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

[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

• Set ALLOWTOPICVIEW =

-- BillRice - 12 Apr 2011