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grid [2018/06/08 14:26]
vodrazka [ÚFAL Grid Engine (LRC)] |
grid [2018/10/01 09:53]
fucik [Basic usage] |
| ====== ÚFAL Grid Engine (LRC) ====== | ====== ÚFAL Grid Engine (LRC) ====== |
| |
| LRC (Linguistic Research Cluster) is a name of ÚFAL's computational grid/cluster, which has (as of 2018/06) about 1416 CPU cores (57 servers + 10 submission heads), with a total 6.33 TiB of RAM. It uses [[https://en.wikipedia.org/wiki/Oracle_Grid_Engine|(Sun/Oracle/Son of) Grid Engine]] software (SGE) for job scheduling etc. You can submit many computing tasks (jobs) at once, they will be placed in a queue and once a machine (slot) with the required capabilities (e.g. RAM, number of cores) is available, your job will be executed (scheduled) on this machine. This way we can maximize the usefulness of the computing resources and divide it among users in a fair way. | LRC (Linguistic Research Cluster) is a name of ÚFAL's computational grid/cluster, which has (as of 2018/06) about 1728 CPU cores (65 servers + 10 submission heads), with a total 7.2 TiB of RAM. It uses [[https://en.wikipedia.org/wiki/Oracle_Grid_Engine|(Sun/Oracle/Son of) Grid Engine]] software (SGE) for job scheduling etc. You can submit many computing tasks (jobs) at once, they will be placed in a queue and once a machine (slot) with the required capabilities (e.g. RAM, number of cores) is available, your job will be executed (scheduled) on this machine. This way we can maximize the usefulness of the computing resources and divide it among users in a fair way. |
| |
| If you need GPU processing, see a special page about our [[:gpu|GPU cluster called DLL]] (which is actually a subsystem of LRC with an independent queue ''gpu-ms.q''). | If you need GPU processing, see a special page about our [[:gpu|GPU cluster called DLL]] (which is actually a subsystem of LRC with an independent queue ''gpu-ms.q''). |
| | andromeda[1-13] | AMD Opteron | 2.8 | 7 | 30 | | | | andromeda[1-13] | AMD Opteron | 2.8 | 7 | 30 | | |
| | lucifer[1-10] | Intel(R) Xeon(R) CPU E5620 | 2.4 | 15 | 122 | | | | lucifer[1-10] | Intel(R) Xeon(R) CPU E5620 | 2.4 | 15 | 122 | | |
| | hydra[1-4] | AMD Opteron SSE4 AVX | 2.6 | 15 | 123 | | | | hydra[1-4] | AMD Opteron SSE4 AVX | 2.6 | 15 | 122 | | |
| | | orion[1-8] | Intel(R) Xeon(R) CPU E5-2630 v4 | 2.2 | 39 | 122 | | |
| | | cosmos | Intel Xeon | 2.9 | 7 | 249 | | |
| | | belzebub | Intel Xeon SSE4 AVX | 2.9 | 31 | 249 | | |
| | | iridium | Intel Xeon SSE4 | 1.9 | 15 | 501 | | |
| |
| Machines from old cluster (do not use!): | Machines from old cluster (do not use!): |
| | fireball[1-10] | Intel Xeon | 3.0 | 4 | 32 | removed | | | fireball[1-10] | Intel Xeon | 3.0 | 4 | 32 | removed | |
| | hyperion[1-9] | Intel Xeon | 3.0 | 4 | 32 | removed | | | hyperion[1-9] | Intel Xeon | 3.0 | 4 | 32 | removed | |
| | orion[1-6] | Intel Xeon | 2.3 | 8 | 32 | removed | | |
| | orion[7-10] | Intel Xeon | 2.0 | 4 | 32 | removed | | |
| | tauri[1-10] | Intel Xeon | 3.0 | 4 | 32 | removed | | | tauri[1-10] | Intel Xeon | 3.0 | 4 | 32 | removed | |
| | cosmos | Intel Xeon | 2.9 | 8 | 256 | migration pending | | | twister[1,2] | Intel Xeon SSE4 | 2.4 | 8 | 48 | moved to GPU cluster| |
| | belzebub | Intel Xeon SSE4 AVX | 2.9 | 32 | 256 | migration pending | | |
