Difference: ClusterUseInstructions (1 vs. 15)

Revision 1507 Feb 2011 - Main.DhireshVyas

 
META TOPICPARENT name="InfotechGroup"
Contents

Cluster Usage Instructions

The Computing Cluster at NYSBC is now fully operational. Requests for processing time can be made to infotech@nysbc.org.

Technical Specifications

Component Description
Architecture Linux AMD Opteron x64
Hardware Head Node HP DL385
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Compute Nodes 15 x HP DL 145
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Software Operating System Red Hat EL4U4 (2.6.9-42.ELsmp)
Compilers Path Scale Complier Suite
Programming Model HP Message Passing Interface (HPMPI)
Scheduler PBS Pro Scheduler
Policies/User Limits Disk Quota Group Quota set at 30GB
Interactive Scratch Quota Currently not set
Maximum disk per Job Currently not set
Maximum CPUs per Job Currently set at 64
Added:
>
>

Connecting to the Cluster

From Outside NYSBC

  1. SSH to the NYSBC Remote Access Server at 207.239.59.21
  2. Once connected, SSH to the cluster at 192.168.5.236

From Within NYSBC

  1. SSH directly to the cluster at 192.168.5.236
 

Compiling Spider Versions

Set the following environment variables -
  1. export F77=pathf90
  2. export F90=pathf90
  3. export MPI_ROOT=/opt/hpmpi/bin
  4. export PATH=/opt/hpmpi/bin:$PATH
  5. export LD_LIBRARY_PATH=/opt/hpmpi/lib/linux_amd64:/opt/hpmpi/include/64
  6. export MPI_F90=pathf90
  7. export PATHSCALE_SUBSCRIPTION_DAEMON=node0
  8. From within the src directory in spider, run this makefile - Makefile_nysbc_cluster

Sample PBS Job File

The PBS job file should be in the format -

#!/bin/sh

#PBS -l nodes=4:ncpus=4

/opt/hpmpi/bin/mpirun -np 16 -hostfile $PBS_NODEFILE <path-to-mpi-app>

To run the job, run qsub <job-file>

Using PBS in SPIDER to replace pubsub

  • Only multiref alignment in spide rhas been optimised in spider mpi -- other commands are not accelerated
  • Additionally, only a subset of commands are mp aware in spider
  • Can use pbs to speed up loops on non-mp aware processes
  • example of a spider script to speed up a non-linear filter
  • Note that this sccript is designed to run such that each node runs one process. This process uses up to 6 GB, so the place=scatter command is used 
;========================input
fr l
[tomo]tomo1_crop.spd
;=========output=================
fr l
[filt]filt
;=========params==============
x90=60          ; cycles
x91=0.1         ; delta t
x92=0           ; sigma
;x93=0.05       ; lambda

;=============================
;---------- following set of commands sets the main qsub script for the cluster, one script per loop event
vm
echo "#!/bin/sh" > qsub-header.txt
vm
echo "#PBS -l select=ncpus=1:mem=6GB " >> qsub-header.txt
vm
echo "#PBS -l place=scatter" >> qsub-header.txt
vm
echo "cd /usr/data/asiebert/30_04_08_Rbs/tomo1" >> qsub-header.txt

;-----------------------------------------------

do lb1 x10=1,10                 ; this loop only makes the scripts using a "slave" script as template

  RR x93             ; adjust lambda according to the following sequence
  0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10                               ;  a nice log sequence

   vm
   echo "x93={**X93}" > filtscript{**x10}.$PRJEXT
   vm
   echo "x10={**X10}" >> filtscript{**x10}.$PRJEXT
   vm
   cat spider_script_filt1_clu_slave.$PRJEXT >> filtscript{**x10}.$PRJEXT
   vm
   cp qsub-header.txt qsub-script{**x10}.txt
   vm
   echo "/usr/apps/spidermp $PRJEXT/$DATEXT @filtscript{**x10}" >> qsub-script{**x10}.txt
   vm
   qsub qsub-script{**x10}.txt
lb1

en      ; end the main script
  • The script which actually does the work: 
;========================input
fr l
[tomo]tomo1_crop.spd
;=========output=================
fr l
[filt]filt
;=========params==============
x90=60          ; cycles
x91=0.1         ; delta t
x92=0           ; sigma
;x93=0.05       ; lambda

