I have a question about vmem and maxvmem. I searched on the web but there are really many confusing explanations of the two words. What I did was to type:
qstat -j 1154926 | grep vmem
The output was: cpu=00:05:25, mem=23.21121 GBs, io=2.70481, vmem=239.277M, maxvmem=351.359M
Can anyone help me to understand the meaning of the variables?
Best
I found this link to be helpful.
qstat
qstat can provide more detailed information about a running job by passing it a job id specified by the '-j' argument:
[jamesa@codon sge_test]$ qstat -j 3804867
==============================================================
job_number: 3804867
exec_file: job_scripts/3804867
submission_time: Wed Jun 29 11:04:02 2011
owner: jamesa
uid: 1001
group: bss-staff
gid: 50001
sge_o_home: /home/jamesa
sge_o_log_name: jamesa
sge_o_path: /usr/lib64/openmpi/bin:/usr/lib64/openmpi/1.4-gcc/bin:/opt/sge/6_2u5_1/bin/lx26-amd64:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/lib/jvm/java/bin:/usr/lib/jvm/jre/bin:/usr/biosoft/bin:/usr/biosoft/perl_modules/bioperl/current/bin:/usr/biosoft/packages/emboss/current/bin:/home/jamesa/bin
sge_o_shell: /bin/bash
sge_o_workdir: /home/jamesa/sge_test
sge_o_host: codon
account: sge
cwd: /home/jamesa/
sge_testmerge: y
hard resource_list: h_rt=3600,h_vmem=2G
mail_list: jamesa@codon.bioinformatics.ic.ac.uk
notify: FALSE
job_name: blast
jobshare: 0
env_list:
script_file: blast.sh
usage 1: cpu=00:01:37, mem=78.06343 GBs, io=0.00002, vmem=925.562M, maxvmem=1.012G
scheduling info: There are no messages available
You can see the resources you requested at submission time on the hard_resource_list line of the qstat output. The actual resources used by the job at the time qstat were executed are shown in the usage line.
Email Reporting
A summary of the jobs resource usage can be obtained by requesting an email report following the jobs completion, using the -m e qsub directive (see advanced submission options for details). An example email report is show below.
Job 3804869 (blast) Complete
User = jamesa
Queue = 3day_16@bss-node11.cluster.bioinformatics.ic.ac.uk
Host = bss-node11.cluster.bioinformatics.ic.ac.uk
Start Time = 06/29/2011 11:26:08
End Time = 06/29/2011 11:30:43
User Time = 00:03:51
System Time = 00:00:12
Wallclock Time = 00:04:35
CPU = 00:04:04
Max vmem = 1.012G
Exit Status = 0
The total memory used is indicated by the Max vmem field, while the total runtime is reported as Wallclock Time. Care should be taken when submitting a large number of jobs with email reporting enabled, since you may find yourself recieving several thousand reports in individual emails.