| | iridium | Intel Xeon SSE4 | 1.9 | 16 | 512 | migration pending | | |
| | twister[1,2] | Intel Xeon SSE4 | 2.4 | 8 | 48 | migration pending | | |
| |
| <html><!-- | <html><!-- |
| ^ Name ^ CPU type ^ GHz ^cores ^ RAM(GB) ^ note ^ | ^ Name ^ CPU type ^ GHz ^cores ^ RAM(GB) ^ note ^ |
| | sol[1-10] | Intel(R) Xeon(R) CPU E5345 | 2.3 | 7 | 31 | you can ssh here and compute or submit jobs | | | sol[1-10] | Intel(R) Xeon(R) CPU E5345 | 2.3 | 7 | 31 | you can ssh here and compute or submit jobs | |
| | | lrc[12] | Intel(R) Xeon(R) CPU E5-2630 v4 | 2.2 | 4 | 4 | you can submit jobs here or monitor job execution - NO COMPUTATION IS ALLOWED HERE !!! | |
| |
| You can ssh to one of the **sol machines** and submit jobs from here. It is allowed to compute here, which is useful e.g. when you have a script which submits your jobs, but it also collects statistics from the jobs outputs (and possibly submits new jobs conditioned on the statistics). However, the sol machines are relatively slow and may be occupied by your colleagues, so for bigger (longer) tasks, always prefer submission as separate jobs. | You can ssh to one of the **sol machines** and submit jobs from here. It is allowed to compute here, which is useful e.g. when you have a script which submits your jobs, but it also collects statistics from the jobs outputs (and possibly submits new jobs conditioned on the statistics). However, the sol machines are relatively slow and may be occupied by your colleagues, so for bigger (longer) tasks, always prefer submission as separate jobs. |
| # prepare a shell script describing your task | # prepare a shell script describing your task |
| qsub -cwd -j y script.sh Hello World | qsub -cwd -j y script.sh Hello World |
| # This submits your job to the default queue, which is currently ''cpu-ms.q''. | # This submits your job to the default queue, which is currently ''cpu-*.q''. |
| # Usually, there is a free slot, so the job will be scheduled within few seconds. | # Usually, there is a free slot, so the job will be scheduled within few seconds. |
| # We have used two handy qsub parameters: | # We have used two handy qsub parameters: |
| ''qsub **-M** popel@ufal.mff.cuni.cz,rosa@ufal.mff.cuni.cz **-m** beas'' | ''qsub **-M** popel@ufal.mff.cuni.cz,rosa@ufal.mff.cuni.cz **-m** beas'' |
| Specify the emails where you want to be notified when the job has been **b** started, **e** ended, **a** aborted or rescheduled, **s** suspended. | Specify the emails where you want to be notified when the job has been **b** started, **e** ended, **a** aborted or rescheduled, **s** suspended. |
| | The default is now ''-m ea'' (TODO check this) and the default email address is forwarded to you (so there is no need to use ''-M''). You can use ''-m n'' to override the defaults and send no emails. |
| |
| ''qsub **-hold_jid** 121144,121145'' (or ''qsub **-hold_jid** get_src.sh,get_tgt.sh'') | ''qsub **-hold_jid** 121144,121145'' (or ''qsub **-hold_jid** get_src.sh,get_tgt.sh'') |
| |
| and you execute it now simply with ''qsub script.sh''. | and you execute it now simply with ''qsub script.sh''. |
| | |
| | === ~/.sge_request === |
| | |