;=============================

   ce ad
   [tomo]
   [filt]{***x10}
   HEG
   x90
   x91
   x92,x93
en d

User Manuals

  1. HP MPI User Manual
  2. Userguide for PathScale compiler suite (F77/90/95, C, C++)
  3. Manpage for PathScale compiler
  4. PBS Pro User Guide

  • Set ALLOWTOPICVIEW =

-- DhireshVyas - 26 Feb 2007

META FILEATTACHMENT attr="" autoattached="1" comment="" date="1181231592" name="Makefile_nysbc_cluster" path="Makefile_nysbc_cluster" size="1426" user="Main.DhireshVyas" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1175623460" name="PBSProUG_7.1.pdf" path="PBSProUG_7.1.pdf" size="2235917" user="Main.DhireshVyas" version="1"

Revision 1414 May 2008 - Main.BillRice

 
META TOPICPARENT name="InfotechGroup"
Contents

Cluster Usage Instructions

The Computing Cluster at NYSBC is now fully operational. Requests for processing time can be made to infotech@nysbc.org.

Technical Specifications

Component Description
Architecture Linux AMD Opteron x64
Hardware Head Node HP DL385
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Compute Nodes 15 x HP DL 145
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Software Operating System Red Hat EL4U4 (2.6.9-42.ELsmp)
Compilers Path Scale Complier Suite
Programming Model HP Message Passing Interface (HPMPI)
Scheduler PBS Pro Scheduler
Policies/User Limits Disk Quota Group Quota set at 30GB
Interactive Scratch Quota Currently not set
Maximum disk per Job Currently not set
Maximum CPUs per Job Currently set at 64

Compiling Spider Versions

Set the following environment variables -
  1. export F77=pathf90
  2. export F90=pathf90
  3. export MPI_ROOT=/opt/hpmpi/bin
  4. export PATH=/opt/hpmpi/bin:$PATH
  5. export LD_LIBRARY_PATH=/opt/hpmpi/lib/linux_amd64:/opt/hpmpi/include/64
  6. export MPI_F90=pathf90
  7. export PATHSCALE_SUBSCRIPTION_DAEMON=node0
  8. From within the src directory in spider, run this makefile - Makefile_nysbc_cluster

Sample PBS Job File

The PBS job file should be in the format -

#!/bin/sh

#PBS -l nodes=4:ncpus=4

/opt/hpmpi/bin/mpirun -np 16 -hostfile $PBS_NODEFILE <path-to-mpi-app>

To run the job, run qsub <job-file>

Using PBS in SPIDER to replace pubsub

  • Only multiref alignment in spide rhas been optimised in spider mpi -- other commands are not accelerated
  • Additionally, only a subset of commands are mp aware in spider
  • Can use pbs to speed up loops on non-mp aware processes
  • example of a spider script to speed up a non-linear filter
Added:
>
>
  • Note that this sccript is designed to run such that each node runs one process. This process uses up to 6 GB, so the place=scatter command is used
 
;========================input
fr l
[tomo]tomo1_crop.spd
;=========output=================
fr l
[filt]filt
;=========params==============
x90=60          ; cycles
x91=0.1         ; delta t
x92=0           ; sigma
;x93=0.05       ; lambda

;=============================
;---------- following set of commands sets the main qsub script for the cluster, one script per loop event
vm
echo "#!/bin/sh" > qsub-header.txt
vm
echo "#PBS -l select=ncpus=1:mem=6GB " >> qsub-header.txt
vm
echo "#PBS -l place=scatter" >> qsub-header.txt
vm
echo "cd /usr/data/asiebert/30_04_08_Rbs/tomo1" >> qsub-header.txt

;-----------------------------------------------

do lb1 x10=1,10                 ; this loop only makes the scripts using a "slave" script as template

  RR x93             ; adjust lambda according to the following sequence
  0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10                               ;  a nice log sequence

   vm
   echo "x93={**X93}" > filtscript{**x10}.$PRJEXT
   vm
   echo "x10={**X10}" >> filtscript{**x10}.$PRJEXT
   vm
   cat spider_script_filt1_clu_slave.$PRJEXT >> filtscript{**x10}.$PRJEXT
   vm
   cp qsub-header.txt qsub-script{**x10}.txt
   vm
   echo "/usr/apps/spidermp $PRJEXT/$DATEXT @filtscript{**x10}" >> qsub-script{**x10}.txt
   vm
   qsub qsub-script{**x10}.txt
lb1

en      ; end the main script
  • The script which actually does the work: 
;========================input
fr l
[tomo]tomo1_crop.spd
;=========output=================
fr l
[filt]filt
;=========params==============
x90=60          ; cycles
x91=0.1         ; delta t
x92=0           ; sigma
;x93=0.05       ; lambda

