Difference between revisions of "QUonG HowTo"
From APEWiki
Jump to navigationJump to searchm |
|||
| Line 37: | Line 37: | ||
'''To run on QUonG:''' | '''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. | + | * 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: | Example: | ||
| − | [user@quong ~]$ salloc -p debug -N | + | [user@quong ~]$ salloc -N 2 -p debug <--- ask for 2 nodes ('''-N''' option) from the 'debug' queue ('''-p''' option) |
salloc: Granted job allocation 656482 | salloc: Granted job allocation 656482 | ||
| − | |||
[user@quong ~]$ mpirun hostname | [user@quong ~]$ mpirun hostname | ||
q002.qng | q002.qng | ||
| Line 49: | Line 48: | ||
q003.qng | q003.qng | ||
q003.qng | q003.qng | ||
| − | |||
[user@quong ~]$ exit | [user@quong ~]$ exit | ||
exit | exit | ||
salloc: Relinquishing job allocation 656482 | salloc: Relinquishing job allocation 656482 | ||
| − | * execute a script with ''' | + | * execute a script with '''sbatch''' asking for a number of nodes from a queue. |
Example: | Example: | ||
| Line 61: | Line 59: | ||
#!/bin/bash | #!/bin/bash | ||
mpirun hostname | mpirun hostname | ||
| + | [fsimula@quong ~]$ sbatch -p run --reservation=apenet_development -N 3 ./test.sh | ||
| + | Submitted batch job 656517 | ||
| + | |||
| + | If not specified, stdout is redirected to a file 'slurm_$jobid.out' | ||
| − | [ | + | [fsimula@quong ~]$ cat slurm-656517.out |
| − | + | q012.qng | |
| − | + | q012.qng | |
| − | + | q014.qng | |
| − | + | q014.qng | |
| + | q013.qng | ||
| + | q013.qng | ||
Revision as of 14:51, 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 -N 2 -p debug <--- ask for 2 nodes (-N option) from the 'debug' queue (-p option) 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 sbatch asking for a number of nodes from a queue.
Example:
[user@quong ~]$ cat test.sh #!/bin/bash mpirun hostname [fsimula@quong ~]$ sbatch -p run --reservation=apenet_development -N 3 ./test.sh Submitted batch job 656517
If not specified, stdout is redirected to a file 'slurm_$jobid.out'
[fsimula@quong ~]$ cat slurm-656517.out q012.qng q012.qng q014.qng q014.qng q013.qng q013.qng
