Re: Warning: Semaphore stuck for 30 seconds

[Ole Tange]

On Tue, Mar 6, 2018 at 10:49 AM, Meli Massimiliano
<massimiliano.meli@gmail.com> wrote:
> 2018-03-05 1:11 GMT+01:00 Ole Tange <ole@tange.dk>:
>> On Wed, Feb 28, 2018 at 12:38 PM, Meli Massimiliano
>> <massimiliano.meli@gmail.com> 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 192.168.4.0/24(rw,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() {
  source program_ene_calc.sh
  mkdir $1
  cd $1
  echo $1

  CALC_program.py -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).


/Ole