;=============================

   ce ad
   [tomo]
   [filt]{***x10}
   HEG
   x90
   x91
   x92,x93
en d

User Manuals

  1. HP MPI User Manual
  2. Userguide for PathScale compiler suite (F77/90/95, C, C++)
  3. Manpage for PathScale compiler
  4. PBS Pro User Guide

  • Set ALLOWTOPICVIEW =

-- DhireshVyas - 26 Feb 2007

META FILEATTACHMENT attr="" autoattached="1" comment="" date="1181231592" name="Makefile_nysbc_cluster" path="Makefile_nysbc_cluster" size="1426" user="Main.DhireshVyas" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1175623460" name="PBSProUG_7.1.pdf" path="PBSProUG_7.1.pdf" size="2235917" user="Main.DhireshVyas" version="1"

Revision 1314 May 2008 - Main.BillRice

 
META TOPICPARENT name="InfotechGroup"
Contents

Cluster Usage Instructions

The Computing Cluster at NYSBC is now fully operational. Requests for processing time can be made to infotech@nysbc.org.

Technical Specifications

Component Description
Architecture Linux AMD Opteron x64
Hardware Head Node HP DL385
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Compute Nodes 15 x HP DL 145
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Software Operating System Red Hat EL4U4 (2.6.9-42.ELsmp)
Compilers Path Scale Complier Suite
Programming Model HP Message Passing Interface (HPMPI)
Scheduler PBS Pro Scheduler
Policies/User Limits Disk Quota Group Quota set at 30GB
Interactive Scratch Quota Currently not set
Maximum disk per Job Currently not set
Maximum CPUs per Job Currently set at 64

Compiling Spider Versions

Set the following environment variables -
  1. export F77=pathf90
  2. export F90=pathf90
  3. export MPI_ROOT=/opt/hpmpi/bin
  4. export PATH=/opt/hpmpi/bin:$PATH
  5. export LD_LIBRARY_PATH=/opt/hpmpi/lib/linux_amd64:/opt/hpmpi/include/64
  6. export MPI_F90=pathf90
  7. export PATHSCALE_SUBSCRIPTION_DAEMON=node0
  8. From within the src directory in spider, run this makefile - Makefile_nysbc_cluster

Sample PBS Job File

The PBS job file should be in the format -

#!/bin/sh

#PBS -l nodes=4:ncpus=4

/opt/hpmpi/bin/mpirun -np 16 -hostfile $PBS_NODEFILE <path-to-mpi-app>

To run the job, run qsub <job-file>

Added:
>
>

Using PBS in SPIDER to replace pubsub

  • Only multiref alignment in spide rhas been optimised in spider mpi -- other commands are not accelerated
  • Additionally, only a subset of commands are mp aware in spider
  • Can use pbs to speed up loops on non-mp aware processes
  • example of a spider script to speed up a non-linear filter 
;========================input
fr l
[tomo]tomo1_crop.spd
;=========output=================
fr l
[filt]filt
;=========params==============
x90=60          ; cycles
x91=0.1         ; delta t
x92=0           ; sigma
;x93=0.05       ; lambda

;=============================
;---------- following set of commands sets the main qsub script for the cluster, one script per loop event
vm
echo "#!/bin/sh" > qsub-header.txt
vm
echo "#PBS -l select=ncpus=1:mem=6GB " >> qsub-header.txt
vm
echo "#PBS -l place=scatter" >> qsub-header.txt
vm
echo "cd /usr/data/asiebert/30_04_08_Rbs/tomo1" >> qsub-header.txt

;-----------------------------------------------

do lb1 x10=1,10                 ; this loop only makes the scripts using a "slave" script as template

  RR x93             ; adjust lambda according to the following sequence
  0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10                               ;  a nice log sequence

   vm
   echo "x93={**X93}" > filtscript{**x10}.$PRJEXT
   vm
   echo "x10={**X10}" >> filtscript{**x10}.$PRJEXT
   vm
   cat spider_script_filt1_clu_slave.$PRJEXT >> filtscript{**x10}.$PRJEXT
   vm
   cp qsub-header.txt qsub-script{**x10}.txt
   vm
   echo "/usr/apps/spidermp $PRJEXT/$DATEXT @filtscript{**x10}" >> qsub-script{**x10}.txt
   vm
   qsub qsub-script{**x10}.txt
lb1

en      ; end the main script
  • The script which actually does the work: 
;========================input
fr l
[tomo]tomo1_crop.spd
;=========output=================
fr l
[filt]filt
;=========params==============
x90=60          ; cycles
x91=0.1         ; delta t
x92=0           ; sigma
;x93=0.05       ; lambda

