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grid [2018/12/17 10:55]
popel [Rules] |
grid [2020/01/27 20:31]
popel link http://aic.ufal.mff.cuni.cz |
| ===== Advanced usage ===== | ===== Advanced usage ===== |
| |
| ''qsub **-q** troja-all.q'' | ''qsub **-q** cpu-troja.q'' |
| This way your job is submitted to the Troja queue. The default is ''ms-all.q''. You can also use e.g. | This way your job is submitted to the Troja queue. The default is ''cpu-ms.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 '(troja*|ms*)''' 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 '[tm]*@!(hector*|iridium)''' to submit on any troja/ms machine except hectors and iridium. |
| However, usually you should specify just the queue (troja-all.q vs. ms-all.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. |
| |
| ''qsub **-l** ...'' | ''qsub **-l** ...'' |
| |
| ''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). |
| |
| ''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'' |
| * ''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 |
| |
| * [[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) |
| |
| ===== 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:** 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]] | * **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). |
