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grid [2019/04/17 09:24]
vodrazka fixed broken links
grid [2020/05/06 14:45] (current)
ufal [Other]
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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 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''​
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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).   * 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

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