「SGE用スクリプトファイルをPBS用に書き換える方法」の版間の差分
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| (同じ利用者による、間の12版が非表示) | |||
| 15行目: | 15行目: | ||
<tr><td></td><th>PBS command</th><th> SGE command</th></tr> | <tr><td></td><th>PBS command</th><th> SGE command</th></tr> | ||
<tr><td>Queue</td><td> #PBS -q [queue] </td><td>#$ -q [queue]</td></tr> | <tr><td>Queue</td><td> #PBS -q [queue] </td><td>#$ -q [queue]</td></tr> | ||
<tr><td> | <tr><td>Processors (Single host) </td><td> #PBS -l select=1:ncpus=[#] </td><td>#$ -pe smp [#]</td></tr> | ||
<tr><td>Wall clock limit</td><td> #PBS -l walltime=[hh:mm:ss] </td><td>#$ -l time=[hh:mm:ss]</td></tr> | <tr><td>Wall clock limit</td><td> #PBS -l walltime=[hh:mm:ss] </td><td>#$ -l time=[hh:mm:ss]</td></tr> | ||
<tr><td>Standard output file</td><td> #PBS -o [file] </td><td>#$ -o [path]</td></tr> | <tr><td>Standard output file</td><td> #PBS -o [file] </td><td>#$ -o [path]</td></tr> | ||
<tr><td>Standard error </td><td>#PBS -e [file] </td><td>#$ -e [path]</td></tr> | <tr><td>Standard error </td><td>#PBS -e [file] </td><td>#$ -e [path]</td></tr> | ||
<tr><td>Array job </td><td>#PBS - | <tr><td>Array job </td><td>#PBS -J [# - #] </td><td>#$ -t [# - #]</td></tr> | ||
<tr><td>Array number Variable name</td><td>${ | <tr><td>Array number Variable name</td><td>${PBS_ARRAY_INDEX}</td><td>${SGE_TASK_ID}</td></tr> | ||
<tr><td>Copy environment</td><td> #PBS -V </td><td>#$ -V</td></tr> | <tr><td>Copy environment</td><td> #PBS -V </td><td>#$ -V</td></tr> | ||
<tr><td>Notification event </td><td>#PBS -m abe </td><td>#$ -m abe</td></tr> | <tr><td>Notification event </td><td>#PBS -m abe </td><td>#$ -m abe</td></tr> | ||
| 28行目: | 27行目: | ||
<tr><td>Job restart </td><td>#PBS -r [y|n] </td><td>#$ -r [yes|no]</td></tr> | <tr><td>Job restart </td><td>#PBS -r [y|n] </td><td>#$ -r [yes|no]</td></tr> | ||
<tr><td>Move current directory </td><td>n/a </td><td>#$ -cwd </td></tr> | <tr><td>Move current directory </td><td>n/a </td><td>#$ -cwd </td></tr> | ||
<tr><td>Memory requirement </td><td>#PBS -l mem=XXXXmb </td><td>#$ -mem [#]G</td></tr> | <tr><td>Memory requirement </td><td>#PBS -l mem=XXXXmb </td><td>#$ -mem [#]G</td></tr> | ||
</table><br> | </table><br> | ||
* -cwd が使えなくなる | * -cwd が使えなくなる | ||
*代替の記述 | *代替の記述 | ||
cd $PBS_O_WORKDIR | cd ${PBS_O_WORKDIR} | ||
== スクリプトファイル SGE -> PBS == | == スクリプトファイル SGE -> PBS == | ||
| 48行目: | 46行目: | ||
#PBS -q medium | #PBS -q medium | ||
#PBS -S /bin/sh | #PBS -S /bin/sh | ||
#PBS - | #PBS -J 1-10<br> | ||
cd ${PBS_O_WORKDIR} <font color="gray">## instead of "#$ -cwd"</font> <br> | cd ${PBS_O_WORKDIR} <font color="gray">## instead of "#$ -cwd"</font> <br> | ||
./myprogram -input=file-${ | ./myprogram -input=file-${PBS_ARRAY_INDEX} | ||
== SGE -> PBS | == SGE -> PBS 変換用 Perl スクリプト == | ||
[https://gist.github.com/piroyon/de5b9890cd4a0c26a07de19f2ba03370 sge2pbs.pl] | [https://gist.github.com/piroyon/de5b9890cd4a0c26a07de19f2ba03370 sge2pbs.pl] | ||
*結果は保障しません... | *結果は保障しません... | ||
perl sge2pbs.pl sge_script_file > pbs_script_file | perl sge2pbs.pl sge_script_file > pbs_script_file | ||
2018年10月25日 (木) 06:30時点における最新版
主なコマンド Common command
| PBS command | SGE command | |
|---|---|---|
| Job submission | qsub [scriptfile] | qsub [scriptfile] |
| Job deletion | qdel [job_id] | qdel [job_id] |
| Job status (for user) | qstat -u [username] | qstat -u [username] |
| Extended job status | qstat -f [job_id] | qstat -f -j [job_id] |
| Hold a job temporarily | qhold [job_id] | qhold [job_id] |
| Release job hold | qrls [job_id] | qrls [job_id] |
| List of usable queues | qstat -Q | qconf -sql |
リソース指定 Resource specifications
| PBS command | SGE command | |
|---|---|---|
| Queue | #PBS -q [queue] | #$ -q [queue] |
| Processors (Single host) | #PBS -l select=1:ncpus=[#] | #$ -pe smp [#] |
| Wall clock limit | #PBS -l walltime=[hh:mm:ss] | #$ -l time=[hh:mm:ss] |
| Standard output file | #PBS -o [file] | #$ -o [path] |
| Standard error | #PBS -e [file] | #$ -e [path] |
| Array job | #PBS -J [# - #] | #$ -t [# - #] |
| Array number Variable name | ${PBS_ARRAY_INDEX} | ${SGE_TASK_ID} |
| Copy environment | #PBS -V | #$ -V |
| Notification event | #PBS -m abe | #$ -m abe |
| Email address | #PBS -M [email] | #$ -M [email] |
| Job name | #PBS -N [name] | #$ -N [name] |
| Job restart | #PBS -r [y|n] | #$ -r [yes|no] |
| Move current directory | n/a | #$ -cwd |
| Memory requirement | #PBS -l mem=XXXXmb | #$ -mem [#]G |
- -cwd が使えなくなる
- 代替の記述
cd ${PBS_O_WORKDIR}
スクリプトファイル SGE -> PBS
- sge
#!/bin/bash #$ -q medium #$ -cwd #$ -S /bin/sh #$ -t 1-10
./myprogram -input=file-${SGE_TASK_ID}
- pbs
#!/bin/bash #PBS -q medium #PBS -S /bin/sh #PBS -J 1-10
cd ${PBS_O_WORKDIR} ## instead of "#$ -cwd"
./myprogram -input=file-${PBS_ARRAY_INDEX}
SGE -> PBS 変換用 Perl スクリプト
- 結果は保障しません...
perl sge2pbs.pl sge_script_file > pbs_script_file