Differences

This shows you the differences between two versions of the page.

--- biac:cluster:submit [2019/02/15 17:54]
cmp12 [Job restrictions]
+++ biac:cluster:submit [2023/02/23 18:43] (current)
@@ Line 20: / Line 20: @@
-====== Job restrictions ======
+====== Job restrictions ====
-Each node has a finite amount of memory installed and due to the disk-less nature of the nodes there are restrictions set on the amount of ram used.  Currently, the default is to assign 8G of ram per job that is submitted.  If your job requires more than 8GB, then you may request a higher limit with the **"-l h_vmem"** directive ... otherwise you don't have to do anything.  This is done to prevent memory over subscription and to better distribute the load across the available machines.
+==
+Each node has a finite amount of memory installed and due to the disk-less nature of the nodes there are restrictions set on the amount of ram used.  Currently, the default is to assign 10G of ram per job that is submitted.  If your job requires more than 10GB, then you may request a higher limit with the **"-l h_vmem"** directive ... otherwise you don't have to do anything.  This is done to prevent memory over subscription and to better distribute the load across the available machines.
-  > qsub -N run_script.1 -l h_vmem=10G,vf=10G script.sh run1
+  > qsub -N run_script.1 -l h_vmem=12G,vf=12G script.sh run1
-The above example will request/reserve 10G of available memory.  **"vf"** will ensure your job will not go to a node unless it has the required amount available.  Also, if you exceed the requested amount of **"h_vmem"** the grid engine will terminate the job and you will receive notice.  In most cases you will not have to do anything, since 8G is a significant amount.  The amount of ram used in your jobs is listed as **"Max vmem"** in the emails set from the cluster.  The restriction is put in place to prevent memory being over allocated and jobs crashing an entire node, which would therefore kill other users' jobs.
+The above example will request/reserve 12G of available memory.  **"vf"** will ensure your job will not go to a node unless it has the required amount available.  Also, if you exceed the requested amount of **"h_vmem"** the grid engine will terminate the job and you will receive notice.  In most cases you will not have to do anything, since 10G is a significant amount.  The amount of ram used in your jobs is listed as **"Max vmem"** in the emails set from the cluster.  The restriction is put in place to prevent memory being over allocated and jobs crashing an entire node, which would therefore kill other users' jobs.
 You can also get it from previous jobs if you have the job number with qacct ( there will be a resulting entry for "maxvmem" ) :
@@ Line 44: / Line 45: @@
 ====== Job status ======
-The current status of a job can be checked with **qstat**. This will return the current list of jobs owned by the user.
+The current statu
+s of a job can be checked with **qstat**. This will return the current list of jobs owned by the user.
   > qstat
   job-ID  prior    name       user      state  submit/start at      queue                        slots ja-task-ID
@@ Line 85: / Line 87: @@
   > qdel -U username
 ====== Template Script ======
-Jobs are usually written in bash. They are similar to local bash scripts in syntax and usage. In  addition, they contain cluster related directives identified by lines starting with " #$ ". These are used to send job related setup information to the cluster. Scripts also contain requests for access to experiment data. The BIAC template script is a good starting point for testing job submission and as a base script for all jobs. Begin, by making a copy of the template script.
+Jobs are usually written in bash. They are similar to local bash scripts in syntax and usage. In  addition, they contain cluster related directives identified by lines starting with " #$ ". These are used to send job related setup information to the cluster. Scripts also contain requests for access to experiment data. The BIAC template script is a good starting point for testing job submission and as a base script for all jobs. Begin, by making a copy of the template script below.
-  cp /usr/local/packages/qsub_templates/basic.sh myscript.sh
 The template script requests access to an experiment folder and lists its contents. It needs a valid BIAC Experiment Name (case-sensitive) that is accessible by the user. Submit myscript.sh using qsub .

Brain Imaging & Analysis Center

User Tools

Site Tools

Differences

Page Tools