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grid [2017/09/29 18:20]
popel [Advanced usage] |
grid [2017/10/02 17:28]
popel [Job monitoring] |
| # We have used two handy qsub parameters: | # We have used two handy qsub parameters: |
| # -cwd ... the script is executed in the current directory (the default is your home) | # -cwd ... the script is executed in the current directory (the default is your home) |
| # -j y ... stdout and stderr outputs are merged and redirected to a file (''script.sh.o*'') | # -j y ... stdout and stderr outputs are merged and redirected to a file (''script.sh.o$JOB_ID'') |
| # We have also provided two parameters for our script "Hello" and "World". | # We have also provided two parameters for our script "Hello" and "World". |
| # The qsub prints something like | # The qsub prints something like |
| ''qsub **-p** -100'' | ''qsub **-p** -100'' |
| Define a priority of your job as a number between -1024 and 0. Only SGE admins may use a number higher than 0. The default is 0, i.e. the highest possible priority. SGE uses the priority to decide when to start which pending job in the queue (it computes a real number called ''prior'', which is reported in ''qstat'', which grows as the job is waiting in the queue). Note that once a job is started, you cannot "unschedule" it, so from that moment on, it is irrelevant what was its priority. | Define a priority of your job as a number between -1024 and 0. Only SGE admins may use a number higher than 0. The default is 0, i.e. the highest possible priority. SGE uses the priority to decide when to start which pending job in the queue (it computes a real number called ''prior'', which is reported in ''qstat'', which grows as the job is waiting in the queue). Note that once a job is started, you cannot "unschedule" it, so from that moment on, it is irrelevant what was its priority. |
| | |
| ''qsub **-o** LOG.stdout **-e** LOG.stderr'' | ''qsub **-o** LOG.stdout **-e** LOG.stderr'' |
| redirect std{out,err} to separate files with given names | redirect std{out,err} to separate files with given names, instead of the defaults ''$JOB_NAME.o$JOB_ID'' and ''$JOB_NAME.e$JOB_ID''. |
| |
| ''qsub **-@** optionfile'' | ''qsub **-@** optionfile'' |
| === Array jobs === | === Array jobs === |
| |
| If you have a set of tasks (of the same type) and want to run them on multiple machines, use ''qsub -t''... | If you have a set of tasks (of the same type) and want to run them on multiple machines, use ''qsub -t''. |
| TODO | * ''-t 1-n'' start array job with n jobs numbered 1 ... n |
| | * environmental variable ''SGE_TASK_ID'' |
| | * output and error files ''$JOB_NAME.[eo]$JOB_ID.$TASK_ID'' |
| | * ''-t m-n[:s]'' start array job with jobs m, m + s, ..., n |
| | * environmental variables ''SGE_TASK_FIRST, SGE_TASK_LAST, SGE_TASK_STEPSIZE'' |
| | * ''-tc j'' run at most j jobs simultaneously |
| | * ''-hold_jid_ad comma_separated_job_list'' array jobs that must finish before this job starts; task //i// of the current job depends only on task //i// of the specified jobs |
| |
| ===== Monitorování úloh ===== | ===== Job monitoring ===== |
| |
| * ''qstat [-u user]'' -- seznam úloh aktuálně běžících / ve frontě | * ''qstat [-u user]'' -- print a list of running/waiting jobs of a given user |
| * ''qhost'' -- dostupné zdroje | * ''qhost'' -- print available/total resources |
| * ''/SGE/REPORTER/LRC-UFAL/bin/lrc_users_real_mem_usage -u user -w'' -- aktuální využití paměti uživatelem | * ''/SGE/REPORTER/LRC-UFAL/bin/lrc_users_real_mem_usage -u user -w'' -- current memory usage of a given user |
| * ''/SGE/REPORTER/LRC-UFAL/bin/lrc_users_limits_requested -w'' -- nárokované požadavky uživatelů | * ''/SGE/REPORTER/LRC-UFAL/bin/lrc_users_limits_requested -w'' -- required resources of all users |
| * ''/SGE/REPORTER/LRC-UFAL/bin/lrc_nodes_meminfo'' -- vypis vsech uzlu a stav vytiznosti pameti. | * ''/SGE/REPORTER/LRC-UFAL/bin/lrc_nodes_meminfo'' -- memory usage of all nodes |
| * mem_total: celkova pamet uzlu | * mem_total: |
| * mem_free: tedy kolik je jeste volne pameti z pametove quoty uzlu | * mem_free: total memory minus reserved memory (using ''qsub -l mem_free'') for each node |
| * act_mem_free: kolik uzlu OPRAVDU zbyva volne pameti | * act_mem_free: really free memory |
| * mem_used: kolik je pameti skutecne pouzito | * mem_used: really used memory |
| * ''/SGE/REPORTER/LRC-UFAL/bin/lrc_state_overview'' -- celkový přehled o clusteru | * ''/SGE/REPORTER/LRC-UFAL/bin/lrc_state_overview'' -- overall summary (with per-user stats for users with running jobs) |
| * celkovy pocet jader, pocet vyuzitych jader | * ''cat /SGE/REPORTER/LRC-UFAL/stats/userlist.weight'' -- all users sorted according to their activity (number of submitted jobs × their average duration), updated each night |
