /hades
   > sudo mount /dev/HADES/hades /hades

nfs configured to export /hades

Setup new workstation fir rice Dec 2014

* Configuration:

- AMD FX-6350 six core processor
- 16 GB RAM
- 650 W power supply
- ATI graphics card
- Crucial MX100 512 GB SSD for OS
- 4X 3 TB WD Red drives for storage
- originally bought as dataserver; found performacs = 2X that of current CEM11 (Fabiana's old workstation)
- Will repurpose cem11 as data server (with Nvidia card) and use new system as my desktop
- keep paris,cem11data in cem11 computer, keep runnina as headless server
- to do later: upgrade to CentOS^? 6

Standard Linux Mint 17.1 install with cinnamon
set up 3 TB drives as RAID 1 0
- format using parted:

   > sudo parted /dev/sdb
   > mklabel gpt
   > mkpart primary ext4 0% 100%
   > quit

repat for /dev/sdc,/dev/sdd/, /dev/sde

Install Linux Mint 17.1 onto 512 GB SDD
Netowrking not working -- ifcofig seems ok but ping does not work
after MUCH strugging, solution was
- go to BIOS
- enable IOMMU
- restart
- edit /etc/default grub: change empty quotes in line to:

GRUB_CMDLINE_LINUX="iommu=soft"

- then run

   sudo update-grub

Now networking, USB2 and USB3 all work

install new drive : 2 TB spare drive
this renumbered disks:
boot is /dev/sdc
spare is /dev/sdb

make RAID on sda,sdd,sde,sdf
re-format sda1,sdd1,sde1,sdf1 as ext4
sudp apt-get install mdadm

 sudo mdadm -v --create /dev/md0 --level=raid10 --raid-devices=4 /dev/sda1 /dev/sdd1 /dev/sde1 /dev/sdf1
mdadm: layout defaults to n2
mdadm: layout defaults to n2
mdadm: chunk size defaults to 512K
mdadm: /dev/sda1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sdd1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sde1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sdf1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: size set to 2930133504K
Continue creating array? y
mdadm: Defaulting to version 1.2 metadata
mdadm: array /dev/md0 started.

Format as follows:

sudo pvcreate /dev/md0
sudo vgcreate PARKING /dev/md0
sudo lvcreate -l100%FREE -n parking PARKING
sudo mkfs.ext4 /dev/PARKING/parking
sudo mkdir /parking
sudo mount /dev/PARKING/parking /parking

mounted OK
for debian-type, need to manually edit mdadm.conf as follows (as root)

 mdadm --examine --scan --config=mdadm.conf >> /etc/mdadm/mdadm.conf

NOTE
tried flag "amd_iommu=on" : USB2 and ethernet still work but no USB3
left as iommu=soft

Added:

>
>

Failing Disk on hades

[rice@styx ~]$ sudo hdparm -i /dev/sda | grep Serial
 Model=WDC, FwRev=02.03B03, SerialNo=WD-WCASY7050076
[rice@styx ~]$ sudo hdparm -i /dev/sdb | grep Serial
 Model=WDC, FwRev=05.01D05, SerialNo=WD-WMAWP0561880
[rice@styx ~]$ sudo hdparm -i /dev/sdc | grep Serial
 Model=WDC, FwRev=80.00A80, SerialNo=WD-WMC1T0928093
[rice@styx ~]$ sudo hdparm -i /dev/sdd | grep Serial
 Model=WDC, FwRev=80.00A80, SerialNo=WD-WMC1T1328932
[rice@styx ~]$ sudo hdparm -i /dev/sde | grep Serial
 Model=WDC, FwRev=80.00A80, SerialNo=WD-WMC1T0906133

Added:

>
>

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Deleted:

<
<

Revision 2102 Jan 2015 - Main.BillRice

   META TOPICPARENT   name="CemITSystem" 

Contents
 
 Administration logs 
  Jan 2011
   April 2011
   May 2011 
  July 2011
  August 2011
   December 2011
   January 2012
   March 2012
  November 2012 
 Setting up new Hp 620z workstation
   linux install details
   desktop details
 
 
   November 26 2012
   January 2 2013 
  Setup Styx /computer for storage 
  details of system install
   preparation of hades RAID5 disk
 
 
   Setup new workstation fir rice Dec 2014
 
 


 Administration logs 

 Jan 2011 
 
 Set up and installed new computer, cem15
  CentOS^? 5.5, RAID5, 5.2 TB disk
  All standard EM software installed
  cem15data drive is nfs shared and exported 
  users added on ad hoc basis
 

 April 2011 
 
 April 7 2011 
 back up svn server from cem100 and move to cem01
  cem01 now running svn server (current revision=48) and apache server
  made very basic web page for cem01 which links to svn repos as well as sesame
 
 
 

 April 8 2011 -- rename computers as follows 
 cem15 --> orpheus
  cem01 -->cronus
  cem02 --> priam
  cem03 --> agamemnon
  cem11 --> tlaloc
  cem12 --> minotaur
 
  made new hosts file listing these changes, and uploaded to svn server
 
 

 TO DO 
 rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
  DONE 04-27-11
 
 
 

 April 10 2011 
 copy all of Kens' data from Tecnai to external hard drive
  delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps
 
 
 

 April 11 2011 -- rename drives as follows: 
 cem02bigdata --> helen
  cem02data --> hector
  cem02data2 --> hecuba
  cem03bigdata --> achilles
  cem03data --> menelaus
  cem03data2 --> iphigenia
  cem11data --> tonatiu
  cem12data --> theseus
  cem15data --> eurydice
 
  exported and mounted all newly named drives
  updated hosts file on jeol1230 pc to reflect these changes
  change backup scripts to reflect these changes
  found problem with leginon not talking to jerol1230 from minotaur (cem12) after change 
 fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
  verified that leginon is still working directly on jeol1230 and remotely from minotaur
 
 
 

 links made to old drive names
  cronus (cem01) now viewable from outside as cronus.nysbc.org 
 verified by browsing cronus.nysbc.org from public network
 
  TO DO 
 rename dl380 to arachne, and make link
  finish renaming, after backup server installed and running 
 rename cem02bigdata_backup to paris
  rename cem03bigdata_backup to odysseus
  find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???
 
 
 
 

 April 20 2011 
 updated IMOD to IMOD 4.1.9 (current version) on /cryoem 
 /cryoem/IMOD now refers to this version
  /cryoem/IMOD3 referes to imod 3.13
  updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  note that priam (centos4) will likely not run this version 
 
 
 
 

 April 21 2011 
 Checked Tecnai F20 computer (Win 2000) 
 19 GB used out of 34 GB
  deleted ~3 GB of images from old tests
  deleted empty folders for several users who are no longer here
  deleted serialem links for users who are no longer here
  shortcut to feispy and teispy found in trash; restored to desktop
  Current disk usage =~ 16 GB, just under 50% capacity
  TODO -- install internal drive temporarily for backup. Do on maintenance day
 
 
 
 

 April 27 2011 
 updated hostname of cem100 to athena
  remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
  ensured that hosts file is updated
  updated hosts file on jeol1230 computer -- cem100 is now athena
  updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
  todo -- fix mounting of cem100 as athena on j1230 -- ckim is using
 
 

 May 2011 
 
 May 24 2011 
 updated imod on /cryoem to IMOD 4.1.10
  installed SerialEM 3 on Tecnai F20
 
 
 

 May 26 2011
  testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work 
 divctf-working-2006 (ELF class 64 shared library)
  hlxavg (ELF class 64 shared library)
  hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
  maskparam (ELF class 64 shared library)
  plotphase (ELF class 64 shared library)
 
 

 July 2011 
 
 update priam to CENTOS5 
 repalced root drive with 500GB drive
  root partition 100GB
  hector partition 350 GB
  memory upgraded to 12GB
  new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
 
  Zeiss Windows 2000PC -- removed Norton antivirus 
 disk nearly 100% full -- this saved 1 GB of space
  computer is isolated from web, so viruses should not be a problem
 
 

 August 2011 
 
 Aug 17-19 -- 
  update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
  now uses BeautifulSoup^? to do most searching 
 need to update  twiki script to do the same
 
  Aug 24 -- set up backup server tartarus: 
 running CENTOS 6
  partitioned backup partiton 23.9 TB (RAID5) with GPT (parted) 
 "mkpart ext4 1 -1"  --> makes a single partiton using all of disk space, named it ext4
 
  xfs format (ext4 currently has 16TB maximum size)
  mount as /pithos/
  installed rdiff-backup: 
 needed to enable rpmforge repository
  installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  no repository for rdiff backup: installation required manually installing  
 pylibacl-0.5.0-1.el6.x86_64.rpm
  pyxattr-0.5.0-1.el6.x86_64.rpm
  gcc using yum
  python-devel using yum
  librsync-devel using yum
  then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
  installed in /usr/local/
 
 
 
 
 

 Aug 23 
 installed gromus on agamemnon 
 required installation of fftw3 libraries in /usr/local
 
 
 

 December 2011 
 
 Agamemnon: menelaus drive moved from /dev/sda5 to /cem03_bigdata_backup 
 menelaus now has lots of space, and root partition can be expanded to take over all of /dev/sda  
 
  Nicolas, Mariena,Ralph PC's are backed up to /hector
 

 January 2012 
 
 Jan 3 
 New PC set up: rhea (one of the old Win2000 Dell PC's)
  purpose is to  
 act as a spare workstation
  drive added - hades, which is exported onto windows drives using samba. 
  EM users who want to copy onto USB flash disks the same day can do safely so via this PC 
 
 
  Jan 16 
 Priam: mounted former /cemo2_bigdatabackup as /paris (1.4 TB drive)
  /paris exported and mounted on eurydice, agamemnon, minotaur,cem11
  /paris set up to be backed up daily on tartarus
  Agamemnon : root partiton resized to 230 GB, from 30 
 root was very full (2Gb free), so expanded ino space formerly used by menelaus
 
 
 

 March 2012 
 
 March 14 
 Set up Ed's PC - Centos5
  install php mrc tools: 
 copied source from cronus (/usr/include/php/ext/mrc) and unzipped in identical location
  downloaded FFTW2 library source (NOT FFTW3 as is mention in docs) and installed:
 
 
 
      ./configure --enable-float --enable-type-prefix --enable-shared
      make
      make install
 
 
 
 
 
 libs were put in /usr/local/lib, however, they are 64-bit libraries so made links in /usr/local/lib64/
  compiled without error however fft power spectrum was invisible
 
 
 


 November 2012 
 Setting up new Hp 620z workstation 
 
 system  
 two six-core Xeon processors (12 cores total)
  32 GB RAM (4* 8 GB; system came with 6*2 GB but this is incompatible; there are 8 slots still free for a max of 96 GB RAM)
  500 GB HD with Windows 7-64 pro installed; 3 extra disks Western Digital 2GB Black 7200rpm
  NVidia Quadro 2000 GPU (192 CUDA cores)
 
  hardware setup 
 Installed RAM and GPU; boots windows
  only 2 bays left for the 3 drives; need to convert one 5.25" bay to 3.5"; adapter on order (Nov 20)
  Attempted to install all RAM simultaneously -- no boot. Removing origina RAM allowed boot.
 
  linux install 
 Choosing CentOS^? 6.3 as a modern system
  system could not boot from DVD: has EFI instead of old-style BIOS
  therefore had to choose install from Centos6.3-64 EFI minimal CD
 
 
 linux install details 
 
 minimal is truly minimal: no graphics, no make, almost nothing but a shell
  set up networking to work  according to http://www.convirture.com/ee_wiki/index.php?title=RedHat_6_Networking 
 plug in ethernet to bottom port (with sticker) -- this is eth0
  /etc/sysconfig/network-scripts/ifcfg-eth0
 
 
       DEVICE="eth0"
      HWADDR=specifc mac address
      NM_CONTROLLED="no"
      ONBOOT="yes"
      BOOTPROTO="static"
      IPADDR=ip address here.
      NETMASK=netmask here.
 
 
 
 /etc/sysconfig/network and /etc/resolv.conf left unchanged (resol.conf was a 0 length file) 
  restart network
 
 
      /etc/init.d/network restart
 
 install some packages 
 yum install kdebase.x86_64   -- get some graphics at least
  yum install firefox -- get a browser
  yum install xorg-x11-server-xorg.X86_64   - - get startx to work
  yum install xorg-x11-xinit-session-1.09-13.el6.x86-64  -- 
  sudo nano vim wget system-config-network-tui kernel-headers make gcc ntp tcsh emacs kernel-devel
  install Nvidia driver NVIDIA-Linux-x86_64-310.19.run 
 problem: complains about Nouveau kernel driver. Alllowed it to disable this. 
  to undo this, need to delete /etd/modprobe.d/nvidia-installer-disable-nouveu.conf
  reboot and try again
  still enabled!
  yum update -y
  edit /boot/efi/EFI/redhat/grub.conf anmd append rdblacklist=nouveau to kernal boot command to disable
  reboot. /sbin/lsmod | grep nouveau indicates that it was not loaded
  install NVIDIA module and run startx. success!
  edit /sbin/inittab to make level 5 the default boot 
 konsole terminal seems messed up a bit
 
  yum groupinstall "Graphical Administration Tools"  -- gui to admin tasks
  now can use gpk-application to install required software
 
 
 
 desktop details 
 
 switchdesk, used to switch between gnome, kde, and others is no longer available
  attempts to make this available by making /etc/sysconfig/desktop did not work
  in home directory, make the file ~/.dmrc as follows:
 

[Desktop]
Session=kde
Language=en_US.utf8

 

 needed to install 32-bit libraries to get web to work: 
 libXmu-1.0.5-1.el6.i686
  libXt-1.0.7-1.el6.i686
  libXtst-1.0.99.2-3.el6.i686
  libXp-1.0.0-15.1.el6.i686
 
 

 November 26 2012 
 
 yum update -y on orpheus, installed latest Nvidia driver, and rebooted
 

 January 2 2013 
 Setup Styx /computer for storage 
 
 Put together Intel Core i3 CPU + motherboard + 8 GB RAM + 450W power supply 
 Motherboard: ASUS P8H61-MLE/CSM
  RAM: 2x 4GB 
 
  Install one boot drive: 500 GB from Kakoli's old RAID system
  Install 5X 2TB drives for storage (configure as RAID5; see below)
  No CD/DVD/floppy
 
 details of system install 
 
 Install CENTOS 6.3 Minimal from external USB DVD drive
  network configured manually as described above
  yum update -y 
  reboot 
  install other essential packages as detailed above
 
 preparation of hades RAID5 disk 
 
 hades: RAID 5 using 5x 2 TB Western Digital drives
  instructions on making these drives a RAID (hdb,hdc,hdd,hde,hdf)
 