;=============================

   ce ad
   [tomo]
   [filt]{***x10}
   HEG
   x90
   x91
   x92,x93
en d
 

User Manuals

  1. HP MPI User Manual
  2. Userguide for PathScale compiler suite (F77/90/95, C, C++)
  3. Manpage for PathScale compiler
  4. PBS Pro User Guide

  • Set ALLOWTOPICVIEW =

-- DhireshVyas - 26 Feb 2007

META FILEATTACHMENT attr="" autoattached="1" comment="" date="1181231592" name="Makefile_nysbc_cluster" path="Makefile_nysbc_cluster" size="1426" user="Main.DhireshVyas" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1175623460" name="PBSProUG_7.1.pdf" path="PBSProUG_7.1.pdf" size="2235917" user="Main.DhireshVyas" version="1"

Revision 1215 Aug 2007 - Main.DhireshVyas

 
META TOPICPARENT name="InfotechGroup"
Contents

Cluster Usage Instructions

The Computing Cluster at NYSBC is now fully operational. Requests for processing time can be made to infotech@nysbc.org.

Technical Specifications

Component Description
Architecture Linux AMD Opteron x64
Hardware Head Node HP DL385
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Compute Nodes 15 x HP DL 145
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Software Operating System Red Hat EL4U4 (2.6.9-42.ELsmp)
Compilers Path Scale Complier Suite
Programming Model HP Message Passing Interface (HPMPI)
Scheduler PBS Pro Scheduler
Policies/User Limits Disk Quota Group Quota set at 30GB
Interactive Scratch Quota Currently not set
Maximum disk per Job Currently not set
Maximum CPUs per Job Currently set at 64

Compiling Spider Versions

Set the following environment variables -
  1. export F77=pathf90
  2. export F90=pathf90
  3. export MPI_ROOT=/opt/hpmpi/bin
  4. export PATH=/opt/hpmpi/bin:$PATH
  5. export LD_LIBRARY_PATH=/opt/hpmpi/lib/linux_amd64:/opt/hpmpi/include/64
  6. export MPI_F90=pathf90
  7. export PATHSCALE_SUBSCRIPTION_DAEMON=node0
  8. From within the src directory in spider, run this makefile - Makefile_nysbc_cluster

Sample PBS Job File

The PBS job file should be in the format -
Changed:
<
<		#!/bin/sh
>
>		 #!/bin/sh
 #PBS -l nodes=4:ncpus=4
Changed:
<
<		/opt/hpmpi/bin/mpirun -np 16 -hostfile $PBS_NODEFILE <path-to-mpi-app>
>
>		/opt/hpmpi/bin/mpirun -np 16 -hostfile $PBS_NODEFILE <path-to-mpi-app>
 To run the job, run qsub <job-file>

User Manuals

  1. HP MPI User Manual
  2. Userguide for PathScale compiler suite (F77/90/95, C, C++)
  3. Manpage for PathScale compiler
  4. PBS Pro User Guide

  • Set ALLOWTOPICVIEW =

-- DhireshVyas - 26 Feb 2007

META FILEATTACHMENT attr="" autoattached="1" comment="" date="1181231592" name="Makefile_nysbc_cluster" path="Makefile_nysbc_cluster" size="1426" user="Main.DhireshVyas" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1175623460" name="PBSProUG_7.1.pdf" path="PBSProUG_7.1.pdf" size="2235917" user="Main.DhireshVyas" version="1"

Revision 1115 Aug 2007 - Main.DhireshVyas

 
META TOPICPARENT name="InfotechGroup"
Contents

Cluster Usage Instructions

The Computing Cluster at NYSBC is now fully operational. Requests for processing time can be made to infotech@nysbc.org.

