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grid [2018/04/25 21:28]
popel all flags in a comment
grid [2018/11/27 16:28] (current)
vidra qalter works on running jobs as well
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 ====== 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 2017/09) about 1800 CPU cores (115 servers + submission heads), with a total 10 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.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''​).
 TODO: describe alternatives,​ e.g.: MetaCentrum / Cesnet cluster (all MFF students can use it), Amazon EC2, Microsoft Azure (some colleagues may have sometime free vouchers). TODO: describe alternatives,​ e.g.: MetaCentrum / Cesnet cluster (all MFF students can use it), Amazon EC2, Microsoft Azure (some colleagues may have sometime free vouchers).
  
 ===== List of Machines ===== ===== List of Machines =====
-Last update: 2017/09. All machines have Ubuntu ​14.04.+Last update: 2017/06. All machines have Ubuntu ​18.04.
 Some machines are at Malá Strana (ground floor, new server room built from Lindat budget), some are at Troja (5 km north-east). Some machines are at Malá Strana (ground floor, new server room built from Lindat budget), some are at Troja (5 km north-east).
 If you need to quickly distinguish which machine is located where, you can use your knowledge of [[https://​en.wikipedia.org/​wiki/​Trojan_War|Trojan war]]-related heroes, ''​qhost -q'',​ or the tables below. ​ If you need to quickly distinguish which machine is located where, you can use your knowledge of [[https://​en.wikipedia.org/​wiki/​Trojan_War|Trojan war]]-related heroes, ''​qhost -q'',​ or the tables below. ​
  
-==== Troja (troja-all.q) ​==== +====== AVX instructions ======
-^ Name                ^ CPU type            ^ GHz ^cores ^RAM(GB)^ note ^ +
-| achilles[1-8] ​      | Intel               | 3.2 |   32 |  128 |  | +
-| hector[1-8] ​        | Intel               | 1.3 |   32 |  128 |  | +
-| helena[1-8] ​        | Intel               | 2.6 |   32 |  128 |  | +
-| paris[1-8] ​         | Intel               | 2.4 |   32 |  128 |  |+
  
-==== MS = Malá Strana ​(ms-all.q) ====+==== Troja (cpu-troja.q) ==== 
 +^ Name                ^ CPU type                                  ^ GHz ^cores ^RAM(GB)^ note ^ 
 +| achilles[1-8] ​      | Intel(R) Xeon(R) CPU E5-2630 v3           | 2.4 |   31 |  123  |  AVX enabled ​   | 
 +| hector[1-8] ​        | Intel(R) Xeon(R) CPU E5-2630 v3           | 2.4 |   31 |  123  |  AVX enabled ​   | 
 +| helena[1-8] ​        | Intel(R) Xeon(R) CPU E5-2630 v3           | 2.4 |   31 |  123  |  AVX enabled ​   | 
 +| paris[1-8] ​         | Intel(R) Xeon(R) CPU E5-2630 v3           | 2.4 |   31 |  123  |  AVX enabled ​   |
  