   > sudo mdadm --create /dev/md0 --level=5 --raid-devices=5 /dev/sd[bcdef]1
   > watch cat /proc/mdstat  (wait until done, about 450 minutes)
 
 mdadm.conf file:
 
DEVICE /dev/sdf1 /dev/sde1 /dev/sdd1 /dev/sdc1 /dev/sdb1
ARRAY /dev/md0 level=raid5 num-devices=5 metadata=1.2 name=styx.nysbc.org:0 UUID=2d2b02fa:a1970439:77152d3a:7d64280e
   devices=/dev/sdb1,/dev/sdc1,/dev/sdd1,/dev/sde1,/dev/sdf1
MAILADDR rice@nysbc.org
 
 set up monitoring:
 
   > sudo chkconfig mdmonitor on
 
 make a logical volume, format it and mount it
 
   > sudo pvcreate /dev/md0     -- creates a physical volume
   > sudo vgvreate HADES /dev/md0   -- creates a volume group on that physical volume
   > sudo lvcreate -L 7.27T -n hades HADES  -- creates a logical volume in that volume group
   > sudo mkfs.ext4 /dev/HADES/hades   -- makes the filesystem on the logical volume
   > sudo mkdir /hades
   > sudo mount /dev/HADES/hades /hades
 
 nfs configured to export /hades
 

 Setup new workstation fir rice Dec 2014 

    * Configuration:  

 
 
 AMD FX-6350 six core processor
  16 GB RAM
  650 W power supply
  ATI graphics card
  Crucial MX100 512 GB SSD for OS
  4X 3 TB WD Red drives for storage
  originally bought as dataserver; found performacs = 2X that of current CEM11 (Fabiana's old workstation)
  Will repurpose cem11 as data server (with Nvidia card) and use new system as  my desktop
  keep paris,cem11data in cem11 computer, keep runnina as headless server
  to do later: upgrade to CentOS^? 6
 
 
 

 Standard Linux Mint 17.1 install with cinnamon
  set up 3 TB drives as RAID 1 0  
 format using parted:
 
 
   > sudo parted /dev/sdb
   > mklabel gpt
   > mkpart primary ext4 0% 100%
   > quit
 
 repat for /dev/sdc,/dev/sdd/, /dev/sde
 
 

 Install Linux Mint 17.1 onto 512 GB SDD
  Netowrking not working -- ifcofig seems ok but ping does not work
  after MUCH strugging, solution was 
 go to BIOS
  enable IOMMU
  restart
  edit /etc/default grub: change empty quotes in line to:
 
 
GRUB_CMDLINE_LINUX="iommu=soft"
 
 
 
 then run
-  META TOPICPARENT
+ name="CemITSystem"
-<
<
+   sudo update grub
->
>
+   sudo update-grub
  Now networking, USB2 and USB3 all work
 
 

 install new drive : 2 TB spare drive
  this renumbered disks:
  boot is /dev/sdc
  spare is /dev/sdb
 
 

 make RAID on sda,sdd,sde,sdf
  re-format sda1,sdd1,sde1,sdf1 as ext4
  sudp apt-get install mdadm
 
 sudo mdadm -v --create /dev/md0 --level=raid10 --raid-devices=4 /dev/sda1 /dev/sdd1 /dev/sde1 /dev/sdf1
mdadm: layout defaults to n2
mdadm: layout defaults to n2
mdadm: chunk size defaults to 512K
mdadm: /dev/sda1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sdd1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sde1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sdf1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: size set to 2930133504K
Continue creating array? y
mdadm: Defaulting to version 1.2 metadata
mdadm: array /dev/md0 started.
->
>
+ Format as follows:
 
sudo pvcreate /dev/md0
sudo vgcreate PARKING /dev/md0
sudo lvcreate -l100%FREE -n parking PARKING
sudo mkfs.ext4 /dev/PARKING/parking
sudo mkdir /parking
sudo mount /dev/PARKING/parking /parking
->
>
+ mounted OK
  for debian-type, need to manually edit mdadm.conf as follows (as root)
 
 mdadm --examine --scan --config=mdadm.conf >> /etc/mdadm/mdadm.conf
->
>
+ NOTE
  tried flag "amd_iommu=on" : USB2 and ethernet still work but no USB3
  left as iommu=soft
->
>
  Set ALLOWTOPICVIEW = 
 

-- BillRice - 12 Apr 2011
->
>

Revision 2031 Dec 2014 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
- DONE 04-27-11

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

April 20 2011
- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

April 21 2011
- Checked Tecnai F20 computer (Win 2000)
  - 19 GB used out of 34 GB
  - deleted ~3 GB of images from old tests
  - deleted empty folders for several users who are no longer here
  - deleted serialem links for users who are no longer here
  - shortcut to feispy and teispy found in trash; restored to desktop
  - Current disk usage =~ 16 GB, just under 50% capacity
  - TODO -- install internal drive temporarily for backup. Do on maintenance day

April 27 2011
- updated hostname of cem100 to athena
- remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
- ensured that hosts file is updated
- updated hosts file on jeol1230 computer -- cem100 is now athena
- updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
- todo -- fix mounting of cem100 as athena on j1230 -- ckim is using

May 2011

May 24 2011
- updated imod on /cryoem to IMOD 4.1.10
- installed SerialEM 3 on Tecnai F20

May 26 2011
testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work
- divctf-working-2006 (ELF class 64 shared library)
- hlxavg (ELF class 64 shared library)
- hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
- maskparam (ELF class 64 shared library)
- plotphase (ELF class 64 shared library)

July 2011

update priam to CENTOS5
- repalced root drive with 500GB drive
- root partition 100GB
- hector partition 350 GB
- memory upgraded to 12GB
- new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
Zeiss Windows 2000PC -- removed Norton antivirus
- disk nearly 100% full -- this saved 1 GB of space
- computer is isolated from web, so viruses should not be a problem

August 2011

Aug 17-19 --
update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
now uses BeautifulSoup^? to do most searching
- need to update twiki script to do the same
Aug 24 -- set up backup server tartarus:
- running CENTOS 6
- partitioned backup partiton 23.9 TB (RAID5) with GPT (parted)
  - "mkpart ext4 1 -1" --> makes a single partiton using all of disk space, named it ext4
- xfs format (ext4 currently has 16TB maximum size)
- mount as /pithos/
- installed rdiff-backup:
  - needed to enable rpmforge repository
  - installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  - no repository for rdiff backup: installation required manually installing
    - pylibacl-0.5.0-1.el6.x86_64.rpm
    - pyxattr-0.5.0-1.el6.x86_64.rpm
    - gcc using yum
    - python-devel using yum
    - librsync-devel using yum
    - then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
    - installed in /usr/local/

Aug 23
- installed gromus on agamemnon
  - required installation of fftw3 libraries in /usr/local

December 2011

Agamemnon: menelaus drive moved from /dev/sda5 to /cem03_bigdata_backup
- menelaus now has lots of space, and root partition can be expanded to take over all of /dev/sda
Nicolas, Mariena,Ralph PC's are backed up to /hector

January 2012

Jan 3
- New PC set up: rhea (one of the old Win2000 Dell PC's)
- purpose is to
  1. act as a spare workstation
  2. drive added - hades, which is exported onto windows drives using samba.
  3. EM users who want to copy onto USB flash disks the same day can do safely so via this PC
Jan 16
- Priam: mounted former /cemo2_bigdatabackup as /paris (1.4 TB drive)
- /paris exported and mounted on eurydice, agamemnon, minotaur,cem11
- /paris set up to be backed up daily on tartarus
- Agamemnon : root partiton resized to 230 GB, from 30
  - root was very full (2Gb free), so expanded ino space formerly used by menelaus

March 2012

March 14
- Set up Ed's PC - Centos5
- install php mrc tools:
  - copied source from cronus (/usr/include/php/ext/mrc) and unzipped in identical location
  - downloaded FFTW2 library source (NOT FFTW3 as is mention in docs) and installed:

      ./configure --enable-float --enable-type-prefix --enable-shared
      make
      make install

- - libs were put in /usr/local/lib, however, they are 64-bit libraries so made links in /usr/local/lib64/
  - compiled without error however fft power spectrum was invisible

November 2012

Setting up new Hp 620z workstation

system
- two six-core Xeon processors (12 cores total)
- 32 GB RAM (4* 8 GB; system came with 6*2 GB but this is incompatible; there are 8 slots still free for a max of 96 GB RAM)
- 500 GB HD with Windows 7-64 pro installed; 3 extra disks Western Digital 2GB Black 7200rpm
- NVidia Quadro 2000 GPU (192 CUDA cores)
hardware setup
- Installed RAM and GPU; boots windows
- only 2 bays left for the 3 drives; need to convert one 5.25" bay to 3.5"; adapter on order (Nov 20)
- Attempted to install all RAM simultaneously -- no boot. Removing origina RAM allowed boot.
linux install
- Choosing CentOS^? 6.3 as a modern system
- system could not boot from DVD: has EFI instead of old-style BIOS
- therefore had to choose install from Centos6.3-64 EFI minimal CD

linux install details

minimal is truly minimal: no graphics, no make, almost nothing but a shell
set up networking to work according to http://www.convirture.com/ee_wiki/index.php?title=RedHat_6_Networking
- plug in ethernet to bottom port (with sticker) -- this is eth0
- /etc/sysconfig/network-scripts/ifcfg-eth0

       DEVICE="eth0"
      HWADDR=specifc mac address
      NM_CONTROLLED="no"
      ONBOOT="yes"
      BOOTPROTO="static"
      IPADDR=ip address here.
      NETMASK=netmask here.

- /etc/sysconfig/network and /etc/resolv.conf left unchanged (resol.conf was a 0 length file)
- restart network

      /etc/init.d/network restart

install some packages
- yum install kdebase.x86_64 -- get some graphics at least
- yum install firefox -- get a browser
- yum install xorg-x11-server-xorg.X86_64 - - get startx to work
- yum install xorg-x11-xinit-session-1.09-13.el6.x86-64 --
- sudo nano vim wget system-config-network-tui kernel-headers make gcc ntp tcsh emacs kernel-devel
- install Nvidia driver NVIDIA-Linux-x86_64-310.19.run
  - problem: complains about Nouveau kernel driver. Alllowed it to disable this.
  - to undo this, need to delete /etd/modprobe.d/nvidia-installer-disable-nouveu.conf
  - reboot and try again
  - still enabled!
  - yum update -y
  - edit /boot/efi/EFI/redhat/grub.conf anmd append rdblacklist=nouveau to kernal boot command to disable
  - reboot. /sbin/lsmod | grep nouveau indicates that it was not loaded
  - install NVIDIA module and run startx. success!
  - edit /sbin/inittab to make level 5 the default boot
    - konsole terminal seems messed up a bit
  - yum groupinstall "Graphical Administration Tools" -- gui to admin tasks
  - now can use gpk-application to install required software

desktop details

switchdesk, used to switch between gnome, kde, and others is no longer available
attempts to make this available by making /etc/sysconfig/desktop did not work
in home directory, make the file ~/.dmrc as follows:


[Desktop]
Session=kde
Language=en_US.utf8

needed to install 32-bit libraries to get web to work:
- libXmu-1.0.5-1.el6.i686
- libXt-1.0.7-1.el6.i686
- libXtst-1.0.99.2-3.el6.i686
- libXp-1.0.0-15.1.el6.i686

November 26 2012

yum update -y on orpheus, installed latest Nvidia driver, and rebooted

January 2 2013

Setup Styx /computer for storage

Put together Intel Core i3 CPU + motherboard + 8 GB RAM + 450W power supply
- Motherboard: ASUS P8H61-MLE/CSM
- RAM: 2x 4GB
Install one boot drive: 500 GB from Kakoli's old RAID system
Install 5X 2TB drives for storage (configure as RAID5; see below)
No CD/DVD/floppy

details of system install

Install CENTOS 6.3 Minimal from external USB DVD drive
network configured manually as described above
yum update -y
reboot
install other essential packages as detailed above

preparation of hades RAID5 disk

hades: RAID 5 using 5x 2 TB Western Digital drives
instructions on making these drives a RAID (hdb,hdc,hdd,hde,hdf)

   > sudo mdadm --create /dev/md0 --level=5 --raid-devices=5 /dev/sd[bcdef]1
   > watch cat /proc/mdstat  (wait until done, about 450 minutes)

mdadm.conf file:

DEVICE /dev/sdf1 /dev/sde1 /dev/sdd1 /dev/sdc1 /dev/sdb1
ARRAY /dev/md0 level=raid5 num-devices=5 metadata=1.2 name=styx.nysbc.org:0 UUID=2d2b02fa:a1970439:77152d3a:7d64280e
   devices=/dev/sdb1,/dev/sdc1,/dev/sdd1,/dev/sde1,/dev/sdf1
MAILADDR rice@nysbc.org

set up monitoring:

   > sudo chkconfig mdmonitor on

make a logical volume, format it and mount it

   > sudo pvcreate /dev/md0     -- creates a physical volume
   > sudo vgvreate HADES /dev/md0   -- creates a volume group on that physical volume
   > sudo lvcreate -L 7.27T -n hades HADES  -- creates a logical volume in that volume group
   > sudo mkfs.ext4 /dev/HADES/hades   -- makes the filesystem on the logical volume
   > sudo mkdir /hades
   > sudo mount /dev/HADES/hades /hades

nfs configured to export /hades

Setup new workstation fir rice Dec 2014

* Configuration:

- AMD FX-6350 six core processor
- 16 GB RAM
- 650 W power supply
- ATI graphics card
- Crucial MX100 512 GB SSD for OS
- 4X 3 TB WD Red drives for storage
- originally bought as dataserver; found performacs = 2X that of current CEM11 (Fabiana's old workstation)
- Will repurpose cem11 as data server (with Nvidia card) and use new system as my desktop
- keep paris,cem11data in cem11 computer, keep runnina as headless server
- to do later: upgrade to CentOS^? 6

Standard Linux Mint 17.1 install with cinnamon
set up 3 TB drives as RAID 1 0
- format using parted:

   > sudo parted /dev/sdb
   > mklabel gpt
   > mkpart primary ext4 0% 100%
   > quit

repat for /dev/sdc,/dev/sdd/, /dev/sde

Install Linux Mint 17.1 onto 512 GB SDD

Added:

>
>

Netowrking not working -- ifcofig seems ok but ping does not work
after MUCH strugging, solution was
- go to BIOS
- enable IOMMU
- restart
- edit /etc/default grub: change empty quotes in line to:

GRUB_CMDLINE_LINUX="iommu=soft"

- then run

   sudo update grub

Now networking, USB2 and USB3 all work

install new drive : 2 TB spare drive
this renumbered disks:
boot is /dev/sdc
spare is /dev/sdb

make RAID on sda,sdd,sde,sdf
re-format sda1,sdd1,sde1,sdf1 as ext4
sudp apt-get install mdadm

 sudo mdadm -v --create /dev/md0 --level=raid10 --raid-devices=4 /dev/sda1 /dev/sdd1 /dev/sde1 /dev/sdf1
mdadm: layout defaults to n2
mdadm: layout defaults to n2
mdadm: chunk size defaults to 512K
mdadm: /dev/sda1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sdd1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sde1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: /dev/sdf1 appears to contain an ext2fs file system
    size=-1364702208K  mtime=Wed Dec 31 19:00:00 1969
mdadm: size set to 2930133504K
Continue creating array? y
mdadm: Defaulting to version 1.2 metadata
mdadm: array /dev/md0 started.

