etap

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etap [2015/06/17 14:30]
meesters
etap [2017/06/11 05:42]
meesters
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 ====== EtapFS ====== ====== EtapFS ======
  
-When using etapfs you should acess these filesystem only within your job and not indicate paths on the command line with LSF commands (e.g. bsub). Especially ''​stdout''​ should not be directed to ''/​etapfs''​ as this can prevent a job to be ended (even if the wall clock time limit is hit), if one such filesystem "​hangs"​.+When using etapfs you should acess these filesystem only within your job and not indicate paths on the command line with SLURM commands (e.g. ''​sbatch''​). Especially ''​stdout''​ should not be directed to ''/​etapfs''​ as this can prevent a job to be ended (even if the wall clock time limit is hit), if one such filesystem "​hangs"​.
  
-This means that the ''​-o'',​ ''​-e''​ and ''​-cwd''​ parameters of bsub should not point to etapfs. However, copying within your script to etapfs is ok, e.g.:+This means that the ''​-o'',​ ''​-e''​ and ''​-D/​--workdir=<​path>​''​ parameters of ''​sbatch'' ​should not point to etapfs. However, copying within your script to etapfs is ok, e.g.:
  
 <code bash> <code bash>
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 </​code>​ </​code>​
  
-Likewise, pointing the output of subshells to etapfs is an alternate solution.+Likewise, pointing the output of subshells to etapfs is an alternate solution. ​ 
 +This helps the scheduler to clean up jobs. 
 + 
 + 
 +<WRAP center round info 80%> 
 +Also, you should not submit jobs when your actual working directory at the time of submit is on an etapfs. Instead, 
 +<code bash> 
 +#SBATCH --workdir=<​path outside etapfs>​ 
 +</​code>​ 
 +can intentionally be used to avoid the mentioned problems, whilst submitting from a working directory in etapfs. 
 +</​WRAP>​ 
  
-**Also, you should not submit jobs when your actual working directory at the time of submit is on an etapfs.** 
  
-The reason is that a "​hanging"​ etapfs (e.g. lost mount) will cause the scheduler to be unable to clean up the job, while a job unable to write to etapfs can still be cleaned up, if the scheduler'​s daemons do not have file handles there. 
  • etap.txt
  • Last modified: 2017/06/30 08:38
  • by meesters