Technical Specifications

Component Description
Architecture Linux AMD Opteron x64
Hardware Head Node HP DL385
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Compute Nodes 15 x HP DL 145
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Software Operating System Red Hat EL4U4 (2.6.9-42.ELsmp)
Compilers Path Scale Complier Suite
Programming Model HP Message Passing Interface (HPMPI)
Scheduler PBS Pro Scheduler
Policies/User Limits Disk Quota Group Quota set at 30GB
Interactive Scratch Quota Currently not set
Maximum disk per Job Currently not set
Maximum CPUs per Job Currently set at 64

Compiling Spider Versions

Set the following environment variables -
  1. export F77=pathf90
  2. export F90=pathf90
  3. export MPI_ROOT=/opt/hpmpi/bin
  4. export PATH=/opt/hpmpi/bin:$PATH
  5. export LD_LIBRARY_PATH=/opt/hpmpi/lib/linux_amd64:/opt/hpmpi/include/64
  6. export MPI_F90=pathf90
  7. export PATHSCALE_SUBSCRIPTION_DAEMON=node0
  8. From within the src directory in spider, run this makefile - Makefile_nysbc_cluster
Added:
>
>

Sample PBS Job File

The PBS job file should be in the format -

#!/bin/sh

#PBS -l nodes=4:ncpus=4

/opt/hpmpi/bin/mpirun -np 16 -hostfile $PBS_NODEFILE <path-to-mpi-app>

To run the job, run qsub <job-file>

 

User Manuals

  1. HP MPI User Manual
  2. Userguide for PathScale compiler suite (F77/90/95, C, C++)
  3. Manpage for PathScale compiler
  4. PBS Pro User Guide

  • Set ALLOWTOPICVIEW =

-- DhireshVyas - 26 Feb 2007

META FILEATTACHMENT attr="" autoattached="1" comment="" date="1181231592" name="Makefile_nysbc_cluster" path="Makefile_nysbc_cluster" size="1426" user="Main.DhireshVyas" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1175623460" name="PBSProUG_7.1.pdf" path="PBSProUG_7.1.pdf" size="2235917" user="Main.DhireshVyas" version="1"

Revision 1007 Jun 2007 - Main.DhireshVyas

 
META TOPICPARENT name="InfotechGroup"
Contents

Cluster Usage Instructions

The Computing Cluster at NYSBC is now fully operational. Requests for processing time can be made to infotech@nysbc.org.

Technical Specifications

Component Description
Architecture Linux AMD Opteron x64
Hardware Head Node HP DL385
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Compute Nodes 15 x HP DL 145
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Software Operating System Red Hat EL4U4 (2.6.9-42.ELsmp)
Compilers Path Scale Complier Suite
Programming Model HP Message Passing Interface (HPMPI)
Scheduler PBS Pro Scheduler
Policies/User Limits Disk Quota Group Quota set at 30GB
Interactive Scratch Quota Currently not set
Maximum disk per Job Currently not set
Maximum CPUs per Job Currently set at 64

Compiling Spider Versions

Set the following environment variables -
  1. export F77=pathf90
  2. export F90=pathf90
  3. export MPI_ROOT=/opt/hpmpi/bin
  4. export PATH=/opt/hpmpi/bin:$PATH
  5. export LD_LIBRARY_PATH=/opt/hpmpi/lib/linux_amd64:/opt/hpmpi/include/64
  6. export MPI_F90=pathf90
  7. export PATHSCALE_SUBSCRIPTION_DAEMON=node0
Added:
>
>
  1. From within the src directory in spider, run this makefile - Makefile_nysbc_cluster
 
Changed:
<
<
>
>

User Manuals

Deleted:
<
<

User Manuals

 
  1. HP MPI User Manual
  2. Userguide for PathScale compiler suite (F77/90/95, C, C++)
  3. Manpage for PathScale compiler
  4. PBS Pro User Guide

  • Set ALLOWTOPICVIEW =

-- DhireshVyas - 26 Feb 2007

Changed:
<
<		 * Makefile_nysbc_cluster: Makefile_nysbc_cluster
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1181231592" name="Makefile_nysbc_cluster" path="Makefile_nysbc_cluster" size="1426" user="Main.DhireshVyas" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1175623460" name="PBSProUG_7.1.pdf" path="PBSProUG_7.1.pdf" size="2235917" user="Main.DhireshVyas" version="1"
Deleted:
<
<
META FILEATTACHMENT attachment="PBSProUG_7.1.pdf" attr="" comment="" date="1175623460" name="PBSProUG_7.1.pdf" path="PBSProUG_7.1.pdf" size="2235917" stream="PBSProUG_7.1.pdf" user="Main.DhireshVyas" version="1"
META FILEATTACHMENT attachment="Makefile_nysbc_cluster" attr="" comment="" date="1181231592" name="Makefile_nysbc_cluster" path="Makefile_nysbc_cluster" size="1426" stream="Makefile_nysbc_cluster" user="Main.DhireshVyas" version="1"
 

Revision 907 Jun 2007 - Main.DhireshVyas

 
META TOPICPARENT name="InfotechGroup"
Contents

Cluster Usage Instructions

The Computing Cluster at NYSBC is now fully operational. Requests for processing time can be made to infotech@nysbc.org.