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Revision 1920 Dec 2014 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
- DONE 04-27-11

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

April 20 2011
- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

April 21 2011
- Checked Tecnai F20 computer (Win 2000)
  - 19 GB used out of 34 GB
  - deleted ~3 GB of images from old tests
  - deleted empty folders for several users who are no longer here
  - deleted serialem links for users who are no longer here
  - shortcut to feispy and teispy found in trash; restored to desktop
  - Current disk usage =~ 16 GB, just under 50% capacity
  - TODO -- install internal drive temporarily for backup. Do on maintenance day

April 27 2011
- updated hostname of cem100 to athena
- remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
- ensured that hosts file is updated
- updated hosts file on jeol1230 computer -- cem100 is now athena
- updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
- todo -- fix mounting of cem100 as athena on j1230 -- ckim is using

May 2011

May 24 2011
- updated imod on /cryoem to IMOD 4.1.10
- installed SerialEM 3 on Tecnai F20

May 26 2011
testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work
- divctf-working-2006 (ELF class 64 shared library)
- hlxavg (ELF class 64 shared library)
- hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
- maskparam (ELF class 64 shared library)
- plotphase (ELF class 64 shared library)

July 2011

update priam to CENTOS5
- repalced root drive with 500GB drive
- root partition 100GB
- hector partition 350 GB
- memory upgraded to 12GB
- new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
Zeiss Windows 2000PC -- removed Norton antivirus
- disk nearly 100% full -- this saved 1 GB of space
- computer is isolated from web, so viruses should not be a problem

August 2011

Aug 17-19 --
update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
now uses BeautifulSoup^? to do most searching
- need to update twiki script to do the same
Aug 24 -- set up backup server tartarus:
- running CENTOS 6
- partitioned backup partiton 23.9 TB (RAID5) with GPT (parted)
  - "mkpart ext4 1 -1" --> makes a single partiton using all of disk space, named it ext4
- xfs format (ext4 currently has 16TB maximum size)
- mount as /pithos/
- installed rdiff-backup:
  - needed to enable rpmforge repository
  - installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  - no repository for rdiff backup: installation required manually installing
    - pylibacl-0.5.0-1.el6.x86_64.rpm
    - pyxattr-0.5.0-1.el6.x86_64.rpm
    - gcc using yum
    - python-devel using yum
    - librsync-devel using yum
    - then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
    - installed in /usr/local/

Aug 23
- installed gromus on agamemnon
  - required installation of fftw3 libraries in /usr/local

December 2011

Agamemnon: menelaus drive moved from /dev/sda5 to /cem03_bigdata_backup
- menelaus now has lots of space, and root partition can be expanded to take over all of /dev/sda
Nicolas, Mariena,Ralph PC's are backed up to /hector

January 2012

Jan 3
- New PC set up: rhea (one of the old Win2000 Dell PC's)
- purpose is to
  1. act as a spare workstation
  2. drive added - hades, which is exported onto windows drives using samba.
  3. EM users who want to copy onto USB flash disks the same day can do safely so via this PC
Jan 16
- Priam: mounted former /cemo2_bigdatabackup as /paris (1.4 TB drive)
- /paris exported and mounted on eurydice, agamemnon, minotaur,cem11
- /paris set up to be backed up daily on tartarus
- Agamemnon : root partiton resized to 230 GB, from 30
  - root was very full (2Gb free), so expanded ino space formerly used by menelaus

March 2012

March 14
- Set up Ed's PC - Centos5
- install php mrc tools:
  - copied source from cronus (/usr/include/php/ext/mrc) and unzipped in identical location
  - downloaded FFTW2 library source (NOT FFTW3 as is mention in docs) and installed:

      ./configure --enable-float --enable-type-prefix --enable-shared
      make
      make install

- - libs were put in /usr/local/lib, however, they are 64-bit libraries so made links in /usr/local/lib64/
  - compiled without error however fft power spectrum was invisible

November 2012

Setting up new Hp 620z workstation

system
- two six-core Xeon processors (12 cores total)
- 32 GB RAM (4* 8 GB; system came with 6*2 GB but this is incompatible; there are 8 slots still free for a max of 96 GB RAM)
- 500 GB HD with Windows 7-64 pro installed; 3 extra disks Western Digital 2GB Black 7200rpm
- NVidia Quadro 2000 GPU (192 CUDA cores)
hardware setup
- Installed RAM and GPU; boots windows
- only 2 bays left for the 3 drives; need to convert one 5.25" bay to 3.5"; adapter on order (Nov 20)
- Attempted to install all RAM simultaneously -- no boot. Removing origina RAM allowed boot.
linux install
- Choosing CentOS^? 6.3 as a modern system
- system could not boot from DVD: has EFI instead of old-style BIOS
- therefore had to choose install from Centos6.3-64 EFI minimal CD

linux install details

minimal is truly minimal: no graphics, no make, almost nothing but a shell
set up networking to work according to http://www.convirture.com/ee_wiki/index.php?title=RedHat_6_Networking
- plug in ethernet to bottom port (with sticker) -- this is eth0
- /etc/sysconfig/network-scripts/ifcfg-eth0

       DEVICE="eth0"
      HWADDR=specifc mac address
      NM_CONTROLLED="no"
      ONBOOT="yes"
      BOOTPROTO="static"
      IPADDR=ip address here.
      NETMASK=netmask here.

- /etc/sysconfig/network and /etc/resolv.conf left unchanged (resol.conf was a 0 length file)
- restart network

      /etc/init.d/network restart

install some packages
- yum install kdebase.x86_64 -- get some graphics at least
- yum install firefox -- get a browser
- yum install xorg-x11-server-xorg.X86_64 - - get startx to work
- yum install xorg-x11-xinit-session-1.09-13.el6.x86-64 --
- sudo nano vim wget system-config-network-tui kernel-headers make gcc ntp tcsh emacs kernel-devel
- install Nvidia driver NVIDIA-Linux-x86_64-310.19.run
  - problem: complains about Nouveau kernel driver. Alllowed it to disable this.
  - to undo this, need to delete /etd/modprobe.d/nvidia-installer-disable-nouveu.conf
  - reboot and try again
  - still enabled!
  - yum update -y
  - edit /boot/efi/EFI/redhat/grub.conf anmd append rdblacklist=nouveau to kernal boot command to disable
  - reboot. /sbin/lsmod | grep nouveau indicates that it was not loaded
  - install NVIDIA module and run startx. success!
  - edit /sbin/inittab to make level 5 the default boot
    - konsole terminal seems messed up a bit
  - yum groupinstall "Graphical Administration Tools" -- gui to admin tasks
  - now can use gpk-application to install required software

desktop details

switchdesk, used to switch between gnome, kde, and others is no longer available
attempts to make this available by making /etc/sysconfig/desktop did not work
in home directory, make the file ~/.dmrc as follows:


[Desktop]
Session=kde
Language=en_US.utf8

needed to install 32-bit libraries to get web to work:
- libXmu-1.0.5-1.el6.i686
- libXt-1.0.7-1.el6.i686
- libXtst-1.0.99.2-3.el6.i686
- libXp-1.0.0-15.1.el6.i686

November 26 2012

yum update -y on orpheus, installed latest Nvidia driver, and rebooted

January 2 2013

Setup Styx /computer for storage

Put together Intel Core i3 CPU + motherboard + 8 GB RAM + 450W power supply
- Motherboard: ASUS P8H61-MLE/CSM
- RAM: 2x 4GB
Install one boot drive: 500 GB from Kakoli's old RAID system
Install 5X 2TB drives for storage (configure as RAID5; see below)
No CD/DVD/floppy

details of system install

Install CENTOS 6.3 Minimal from external USB DVD drive
network configured manually as described above
yum update -y
reboot
install other essential packages as detailed above

preparation of hades RAID5 disk

hades: RAID 5 using 5x 2 TB Western Digital drives
instructions on making these drives a RAID (hdb,hdc,hdd,hde,hdf)

   > sudo mdadm --create /dev/md0 --level=5 --raid-devices=5 /dev/sd[bcdef]1
   > watch cat /proc/mdstat  (wait until done, about 450 minutes)

mdadm.conf file:

DEVICE /dev/sdf1 /dev/sde1 /dev/sdd1 /dev/sdc1 /dev/sdb1
ARRAY /dev/md0 level=raid5 num-devices=5 metadata=1.2 name=styx.nysbc.org:0 UUID=2d2b02fa:a1970439:77152d3a:7d64280e
   devices=/dev/sdb1,/dev/sdc1,/dev/sdd1,/dev/sde1,/dev/sdf1
MAILADDR rice@nysbc.org

set up monitoring:

   > sudo chkconfig mdmonitor on

make a logical volume, format it and mount it

   > sudo pvcreate /dev/md0     -- creates a physical volume
   > sudo vgvreate HADES /dev/md0   -- creates a volume group on that physical volume
   > sudo lvcreate -L 7.27T -n hades HADES  -- creates a logical volume in that volume group
   > sudo mkfs.ext4 /dev/HADES/hades   -- makes the filesystem on the logical volume
   > sudo mkdir /hades
   > sudo mount /dev/HADES/hades /hades

nfs configured to export /hades

Added:

>
>

Setup new workstation fir rice Dec 2014

* Configuration:

- AMD FX-6350 six core processor
- 16 GB RAM
- 650 W power supply
- ATI graphics card
- Crucial MX100 512 GB SSD for OS
- 4X 3 TB WD Red drives for storage
- originally bought as dataserver; found performacs = 2X that of current CEM11 (Fabiana's old workstation)
- Will repurpose cem11 as data server (with Nvidia card) and use new system as my desktop
- keep paris,cem11data in cem11 computer, keep runnina as headless server
- to do later: upgrade to CentOS^? 6

Standard Linux Mint 17.1 install with cinnamon
set up 3 TB drives as RAID 1 0
- format using parted:

   > sudo parted /dev/sdb
   > mklabel gpt
   > mkpart primary ext4 0% 100%
   > quit

repat for /dev/sdc,/dev/sdd/, /dev/sde

Install Linux Mint 17.1 onto 512 GB SDD

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Deleted:

<
<

Revision 1804 Jan 2013 - Main.BillRice

   META TOPICPARENT   name="CemITSystem" 

Contents
 
 Administration logs 
  Jan 2011
   April 2011
   May 2011 
  July 2011
  August 2011
   December 2011
   January 2012
   March 2012
  November 2012 
 Setting up new Hp 620z workstation
   linux install details
   desktop details
 
 
   November 26 2012
 
 


 Administration logs 

 Jan 2011 
 
 Set up and installed new computer, cem15
  CentOS^? 5.5, RAID5, 5.2 TB disk
  All standard EM software installed
  cem15data drive is nfs shared and exported 
  users added on ad hoc basis
 

 April 2011 
 
 April 7 2011 
 back up svn server from cem100 and move to cem01
  cem01 now running svn server (current revision=48) and apache server
  made very basic web page for cem01 which links to svn repos as well as sesame
 
 
 

 April 8 2011 -- rename computers as follows 
 cem15 --> orpheus
  cem01 -->cronus
  cem02 --> priam
  cem03 --> agamemnon
  cem11 --> tlaloc
  cem12 --> minotaur
 
  made new hosts file listing these changes, and uploaded to svn server
 
 

 TO DO 
 rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
  DONE 04-27-11
 
 
 

 April 10 2011 
 copy all of Kens' data from Tecnai to external hard drive
  delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps
 
 
 

 April 11 2011 -- rename drives as follows: 
 cem02bigdata --> helen
  cem02data --> hector
  cem02data2 --> hecuba
  cem03bigdata --> achilles
  cem03data --> menelaus
  cem03data2 --> iphigenia
  cem11data --> tonatiu
  cem12data --> theseus
  cem15data --> eurydice
 
  exported and mounted all newly named drives
  updated hosts file on jeol1230 pc to reflect these changes
  change backup scripts to reflect these changes
  found problem with leginon not talking to jerol1230 from minotaur (cem12) after change 
 fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
  verified that leginon is still working directly on jeol1230 and remotely from minotaur
 
 
 

 links made to old drive names
  cronus (cem01) now viewable from outside as cronus.nysbc.org 
 verified by browsing cronus.nysbc.org from public network
 
  TO DO 
 rename dl380 to arachne, and make link
  finish renaming, after backup server installed and running 
 rename cem02bigdata_backup to paris
  rename cem03bigdata_backup to odysseus
  find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???
 