| * celkova velikost RAM, kolik je ji fyzicky nepouzite, kolik je ji jeste nerezervovane | * [[https://ufaladm2.ufal.hide.ms.mff.cuni.cz/munin/ufal.hide.ms.mff.cuni.cz/lrc1.ufal.hide.ms.mff.cuni.cz/lrc_users.html|Munin: graph of cluster usage by day and user]] (accessible only from ÚFAL network, after accepting a security exception) |
| * po jednotlivych uzivatelich (zrovna pocitajicich) -- kolik jim bezi uloh, kolik jich maji ve fronte a kolik z nich je ve stavu hold | |
| * ''cat /SGE/REPORTER/LRC-UFAL/stats/userlist.weight'' -- seznam uživatelů clusteru seřazený podle dosavadní aktivity (počet odeslaných úloh × čas, který běžely), aktualizovaný každý den v noci | |
| * [[https://ufaladm2.ufal.hide.ms.mff.cuni.cz/munin/ufal.hide.ms.mff.cuni.cz/lrc1.ufal.hide.ms.mff.cuni.cz/lrc_users.html|Munin: graf vytíženosti clusteru podle uživatelů]] (viditelný pouze ze sítě ÚFAL) | |
| | |
| ===== Časté a záludné problémy ===== | |
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| ==== Submitnutý job může znovu submitovat ==== | |
| | |
| Danovy starší zkušenosti s clusterem PBS (nikoli SGE) říkaly, že tohle nejde. Ale jde to, aspoň u nás. Příkazy ''qsub'' a spol. jsou kromě hlavy clusteru dostupné i na všech strojích clusteru, samozřejmě pokud váš soubor ''.bashrc'', ''.cshrc'' apod. zajistí, že se i na nich provede inicializace prostředí SGE. | |
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| ==== Proměnné prostředí, nastavení vlastního prostředí ==== | |
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| SGE spouští skripty v čistém prostředí. Nebuďte proto překvapeni, když vám skript na konzoli poběží dobře, ale po submitnutí fungovat nebude. Třeba nenašel potřebné programy v ''$PATH'' | |
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| Zatím nevím přesně, které ze souborů ''.login'', ''.bashrc'' ap. SGE spouští, jestli vůbec nějaké. Naopak, experimentálně jsem ověřil, že ''qsub -S /bin/bash skript'' nenačte žádný z ''.bashrc'', ''.bash_profile'', ''.login'', ani ''.profile''. | |
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| Z toho například také vyplývá, že bez ošetření se jako **Java** používá | |
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| java version "1.5.0" | |
| gij (GNU libgcj) version 4.1.2 20070502 (Red Hat 4.1.2-12) | |
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| Pokud chcete submittovaný program pouštět ve svém oblíbeném prostředí (např. nastavení ''PATH''), musíte v obalujícím skriptu příslušné ''.bash*'' načíst. Vždy je ale bezpečnější všude psát plné cesty, než spoléhat na PATH. | |
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| ==== bashrc a podobné nesmí nic vypisovat na konzoli ==== | |
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| Opsáno z [[http://www.sara.nl/userinfo/lisa/usage/batch/index.html]]. | |
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| It is important, that the files that are sourced during a login such as .bash_profile .profile .bashrc .login .cshrc don't produce any output when a non-interactive login is done. If they do, changes are that your job will run, but that the batch system is unable to deliver to you the standard output and error files. In that case the status of your job will be 'E' after the job is finished. Here is an example how you can test in a .bash_profile or .bashrc if this is an interactive login: | |
| |
| | ==== Other ==== |
| | * You can use environment variables ''$JOB_ID'', ''$JOB_NAME''. |
| | * One job can submit other jobs (but be careful with recursive:-)). A job submitted to the CPU cluster may submit GPU jobs (to the ''qpu.q'' queue). |
| | * It is important, that the files that are sourced during a login such as .bash_profile, .profile, .bashrc, .login etc. don't produce any output when a non-interactive login is done. If they do, changes are that your job will run, but that the batch system is unable to deliver to you the standard output and error files. In that case the status of your job will be 'E' after the job is finished. Here is an example how you can test in a .bash_profile or .bashrc if this is an interactive login: |
| <code> | <code> |
| unset INTERACTIVE | unset INTERACTIVE |
| fi | fi |
| </code> | </code> |
| | TODO: Is this restriction still true (for our cluster)? E.g. .bash_profile with /net/projects/SGE/user/sge_profile prints info messages on stderr and it is OK. |
| ==== Jak zjistit, jaké zdroje jsem pro svou úlohu požadoval ==== | |
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| <code>qstat -j 973884,982737,984029,984030,984031,984034,984036 | grep resource | |
| hard resource_list: mem_free=50g | |
| hard resource_list: mem_free=200g | |
| hard resource_list: mem_free=16g | |
| hard resource_list: mem_free=16g | |
| hard resource_list: mem_free=16g | |
| hard resource_list: mem_free=31g</code> | |
| |
