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cluster:103 [2011/12/21 19:47]
hmeij [Best Practices] 		cluster:103 [2011/12/22 19:34] (current)
hmeij [Submit 2]
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 On the back end compute nodes, unless specified, the job runs inside your home directory.  That job competes with other activities inside /home.  Compute nodes have two other areas where the jobs could be submitted: /localscratch and /sanscratch.  The former is a local filesystem for each node and should be used if file locking is essential. The later is a filesystem from greentails diskarray (5 TB) served vi IPoIB (that is NFS traffic over fast interconnects switches, the performance should be much better than gigabit ethernet switches).  It is comprised of disks and spindles that are not impacted by what happens on /home.  So we're going to use that. On the back end compute nodes, unless specified, the job runs inside your home directory.  That job competes with other activities inside /home.  Compute nodes have two other areas where the jobs could be submitted: /localscratch and /sanscratch.  The former is a local filesystem for each node and should be used if file locking is essential. The later is a filesystem from greentails diskarray (5 TB) served vi IPoIB (that is NFS traffic over fast interconnects switches, the performance should be much better than gigabit ethernet switches).  It is comprised of disks and spindles that are not impacted by what happens on /home.  So we're going to use that.
 +
 +In the SAS program we add the following lines
 +
 +<code>
 +%let jobpid = %sysget(LSB_JOBID);
 +libname here "/sanscratch/&jobpid";
 +</code>
 +
 +And change this line to use local disks for storage
 +
 +<code>
 +data here.one;
 +</code>
 +
 +In the submission script we change the following
  
   * new submission file with edits   * new submission file with edits
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   * -R reserves memory, for example, reserve 200 MB of memory on target compute node   * -R reserves memory, for example, reserve 200 MB of memory on target compute node
   * scheduler creates unique dirs in scratch by JOBPID for you, so we'll stage the job there   * scheduler creates unique dirs in scratch by JOBPID for you, so we'll stage the job there
-  * but now we must copy relevant to scratch dir and results back to home dir+  * but now we must copy relevant files //to// scratch dir and results back //to// home dir 
  
 <code> <code>
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   * Reserve resources if you know what you need, especially memory   * Reserve resources if you know what you need, especially memory
   * Use /sanscratch for large data jobs with heavy read/write operations   * Use /sanscratch for large data jobs with heavy read/write operations
-  * Queue ehwfd is preferentially for Gaussian users and stay off the stata and matlab queues+  * Queue ehwfd is preferentially for Gaussian users and stay off the stata and matlab queues please
   * Write smart SAS code, for example, use data set indexes and PROC SQL (this can be your best friend)   * Write smart SAS code, for example, use data set indexes and PROC SQL (this can be your best friend)
 +  * ... suggestions will be added to this page
  
 \\ \\
 **[[cluster:0|Back]]** **[[cluster:0|Back]]**
cluster/103.1324496864.txt.gz · Last modified: 2011/12/21 19:47 by hmeij

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