| | You can change the defaults for any option by creating a personal configuration file ''~/.sge_request''. For example, you can add there a line ''-m n'', so you will get no email notifications (unless overridden from the command line or in-script options). |
| |
| === Array jobs === | === Array jobs === |
| === Ssh to random sol === | === Ssh to random sol === |
| Ondřej Bojar suggests to add the following alias to your .bashrc (cf. [[#sshcwd]]): | Ondřej Bojar suggests to add the following alias to your .bashrc (cf. [[#sshcwd]]): |
| <code>alias cluster='comp=$(($RANDOM /4095 +1)); ssh -o "StrictHostKeyChecking no" sol$comp'</code> | <code>alias cluster='comp=$(( (RANDOM % 10) +1)); ssh -o "StrictHostKeyChecking no" sol$comp'</code> |
| |
| ===== Job monitoring ===== | ===== Job monitoring ===== |
| * ''qstat [-u user]'' -- print a list of running/waiting jobs of a given user | * ''qstat [-u user]'' -- print a list of running/waiting jobs of a given user |
| * ''qhost'' -- print available/total resources | * ''qhost'' -- print available/total resources |
| * ''/SGE/REPORTER/LRC-UFAL/bin/lrc_users_real_mem_usage -u user -w'' -- current memory usage of a given user | * ''qacct -j job_id'' -- print info even for ended job (for which ''qstat -j job_id'' does not work). See ''man qacct'' for more. |
| * ''/SGE/REPORTER/LRC-UFAL/bin/lrc_users_limits_requested -w'' -- required resources of all users | |
| * ''/SGE/REPORTER/LRC-UFAL/bin/lrc_nodes_meminfo'' -- memory usage of all nodes | * ''/opt/LRC/REPORTER/LRC-UFAL/bin/lrc_users_real_mem_usage -u user -w'' -- current memory usage of a given user |
| | * ''/opt/LRC/REPORTER/LRC-UFAL/bin/lrc_users_limits_requested -w'' -- required resources of all users |
| | * ''/opt/LRC/REPORTER/LRC-UFAL/bin/lrc_nodes_meminfo'' -- memory usage of all nodes |
| * mem_total: | * mem_total: |
| * mem_free: total memory minus reserved memory (using ''qsub -l mem_free'') for each node | * mem_free: total memory minus reserved memory (using ''qsub -l mem_free'') for each node |
| * act_mem_free: really free memory | * act_mem_free: really free memory |
| * mem_used: really used memory | * mem_used: really used memory |
| * ''/SGE/REPORTER/LRC-UFAL/bin/lrc_state_overview'' -- overall summary (with per-user stats for users with running jobs) | * ''/opt/LRC/REPORTER/LRC-UFAL/bin/lrc_state_overview'' -- overall summary (with per-user stats for users with running jobs) |
| * ''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 | * ''cat /opt/LRC/REPORTER/LRC-UFAL/stats/userlist.weight'' -- all users sorted according to their activity (number of submitted jobs × their average duration), updated each night |
| * [[http://ufaladm2/munin/ufal.hide.ms.mff.cuni.cz/lrc-headnode.ufal.hide.ms.mff.cuni.cz/index.html|Munin: graph of cluster usage by day and user]] and [[http://ufaladm2/munin/ufal.hide.ms.mff.cuni.cz/apophis.ufal.hide.ms.mff.cuni.cz/index.html|Munin monitoring of Apophis disk server]] (both accessible only from ÚFAL network) | * [[http://ufaladm2/munin/ufal.hide.ms.mff.cuni.cz/lrc-headnode.ufal.hide.ms.mff.cuni.cz/index.html|Munin: graph of cluster usage by day and user]] and [[http://ufaladm2/munin/ufal.hide.ms.mff.cuni.cz/apophis.ufal.hide.ms.mff.cuni.cz/index.html|Munin monitoring of Apophis disk server]] (both accessible only from ÚFAL network) |
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