 
 
 

 April 20 2011 
 updated IMOD to IMOD 4.1.9 (current version) on /cryoem 
 /cryoem/IMOD now refers to this version
  /cryoem/IMOD3 referes to imod 3.13
  updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  note that priam (centos4) will likely not run this version 
 
 
 
 

 April 21 2011 
 Checked Tecnai F20 computer (Win 2000) 
 19 GB used out of 34 GB
  deleted ~3 GB of images from old tests
  deleted empty folders for several users who are no longer here
  deleted serialem links for users who are no longer here
  shortcut to feispy and teispy found in trash; restored to desktop
  Current disk usage =~ 16 GB, just under 50% capacity
  TODO -- install internal drive temporarily for backup. Do on maintenance day
 
 
 
 

 April 27 2011 
 updated hostname of cem100 to athena
  remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
  ensured that hosts file is updated
  updated hosts file on jeol1230 computer -- cem100 is now athena
  updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
  todo -- fix mounting of cem100 as athena on j1230 -- ckim is using
 
 

 May 2011 
 
 May 24 2011 
 updated imod on /cryoem to IMOD 4.1.10
  installed SerialEM 3 on Tecnai F20
 
 
 

 May 26 2011
  testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work 
 divctf-working-2006 (ELF class 64 shared library)
  hlxavg (ELF class 64 shared library)
  hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
  maskparam (ELF class 64 shared library)
  plotphase (ELF class 64 shared library)
 
 

 July 2011 
 
 update priam to CENTOS5 
 repalced root drive with 500GB drive
  root partition 100GB
  hector partition 350 GB
  memory upgraded to 12GB
  new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
 
  Zeiss Windows 2000PC -- removed Norton antivirus 
 disk nearly 100% full -- this saved 1 GB of space
  computer is isolated from web, so viruses should not be a problem
 
 

 August 2011 
 
 Aug 17-19 -- 
  update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
  now uses BeautifulSoup^? to do most searching 
 need to update  twiki script to do the same
 
  Aug 24 -- set up backup server tartarus: 
 running CENTOS 6
  partitioned backup partiton 23.9 TB (RAID5) with GPT (parted) 
 "mkpart ext4 1 -1"  --> makes a single partiton using all of disk space, named it ext4
 
  xfs format (ext4 currently has 16TB maximum size)
  mount as /pithos/
  installed rdiff-backup: 
 needed to enable rpmforge repository
  installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  no repository for rdiff backup: installation required manually installing  
 pylibacl-0.5.0-1.el6.x86_64.rpm
  pyxattr-0.5.0-1.el6.x86_64.rpm
  gcc using yum
  python-devel using yum
  librsync-devel using yum
  then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
  installed in /usr/local/
 
 
 
 
 

 Aug 23 
 installed gromus on agamemnon 
 required installation of fftw3 libraries in /usr/local
 
 
 

 December 2011 
 
 Agamemnon: menelaus drive moved from /dev/sda5 to /cem03_bigdata_backup 
 menelaus now has lots of space, and root partition can be expanded to take over all of /dev/sda  
 
  Nicolas, Mariena,Ralph PC's are backed up to /hector
 

 January 2012 
 
 Jan 3 
 New PC set up: rhea (one of the old Win2000 Dell PC's)
  purpose is to  
 act as a spare workstation
  drive added - hades, which is exported onto windows drives using samba. 
  EM users who want to copy onto USB flash disks the same day can do safely so via this PC 
 
 
  Jan 16 
 Priam: mounted former /cemo2_bigdatabackup as /paris (1.4 TB drive)
  /paris exported and mounted on eurydice, agamemnon, minotaur,cem11
  /paris set up to be backed up daily on tartarus
  Agamemnon : root partiton resized to 230 GB, from 30 
 root was very full (2Gb free), so expanded ino space formerly used by menelaus
 
 
 

 March 2012 
 
 March 14 
 Set up Ed's PC - Centos5
  install php mrc tools: 
 copied source from cronus (/usr/include/php/ext/mrc) and unzipped in identical location
  downloaded FFTW2 library source (NOT FFTW3 as is mention in docs) and installed:
 
 
 
      ./configure --enable-float --enable-type-prefix --enable-shared
      make
      make install
 
 
 
 
 
 libs were put in /usr/local/lib, however, they are 64-bit libraries so made links in /usr/local/lib64/
  compiled without error however fft power spectrum was invisible
 
 
 


 November 2012 
 Setting up new Hp 620z workstation 
 
 system  
 two six-core Xeon processors (12 cores total)
  32 GB RAM (4* 8 GB; system came with 6*2 GB but this is incompatible; there are 8 slots still free for a max of 96 GB RAM)
  500 GB HD with Windows 7-64 pro installed; 3 extra disks Western Digital 2GB Black 7200rpm
  NVidia Quadro 2000 GPU (192 CUDA cores)
 
  hardware setup 
 Installed RAM and GPU; boots windows
  only 2 bays left for the 3 drives; need to convert one 5.25" bay to 3.5"; adapter on order (Nov 20)
  Attempted to install all RAM simultaneously -- no boot. Removing origina RAM allowed boot.
 
  linux install 
 Choosing CentOS^? 6.3 as a modern system
  system could not boot from DVD: has EFI instead of old-style BIOS
  therefore had to choose install from Centos6.3-64 EFI minimal CD
 
 
 linux install details 
 
 minimal is truly minimal: no graphics, no make, almost nothing but a shell
  set up networking to work  according to http://www.convirture.com/ee_wiki/index.php?title=RedHat_6_Networking 
 plug in ethernet to bottom port (with sticker) -- this is eth0
  /etc/sysconfig/network-scripts/ifcfg-eth0
 
 
       DEVICE="eth0"
      HWADDR=specifc mac address
      NM_CONTROLLED="no"
      ONBOOT="yes"
      BOOTPROTO="static"
      IPADDR=ip address here.
      NETMASK=netmask here.
 
 
 
 /etc/sysconfig/network and /etc/resolv.conf left unchanged (resol.conf was a 0 length file) 
  restart network
 
 
      /etc/init.d/network restart
 
 install some packages 
 yum install kdebase.x86_64   -- get some graphics at least
  yum install firefox -- get a browser
  yum install xorg-x11-server-xorg.X86_64   - - get startx to work
  yum install xorg-x11-xinit-session-1.09-13.el6.x86-64  -- 
  sudo nano vim wget system-config-network-tui kernel-headers make gcc ntp tcsh emacs kernel-devel
  install Nvidia driver NVIDIA-Linux-x86_64-310.19.run 
 problem: complains about Nouveau kernel driver. Alllowed it to disable this. 
  to undo this, need to delete /etd/modprobe.d/nvidia-installer-disable-nouveu.conf
  reboot and try again
  still enabled!
  yum update -y
  edit /boot/efi/EFI/redhat/grub.conf anmd append rdblacklist=nouveau to kernal boot command to disable
  reboot. /sbin/lsmod | grep nouveau indicates that it was not loaded
  install NVIDIA module and run startx. success!
  edit /sbin/inittab to make level 5 the default boot 
 konsole terminal seems messed up a bit
 
  yum groupinstall "Graphical Administration Tools"  -- gui to admin tasks
  now can use gpk-application to install required software
 
 
 
 desktop details 
 
 switchdesk, used to switch between gnome, kde, and others is no longer available
  attempts to make this available by making /etc/sysconfig/desktop did not work
  in home directory, make the file ~/.dmrc as follows:
 

[Desktop]
Session=kde
Language=en_US.utf8

 

 needed to install 32-bit libraries to get web to work: 
 libXmu-1.0.5-1.el6.i686
  libXt-1.0.7-1.el6.i686
  libXtst-1.0.99.2-3.el6.i686
  libXp-1.0.0-15.1.el6.i686
 
 

 November 26 2012
-  META TOPICPARENT
+ name="CemITSystem"
-<
<
+ yum update -y on oroheus, installed latest Nvidia driver, and rebooted
->
>
+ yum update -y on orpheus, installed latest Nvidia driver, and rebooted
  January 2 2013 
 Setup Styx /computer for storage 
 
 Put together Intel Core i3 CPU + motherboard + 8 GB RAM + 450W power supply 
 Motherboard: ASUS P8H61-MLE/CSM
  RAM: 2x 4GB 
 
  Install one boot drive: 500 GB from Kakoli's old RAID system
  Install 5X 2TB drives for storage (configure as RAID5; see below)
  No CD/DVD/floppy
 
 details of system install 
 
 Install CENTOS 6.3 Minimal from external USB DVD drive
  network configured manually as described above
  yum update -y 
  reboot
->
>
+ install other essential packages as detailed above
 
 preparation of hades RAID5 disk 
 
 hades: RAID 5 using 5x 2 TB Western Digital drives
  instructions on making these drives a RAID (hdb,hdc,hdd,hde,hdf)
 
   > sudo mdadm --create /dev/md0 --level=5 --raid-devices=5 /dev/sd[bcdef]1
   > watch cat /proc/mdstat  (wait until done, about 450 minutes)
 
 mdadm.conf file:
 
DEVICE /dev/sdf1 /dev/sde1 /dev/sdd1 /dev/sdc1 /dev/sdb1
ARRAY /dev/md0 level=raid5 num-devices=5 metadata=1.2 name=styx.nysbc.org:0 UUID=2d2b02fa:a1970439:77152d3a:7d64280e
   devices=/dev/sdb1,/dev/sdc1,/dev/sdd1,/dev/sde1,/dev/sdf1
MAILADDR rice@nysbc.org
 
 set up monitoring:
 
   > sudo chkconfig mdmonitor on
 
 make a logical volume, format it and mount it
 
   > sudo pvcreate /dev/md0     -- creates a physical volume
   > sudo vgvreate HADES /dev/md0   -- creates a volume group on that physical volume
   > sudo lvcreate -L 7.27T -n hades HADES  -- creates a logical volume in that volume group
   > sudo mkfs.ext4 /dev/HADES/hades   -- makes the filesystem on the logical volume
   > sudo mkdir /hades
   > sudo mount /dev/HADES/hades /hades
 
 nfs configured to export /hades
  Set ALLOWTOPICVIEW = 
 

-- BillRice - 12 Apr 2011
->
>

Revision 1702 Jan 2013 - Main.BillRice

   META TOPICPARENT   name="CemITSystem" 

Contents
 
 Administration logs 
  Jan 2011
   April 2011
   May 2011 
  July 2011
  August 2011
   December 2011
   January 2012
   March 2012
  November 2012 
 Setting up new Hp 620z workstation
   linux install details
   desktop details
 
 
   November 26 2012
 
 


 Administration logs 

 Jan 2011 
 
 Set up and installed new computer, cem15
  CentOS^? 5.5, RAID5, 5.2 TB disk
  All standard EM software installed
  cem15data drive is nfs shared and exported 
  users added on ad hoc basis
 

 April 2011 
 
 April 7 2011 
 back up svn server from cem100 and move to cem01
  cem01 now running svn server (current revision=48) and apache server
  made very basic web page for cem01 which links to svn repos as well as sesame
 
 
 

 April 8 2011 -- rename computers as follows 
 cem15 --> orpheus
  cem01 -->cronus
  cem02 --> priam
  cem03 --> agamemnon
  cem11 --> tlaloc
  cem12 --> minotaur
 
  made new hosts file listing these changes, and uploaded to svn server
 
 

 TO DO 
 rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
  DONE 04-27-11
 
 
 

 April 10 2011 
 copy all of Kens' data from Tecnai to external hard drive
  delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps
 
 
 

 April 11 2011 -- rename drives as follows: 
 cem02bigdata --> helen
  cem02data --> hector
  cem02data2 --> hecuba
  cem03bigdata --> achilles
  cem03data --> menelaus
  cem03data2 --> iphigenia
  cem11data --> tonatiu
  cem12data --> theseus
  cem15data --> eurydice
 
  exported and mounted all newly named drives
  updated hosts file on jeol1230 pc to reflect these changes
  change backup scripts to reflect these changes
  found problem with leginon not talking to jerol1230 from minotaur (cem12) after change 
 fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
  verified that leginon is still working directly on jeol1230 and remotely from minotaur
 
 
 

 links made to old drive names
  cronus (cem01) now viewable from outside as cronus.nysbc.org 
 verified by browsing cronus.nysbc.org from public network
 
  TO DO 
 rename dl380 to arachne, and make link
  finish renaming, after backup server installed and running 
 rename cem02bigdata_backup to paris
  rename cem03bigdata_backup to odysseus
  find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???
 
 
 
 

 April 20 2011 
 updated IMOD to IMOD 4.1.9 (current version) on /cryoem 
 /cryoem/IMOD now refers to this version
  /cryoem/IMOD3 referes to imod 3.13
  updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  note that priam (centos4) will likely not run this version 
 
 
 
 

 April 21 2011 
 Checked Tecnai F20 computer (Win 2000) 
 19 GB used out of 34 GB
  deleted ~3 GB of images from old tests
  deleted empty folders for several users who are no longer here
  deleted serialem links for users who are no longer here
  shortcut to feispy and teispy found in trash; restored to desktop
  Current disk usage =~ 16 GB, just under 50% capacity
  TODO -- install internal drive temporarily for backup. Do on maintenance day
 
 
 
 

 April 27 2011 
 updated hostname of cem100 to athena
  remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
  ensured that hosts file is updated
  updated hosts file on jeol1230 computer -- cem100 is now athena
  updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
  todo -- fix mounting of cem100 as athena on j1230 -- ckim is using
 
 

 May 2011 
 
 May 24 2011 
 updated imod on /cryoem to IMOD 4.1.10
  installed SerialEM 3 on Tecnai F20
 
 
 

 May 26 2011
  testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work 
 divctf-working-2006 (ELF class 64 shared library)
  hlxavg (ELF class 64 shared library)
  hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
  maskparam (ELF class 64 shared library)
  plotphase (ELF class 64 shared library)
 
 

 July 2011 
 
 update priam to CENTOS5 
 repalced root drive with 500GB drive
  root partition 100GB
  hector partition 350 GB
  memory upgraded to 12GB
  new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
 
  Zeiss Windows 2000PC -- removed Norton antivirus 
 disk nearly 100% full -- this saved 1 GB of space
  computer is isolated from web, so viruses should not be a problem
 
 

 August 2011 
 
 Aug 17-19 -- 
  update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
  now uses BeautifulSoup^? to do most searching 
 need to update  twiki script to do the same
 
  Aug 24 -- set up backup server tartarus: 
 running CENTOS 6
  partitioned backup partiton 23.9 TB (RAID5) with GPT (parted) 
 "mkpart ext4 1 -1"  --> makes a single partiton using all of disk space, named it ext4
 
  xfs format (ext4 currently has 16TB maximum size)
  mount as /pithos/
  installed rdiff-backup: 
 needed to enable rpmforge repository
  installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  no repository for rdiff backup: installation required manually installing  
 pylibacl-0.5.0-1.el6.x86_64.rpm
  pyxattr-0.5.0-1.el6.x86_64.rpm
  gcc using yum
  python-devel using yum
  librsync-devel using yum
  then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
  installed in /usr/local/
 
 
 
 
 

 Aug 23 
 installed gromus on agamemnon 
 required installation of fftw3 libraries in /usr/local
 
 
 

 December 2011 
 
 Agamemnon: menelaus drive moved from /dev/sda5 to /cem03_bigdata_backup 
 menelaus now has lots of space, and root partition can be expanded to take over all of /dev/sda  
 
  Nicolas, Mariena,Ralph PC's are backed up to /hector
 

 January 2012 
 
 Jan 3 
 New PC set up: rhea (one of the old Win2000 Dell PC's)
  purpose is to  
 act as a spare workstation
  drive added - hades, which is exported onto windows drives using samba. 
  EM users who want to copy onto USB flash disks the same day can do safely so via this PC 
 
 
  Jan 16 
 Priam: mounted former /cemo2_bigdatabackup as /paris (1.4 TB drive)
  /paris exported and mounted on eurydice, agamemnon, minotaur,cem11
  /paris set up to be backed up daily on tartarus
  Agamemnon : root partiton resized to 230 GB, from 30 
 root was very full (2Gb free), so expanded ino space formerly used by menelaus
 
 
 

 March 2012 
 
 March 14 
 Set up Ed's PC - Centos5
  install php mrc tools: 
 copied source from cronus (/usr/include/php/ext/mrc) and unzipped in identical location
  downloaded FFTW2 library source (NOT FFTW3 as is mention in docs) and installed:
 
 
 
      ./configure --enable-float --enable-type-prefix --enable-shared
      make
      make install
 
 
 
 
 
 libs were put in /usr/local/lib, however, they are 64-bit libraries so made links in /usr/local/lib64/
  compiled without error however fft power spectrum was invisible
 
 
 


 November 2012 
 Setting up new Hp 620z workstation 
 
 system  
 two six-core Xeon processors (12 cores total)
  32 GB RAM (4* 8 GB; system came with 6*2 GB but this is incompatible; there are 8 slots still free for a max of 96 GB RAM)
  500 GB HD with Windows 7-64 pro installed; 3 extra disks Western Digital 2GB Black 7200rpm
  NVidia Quadro 2000 GPU (192 CUDA cores)
 
  hardware setup 
 Installed RAM and GPU; boots windows
  only 2 bays left for the 3 drives; need to convert one 5.25" bay to 3.5"; adapter on order (Nov 20)
  Attempted to install all RAM simultaneously -- no boot. Removing origina RAM allowed boot.
 
  linux install 
 Choosing CentOS^? 6.3 as a modern system
  system could not boot from DVD: has EFI instead of old-style BIOS
  therefore had to choose install from Centos6.3-64 EFI minimal CD
 
 
 linux install details 
 
 minimal is truly minimal: no graphics, no make, almost nothing but a shell
  set up networking to work  according to http://www.convirture.com/ee_wiki/index.php?title=RedHat_6_Networking 
 plug in ethernet to bottom port (with sticker) -- this is eth0
  /etc/sysconfig/network-scripts/ifcfg-eth0
 
 
       DEVICE="eth0"
      HWADDR=specifc mac address
      NM_CONTROLLED="no"
      ONBOOT="yes"
      BOOTPROTO="static"
      IPADDR=ip address here.
      NETMASK=netmask here.
 