-^ Name                ^ CPU type and flags   ​^ GHz ^cores ^RAM(GB)^ note ^ +==== MS = Malá Strana (cpu-ms.q) ==== 
-| andromeda[1-13] ​    | AMD Opteron ​         | 2.8 |    ​|   32 |  | + 
-| hydra[1-4] ​         | AMD Opteron SSE4 AVX | 2.6 |   16 |  ​128 |  | +^ Name                ^ CPU type and flags              ^ GHz ^cores ^RAM(GB)^ note ^ 
-fireball[1-10     | Intel Xeon           ​3.0 |    4 |   32 |  | +| andromeda[1-13] ​    | AMD Opteron ​                    ​| 2.8 |    ​|   30  |      | 
-hyperion[1-9] ​      | Intel Xeon           ​3.|    ​4 |   ​32 ​|  | +| lucifer[1-10] ​      | Intel(R) Xeon(R) CPU E5620      | 2.4 |   ​15 ​|  ​122  |      ​
-lucifer[1-10] ​      | Intel Xeon SSE4      | 2.|   16 |  ​128 |  | +| hydra[1-4] ​         | AMD Opteron SSE4 AVX            | 2.6 |   15 |  ​122  |   AVX enabled ​  
-orion[1-6] ​         ​| Intel Xeon           ​2.3 |    8 |   32 |  | +orion[1-8         | Intel(R) Xeon(R) CPU E5-2630 v4 2.|   39 |  ​122  |   AVX enabled ​  
-orion[7-10]         ​| Intel Xeon           ​| ​2.0 |    4 |   32 |  +cosmos ​             ​| Intel Xeon                      2.|    ​|  ​249  |      ​
-tauri[1-10        ​| Intel Xeon           | 3.0 |    4 |   32 |  +belzebub ​           ​| Intel Xeon SSE4 AVX             | 2.|   31 |  ​249  |   AVX enabled ​  
-cosmos ​             ​| Intel Xeon           ​| ​2.|    ​8 |  256 |  | +iridium ​            | Intel Xeon SSE4                 1.|   15 |  ​501  |      ​| 
-| belzebub ​           | Intel Xeon SSE4 AVX  | 2.9 |   32 |  256 |  | + 
-| iridium ​            | Intel Xeon SSE4      | 1.9 |   16 |  512 | also in ''​gpu.q'' ​+Machines from old cluster (do not use!): 
-| twister[1,​2] ​       | Intel Xeon SSE4      | 2.4 |    8 |   48 | also in ''​gpu.q'' ​|+ 
 +^ Name                ^ CPU type and flags              ^ GHz ^cores ^RAM(GB)^ note ^ 
 +fireball[1-10]      | Intel Xeon           ​| ​3.0 |    4 |   32 | removed ​
 +hyperion[1-9      ​| Intel Xeon           | 3.0 |    4 |   32 | removed ​
 +tauri[1-10] ​        | Intel Xeon           ​| ​3.|    ​|   32 | removed ​
 +| twister[1,​2] ​       | Intel Xeon SSE4      | 2.4 |    8 |   48 | moved to GPU cluster|
  
 <​html><​!-- <​html><​!--
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 --> -->
 </​html>​ </​html>​
-=== Outside LRC cluster (but located as MS) === +=== Submit hosts / test machines ​=== 
-^ Name                ^ CPU type            ^ GHz ^cores ^ RAM(GB)^ note  ^ +^ Name                ^ CPU type                        ^ GHz ^cores ^ RAM(GB) ^ note  ^ 
-lrc[1,2           | Intel               ​| 2.3 |    ​|   45 | **no computing here**, just submit jobs | +sol[1-10          ​| Intel(R) Xeon(R) CPU E5345      ​| 2.3 |    ​|   31    | you can ssh here and compute ​or submit jobs 
-| sol[1-5] ​           | Intel               | 2.6 |    4 |   ​16 ​| you can ssh here and compute | +lrc[12            ​| Intel(R) Xeon(R) CPU E5-2630 v4 | 2.|    ​   ​4 ​   ​| you can submit jobs here or monitor job execution - NO COMPUTATION IS ALLOWED HERE !!! |
-sol[6-8           | Intel               ​| 2.|    ​  16 | you can ssh here and compute ​|+
  
-The two **lrc machines** are so called heads of the cluster. **No computation is allowed here**, i.e. no CPU-intensive,​ disk-intensive nor RAM-intensive computation (very simple scripts are OK). You should just ssh to ''​lrc1''​ or ''​lrc2''​ and submit your jobs as described bellow. +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.
- +
-Alternatively,​ 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.+
  
 ===== Installation ===== ===== Installation =====
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 Add the following line into your '​~/​.bash_profile'​. Add the following line into your '​~/​.bash_profile'​.
  