Technical Specifications

Component Description
Architecture Linux AMD Opteron x64
Hardware Head Node HP DL385
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Compute Nodes 15 x HP DL 145
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Software Operating System Red Hat EL4U4 (2.6.9-42.ELsmp)
Compilers Path Scale Complier Suite
Programming Model HP Message Passing Interface (HPMPI)
Scheduler PBS Pro Scheduler
Policies/User Limits Disk Quota Group Quota set at 30GB
Interactive Scratch Quota Currently not set
Maximum disk per Job Currently not set
Maximum CPUs per Job Currently set at 64

Compiling Spider Versions

Set the following environment variables -
  1. export F77=pathf90
  2. export F90=pathf90
  3. export MPI_ROOT=/opt/hpmpi/bin
  4. export PATH=/opt/hpmpi/bin:$PATH
  5. export LD_LIBRARY_PATH=/opt/hpmpi/lib/linux_amd64:/opt/hpmpi/include/64
  6. export MPI_F90=pathf90
  7. export PATHSCALE_SUBSCRIPTION_DAEMON=node0

User Manuals

  1. HP MPI User Manual
  2. Userguide for PathScale compiler suite (F77/90/95, C, C++)
  3. Manpage for PathScale compiler
  4. PBS Pro User Guide

  • Set ALLOWTOPICVIEW =

-- DhireshVyas - 26 Feb 2007

Added:
>
>		 * Makefile_nysbc_cluster: Makefile_nysbc_cluster
 
META FILEATTACHMENT attachment="PBSProUG_7.1.pdf" attr="" comment="" date="1175623460" name="PBSProUG_7.1.pdf" path="PBSProUG_7.1.pdf" size="2235917" stream="PBSProUG_7.1.pdf" user="Main.DhireshVyas" version="1"
Added:
>
>
META FILEATTACHMENT attachment="Makefile_nysbc_cluster" attr="" comment="" date="1181231592" name="Makefile_nysbc_cluster" path="Makefile_nysbc_cluster" size="1426" stream="Makefile_nysbc_cluster" user="Main.DhireshVyas" version="1"
 

Revision 807 Jun 2007 - Main.DhireshVyas

 
META TOPICPARENT name="InfotechGroup"
Contents

Cluster Usage Instructions

The Computing Cluster at NYSBC is now fully operational. Requests for processing time can be made to infotech@nysbc.org.

Technical Specifications

Component Description
Architecture Linux AMD Opteron x64
Hardware Head Node HP DL385
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Compute Nodes 15 x HP DL 145
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Software Operating System Red Hat EL4U4 (2.6.9-42.ELsmp)
Compilers Path Scale Complier Suite
Programming Model HP Message Passing Interface (HPMPI)
Scheduler PBS Pro Scheduler
Policies/User Limits Disk Quota Group Quota set at 30GB
Interactive Scratch Quota Currently not set
Maximum disk per Job Currently not set
Maximum CPUs per Job Currently set at 64
Added:
>
>

Compiling Spider Versions

Set the following environment variables -
  1. export F77=pathf90
  2. export F90=pathf90
  3. export MPI_ROOT=/opt/hpmpi/bin
  4. export PATH=/opt/hpmpi/bin:$PATH
  5. export LD_LIBRARY_PATH=/opt/hpmpi/lib/linux_amd64:/opt/hpmpi/include/64
  6. export MPI_F90=pathf90
  7. export PATHSCALE_SUBSCRIPTION_DAEMON=node0
 

User Manuals

  1. HP MPI User Manual
  2. Userguide for PathScale compiler suite (F77/90/95, C, C++)
  3. Manpage for PathScale compiler
  4. PBS Pro User Guide

  • Set ALLOWTOPICVIEW =

-- DhireshVyas - 26 Feb 2007

META FILEATTACHMENT attachment="PBSProUG_7.1.pdf" attr="" comment="" date="1175623460" name="PBSProUG_7.1.pdf" path="PBSProUG_7.1.pdf" size="2235917" stream="PBSProUG_7.1.pdf" user="Main.DhireshVyas" version="1"

Revision 703 Apr 2007 - Main.DhireshVyas

 
META TOPICPARENT name="InfotechGroup"
Contents

Cluster Usage Instructions

The Computing Cluster at NYSBC is now fully operational. Requests for processing time can be made to infotech@nysbc.org.

