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grid [2017/10/02 17:33]
popel |
grid [2017/10/03 15:21]
popel [Other] |
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| 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.q''). |
| TODO: describe alternatives, e.g.: ms-guests tiny cluster, 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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| ===== List of Machines ===== | ===== List of Machines ===== |
| ^ Name ^ CPU type ^ GHz ^cores ^ RAM(GB)^ note ^ | ^ Name ^ CPU type ^ GHz ^cores ^ RAM(GB)^ note ^ |
| | lrc[1,2] | Intel | 2.3 | 4 | 45 | **no computing here**, just submit jobs | | | lrc[1,2] | Intel | 2.3 | 4 | 45 | **no computing here**, just submit jobs | |
| | pandora[1-10] | 2xCore2 Intel Xeon | 2.6 | | 16 | special cluster&queue ''ms-guests.q'' | | |
| | sol[1-5] | Intel | 2.6 | 4 | 16 | you can ssh here and compute | | | sol[1-5] | Intel | 2.6 | 4 | 16 | you can ssh here and compute | |
| | sol[6-8] | Intel | 2.0 | 8 | 16 | you can ssh here and compute | | | sol[6-8] | Intel | 2.0 | 8 | 16 | you can ssh here and compute | |
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| 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. | 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. |
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| The **pandora machines** are in a special cluster (not accessible from lrc) and queue **ms-guests.q** available for our colleagues from KSVI and for students of [[http://ufal.mff.cuni.cz/courses/npfl102|Data intensive computing]] (see the 2016 handouts if you missed the course). | |
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| ===== Installation ===== | ===== Installation ===== |
| ''qsub **-N** my-name'' | ''qsub **-N** my-name'' |
| By default the name of a job (which you can see e.g. in ''qstat'') is the name of the ''script.sh''. This way you can override it. | By default the name of a job (which you can see e.g. in ''qstat'') is the name of the ''script.sh''. This way you can override it. |
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| ''qsub **-S** /bin/bash'' | ''qsub **-S** /bin/bash'' |
| * ''/SGE/REPORTER/LRC-UFAL/bin/lrc_state_overview'' -- overall summary (with per-user stats for users with running jobs) | * ''/SGE/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 /SGE/REPORTER/LRC-UFAL/stats/userlist.weight'' -- all users sorted according to their activity (number of submitted jobs × their average duration), updated each night |
| * [[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) | * [[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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| ===== 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). |
| | * 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. |
| * 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). |