 
 
 /etc/sysconfig/network and /etc/resolv.conf left unchanged (resol.conf was a 0 length file) 
  restart network
 
 
      /etc/init.d/network restart
 
 install some packages 
 yum install kdebase.x86_64   -- get some graphics at least
  yum install firefox -- get a browser
  yum install xorg-x11-server-xorg.X86_64   - - get startx to work
  yum install xorg-x11-xinit-session-1.09-13.el6.x86-64  -- 
  sudo nano vim wget system-config-network-tui kernel-headers make gcc ntp tcsh emacs kernel-devel
  install Nvidia driver NVIDIA-Linux-x86_64-310.19.run 
 problem: complains about Nouveau kernel driver. Alllowed it to disable this. 
  to undo this, need to delete /etd/modprobe.d/nvidia-installer-disable-nouveu.conf
  reboot and try again
  still enabled!
  yum update -y
  edit /boot/efi/EFI/redhat/grub.conf anmd append rdblacklist=nouveau to kernal boot command to disable
  reboot. /sbin/lsmod | grep nouveau indicates that it was not loaded
  install NVIDIA module and run startx. success!
  edit /sbin/inittab to make level 5 the default boot 
 konsole terminal seems messed up a bit
 
  yum groupinstall "Graphical Administration Tools"  -- gui to admin tasks
  now can use gpk-application to install required software
 
 
 
 desktop details 
 
 switchdesk, used to switch between gnome, kde, and others is no longer available
  attempts to make this available by making /etc/sysconfig/desktop did not work
  in home directory, make the file ~/.dmrc as follows:
 

[Desktop]
Session=kde
Language=en_US.utf8

 

 needed to install 32-bit libraries to get web to work: 
 libXmu-1.0.5-1.el6.i686
  libXt-1.0.7-1.el6.i686
  libXtst-1.0.99.2-3.el6.i686
  libXp-1.0.0-15.1.el6.i686
 
 

 November 26 2012 
 
 yum update -y on oroheus, installed latest Nvidia driver, and rebooted
-  META TOPICPARENT
+ name="CemITSystem"
-<
<
+a263 1
->
>
+ January 2 2013
->
>
+ Setup Styx /computer for storage 
 
 Put together Intel Core i3 CPU + motherboard + 8 GB RAM + 450W power supply 
 Motherboard: ASUS P8H61-MLE/CSM
  RAM: 2x 4GB 
 
  Install one boot drive: 500 GB from Kakoli's old RAID system
  Install 5X 2TB drives for storage (configure as RAID5; see below)
  No CD/DVD/floppy
 
 details of system install 
 
 Install CENTOS 6.3 Minimal from external USB DVD drive
  network configured manually as described above
  yum update -y 
  reboot
  Set ALLOWTOPICVIEW = 
 

-- BillRice - 12 Apr 2011

Revision 1626 Nov 2012 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
- DONE 04-27-11

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

April 20 2011
- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

April 21 2011
- Checked Tecnai F20 computer (Win 2000)
  - 19 GB used out of 34 GB
  - deleted ~3 GB of images from old tests
  - deleted empty folders for several users who are no longer here
  - deleted serialem links for users who are no longer here
  - shortcut to feispy and teispy found in trash; restored to desktop
  - Current disk usage =~ 16 GB, just under 50% capacity
  - TODO -- install internal drive temporarily for backup. Do on maintenance day

April 27 2011
- updated hostname of cem100 to athena
- remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
- ensured that hosts file is updated
- updated hosts file on jeol1230 computer -- cem100 is now athena
- updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
- todo -- fix mounting of cem100 as athena on j1230 -- ckim is using

May 2011

May 24 2011
- updated imod on /cryoem to IMOD 4.1.10
- installed SerialEM 3 on Tecnai F20

May 26 2011
testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work
- divctf-working-2006 (ELF class 64 shared library)
- hlxavg (ELF class 64 shared library)
- hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
- maskparam (ELF class 64 shared library)
- plotphase (ELF class 64 shared library)

July 2011

update priam to CENTOS5
- repalced root drive with 500GB drive
- root partition 100GB
- hector partition 350 GB
- memory upgraded to 12GB
- new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
Zeiss Windows 2000PC -- removed Norton antivirus
- disk nearly 100% full -- this saved 1 GB of space
- computer is isolated from web, so viruses should not be a problem

August 2011

Aug 17-19 --
update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
now uses BeautifulSoup^? to do most searching
- need to update twiki script to do the same
Aug 24 -- set up backup server tartarus:
- running CENTOS 6
- partitioned backup partiton 23.9 TB (RAID5) with GPT (parted)
  - "mkpart ext4 1 -1" --> makes a single partiton using all of disk space, named it ext4
- xfs format (ext4 currently has 16TB maximum size)
- mount as /pithos/
- installed rdiff-backup:
  - needed to enable rpmforge repository
  - installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  - no repository for rdiff backup: installation required manually installing
    - pylibacl-0.5.0-1.el6.x86_64.rpm
    - pyxattr-0.5.0-1.el6.x86_64.rpm
    - gcc using yum
    - python-devel using yum
    - librsync-devel using yum
    - then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
    - installed in /usr/local/

Aug 23
- installed gromus on agamemnon
  - required installation of fftw3 libraries in /usr/local

December 2011

Agamemnon: menelaus drive moved from /dev/sda5 to /cem03_bigdata_backup
- menelaus now has lots of space, and root partition can be expanded to take over all of /dev/sda
Nicolas, Mariena,Ralph PC's are backed up to /hector

January 2012

Jan 3
- New PC set up: rhea (one of the old Win2000 Dell PC's)
- purpose is to
  1. act as a spare workstation
  2. drive added - hades, which is exported onto windows drives using samba.
  3. EM users who want to copy onto USB flash disks the same day can do safely so via this PC
Jan 16
- Priam: mounted former /cemo2_bigdatabackup as /paris (1.4 TB drive)
- /paris exported and mounted on eurydice, agamemnon, minotaur,cem11
- /paris set up to be backed up daily on tartarus
- Agamemnon : root partiton resized to 230 GB, from 30
  - root was very full (2Gb free), so expanded ino space formerly used by menelaus

March 2012

March 14
- Set up Ed's PC - Centos5
- install php mrc tools:
  - copied source from cronus (/usr/include/php/ext/mrc) and unzipped in identical location
  - downloaded FFTW2 library source (NOT FFTW3 as is mention in docs) and installed:

      ./configure --enable-float --enable-type-prefix --enable-shared
      make
      make install

- - libs were put in /usr/local/lib, however, they are 64-bit libraries so made links in /usr/local/lib64/
  - compiled without error however fft power spectrum was invisible

November 2012

Setting up new Hp 620z workstation

system
- two six-core Xeon processors (12 cores total)
- 32 GB RAM (4* 8 GB; system came with 6*2 GB but this is incompatible; there are 8 slots still free for a max of 96 GB RAM)
- 500 GB HD with Windows 7-64 pro installed; 3 extra disks Western Digital 2GB Black 7200rpm
- NVidia Quadro 2000 GPU (192 CUDA cores)
hardware setup
- Installed RAM and GPU; boots windows
- only 2 bays left for the 3 drives; need to convert one 5.25" bay to 3.5"; adapter on order (Nov 20)
- Attempted to install all RAM simultaneously -- no boot. Removing origina RAM allowed boot.
linux install
- Choosing CentOS^? 6.3 as a modern system
- system could not boot from DVD: has EFI instead of old-style BIOS
- therefore had to choose install from Centos6.3-64 EFI minimal CD

linux install details

minimal is truly minimal: no graphics, no make, almost nothing but a shell
set up networking to work according to http://www.convirture.com/ee_wiki/index.php?title=RedHat_6_Networking
- plug in ethernet to bottom port (with sticker) -- this is eth0
- /etc/sysconfig/network-scripts/ifcfg-eth0

       DEVICE="eth0"
      HWADDR=specifc mac address
      NM_CONTROLLED="no"
      ONBOOT="yes"
      BOOTPROTO="static"
      IPADDR=ip address here.
      NETMASK=netmask here.

- /etc/sysconfig/network and /etc/resolv.conf left unchanged (resol.conf was a 0 length file)
- restart network

      /etc/init.d/network restart

install some packages
- yum install kdebase.x86_64 -- get some graphics at least
- yum install firefox -- get a browser
- yum install xorg-x11-server-xorg.X86_64 - - get startx to work
- yum install xorg-x11-xinit-session-1.09-13.el6.x86-64 --
- sudo nano vim wget system-config-network-tui kernel-headers make gcc ntp tcsh emacs kernel-devel
- install Nvidia driver NVIDIA-Linux-x86_64-310.19.run
  - problem: complains about Nouveau kernel driver. Alllowed it to disable this.
  - to undo this, need to delete /etd/modprobe.d/nvidia-installer-disable-nouveu.conf
  - reboot and try again
  - still enabled!
  - yum update -y
  - edit /boot/efi/EFI/redhat/grub.conf anmd append rdblacklist=nouveau to kernal boot command to disable
  - reboot. /sbin/lsmod | grep nouveau indicates that it was not loaded
  - install NVIDIA module and run startx. success!
  - edit /sbin/inittab to make level 5 the default boot
    - konsole terminal seems messed up a bit
  - yum groupinstall "Graphical Administration Tools" -- gui to admin tasks
  - now can use gpk-application to install required software

desktop details

switchdesk, used to switch between gnome, kde, and others is no longer available
attempts to make this available by making /etc/sysconfig/desktop did not work
in home directory, make the file ~/.dmrc as follows:


[Desktop]
Session=kde
Language=en_US.utf8

Added:

>
>

needed to install 32-bit libraries to get web to work:
- libXmu-1.0.5-1.el6.i686
- libXt-1.0.7-1.el6.i686
- libXtst-1.0.99.2-3.el6.i686
- libXp-1.0.0-15.1.el6.i686

November 26 2012

yum update -y on oroheus, installed latest Nvidia driver, and rebooted

a263 1

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Revision 1526 Nov 2012 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
- DONE 04-27-11

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

April 20 2011
- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

April 21 2011
- Checked Tecnai F20 computer (Win 2000)
  - 19 GB used out of 34 GB
  - deleted ~3 GB of images from old tests
  - deleted empty folders for several users who are no longer here
  - deleted serialem links for users who are no longer here
  - shortcut to feispy and teispy found in trash; restored to desktop
  - Current disk usage =~ 16 GB, just under 50% capacity
  - TODO -- install internal drive temporarily for backup. Do on maintenance day

April 27 2011
- updated hostname of cem100 to athena
- remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
- ensured that hosts file is updated
- updated hosts file on jeol1230 computer -- cem100 is now athena
- updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
- todo -- fix mounting of cem100 as athena on j1230 -- ckim is using

May 2011

May 24 2011
- updated imod on /cryoem to IMOD 4.1.10
- installed SerialEM 3 on Tecnai F20

May 26 2011
testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work
- divctf-working-2006 (ELF class 64 shared library)
- hlxavg (ELF class 64 shared library)
- hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
- maskparam (ELF class 64 shared library)
- plotphase (ELF class 64 shared library)

July 2011

update priam to CENTOS5
- repalced root drive with 500GB drive
- root partition 100GB
- hector partition 350 GB
- memory upgraded to 12GB
- new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
Zeiss Windows 2000PC -- removed Norton antivirus
- disk nearly 100% full -- this saved 1 GB of space
- computer is isolated from web, so viruses should not be a problem

August 2011

Aug 17-19 --
update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
now uses BeautifulSoup^? to do most searching
- need to update twiki script to do the same
Aug 24 -- set up backup server tartarus:
- running CENTOS 6
- partitioned backup partiton 23.9 TB (RAID5) with GPT (parted)
  - "mkpart ext4 1 -1" --> makes a single partiton using all of disk space, named it ext4
- xfs format (ext4 currently has 16TB maximum size)
- mount as /pithos/
- installed rdiff-backup:
  - needed to enable rpmforge repository
  - installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  - no repository for rdiff backup: installation required manually installing
    - pylibacl-0.5.0-1.el6.x86_64.rpm
    - pyxattr-0.5.0-1.el6.x86_64.rpm
    - gcc using yum
    - python-devel using yum
    - librsync-devel using yum
    - then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
    - installed in /usr/local/

Aug 23
- installed gromus on agamemnon
  - required installation of fftw3 libraries in /usr/local

December 2011

Agamemnon: menelaus drive moved from /dev/sda5 to /cem03_bigdata_backup
- menelaus now has lots of space, and root partition can be expanded to take over all of /dev/sda
Nicolas, Mariena,Ralph PC's are backed up to /hector

