[gmx-users] time estimation script

Stéphane Téletchéa steletch at jouy.inra.fr
Tue Feb 27 11:13:59 CET 2007

Martin Höfling a écrit :
> Am Dienstag, 27. Februar 2007 schrieb David van der Spoel:
>> mdrun -v
> Yep, I know that :-)
> But maybe someone has already implemented a script parsing the output of a 
> test mdrun?

Something like what i've attached ?

I used this script to parse the benchmark results of gmxbench, i could 
post it on the list (or on contributions) if there a need for it.

The main function is (in French) trie_fichier ()

It takes as inputs the rundir, the number of processors used, the 
extension of the file to read, the file itself and the gromacs version 
(since 3.2.1 and 3.3+ output are a little bit different).

Main info are easily available via theses grep commands on the output file:
tmptime=`grep -m 1 "Time:" $nomfichrech`
tmpperf=`grep -m 1 "Performance" $nomfichrech`

# Le format de sortie de gromacs 3.2.1 est légèrement différent de celui 
de gromacs 3.3, il faut
[ $5 == '3.2.1' ] && tmpperf2=`echo "scale=3;${tmpperf:36:9} * 24 / 

# La sortie est faite en mFlops ou Gflops, pour être sûr de la bonne 
valeur, il faut vérifier la lettre utilisée
tmpnom=`grep -m 1 "Flops)" $nomfichrech`

In short, grep matches the line to parse, and i use bash built-in 
functions to extract the value directly, with a different rule if it is 
gromacs 3.2.1 or 3.3+.

The attached program itself creates data files in a destination dir 
where a batch file can be used for seing the datas with xmgrace. (Of 
course i have also a script for producing it ;-).



Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901
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