[gmx-users] Joining log files ?

Stéphane Teletchéa steletch at jouy.inra.fr
Mon Jan 23 16:22:53 CET 2006

Lubos Vrbka a écrit :
> hi,
>> While submitting a parallel job (lam/MPI + gromacs 3.3), i'm facing a 
>> little problem : all processors logs are in a separate file (q0.log, 
>> q1.log, q2.log ... qn.log), and if the directory origin is not shared 
>> (for instance via an nfs connection), all theses files are output in 
>> different directories (i've put /tmp for all as for now).
>> Is there a way to tell the master node to use its own *scratch* for 
>> writing all information in one big log ? I assumed the compact option 
>> had this purposed but it seems this is not its role.
> i had very similar question some time ago and the answer was (search the 
> archives if you want to know more):
> no, it's not possible however, if everything works fine the files 
> q1.log, q2.log, q3.log, ... do not contain any really useful information 
> (iirc, it was just lincs output in my case) and can be safely deleted.
> if you insist on having these files together you have to use facilities 
> provided by your batch system (if you have any) - in my case i run under 
> pbspro and the command of choice is pbsdsh - it can be used to execute a 
> command on all nodes the job is running on. the scp/rcp command running 
> in pbsdsh then does the trick...
> regards,

Thanks a lot for the answer, i should have went through the archive this 
time ...

In short, no way to do it. I'm using SGE but there is probably an option 
similar to create an all nodes the necessary directories, otherwise, 
i'll use a regular one as scratch.



Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 121 / 3086
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

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