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grid [2019/02/14 17:49]
dusek [Advanced usage] |
grid [2024/10/02 15:21] (current)
popel |
| 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''). |
| 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). |
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| | **TODO: IN 2022 MOVING FROM SGE TO SLURM** (see [[slurm|slurm guidelines]]) -- **commands like ''qsub'' and ''qstat'' will stop working!** |
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| | **IN 2024: Newly, all the documentation is at a dedicated wiki https://ufal.mff.cuni.cz/lrc (you need to use ufal and [[internal:welcome-at-ufal#small-linguistic-password|small-linguistic password]] to access the wiki from outside of the UFAL network).*** |
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| ===== List of Machines ===== | ===== List of Machines ===== |
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| ^ Name ^ CPU type and flags ^ GHz ^cores ^RAM(GB)^ note ^ | ^ Name ^ CPU type and flags ^ GHz ^cores ^RAM(GB)^ note ^ |
| | andromeda[1-13] | AMD Opteron | 2.8 | 7 | 30 | | | |
| | lucifer[1-10] | Intel(R) Xeon(R) CPU E5620 | 2.4 | 15 | 122 | | | |
| | hydra[1-4] | AMD Opteron SSE4 AVX | 2.6 | 15 | 122 | AVX enabled | | | hydra[1-4] | AMD Opteron SSE4 AVX | 2.6 | 15 | 122 | AVX enabled | |
| | orion[1-8] | Intel(R) Xeon(R) CPU E5-2630 v4 | 2.2 | 39 | 122 | AVX enabled | | | orion[1-8] | Intel(R) Xeon(R) CPU E5-2630 v4 | 2.2 | 39 | 122 | AVX enabled | |
| | cosmos | Intel Xeon | 2.9 | 7 | 249 | | | |
| | belzebub | Intel Xeon SSE4 AVX | 2.9 | 31 | 249 | AVX enabled | | | belzebub | Intel Xeon SSE4 AVX | 2.9 | 31 | 249 | AVX enabled | |
| | iridium | Intel Xeon SSE4 | 1.9 | 15 | 501 | | | | iridium | Intel Xeon SSE4 | 1.9 | 15 | 501 | | |
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| Machines from old cluster (do not use!): | |
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| ^ 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 | 3.0 | 4 | 32 | removed | | |
| | twister[1,2] | Intel Xeon SSE4 | 2.4 | 8 | 48 | moved to GPU cluster| | |
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| <html><!-- | <html><!-- |
| === Submit hosts / test machines === | === Submit hosts / test machines === |
| ^ 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[1-8] | Intel(R) Xeon(R) CPU E5-2630 v3 | 2.4 | 7 | 28 | 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 !!! | | | 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 !!! | |
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| ''qsub **-q** cpu-troja.q'' | ''qsub **-q** cpu-troja.q'' |
| This way your job is submitted to the Troja queue. The default is ''cpu-ms.q''. You can also use e.g. | This way your job is submitted to the Troja queue. The default is ''cpu-*.q''. You can also use e.g. |
| ''-q '(troja*|ms*)''' to submit on any machine in those two queues (but **don't use ''-q '*'''** as this includes also [[:gpu|gpu.q]]), | ''-q '(cpu-t*|cpu-m*)''' to submit on any machine in those two queues (but **don't use ''-q '*'''** as this includes also [[:gpu|gpu.q]]), |
| ''-q '*@hector[14]''' to submit on hector1 or hector4, | ''-q '*@hector[14]''' to submit on hector1 or hector4, |
| ''-q '[tm]*@!(hector*|iridium)''' to submit on any troja/ms machine except hectors and iridium. | ''-q 'cpu-*@!(hector*|iridium)''' to submit on any troja/ms machine except hectors and iridium. |
| However, usually you should specify just the queue (cpu-troja.q vs. cpu-ms.q), not a particular machine, and instead use ''-l'' to specify the needed resources in a general way. | However, usually you should specify just the queue (cpu-troja.q vs. cpu-ms.q), not a particular machine, and instead use ''-l'' to specify the needed resources in a general way. |
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| ''qsub **-b** y'' | ''qsub **-b** y'' |
