Difference between revisions of "Sungrid Use"
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== Basic Commands == | == Basic Commands == | ||
| − | We have our machines setup in a grid using a batch queue system. You can check your job status with: | + | We have our machines setup in a grid using a batch queue system. You must run the job on one of the sungrid machines (qconf -sh to see them). You can check your job status with: |
qstat | qstat | ||
| Line 11: | Line 11: | ||
where you can specify a specific job ID or all your jobs with "-u yourid". | where you can specify a specific job ID or all your jobs with "-u yourid". | ||
| − | To submit jobs, you use qsub. | + | To submit jobs, you use qsub as shown later. |
== Common Options == | == Common Options == | ||
| Line 17: | Line 17: | ||
-S /bin/sh | -S /bin/sh | ||
| − | For the script option | + | For the script option (you did not specify -b y), this specifies which interpreter to use. |
-m es | -m es | ||
| Line 46: | Line 46: | ||
Specify that the executable is a binary and not a script. | Specify that the executable is a binary and not a script. | ||
| − | == Command Line == | + | |
| + | -V | ||
| + | |||
| + | Specify that the job and the shells environmental variables should be the same. | ||
| + | |||
| + | == Submitting Jobs == | ||
| + | |||
| + | When you submit a job, it sources your ".profile" instead of your ".bashrc" for configuration since it is a "non-interactive" shell. | ||
| + | |||
| + | You can submit jobs in one of two ways: | ||
| + | |||
| + | === Command Line === | ||
| + | |||
| + | |||
qsub <options> -b y <binary> -- <options for the binary> | qsub <options> -b y <binary> -- <options for the binary> | ||
| Line 52: | Line 65: | ||
Example: | Example: | ||
| − | qsub -S /bin/sh -m es -M myid@soe.ucsc.edu -cwd -b y -N "myid_hard_area_FP" -e hard_results/n10.err -o hard_results/n10.log ../simanneal/simanneal -- -i ../benchmarks/hard/n10 -o hard_results/n10 | + | qsub -S /bin/sh -m es -M myid@soe.ucsc.edu -cwd -b y -N "myid_hard_area_FP" \ |
| + | -e hard_results/n10.err -o hard_results/n10.log ../simanneal/simanneal -- -i ../benchmarks/hard/n10 -o hard_results/n10 | ||
| − | == Script == | + | Sometimes, I have found that the "--" isn't needed... I'm not sure why. |
| + | |||
| + | === Script === | ||
Instead of specifying all the options on the command line, you can specify them in a script like this: | Instead of specifying all the options on the command line, you can specify them in a script like this: | ||
| Line 68: | Line 84: | ||
../simanneal/simanneal -i ../benchmarks/hard/n10 -o hard_results/n10 | ../simanneal/simanneal -i ../benchmarks/hard/n10 -o hard_results/n10 | ||
exit 0 | exit 0 | ||
| + | |||
| + | == Restricting to the same machines == | ||
| + | |||
| + | Often for papers, you will want to restrict your simualtions to identical machines (e.g. you want to compare run-times). In order to do this, we have a hostgroup for all of the mada servers (mada1-7). You can submit to these machines by doing: | ||
| + | |||
| + | qsub -q *@@mada <other arguments> | ||
| + | |||
| + | You can also specify other requirements such as available memory with the "-l" command. | ||
| + | |||
| + | To list a all hosts | ||
| + | qconf -ss | ||
| + | |||
| + | To list of cluster queues | ||
| + | qconf -sql | ||
| + | |||
| + | == Administraiton == | ||
| + | |||
| + | Somtimes the machines will get in an error state (E): | ||
| + | |||
| + | qstat -f | ||
| + | |||
| + | will show | ||
| + | |||
| + | ---------------------------------------------------------------------------- | ||
| + | all.q@mada3.cse.ucsc.edu BIP 0/4 0.00 lx24-amd64 E | ||
| + | |||
| + | You can diagnose the error by typing: | ||
| + | |||
| + | qstat -explain E | ||
| + | |||
| + | ---------------------------------------------------------------------------- | ||
| + | all.q@mada3.cse.ucsc.edu BIP 0/4 0.00 lx24-amd64 E | ||
| + | queue all.q marked QERROR as result of job 18526's failure at host mada3.cse.ucsc.edu | ||
| + | |||
| + | Then you can force clear a queue with: | ||
| + | |||
| + | qmod -cq all.q@mada3.cse.ucsc.edu | ||
| + | |||
| + | or the entire queue with: | ||
| + | qmod -c '*' | ||
Latest revision as of 06:50, 12 July 2012
Contents
Basic Commands
We have our machines setup in a grid using a batch queue system. You must run the job on one of the sungrid machines (qconf -sh to see them). You can check your job status with:
qstat
You can delete jobs with:
qdel
where you can specify a specific job ID or all your jobs with "-u yourid".
To submit jobs, you use qsub as shown later.
Common Options
-S /bin/sh
For the script option (you did not specify -b y), this specifies which interpreter to use.
-m es
Mail the user on the end or suspension.
-M user@soe.ucsc.edu
What email address to send to.
-cwd
Start the simulation from the current working directory.
-o soc_fpu.log
Standard output.
-e soc_fpu.err
Standard error.
-N "fpu SOC P&R"
A name for the job.
-b y
Specify that the executable is a binary and not a script.
-V
Specify that the job and the shells environmental variables should be the same.
Submitting Jobs
When you submit a job, it sources your ".profile" instead of your ".bashrc" for configuration since it is a "non-interactive" shell.
You can submit jobs in one of two ways:
Command Line
qsub <options> -b y <binary> -- <options for the binary>
Example:
qsub -S /bin/sh -m es -M myid@soe.ucsc.edu -cwd -b y -N "myid_hard_area_FP" \ -e hard_results/n10.err -o hard_results/n10.log ../simanneal/simanneal -- -i ../benchmarks/hard/n10 -o hard_results/n10
Sometimes, I have found that the "--" isn't needed... I'm not sure why.
Script
Instead of specifying all the options on the command line, you can specify them in a script like this:
#!/bin/sh #$ -S /bin/sh #$ -m es #$ -M myid #$ -cwd #$ -o hard_results/n10.log #$ -e hard_results/n10.err #$ -N "myid_hard_area_FP" ../simanneal/simanneal -i ../benchmarks/hard/n10 -o hard_results/n10 exit 0
Restricting to the same machines
Often for papers, you will want to restrict your simualtions to identical machines (e.g. you want to compare run-times). In order to do this, we have a hostgroup for all of the mada servers (mada1-7). You can submit to these machines by doing:
qsub -q *@@mada <other arguments>
You can also specify other requirements such as available memory with the "-l" command.
To list a all hosts
qconf -ss
To list of cluster queues
qconf -sql
Administraiton
Somtimes the machines will get in an error state (E):
qstat -f
will show
---------------------------------------------------------------------------- all.q@mada3.cse.ucsc.edu BIP 0/4 0.00 lx24-amd64 E
You can diagnose the error by typing:
qstat -explain E
----------------------------------------------------------------------------
all.q@mada3.cse.ucsc.edu BIP 0/4 0.00 lx24-amd64 E
queue all.q marked QERROR as result of job 18526's failure at host mada3.cse.ucsc.edu
Then you can force clear a queue with:
qmod -cq all.q@mada3.cse.ucsc.edu
or the entire queue with:
qmod -c '*'
