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Re: Warning: Semaphore stuck for 30 seconds

From: Ole Tange
Subject: Re: Warning: Semaphore stuck for 30 seconds
Date: Tue, 6 Mar 2018 23:27:57 +0100

On Tue, Mar 6, 2018 at 10:49 AM, Meli Massimiliano
<address@hidden> wrote:
> 2018-03-05 1:11 GMT+01:00 Ole Tange <address@hidden>:
>> On Wed, Feb 28, 2018 at 12:38 PM, Meli Massimiliano
>> <address@hidden> wrote:
>> > The error messages that sometimes block the production of the output is:
>> >
>> > parallel: Warning: Semaphore stuck for 30 seconds. Consider using
>> > --semaphoretimeout.
>> > the is any way to move this directory in a different position?
>> The semaphores are in: ~/.parallel/semaphores so you can symlink that
>> to somewhere else.
> The home are exported along each cluster nodes by NFS:
> /data01/home,no_root_squash)

Annoying: So this means that we still have not fixed the NFS issue completely.

> each node have 32 processors. The script that are:

This could be rewritten as:

ene_calc() {
  mkdir $1
  cd $1
  echo $1 -O ................. -o RESULTS.dat.$1

  mv RESULTS.dat.$1 ../Files/
  gzip ../Files/RESULTS.dat.$1&

  cd ..
  rm -rf $1
export -f ene_calc
mkdir Files
# Why not just remove -j 30 and have GNU Parallel run one on each core?
parallel -j 30 ./ene_calc ::: {1..1000}
echo all done

GNU Parallel will be faster and NFS will not be an issue. (And IMHO it
is more readable).


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