January 2012

Jan 3
- New PC set up: rhea (one of the old Win2000 Dell PC's)
- purpose is to
  1. act as a spare workstation
  2. drive added - hades, which is exported onto windows drives using samba.
  3. EM users who want to copy onto USB flash disks the same day can do safely so via this PC
Jan 16
- Priam: mounted former /cemo2_bigdatabackup as /paris (1.4 TB drive)
- /paris exported and mounted on eurydice, agamemnon, minotaur,cem11
- /paris set up to be backed up daily on tartarus
- Agamemnon : root partiton resized to 230 GB, from 30
  - root was very full (2Gb free), so expanded ino space formerly used by menelaus

March 2012

March 14
- Set up Ed's PC - Centos5
- install php mrc tools:
  - copied source from cronus (/usr/include/php/ext/mrc) and unzipped in identical location
  - downloaded FFTW2 library source (NOT FFTW3 as is mention in docs) and installed:

      ./configure --enable-float --enable-type-prefix --enable-shared
      make
      make install

- - libs were put in /usr/local/lib, however, they are 64-bit libraries so made links in /usr/local/lib64/
  - compiled without error however fft power spectrum was invisible

November 2012

Setting up new Hp 620z workstation

system
- two six-core Xeon processors (12 cores total)
- 32 GB RAM (4* 8 GB; system came with 6*2 GB but this is incompatible; there are 8 slots still free for a max of 96 GB RAM)
- 500 GB HD with Windows 7-64 pro installed; 3 extra disks Western Digital 2GB Black 7200rpm
- NVidia Quadro 2000 GPU (192 CUDA cores)
hardware setup
- Installed RAM and GPU; boots windows
- only 2 bays left for the 3 drives; need to convert one 5.25" bay to 3.5"; adapter on order (Nov 20)
- Attempted to install all RAM simultaneously -- no boot. Removing origina RAM allowed boot.
linux install
- Choosing CentOS^? 6.3 as a modern system
- system could not boot from DVD: has EFI instead of old-style BIOS
- therefore had to choose install from Centos6.3-64 EFI minimal CD

linux install details

minimal is truly minimal: no graphics, no make, almost nothing but a shell
set up networking to work according to http://www.convirture.com/ee_wiki/index.php?title=RedHat_6_Networking
- plug in ethernet to bottom port (with sticker) -- this is eth0
- /etc/sysconfig/network-scripts/ifcfg-eth0

       DEVICE="eth0"
      HWADDR=specifc mac address
      NM_CONTROLLED="no"
      ONBOOT="yes"
      BOOTPROTO="static"
      IPADDR=ip address here.
      NETMASK=netmask here.

- /etc/sysconfig/network and /etc/resolv.conf left unchanged (resol.conf was a 0 length file)
- restart network

      /etc/init.d/network restart

install some packages
- yum install kdebase.x86_64 -- get some graphics at least
- yum install firefox -- get a browser
- yum install xorg-x11-server-xorg.X86_64 - - get startx to work
- yum install xorg-x11-xinit-session-1.09-13.el6.x86-64 --
- sudo nano vim wget system-config-network-tui kernel-headers make gcc ntp tcsh emacs kernel-devel
- install Nvidia driver NVIDIA-Linux-x86_64-310.19.run
  - problem: complains about Nouveau kernel driver. Alllowed it to disable this.
  - to undo this, need to delete /etd/modprobe.d/nvidia-installer-disable-nouveu.conf
  - reboot and try again
  - still enabled!
  - yum update -y
  - edit /boot/efi/EFI/redhat/grub.conf anmd append rdblacklist=nouveau to kernal boot command to disable
  - reboot. /sbin/lsmod | grep nouveau indicates that it was not loaded
  - install NVIDIA module and run startx. success!
  - edit /sbin/inittab to make level 5 the default boot
    - konsole terminal seems messed up a bit
  - yum groupinstall "Graphical Administration Tools" -- gui to admin tasks
  - now can use gpk-application to install required software

Added:

>
>

desktop details

switchdesk, used to switch between gnome, kde, and others is no longer available
attempts to make this available by making /etc/sysconfig/desktop did not work
in home directory, make the file ~/.dmrc as follows:

Added:

>
>

[Desktop] Session=kde Language=en_US.utf8

Added:

>
>

November 26 2012

yum update -y on oroheus, installed latest Nvidia driver, and rebooted

a263 1

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Revision 1421 Nov 2012 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
- DONE 04-27-11

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

April 20 2011
- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

April 21 2011
- Checked Tecnai F20 computer (Win 2000)
  - 19 GB used out of 34 GB
  - deleted ~3 GB of images from old tests
  - deleted empty folders for several users who are no longer here
  - deleted serialem links for users who are no longer here
  - shortcut to feispy and teispy found in trash; restored to desktop
  - Current disk usage =~ 16 GB, just under 50% capacity
  - TODO -- install internal drive temporarily for backup. Do on maintenance day

April 27 2011
- updated hostname of cem100 to athena
- remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
- ensured that hosts file is updated
- updated hosts file on jeol1230 computer -- cem100 is now athena
- updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
- todo -- fix mounting of cem100 as athena on j1230 -- ckim is using

May 2011

May 24 2011
- updated imod on /cryoem to IMOD 4.1.10
- installed SerialEM 3 on Tecnai F20

May 26 2011
testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work
- divctf-working-2006 (ELF class 64 shared library)
- hlxavg (ELF class 64 shared library)
- hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
- maskparam (ELF class 64 shared library)
- plotphase (ELF class 64 shared library)

July 2011

update priam to CENTOS5
- repalced root drive with 500GB drive
- root partition 100GB
- hector partition 350 GB
- memory upgraded to 12GB
- new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
Zeiss Windows 2000PC -- removed Norton antivirus
- disk nearly 100% full -- this saved 1 GB of space
- computer is isolated from web, so viruses should not be a problem

August 2011

Aug 17-19 --
update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
now uses BeautifulSoup^? to do most searching
- need to update twiki script to do the same
Aug 24 -- set up backup server tartarus:
- running CENTOS 6
- partitioned backup partiton 23.9 TB (RAID5) with GPT (parted)
  - "mkpart ext4 1 -1" --> makes a single partiton using all of disk space, named it ext4
- xfs format (ext4 currently has 16TB maximum size)
- mount as /pithos/
- installed rdiff-backup:
  - needed to enable rpmforge repository
  - installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  - no repository for rdiff backup: installation required manually installing
    - pylibacl-0.5.0-1.el6.x86_64.rpm
    - pyxattr-0.5.0-1.el6.x86_64.rpm
    - gcc using yum
    - python-devel using yum
    - librsync-devel using yum
    - then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
    - installed in /usr/local/

Aug 23
- installed gromus on agamemnon
  - required installation of fftw3 libraries in /usr/local

December 2011

Agamemnon: menelaus drive moved from /dev/sda5 to /cem03_bigdata_backup
- menelaus now has lots of space, and root partition can be expanded to take over all of /dev/sda
Nicolas, Mariena,Ralph PC's are backed up to /hector

January 2012

Jan 3
- New PC set up: rhea (one of the old Win2000 Dell PC's)
- purpose is to
  1. act as a spare workstation
  2. drive added - hades, which is exported onto windows drives using samba.
  3. EM users who want to copy onto USB flash disks the same day can do safely so via this PC
Jan 16
- Priam: mounted former /cemo2_bigdatabackup as /paris (1.4 TB drive)
- /paris exported and mounted on eurydice, agamemnon, minotaur,cem11
- /paris set up to be backed up daily on tartarus
- Agamemnon : root partiton resized to 230 GB, from 30
  - root was very full (2Gb free), so expanded ino space formerly used by menelaus

March 2012

March 14
- Set up Ed's PC - Centos5
- install php mrc tools:
  - copied source from cronus (/usr/include/php/ext/mrc) and unzipped in identical location
  - downloaded FFTW2 library source (NOT FFTW3 as is mention in docs) and installed:

      ./configure --enable-float --enable-type-prefix --enable-shared
      make
      make install

- - libs were put in /usr/local/lib, however, they are 64-bit libraries so made links in /usr/local/lib64/
  - compiled without error however fft power spectrum was invisible

November 2012

Setting up new Hp 620z workstation

system
- two six-core Xeon processors (12 cores total)
- 32 GB RAM (4* 8 GB; system came with 6*2 GB but this is incompatible; there are 8 slots still free for a max of 96 GB RAM)
- 500 GB HD with Windows 7-64 pro installed; 3 extra disks Western Digital 2GB Black 7200rpm
- NVidia Quadro 2000 GPU (192 CUDA cores)
hardware setup
- Installed RAM and GPU; boots windows
- only 2 bays left for the 3 drives; need to convert one 5.25" bay to 3.5"; adapter on order (Nov 20)
- Attempted to install all RAM simultaneously -- no boot. Removing origina RAM allowed boot.
linux install
- Choosing CentOS^? 6.3 as a modern system
- system could not boot from DVD: has EFI instead of old-style BIOS
- therefore had to choose install from Centos6.3-64 EFI minimal CD

linux install details

minimal is truly minimal: no graphics, no make, almost nothing but a shell
set up networking to work according to http://www.convirture.com/ee_wiki/index.php?title=RedHat_6_Networking
- plug in ethernet to bottom port (with sticker) -- this is eth0
- /etc/sysconfig/network-scripts/ifcfg-eth0

       DEVICE="eth0"
      HWADDR=specifc mac address
      NM_CONTROLLED="no"
      ONBOOT="yes"
      BOOTPROTO="static"
      IPADDR=ip address here.
      NETMASK=netmask here.

- /etc/sysconfig/network and /etc/resolv.conf left unchanged (resol.conf was a 0 length file)
- restart network

      /etc/init.d/network restart

install some packages
- yum install kdebase.x86_64 -- get some graphics at least
- yum install firefox -- get a browser
- yum install xorg-x11-server-xorg.X86_64 - - get startx to work
- yum install xorg-x11-xinit-session-1.09-13.el6.x86-64 --
- sudo nano vim wget system-config-network-tui kernel-headers make gcc ntp tcsh emacs kernel-devel
- install Nvidia driver NVIDIA-Linux-x86_64-310.19.run
  - problem: complains about Nouveau kernel driver. Alllowed it to disable this.
  - to undo this, need to delete /etd/modprobe.d/nvidia-installer-disable-nouveu.conf
  - reboot and try again
  - still enabled!
  - yum update -y
  - edit /boot/efi/EFI/redhat/grub.conf anmd append rdblacklist=nouveau to kernal boot command to disable
  - reboot. /sbin/lsmod | grep nouveau indicates that it was not loaded
  - install NVIDIA module and run startx. success!
  - edit /sbin/inittab to make level 5 the default boot
    - konsole terminal seems messed up a bit

Added:

>
>

- - yum groupinstall "Graphical Administration Tools" -- gui to admin tasks
  - now can use gpk-application to install required software

a263 1

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Revision 1320 Nov 2012 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
- DONE 04-27-11

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

April 20 2011
- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

April 21 2011
- Checked Tecnai F20 computer (Win 2000)
  - 19 GB used out of 34 GB
  - deleted ~3 GB of images from old tests
  - deleted empty folders for several users who are no longer here
  - deleted serialem links for users who are no longer here
  - shortcut to feispy and teispy found in trash; restored to desktop
  - Current disk usage =~ 16 GB, just under 50% capacity
  - TODO -- install internal drive temporarily for backup. Do on maintenance day

April 27 2011
- updated hostname of cem100 to athena
- remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
- ensured that hosts file is updated
- updated hosts file on jeol1230 computer -- cem100 is now athena
- updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
- todo -- fix mounting of cem100 as athena on j1230 -- ckim is using

May 2011

May 24 2011
- updated imod on /cryoem to IMOD 4.1.10
- installed SerialEM 3 on Tecnai F20

May 26 2011
testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work
- divctf-working-2006 (ELF class 64 shared library)
- hlxavg (ELF class 64 shared library)
- hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
- maskparam (ELF class 64 shared library)
- plotphase (ELF class 64 shared library)

July 2011

update priam to CENTOS5
- repalced root drive with 500GB drive
- root partition 100GB
- hector partition 350 GB
- memory upgraded to 12GB
- new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
Zeiss Windows 2000PC -- removed Norton antivirus
- disk nearly 100% full -- this saved 1 GB of space
- computer is isolated from web, so viruses should not be a problem

August 2011

Aug 17-19 --
update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
now uses BeautifulSoup^? to do most searching
- need to update twiki script to do the same
Aug 24 -- set up backup server tartarus:
- running CENTOS 6
- partitioned backup partiton 23.9 TB (RAID5) with GPT (parted)
  - "mkpart ext4 1 -1" --> makes a single partiton using all of disk space, named it ext4
- xfs format (ext4 currently has 16TB maximum size)
- mount as /pithos/
- installed rdiff-backup:
  - needed to enable rpmforge repository
  - installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  - no repository for rdiff backup: installation required manually installing
    - pylibacl-0.5.0-1.el6.x86_64.rpm
    - pyxattr-0.5.0-1.el6.x86_64.rpm
    - gcc using yum
    - python-devel using yum
    - librsync-devel using yum
    - then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
    - installed in /usr/local/

Aug 23
- installed gromus on agamemnon
  - required installation of fftw3 libraries in /usr/local

December 2011

Agamemnon: menelaus drive moved from /dev/sda5 to /cem03_bigdata_backup
- menelaus now has lots of space, and root partition can be expanded to take over all of /dev/sda
Nicolas, Mariena,Ralph PC's are backed up to /hector

January 2012

Jan 3
- New PC set up: rhea (one of the old Win2000 Dell PC's)
- purpose is to
  1. act as a spare workstation
  2. drive added - hades, which is exported onto windows drives using samba.
  3. EM users who want to copy onto USB flash disks the same day can do safely so via this PC
Jan 16
- Priam: mounted former /cemo2_bigdatabackup as /paris (1.4 TB drive)
- /paris exported and mounted on eurydice, agamemnon, minotaur,cem11
- /paris set up to be backed up daily on tartarus
- Agamemnon : root partiton resized to 230 GB, from 30
  - root was very full (2Gb free), so expanded ino space formerly used by menelaus

March 2012

March 14
- Set up Ed's PC - Centos5
- install php mrc tools:
  - copied source from cronus (/usr/include/php/ext/mrc) and unzipped in identical location
  - downloaded FFTW2 library source (NOT FFTW3 as is mention in docs) and installed:

      ./configure --enable-float --enable-type-prefix --enable-shared
      make
      make install

- - libs were put in /usr/local/lib, however, they are 64-bit libraries so made links in /usr/local/lib64/
  - compiled without error however fft power spectrum was invisible

Added:

>
>

November 2012

Setting up new Hp 620z workstation

system
- two six-core Xeon processors (12 cores total)
- 32 GB RAM (4* 8 GB; system came with 6*2 GB but this is incompatible; there are 8 slots still free for a max of 96 GB RAM)
- 500 GB HD with Windows 7-64 pro installed; 3 extra disks Western Digital 2GB Black 7200rpm
- NVidia Quadro 2000 GPU (192 CUDA cores)
hardware setup
- Installed RAM and GPU; boots windows
- only 2 bays left for the 3 drives; need to convert one 5.25" bay to 3.5"; adapter on order (Nov 20)
- Attempted to install all RAM simultaneously -- no boot. Removing origina RAM allowed boot.
linux install
- Choosing CentOS^? 6.3 as a modern system
- system could not boot from DVD: has EFI instead of old-style BIOS
- therefore had to choose install from Centos6.3-64 EFI minimal CD

linux install details

minimal is truly minimal: no graphics, no make, almost nothing but a shell
set up networking to work according to http://www.convirture.com/ee_wiki/index.php?title=RedHat_6_Networking
- plug in ethernet to bottom port (with sticker) -- this is eth0
- /etc/sysconfig/network-scripts/ifcfg-eth0

       DEVICE="eth0"
      HWADDR=specifc mac address
      NM_CONTROLLED="no"
      ONBOOT="yes"
      BOOTPROTO="static"
      IPADDR=ip address here.
      NETMASK=netmask here.