Technical Specifications

Component Description
Architecture Linux AMD Opteron x64
Hardware Head Node HP DL385
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Compute Nodes 15 x HP DL 145
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Software Operating System Red Hat EL4U4 (2.6.9-42.ELsmp)
Compilers Path Scale Complier Suite
Programming Model HP Message Passing Interface (HPMPI)
Scheduler PBS Pro Scheduler
Policies/User Limits Disk Quota Group Quota set at 30GB
Interactive Scratch Quota Currently not set
Maximum disk per Job Currently not set
Maximum CPUs per Job Currently set at 64

User Manuals

  1. HP MPI User Manual
  2. Userguide for PathScale compiler suite (F77/90/95, C, C++)
  3. Manpage for PathScale compiler
Added:
>
>
  1. PBS Pro User Guide
 
Deleted:
<
<
 
  • Set ALLOWTOPICVIEW =

-- DhireshVyas - 26 Feb 2007

Changed:
<
<		 * PBSProUG_7.1.pdf: PBSProUG?_7.1.pdf
>
>
 
META FILEATTACHMENT attachment="PBSProUG_7.1.pdf" attr="" comment="" date="1175623460" name="PBSProUG_7.1.pdf" path="PBSProUG_7.1.pdf" size="2235917" stream="PBSProUG_7.1.pdf" user="Main.DhireshVyas" version="1"

Revision 603 Apr 2007 - Main.DhireshVyas

 
META TOPICPARENT name="InfotechGroup"
Contents

Cluster Usage Instructions

The Computing Cluster at NYSBC is now fully operational. Requests for processing time can be made to infotech@nysbc.org.

Technical Specifications

Component Description
Architecture Linux AMD Opteron x64
Hardware Head Node HP DL385
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Compute Nodes 15 x HP DL 145
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Software Operating System Red Hat EL4U4 (2.6.9-42.ELsmp)
Compilers Path Scale Complier Suite
Programming Model HP Message Passing Interface (HPMPI)
Scheduler PBS Pro Scheduler
Policies/User Limits Disk Quota Group Quota set at 30GB
Interactive Scratch Quota Currently not set
Maximum disk per Job Currently not set
Maximum CPUs per Job Currently set at 64

User Manuals

  1. HP MPI User Manual
  2. Userguide for PathScale compiler suite (F77/90/95, C, C++)
  3. Manpage for PathScale compiler

  • Set ALLOWTOPICVIEW =

-- DhireshVyas - 26 Feb 2007

Added:
>
>		 * PBSProUG_7.1.pdf: PBSProUG?_7.1.pdf

META FILEATTACHMENT attachment="PBSProUG_7.1.pdf" attr="" comment="" date="1175623460" name="PBSProUG_7.1.pdf" path="PBSProUG_7.1.pdf" size="2235917" stream="PBSProUG_7.1.pdf" user="Main.DhireshVyas" version="1"
 

Revision 526 Feb 2007 - Main.DhireshVyas

 
META TOPICPARENT name="InfotechGroup"
Contents

Cluster Usage Instructions

The Computing Cluster at NYSBC is now fully operational. Requests for processing time can be made to infotech@nysbc.org.

Technical Specifications

Changed:
<
<
Component Description
>
>
Component Description
 
Architecture Linux AMD Opteron x64
Hardware Head Node HP DL385
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Compute Nodes 15 x HP DL 145
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Software Operating System Red Hat EL4U4 (2.6.9-42.ELsmp)
Compilers Path Scale Complier Suite
Programming Model HP Message Passing Interface (HPMPI)
Scheduler PBS Pro Scheduler
Policies/User Limits Disk Quota Group Quota set at 30GB
Interactive Scratch Quota Currently not set
Maximum disk per Job Currently not set
Maximum CPUs per Job Currently set at 64

User Manuals

  1. HP MPI User Manual
  2. Userguide for PathScale compiler suite (F77/90/95, C, C++)
  3. Manpage for PathScale compiler

  • Set ALLOWTOPICVIEW =

-- DhireshVyas - 26 Feb 2007

Revision 426 Feb 2007 - Main.DhireshVyas

 
META TOPICPARENT name="InfotechGroup"
Contents

Cluster Usage Instructions

The Computing Cluster at NYSBC is now fully operational. Requests for processing time can be made to infotech@nysbc.org.

