[gmx-users] Joining log files ?

Lubos Vrbka lubos.vrbka at gmail.com
Mon Jan 23 15:41:49 CET 2006


> 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...


_ at _"

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