-  source /net/projects/SGE/user/sge_profile+  source /opt/LRC/sge_profile 
 + 
 +Or call one of these scripts directly: 
 + 
 +  ​/opt/LRC/​common/​settings.sh (for bash)  
 +  /​opt/​LRC/​common/​settings.csh (for tcsh/csh)
  
-This detects if you are on one of the cluster machines (including ​lrc and sol) and sets env variables accordingly. It also prints a status message.+This detects if you are on one of the cluster machines (including sol) and sets env variables accordingly. It also prints a status message.
 Usually, this is the first line of your '​~/​.bash_profile'​ and the second-and-last line is Usually, this is the first line of your '​~/​.bash_profile'​ and the second-and-last line is
  
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   export LC_ALL=en_US.UTF-8   export LC_ALL=en_US.UTF-8
 +  ​
 +If you are curious about purpose of .bashrc and .bash_profile and you need to know when they should be used you may read [[https://​stackoverflow.com/​a/​415444|this]].
 +  ​
 ===== Basic usage ===== ===== Basic usage =====
  
-First, you need to ssh to the cluster head (lrc1 or lrc2) or to one of the sol machines. The full address is ''​lrc1.ufal.hide.ms.mff.cuni.cz'',​ but you can use just ''​ssh ​lrc1''​ ("​hide"​ means it is accessible only from the ÚFAL network, not from outside; if working from home/​Eduroam,​ you need to [[internal:​remote-access|login/​VPN]] to the ÚFAL network first).+First, you need to ssh to one of the submit hosts (sol[1-10]). The full address is (for example) ​''​sol1.ufal.hide.ms.mff.cuni.cz'',​ but you can use just ''​ssh ​sol1''​ ("​hide"​ means it is accessible only from the ÚFAL network, not from outside; if working from home/​Eduroam,​ you need to [[internal:​remote-access|login/​VPN]] to the ÚFAL network first).
 In the following tutorial, we will prepare a wrapper shell script ''​script.sh''​ with a toy task. In practice you can name the script whatever you want and you can execute the real task, e.g. a Python/​Perl/​... script. It is recommended to use the wrapper shell scripts, but with ''​-b y''​ (see [[#advanced usage]]) you can execute a Python/​Perl/​... directly without any wrapper. In the following tutorial, we will prepare a wrapper shell script ''​script.sh''​ with a toy task. In practice you can name the script whatever you want and you can execute the real task, e.g. a Python/​Perl/​... script. It is recommended to use the wrapper shell scripts, but with ''​-b y''​ (see [[#advanced usage]]) you can execute a Python/​Perl/​... directly without any wrapper.
  
 <​code>​ <​code>​
-ssh lrc1+ssh sol1
 echo '​hostname;​ pwd; echo The second parameter is $2' > script.sh echo '​hostname;​ pwd; echo The second parameter is $2' > script.sh
   # 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 ''​ms-all.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:
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 See ''​man complex''​ (run it on lrc or sol machines) for a list of possible resources you may require (in addition to ''​mem_free''​ etc. discussed above). See ''​man complex''​ (run it on lrc or sol machines) for a list of possible resources you may require (in addition to ''​mem_free''​ etc. discussed above).
  
-''​qsub **-p** -99''​ +''​qsub **-p** -200''​ 
-Define a priority of your job as a number between -1024 and 0. Only SGE admins may use a number higher than 0. In January 2018, we changed the default to -100 (it used to be 0). 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. You can ask for a higher priority (-99...0) if your job is urgent and/or will finish soon and you want to skip your colleagues'​ jobs in the queue. You should ask for lower priority (-1024..-101) if you submit many jobs at once or if the jobs are not urgent.+Define a priority of your job as a number between -1024 and 0. Only SGE admins may use a number higher than 0. In January 2018, we changed the default to -100 (it used to be 0). Please, do not use priority between -99 and 0 for jobs taking longer than a few hours, unless it is absolutely necessary for a deadline. In that case, please notify other GPU users. You should ask for lower priority (-1024..-101) if you submit many jobs at once or if the jobs are not urgent. 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''​
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 ''​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 a''​ 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''​)
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 ''​**qalter**''​ ''​**qalter**''​
-You can change some properties of already submitted jobs, which are still waiting in the queue (//​pending//​).+You can change some properties of already submitted jobs (both waiting in the queue and running). Changeable properties are listed in ''​man qsub''​.
  
 ''​**man** qsub qstat qalter qhold queue_conf sge_types complex''​ ''​**man** qsub qstat qalter qhold queue_conf sge_types complex''​
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 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 ===
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 === 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 =====
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   * ''​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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