[gmx-users] g_tcaf issue

Jones de Andrade johannesrs at gmail.com
Fri Dec 13 20:02:18 CET 2013

Hi all.

We are having some problem running g_tcaf here. It keeps yielding
"segmentation faults".

We first thought it was because of the single-precision calculations
of the first run, or the exceedingly large trajectory file. Both were
changed for a second trial, which still yielded the same error.

Also, we are aware of the similar error posted in this thread at this mail-list:


Unfortunately, it seems to be a different issue.

We are also writing a full trajectory file in the .trr file, as can be
seen below on the excerpt from the .mdp file below:

dt                  =  0.002
nsteps              =  100000
nstcomm             =  1
nstxout             =  0
nstvout             =  10
nstfout             =  10
nstlog              =  10
nstenergy           =  100
nstlist             =  5

The precise line our cluster script is trying to execute is:

echo 0 | g_tcaf -f BMIm.AlCl4.md14.trr -s BMIm.AlCl4.md14.tpr -oa
BMIm.AlCl4.md14.all.xvg -o BMIm.AlCl4.md14.tcaf.xvg -of
BMIm.AlCl4.md14.fit.xvg -ov BMIm.AlCl4.md14.visc.xvg >& md14.tcaf.out

The "echo 0" assures that the needed parameter is passed to g_tcaf. By
the way, in our last test the pbs parameters for resources request

#PBS -l ncpus=8
#PBS -l mem=16GB

We know that it's pointless to ask for extra cpus, it's in there just
for a matter involving the machine architecture. But the 16 GB of
memory, despite available, are just our guess on how much it will
need. We also tested it out of the queue to be certain, but it still
fails at the same point.

Does anybody has any suggestion please? I would be really helpful.

Thanks a lot in advance for any help,


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