Difference between revisions of "QUonG HowTo"

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Work in progress...
 
 
'''Available Resources on QUonG:'''
 
'''Available Resources on QUonG:'''
−
* 16 nodes
+
* 16 nodes (SuperMicro X8DTG-D)
 
* each node is dual socket, with one 4-core Intel Xeon E5620 2.40GHz per socket
 
* each node is dual socket, with one 4-core Intel Xeon E5620 2.40GHz per socket
 
* each node OS is (diskless, boot from network) Centos 6.4 with kernel 2.6.32-358.2.1.el6.x86_64 (x86_64 arch)
 
* each node OS is (diskless, boot from network) Centos 6.4 with kernel 2.6.32-358.2.1.el6.x86_64 (x86_64 arch)
 
* GNU C/C++ compiler is version 4.4.7
 
* GNU C/C++ compiler is version 4.4.7
 +
 +
'''Available SLURM queues on QUonG'''
 +
* 4 nodes (q000-03) in the '''debug''' queue (30 min. run time limit)
 +
* 8 nodes (q004-11) in the '''run''' queue (4 hrs. run time limit)
 +
* remaining 4 nodes (q012-15) in the '''run''' queue under SLURM reservation, needs permission for '--reservation=apenet_development' option - ask us if you need access
 +
 +
'''To view resources on QUonG:'''
 +
* 'sinfo': list of currently available queues and their status
 +
 +
Example output:
 +
 +
  PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
 +
debug*      up      30:00      2  alloc q[000-001]
 +
debug*      up      30:00      2  idle q[002-003]
 +
run          up    4:00:00      4  maint q[012-015]
 +
run          up    4:00:00      6  alloc q[004-009]
 +
run          up    4:00:00      2  idle q[010-011]
 +
 +
* 'squeue': list of currently queued jobs in the available queues
 +
 +
Example output:
 +
 +
  JOBID PARTITION    NAME    USER  ST      TIME  NODES NODELIST(REASON)
 +
656479    debug  job7.sh    delia  R      4:32      1 q001
 +
656480    debug  job8.sh    delia  R      4:24      1 q000
 +
656473      run  job1.sh    delia  R      5:07      1 q008
 +
656474      run  job2.sh    delia  R      5:04      1 q009
 +
656475      run  job3.sh    delia  R      4:57      1 q004
 +
656476      run  job4.sh    delia  R      4:44      1 q005
 +
656477      run  job5.sh    delia  R      4:42      1 q006
 +
656478      run  job6.sh    delia  R      4:36      1 q007
 +
 +
'''To run on QUonG:'''
 +
* allocate a number of nodes from a queue with 'salloc', get an interactive shell and run from there, exit the shell to relinquish the resources.
 +
 +
Example:
 +
 +
[user@quong ~]$ salloc -p debug -N 2
 +
salloc: Granted job allocation 656482
 +
 +
[user@quong ~]$ mpirun hostname
 +
q002.qng
 +
q002.qng
 +
q003.qng
 +
q003.qng
 +
 +
[user@quong ~]$ exit
 +
exit
 +
salloc: Relinquishing job allocation 656482
 +
 +
* execute a script with '''srun''' asking for a number of nodes from a queue.
 +
 +
Example:
 +
 +
[user@quong ~]$ cat test.sh
 +
#!/bin/bash
 +
mpirun hostname
 +
 +
[user@quong ~]$ srun -p run -N 2 ./test.sh
 +
q010.qng
 +
q011.qng
 +
q011.qng
 +
q010.qng

Revision as of 14:27, 11 November 2013

Available Resources on QUonG:

  • 16 nodes (SuperMicro X8DTG-D)
  • each node is dual socket, with one 4-core Intel Xeon E5620 2.40GHz per socket
  • each node OS is (diskless, boot from network) Centos 6.4 with kernel 2.6.32-358.2.1.el6.x86_64 (x86_64 arch)
  • GNU C/C++ compiler is version 4.4.7

Available SLURM queues on QUonG

  • 4 nodes (q000-03) in the debug queue (30 min. run time limit)
  • 8 nodes (q004-11) in the run queue (4 hrs. run time limit)
  • remaining 4 nodes (q012-15) in the run queue under SLURM reservation, needs permission for '--reservation=apenet_development' option - ask us if you need access

To view resources on QUonG:

  • 'sinfo': list of currently available queues and their status

Example output: 

 PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
debug*       up      30:00      2  alloc q[000-001]
debug*       up      30:00      2   idle q[002-003]
run          up    4:00:00      4  maint q[012-015]
run          up    4:00:00      6  alloc q[004-009]
run          up    4:00:00      2   idle q[010-011]
  • 'squeue': list of currently queued jobs in the available queues

Example output: 

 JOBID PARTITION     NAME     USER  ST       TIME  NODES NODELIST(REASON)
656479     debug  job7.sh    delia   R       4:32      1 q001
656480     debug  job8.sh    delia   R       4:24      1 q000
656473       run  job1.sh    delia   R       5:07      1 q008
656474       run  job2.sh    delia   R       5:04      1 q009
656475       run  job3.sh    delia   R       4:57      1 q004
656476       run  job4.sh    delia   R       4:44      1 q005
656477       run  job5.sh    delia   R       4:42      1 q006
656478       run  job6.sh    delia   R       4:36      1 q007

To run on QUonG:

  • allocate a number of nodes from a queue with 'salloc', get an interactive shell and run from there, exit the shell to relinquish the resources.

Example: 

[user@quong ~]$ salloc -p debug -N 2
salloc: Granted job allocation 656482

[user@quong ~]$ mpirun hostname
q002.qng
q002.qng
q003.qng
q003.qng

[user@quong ~]$ exit
exit
salloc: Relinquishing job allocation 656482
  • execute a script with srun asking for a number of nodes from a queue.

Example: 

[user@quong ~]$ cat test.sh
#!/bin/bash
mpirun hostname

[user@quong ~]$ srun -p run -N 2 ./test.sh 
q010.qng
q011.qng
q011.qng
q010.qng
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