Technical Specifications

Changed:
<
<
Component Description
>
>
Component Description
 
Architecture Linux AMD Opteron x64
Hardware Head Node HP DL385
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Compute Nodes 15 x HP DL 145
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Software Operating System Red Hat EL4U4 (2.6.9-42.ELsmp)
Compilers Path Scale Complier Suite
Programming Model HP Message Passing Interface (HPMPI)
Scheduler PBS Pro Scheduler
Policies/User Limits Disk Quota Group Quota set at 30GB
Interactive Scratch Quota Currently not set
Maximum disk per Job Currently not set
Maximum CPUs per Job Currently set at 64

User Manuals

  1. HP MPI User Manual
  2. Userguide for PathScale compiler suite (F77/90/95, C, C++)
  3. Manpage for PathScale compiler

  • Set ALLOWTOPICVIEW =

-- DhireshVyas - 26 Feb 2007

Revision 326 Feb 2007 - Main.DhireshVyas

 
META TOPICPARENT name="InfotechGroup"
Contents

Cluster Usage Instructions

Changed:
<
<		The Computing Cluster at NYSBC is now fully operational. Requests for processing time can now be made to infotech@nysbc.org.
>
>		The Computing Cluster at NYSBC is now fully operational. Requests for processing time can be made to infotech@nysbc.org.
 

Technical Specifications

Component Description
Architecture Linux AMD Opteron x64
Hardware Head Node HP DL385
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Compute Nodes 15 x HP DL 145
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Software Operating System Red Hat EL4U4 (2.6.9-42.ELsmp)
Compilers Path Scale Complier Suite
Programming Model HP Message Passing Interface (HPMPI)
Scheduler PBS Pro Scheduler
Policies/User Limits Disk Quota Group Quota set at 30GB
Interactive Scratch Quota Currently not set
Maximum disk per Job Currently not set
Maximum CPUs per Job Currently set at 64

User Manuals

  1. HP MPI User Manual
  2. Userguide for PathScale compiler suite (F77/90/95, C, C++)
  3. Manpage for PathScale compiler

  • Set ALLOWTOPICVIEW =

-- DhireshVyas - 26 Feb 2007

Revision 226 Feb 2007 - Main.DhireshVyas

 
META TOPICPARENT name="InfotechGroup"
Contents

Cluster Usage Instructions

The Computing Cluster at NYSBC is now fully operational. Requests for processing time can now be made to infotech@nysbc.org.

Technical Specifications

Component Description
Architecture Linux AMD Opteron x64
Hardware Head Node HP DL385
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Compute Nodes 15 x HP DL 145
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Software Operating System Red Hat EL4U4 (2.6.9-42.ELsmp)
Compilers Path Scale Complier Suite
Programming Model HP Message Passing Interface (HPMPI)
Scheduler PBS Pro Scheduler
Policies/User Limits Disk Quota Group Quota set at 30GB
Interactive Scratch Quota Currently not set
Maximum disk per Job Currently not set
Maximum CPUs per Job Currently set at 64

User Manuals

  1. HP MPI User Manual
Added:
>
>
  1. Userguide for PathScale compiler suite (F77/90/95, C, C++)
  2. Manpage for PathScale compiler
 

  • Set ALLOWTOPICVIEW =

-- DhireshVyas - 26 Feb 2007

Revision 126 Feb 2007 - Main.DhireshVyas

 
META TOPICPARENT name="InfotechGroup"
Contents

Cluster Usage Instructions

The Computing Cluster at NYSBC is now fully operational. Requests for processing time can now be made to infotech@nysbc.org.

Technical Specifications

Component Description
Architecture Linux AMD Opteron x64
Hardware Head Node HP DL385
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Compute Nodes 15 x HP DL 145
CPU AMD Opteron 280 DC - 2.4Ghz Dual Core
RAM - 8GB
Software Operating System Red Hat EL4U4 (2.6.9-42.ELsmp)
Compilers Path Scale Complier Suite
Programming Model HP Message Passing Interface (HPMPI)
Scheduler PBS Pro Scheduler
Policies/User Limits Disk Quota Group Quota set at 30GB
Interactive Scratch Quota Currently not set
Maximum disk per Job Currently not set
Maximum CPUs per Job Currently set at 64

User Manuals

  1. HP MPI User Manual

  • Set ALLOWTOPICVIEW =

-- DhireshVyas - 26 Feb 2007

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