| Treat ''script.sh'' (or whatever is the name of the command you execute) as a binary, i.e. don't search for [[#in-script options]] within the file, don't transfer it to the qmaster and then to the execution node. This makes the execution a bit faster and it may prevent some rare but hard-to-detect errors caused SGE interpreting the script. The script must be available on the execution node via NFS, Lustre (which is our case), etc. With ''-b y'' (shortcut for ''-b yes''), ''script.sh'' can be a script or a binary. With ''-b n'' (which is the default for ''qsub''), ''script.sh'' must be a script (text file). | Treat ''script.sh'' (or whatever is the name of the command you execute) as a binary, i.e. don't search for [[#in-script options]] within the file, don't transfer it to the qmaster and then to the execution node. This makes the execution a bit faster and it may prevent some rare but hard-to-detect errors caused SGE interpreting the script. The script must be available on the execution node via NFS, Lustre (which is our case), etc. With ''-b y'' (shortcut for ''-b yes''), ''script.sh'' can be an executable script or a binary (and you must provide full path, e.g. ''./script.sh''). With ''-b n'' (which is the default for ''qsub''), ''script.sh'' must be a script (text file). |
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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'' |
| You can change some properties of already submitted jobs (both waiting in the queue and running). Changeable properties are listed in ''man qsub''. | You can change some properties of already submitted jobs (both waiting in the queue and running). Changeable properties are listed in ''man qsub''. |
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| ''**man** qsub qstat qalter qhold queue_conf sge_types complex'' | ''[[https://gridscheduler.sourceforge.net/htmlman/htmlman1/qsub.html|man qsub]] qstat qalter qhold queue_conf sge_types complex'' |
| Find out all the gory details which are missing here. You'll have to do it one day anyway:-). | Find out all the gory details which are missing here. You'll have to do it one day anyway:-). |
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| * ''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 | * ''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 |
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| * [[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) | * [[https://ufaladm2.ufal.hide.ms.mff.cuni.cz/munin/ufal.hide.ms.mff.cuni.cz/lrc-master.ufal.hide.ms.mff.cuni.cz/index.html|Munin: graph of cluster usage by day and user]] and [[https://ufaladm2.ufal.hide.ms.mff.cuni.cz/munin/ufal.hide.ms.mff.cuni.cz/nfs-core.ufal.hide.ms.mff.cuni.cz/index.html|Munin monitoring of disk storage]] (both accessible only from ÚFAL network) |
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| ===== Profiling ===== | ===== Profiling ===== |
| ===== Other ===== | ===== Other ===== |
| * There is a **great course [[http://ufal.mff.cuni.cz/courses/npfl102|Data intensive computing]]**, see the 2016 handouts if you missed the course. It covers the usage of [[http://spark.apache.org/|Spark]] (MapReduce/Hadoop alternative, but better) and HDFS (Hadoop filesystem). | * There is a **great course [[http://ufal.mff.cuni.cz/courses/npfl102|Data intensive computing]]**, see the 2016 handouts if you missed the course. It covers the usage of [[http://spark.apache.org/|Spark]] (MapReduce/Hadoop alternative, but better) and HDFS (Hadoop filesystem). |
| * This course had used a special **DLRC (Demo LRC) cluster** (students had to login with ''ssh -p 11422 ufallab.ms.mff.cuni.cz'' and special NPFL102-only LDAP logins) with six virtual machines on one physical. During the years when NPFL102 is not taught (e.g. 2017), the DLRC cluster has just one virtual machine. | * **Note:** some hadoop basics and a lot of NoSQL technologies are covered by [[https://is.cuni.cz/studium/predmety/index.php?do=predmet&kod=NDBI040|Big Data Management and NoSQL Databases]] |
| * **Note:** soma hadoop basics and a lot of NoSQL technologies are covered by [[https://is.cuni.cz/studium/predmety/index.php?do=predmet&kod=NDBI040|Big Data Management and NoSQL Databases]] | * There is a special cluster for Mgr (and Bc) students (but not for PhD and UFAL members): http://aic.ufal.mff.cuni.cz/ |
| * You can use environment variables ''$JOB_ID'', ''$JOB_NAME''. | * 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). | * 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: | * 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, chances 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 |