- /etc/sysconfig/network and /etc/resolv.conf left unchanged (resol.conf was a 0 length file)
- restart network

      /etc/init.d/network restart

install some packages
- yum install kdebase.x86_64 -- get some graphics at least
- yum install firefox -- get a browser
- yum install xorg-x11-server-xorg.X86_64 - - get startx to work
- yum install xorg-x11-xinit-session-1.09-13.el6.x86-64 --
- sudo nano vim wget system-config-network-tui kernel-headers make gcc ntp tcsh emacs kernel-devel
- install Nvidia driver NVIDIA-Linux-x86_64-310.19.run
  - problem: complains about Nouveau kernel driver. Alllowed it to disable this.
  - to undo this, need to delete /etd/modprobe.d/nvidia-installer-disable-nouveu.conf
  - reboot and try again
  - still enabled!
  - yum update -y
  - edit /boot/efi/EFI/redhat/grub.conf anmd append rdblacklist=nouveau to kernal boot command to disable
  - reboot. /sbin/lsmod | grep nouveau indicates that it was not loaded
  - install NVIDIA module and run startx. success!
  - edit /sbin/inittab to make level 5 the default boot
    - konsole terminal seems messed up a bit

a263 1

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Revision 1214 Mar 2012 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
- DONE 04-27-11

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

April 20 2011
- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

April 21 2011
- Checked Tecnai F20 computer (Win 2000)
  - 19 GB used out of 34 GB
  - deleted ~3 GB of images from old tests
  - deleted empty folders for several users who are no longer here
  - deleted serialem links for users who are no longer here
  - shortcut to feispy and teispy found in trash; restored to desktop
  - Current disk usage =~ 16 GB, just under 50% capacity
  - TODO -- install internal drive temporarily for backup. Do on maintenance day

April 27 2011
- updated hostname of cem100 to athena
- remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
- ensured that hosts file is updated
- updated hosts file on jeol1230 computer -- cem100 is now athena
- updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
- todo -- fix mounting of cem100 as athena on j1230 -- ckim is using

May 2011

May 24 2011
- updated imod on /cryoem to IMOD 4.1.10
- installed SerialEM 3 on Tecnai F20

May 26 2011
testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work
- divctf-working-2006 (ELF class 64 shared library)
- hlxavg (ELF class 64 shared library)
- hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
- maskparam (ELF class 64 shared library)
- plotphase (ELF class 64 shared library)

July 2011

update priam to CENTOS5
- repalced root drive with 500GB drive
- root partition 100GB
- hector partition 350 GB
- memory upgraded to 12GB
- new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
Zeiss Windows 2000PC -- removed Norton antivirus
- disk nearly 100% full -- this saved 1 GB of space
- computer is isolated from web, so viruses should not be a problem

August 2011

Aug 17-19 --
update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
now uses BeautifulSoup^? to do most searching
- need to update twiki script to do the same
Aug 24 -- set up backup server tartarus:
- running CENTOS 6
- partitioned backup partiton 23.9 TB (RAID5) with GPT (parted)
  - "mkpart ext4 1 -1" --> makes a single partiton using all of disk space, named it ext4
- xfs format (ext4 currently has 16TB maximum size)
- mount as /pithos/
- installed rdiff-backup:
  - needed to enable rpmforge repository
  - installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  - no repository for rdiff backup: installation required manually installing
    - pylibacl-0.5.0-1.el6.x86_64.rpm
    - pyxattr-0.5.0-1.el6.x86_64.rpm
    - gcc using yum
    - python-devel using yum
    - librsync-devel using yum
    - then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
    - installed in /usr/local/

Aug 23
- installed gromus on agamemnon
  - required installation of fftw3 libraries in /usr/local

December 2011

Agamemnon: menelaus drive moved from /dev/sda5 to /cem03_bigdata_backup
- menelaus now has lots of space, and root partition can be expanded to take over all of /dev/sda
Nicolas, Mariena,Ralph PC's are backed up to /hector

January 2012

Jan 3
- New PC set up: rhea (one of the old Win2000 Dell PC's)
- purpose is to
  1. act as a spare workstation
  2. drive added - hades, which is exported onto windows drives using samba.
  3. EM users who want to copy onto USB flash disks the same day can do safely so via this PC
Jan 16
- Priam: mounted former /cemo2_bigdatabackup as /paris (1.4 TB drive)
- /paris exported and mounted on eurydice, agamemnon, minotaur,cem11
- /paris set up to be backed up daily on tartarus
- Agamemnon : root partiton resized to 230 GB, from 30
  - root was very full (2Gb free), so expanded ino space formerly used by menelaus

Added:

>
>

March 2012

March 14
- Set up Ed's PC - Centos5
- install php mrc tools:
  - copied source from cronus (/usr/include/php/ext/mrc) and unzipped in identical location
  - downloaded FFTW2 library source (NOT FFTW3 as is mention in docs) and installed:

      ./configure --enable-float --enable-type-prefix --enable-shared
      make
      make install

- - libs were put in /usr/local/lib, however, they are 64-bit libraries so made links in /usr/local/lib64/
  - compiled without error however fft power spectrum was invisible

a263 1

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Revision 1116 Jan 2012 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
- DONE 04-27-11

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

April 20 2011
- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

April 21 2011
- Checked Tecnai F20 computer (Win 2000)
  - 19 GB used out of 34 GB
  - deleted ~3 GB of images from old tests
  - deleted empty folders for several users who are no longer here
  - deleted serialem links for users who are no longer here
  - shortcut to feispy and teispy found in trash; restored to desktop
  - Current disk usage =~ 16 GB, just under 50% capacity
  - TODO -- install internal drive temporarily for backup. Do on maintenance day

April 27 2011
- updated hostname of cem100 to athena
- remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
- ensured that hosts file is updated
- updated hosts file on jeol1230 computer -- cem100 is now athena
- updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
- todo -- fix mounting of cem100 as athena on j1230 -- ckim is using

May 2011

May 24 2011
- updated imod on /cryoem to IMOD 4.1.10
- installed SerialEM 3 on Tecnai F20

May 26 2011
testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work
- divctf-working-2006 (ELF class 64 shared library)
- hlxavg (ELF class 64 shared library)
- hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
- maskparam (ELF class 64 shared library)
- plotphase (ELF class 64 shared library)

July 2011

update priam to CENTOS5
- repalced root drive with 500GB drive
- root partition 100GB
- hector partition 350 GB
- memory upgraded to 12GB
- new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
Zeiss Windows 2000PC -- removed Norton antivirus
- disk nearly 100% full -- this saved 1 GB of space
- computer is isolated from web, so viruses should not be a problem

August 2011

Aug 17-19 --
update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
now uses BeautifulSoup^? to do most searching
- need to update twiki script to do the same
Aug 24 -- set up backup server tartarus:
- running CENTOS 6
- partitioned backup partiton 23.9 TB (RAID5) with GPT (parted)
  - "mkpart ext4 1 -1" --> makes a single partiton using all of disk space, named it ext4
- xfs format (ext4 currently has 16TB maximum size)
- mount as /pithos/
- installed rdiff-backup:
  - needed to enable rpmforge repository
  - installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  - no repository for rdiff backup: installation required manually installing
    - pylibacl-0.5.0-1.el6.x86_64.rpm
    - pyxattr-0.5.0-1.el6.x86_64.rpm
    - gcc using yum
    - python-devel using yum
    - librsync-devel using yum
    - then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
    - installed in /usr/local/

Aug 23
- installed gromus on agamemnon
  - required installation of fftw3 libraries in /usr/local

Added:

>
>

December 2011

Agamemnon: menelaus drive moved from /dev/sda5 to /cem03_bigdata_backup
- menelaus now has lots of space, and root partition can be expanded to take over all of /dev/sda
Nicolas, Mariena,Ralph PC's are backed up to /hector

January 2012

Jan 3
- New PC set up: rhea (one of the old Win2000 Dell PC's)
- purpose is to
  1. act as a spare workstation
  2. drive added - hades, which is exported onto windows drives using samba.
  3. EM users who want to copy onto USB flash disks the same day can do safely so via this PC
Jan 16
- Priam: mounted former /cemo2_bigdatabackup as /paris (1.4 TB drive)
- /paris exported and mounted on eurydice, agamemnon, minotaur,cem11
- /paris set up to be backed up daily on tartarus
- Agamemnon : root partiton resized to 230 GB, from 30
  - root was very full (2Gb free), so expanded ino space formerly used by menelaus

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Deleted:

<
<

Revision 1024 Aug 2011 - Main.BillRice

   META TOPICPARENT   name="CemITSystem" 

Contents
 
 Administration logs 
  Jan 2011
   April 2011
   May 2011 
  July 2011
 
 
 


 Administration logs 

 Jan 2011 
 
 Set up and installed new computer, cem15
  CentOS^? 5.5, RAID5, 5.2 TB disk
  All standard EM software installed
  cem15data drive is nfs shared and exported 
  users added on ad hoc basis
 

 April 2011 
 
 April 7 2011 
 back up svn server from cem100 and move to cem01
  cem01 now running svn server (current revision=48) and apache server
  made very basic web page for cem01 which links to svn repos as well as sesame
 
 
 

 April 8 2011 -- rename computers as follows 
 cem15 --> orpheus
  cem01 -->cronus
  cem02 --> priam
  cem03 --> agamemnon
  cem11 --> tlaloc
  cem12 --> minotaur
 
  made new hosts file listing these changes, and uploaded to svn server
 
 

 TO DO 
 rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
  DONE 04-27-11
 
 
 

 April 10 2011 
 copy all of Kens' data from Tecnai to external hard drive
  delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps
 
 
 

 April 11 2011 -- rename drives as follows: 
 cem02bigdata --> helen
  cem02data --> hector
  cem02data2 --> hecuba
  cem03bigdata --> achilles
  cem03data --> menelaus
  cem03data2 --> iphigenia
  cem11data --> tonatiu
  cem12data --> theseus
  cem15data --> eurydice
 
  exported and mounted all newly named drives
  updated hosts file on jeol1230 pc to reflect these changes
  change backup scripts to reflect these changes
  found problem with leginon not talking to jerol1230 from minotaur (cem12) after change 
 fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
  verified that leginon is still working directly on jeol1230 and remotely from minotaur
 
 
 

 links made to old drive names
  cronus (cem01) now viewable from outside as cronus.nysbc.org 
 verified by browsing cronus.nysbc.org from public network
 
  TO DO 
 rename dl380 to arachne, and make link
  finish renaming, after backup server installed and running 
 rename cem02bigdata_backup to paris
  rename cem03bigdata_backup to odysseus
  find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???
 
 
 
 

 April 20 2011 
 updated IMOD to IMOD 4.1.9 (current version) on /cryoem 
 /cryoem/IMOD now refers to this version
  /cryoem/IMOD3 referes to imod 3.13
  updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  note that priam (centos4) will likely not run this version 
 
 
 
 

 April 21 2011 
 Checked Tecnai F20 computer (Win 2000) 
 19 GB used out of 34 GB
  deleted ~3 GB of images from old tests
  deleted empty folders for several users who are no longer here
  deleted serialem links for users who are no longer here
  shortcut to feispy and teispy found in trash; restored to desktop
  Current disk usage =~ 16 GB, just under 50% capacity
  TODO -- install internal drive temporarily for backup. Do on maintenance day
 
 
 
 

 April 27 2011 
 updated hostname of cem100 to athena
  remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
  ensured that hosts file is updated
  updated hosts file on jeol1230 computer -- cem100 is now athena
  updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
  todo -- fix mounting of cem100 as athena on j1230 -- ckim is using
 
 

 May 2011 
 
 May 24 2011 
 updated imod on /cryoem to IMOD 4.1.10
  installed SerialEM 3 on Tecnai F20
 
 
 

 May 26 2011
  testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work 
 divctf-working-2006 (ELF class 64 shared library)
  hlxavg (ELF class 64 shared library)
  hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
  maskparam (ELF class 64 shared library)
  plotphase (ELF class 64 shared library)
 
 

 July 2011 
 
 update priam to CENTOS5 
 repalced root drive with 500GB drive
  root partition 100GB
  hector partition 350 GB
  memory upgraded to 12GB
  new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
-  META TOPICPARENT
+ name="CemITSystem"
->
>
+ Zeiss Windows 2000PC -- removed Norton antivirus 
 disk nearly 100% full -- this saved 1 GB of space
  computer is isolated from web, so viruses should not be a problem
  August 2011 
 
 Aug 17-19 -- 
  update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
  now uses BeautifulSoup^? to do most searching 
 need to update  twiki script to do the same
 
  Aug 24 -- set up backup server tartarus: 
 running CENTOS 6
  partitioned backup partiton 23.9 TB (RAID5) with GPT (parted)
-<
<
+ ext4 format
->
>
+ "mkpart ext4 1 -1"  --> makes a single partiton using all of disk space, named it ext4
->
>
+ xfs format (ext4 currently has 16TB maximum size)
  mount as /pithos/
  installed rdiff-backup: 
 needed to enable rpmforge repository
  installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  no repository for rdiff backup: installation required manually installing  
 pylibacl-0.5.0-1.el6.x86_64.rpm
  pyxattr-0.5.0-1.el6.x86_64.rpm
  gcc using yum
  python-devel using yum
  librsync-devel using yum
  then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
  installed in /usr/local/
->
>
+ Aug 23 
 installed gromus on agamemnon 
 required installation of fftw3 libraries in /usr/local
  Set ALLOWTOPICVIEW = 
 

-- BillRice - 12 Apr 2011
->
>

Revision 924 Aug 2011 - Main.BillRice

   META TOPICPARENT   name="CemITSystem" 

Contents
 
 Administration logs 
  Jan 2011
   April 2011
   May 2011
 
 


 Administration logs 

 Jan 2011 
 
 Set up and installed new computer, cem15
  CentOS^? 5.5, RAID5, 5.2 TB disk
  All standard EM software installed
  cem15data drive is nfs shared and exported 
  users added on ad hoc basis
 

 April 2011 
 
 April 7 2011 
 back up svn server from cem100 and move to cem01
  cem01 now running svn server (current revision=48) and apache server
  made very basic web page for cem01 which links to svn repos as well as sesame
 
 
 

 April 8 2011 -- rename computers as follows 
 cem15 --> orpheus
  cem01 -->cronus
  cem02 --> priam
  cem03 --> agamemnon
  cem11 --> tlaloc
  cem12 --> minotaur
 
  made new hosts file listing these changes, and uploaded to svn server
 
 

 TO DO 
 rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
  DONE 04-27-11
 
 
 

 April 10 2011 
 copy all of Kens' data from Tecnai to external hard drive
  delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps
 
 
 

 April 11 2011 -- rename drives as follows: 
 cem02bigdata --> helen
  cem02data --> hector
  cem02data2 --> hecuba
  cem03bigdata --> achilles
  cem03data --> menelaus
  cem03data2 --> iphigenia
  cem11data --> tonatiu
  cem12data --> theseus
  cem15data --> eurydice
 
  exported and mounted all newly named drives
  updated hosts file on jeol1230 pc to reflect these changes
  change backup scripts to reflect these changes
  found problem with leginon not talking to jerol1230 from minotaur (cem12) after change 
 fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
  verified that leginon is still working directly on jeol1230 and remotely from minotaur
 
 
 

 links made to old drive names
  cronus (cem01) now viewable from outside as cronus.nysbc.org 
 verified by browsing cronus.nysbc.org from public network
 
  TO DO 
 rename dl380 to arachne, and make link
  finish renaming, after backup server installed and running 
 rename cem02bigdata_backup to paris
  rename cem03bigdata_backup to odysseus
  find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???
 
 
 
 

 April 20 2011 
 updated IMOD to IMOD 4.1.9 (current version) on /cryoem 
 /cryoem/IMOD now refers to this version
  /cryoem/IMOD3 referes to imod 3.13
  updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  note that priam (centos4) will likely not run this version 
 
 
 
 

 April 21 2011 
 Checked Tecnai F20 computer (Win 2000) 
 19 GB used out of 34 GB
  deleted ~3 GB of images from old tests
  deleted empty folders for several users who are no longer here
  deleted serialem links for users who are no longer here
  shortcut to feispy and teispy found in trash; restored to desktop
  Current disk usage =~ 16 GB, just under 50% capacity
  TODO -- install internal drive temporarily for backup. Do on maintenance day
 
 
 
 

 April 27 2011 
 updated hostname of cem100 to athena
  remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
  ensured that hosts file is updated
  updated hosts file on jeol1230 computer -- cem100 is now athena
  updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
  todo -- fix mounting of cem100 as athena on j1230 -- ckim is using
 
 

 May 2011 
 
 May 24 2011 
 updated imod on /cryoem to IMOD 4.1.10
  installed SerialEM 3 on Tecnai F20
 
 
 

 May 26 2011
  testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work 
 divctf-working-2006 (ELF class 64 shared library)
  hlxavg (ELF class 64 shared library)
  hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
  maskparam (ELF class 64 shared library)
  plotphase (ELF class 64 shared library)
-  META TOPICPARENT
+ name="CemITSystem"
->
>
+ July 2011 
 
 update priam to CENTOS5 
 repalced root drive with 500GB drive
  root partition 100GB
  hector partition 350 GB
  memory upgraded to 12GB
  new GPU installed from cem11 (Ruben's) so GPU can be used for calculations (CUDA)
-<
<
->
>
+ August 2011 
 
 Aug 17-19 --
->
>
+ update temimps2twiki.py on athena -- now downloads all attachments (ppt,pdf,zip,...)
  now uses BeautifulSoup^? to do most searching 
 need to update  twiki script to do the same
 
  Aug 24 -- set up backup server tartarus: 
 running CENTOS 6
  partitioned backup partiton 23.9 TB (RAID5) with GPT (parted)
  ext4 format
  mount as /pithos/
  installed rdiff-backup: 
 needed to enable rpmforge repository
  installed yum-priorities -- put CentOS^? priorities at 1, rpmforge at 10 to prevent rpmforge from overtaking centos
  no repository for rdiff backup: installation required manually installing  
 pylibacl-0.5.0-1.el6.x86_64.rpm
  pyxattr-0.5.0-1.el6.x86_64.rpm
  gcc using yum
  python-devel using yum
  librsync-devel using yum
  then needed to manually install and compile rdiff-backup-1.2.8 (rpm did not work)
  installed in /usr/local/
  Set ALLOWTOPICVIEW = 
 

-- BillRice - 12 Apr 2011

Revision 827 May 2011 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs
- Jan 2011
- April 2011

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
- DONE 04-27-11

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

April 20 2011
- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

April 21 2011
- Checked Tecnai F20 computer (Win 2000)
  - 19 GB used out of 34 GB
  - deleted ~3 GB of images from old tests
  - deleted empty folders for several users who are no longer here
  - deleted serialem links for users who are no longer here
  - shortcut to feispy and teispy found in trash; restored to desktop
  - Current disk usage =~ 16 GB, just under 50% capacity
  - TODO -- install internal drive temporarily for backup. Do on maintenance day

April 27 2011
- updated hostname of cem100 to athena
- remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
- ensured that hosts file is updated
- updated hosts file on jeol1230 computer -- cem100 is now athena
- updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
- todo -- fix mounting of cem100 as athena on j1230 -- ckim is using

Changed:

<
<

April 2011

>
>

May 2011

May 24 2011
- updated imod on /cryoem to IMOD 4.1.10
- installed SerialEM 3 on Tecnai F20

Added:

>
>

May 26 2011
testing of 32-bit helix programs in kubuntu 9 (lab laptop) to see which need recompiling: listing of progs which do not work
- divctf-working-2006 (ELF class 64 shared library)
- hlxavg (ELF class 64 shared library)
- hlxresidual.pyc (should not be included -- need hlxresidual.py instead)
- maskparam (ELF class 64 shared library)
- plotphase (ELF class 64 shared library)

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Revision 724 May 2011 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs
- Jan 2011
- April 2011

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
- DONE 04-27-11

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

April 20 2011
- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

April 21 2011
- Checked Tecnai F20 computer (Win 2000)
  - 19 GB used out of 34 GB
  - deleted ~3 GB of images from old tests
  - deleted empty folders for several users who are no longer here
  - deleted serialem links for users who are no longer here
  - shortcut to feispy and teispy found in trash; restored to desktop
  - Current disk usage =~ 16 GB, just under 50% capacity
  - TODO -- install internal drive temporarily for backup. Do on maintenance day

April 27 2011
- updated hostname of cem100 to athena
- remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
- ensured that hosts file is updated
- updated hosts file on jeol1230 computer -- cem100 is now athena
- updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
- todo -- fix mounting of cem100 as athena on j1230 -- ckim is using

Added:

>
>

April 2011

May 24 2011
- updated imod on /cryoem to IMOD 4.1.10
- installed SerialEM 3 on Tecnai F20

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Revision 628 Apr 2011 - Main.BillRice

   META TOPICPARENT   name="CemITSystem" 

Contents
 
 Administration logs 
  Jan 2011
   April 2011
 
 


 Administration logs 

 Jan 2011 
 
 Set up and installed new computer, cem15
  CentOS^? 5.5, RAID5, 5.2 TB disk
  All standard EM software installed
  cem15data drive is nfs shared and exported 
  users added on ad hoc basis
 

 April 2011 
 
 April 7 2011 
 back up svn server from cem100 and move to cem01
  cem01 now running svn server (current revision=48) and apache server
  made very basic web page for cem01 which links to svn repos as well as sesame
 
 
 

 April 8 2011 -- rename computers as follows 
 cem15 --> orpheus
  cem01 -->cronus
  cem02 --> priam
  cem03 --> agamemnon
  cem11 --> tlaloc
  cem12 --> minotaur
 
  made new hosts file listing these changes, and uploaded to svn server
 
 

 TO DO 
 rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break
-  META TOPICPARENT
+ name="CemITSystem"
->
>
+ DONE 04-27-11
  April 10 2011 
 copy all of Kens' data from Tecnai to external hard drive
  delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps
 
 
 

 April 11 2011 -- rename drives as follows: 
 cem02bigdata --> helen
  cem02data --> hector
  cem02data2 --> hecuba
  cem03bigdata --> achilles
  cem03data --> menelaus
  cem03data2 --> iphigenia
  cem11data --> tonatiu
  cem12data --> theseus
  cem15data --> eurydice
 
  exported and mounted all newly named drives
  updated hosts file on jeol1230 pc to reflect these changes
  change backup scripts to reflect these changes
  found problem with leginon not talking to jerol1230 from minotaur (cem12) after change 
 fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
  verified that leginon is still working directly on jeol1230 and remotely from minotaur
 
 
 

 links made to old drive names
  cronus (cem01) now viewable from outside as cronus.nysbc.org 
 verified by browsing cronus.nysbc.org from public network
 
  TO DO 
 rename dl380 to arachne, and make link
  finish renaming, after backup server installed and running 
 rename cem02bigdata_backup to paris
  rename cem03bigdata_backup to odysseus
  find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???
 
 
 
 

 April 20 2011 
 updated IMOD to IMOD 4.1.9 (current version) on /cryoem 
 /cryoem/IMOD now refers to this version
  /cryoem/IMOD3 referes to imod 3.13
  updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  note that priam (centos4) will likely not run this version 
 
 
 
 

 April 21 2011 
 Checked Tecnai F20 computer (Win 2000) 
 19 GB used out of 34 GB
  deleted ~3 GB of images from old tests
  deleted empty folders for several users who are no longer here
  deleted serialem links for users who are no longer here
  shortcut to feispy and teispy found in trash; restored to desktop
  Current disk usage =~ 16 GB, just under 50% capacity
  TODO -- install internal drive temporarily for backup. Do on maintenance day
-<
<
->
>
+ April 27 2011
->
>
+ updated hostname of cem100 to athena
  remounted cem100/data as athena/data on cronus,priam,agamemnon,minotaur
  ensured that hosts file is updated
  updated hosts file on jeol1230 computer -- cem100 is now athena
  updated sinedon.cfg on j1230 and minotaur -- now has athena as db host
  todo -- fix mounting of cem100 as athena on j1230 -- ckim is using
  Set ALLOWTOPICVIEW = 
 

-- BillRice - 12 Apr 2011

Revision 521 Apr 2011 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs
- Jan 2011
- April 2011

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

April 20 2011
- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

Added:

>
>

April 21 2011
- Checked Tecnai F20 computer (Win 2000)
  - 19 GB used out of 34 GB
  - deleted ~3 GB of images from old tests
  - deleted empty folders for several users who are no longer here
  - deleted serialem links for users who are no longer here
  - shortcut to feispy and teispy found in trash; restored to desktop
  - Current disk usage =~ 16 GB, just under 50% capacity
  - TODO -- install internal drive temporarily for backup. Do on maintenance day

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Revision 420 Apr 2011 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs
- Jan 2011
- April 2011

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

Changed:

<
<

April 20 2010

>
>

April 20 2011

- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Revision 320 Apr 2011 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs
- Jan 2011
- April 2011

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
change backup scripts to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link
- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

Added:

>
>

April 20 2010
- updated IMOD to IMOD 4.1.9 (current version) on /cryoem
  - /cryoem/IMOD now refers to this version
  - /cryoem/IMOD3 referes to imod 3.13
  - updated .cshrc fil on orpheus, agamemnon, minotaur to reflect this
  - note that priam (centos4) will likely not run this version

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Revision 212 Apr 2011 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs
- Jan 2011
- April 2011

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes

Added:

>
>

change backup scripts to reflect these changes

found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link

Added:

>
>

- finish renaming, after backup server installed and running
  - rename cem02bigdata_backup to paris
  - rename cem03bigdata_backup to odysseus
  - find use for external USB RAID on minotaur, since it will no longer be used for backup. Kens data???

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

Revision 112 Apr 2011 - Main.BillRice

META TOPICPARENT	name="CemITSystem"

Contents

Administration logs
- Jan 2011
- April 2011

Administration logs

Jan 2011

Set up and installed new computer, cem15
CentOS^? 5.5, RAID5, 5.2 TB disk
All standard EM software installed
cem15data drive is nfs shared and exported
users added on ad hoc basis

April 2011

April 7 2011
- back up svn server from cem100 and move to cem01
- cem01 now running svn server (current revision=48) and apache server
- made very basic web page for cem01 which links to svn repos as well as sesame

April 8 2011 -- rename computers as follows
- cem15 --> orpheus
- cem01 -->cronus
- cem02 --> priam
- cem03 --> agamemnon
- cem11 --> tlaloc
- cem12 --> minotaur
made new hosts file listing these changes, and uploaded to svn server

TO DO
- rename cem100 to athena -- this will be done after the 2dx meeting at nysbc, so thigns will not break

April 10 2011
- copy all of Kens' data from Tecnai to external hard drive
- delete original copy of tomograms from Tecnai hard drive, leaving only navigator maps

April 11 2011 -- rename drives as follows:
- cem02bigdata --> helen
- cem02data --> hector
- cem02data2 --> hecuba
- cem03bigdata --> achilles
- cem03data --> menelaus
- cem03data2 --> iphigenia
- cem11data --> tonatiu
- cem12data --> theseus
- cem15data --> eurydice
exported and mounted all newly named drives
updated hosts file on jeol1230 pc to reflect these changes
found problem with leginon not talking to jerol1230 from minotaur (cem12) after change
- fixed by replacing minotaur entry with minotaur.nysbc.org in cd:\windows\system32\drivers\etc\hosts file
- verified that leginon is still working directly on jeol1230 and remotely from minotaur

links made to old drive names
cronus (cem01) now viewable from outside as cronus.nysbc.org
- verified by browsing cronus.nysbc.org from public network
TO DO
- rename dl380 to arachne, and make link

Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011

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