Justin A. Lemkul wrote:
ABEL Stephane 175950 wrote:
Dear GMX Users,
I ask this question in this mailing list since probably a user have
already
encountered this similar problem. I would like to post-process my
trajectory
with the command trjconv (in mpi mode). For this I use the following
shell
command:
Is trjconv parallelizable? This is nowhere in the documentation, but if
it is, that would be very interesting...
No. There are no 4.0.x tools that use MPI. Hence the wiki advice not to
bother compiling tools in parallel, and the old website installation
guide directing the use of only "make mdrun" after reconfiguring with
--enable-mpi.
echo 0 | /usr/pbs/bin/mpiexec
/scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s
Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o
./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0
("System")
It works but since my simulations is very long (> 300ns) the command
stops in
the middle of the trajectory before to finish the process ( i suspect
a time
limit for using the interactive mode). So i would like to use a script
to do
the task. How to pass the choice 0 in the script (i.e. equivalent to
the echo
0). I use a bash shell and the command qsub to launch a mpi job.
I have tried to adapt the examples available in the GMX website with a
text
file as suggested by the author in GROMACS site with no success.
I routinely use a text file for scripted jobs. Odd that yours isn't
working. Is it just that the command still exits before finishing? In
any case, you can make an .ndx file with only an entry for [System].
When presented with one choice, trjconv has to choose it.
Recompiling without mpi, and doing non-mdrun operations on your local
machine / cluster login node is usually the approach simplest to use.
Yes, it's more work when you configure and compile, but you only do that
every once in a while right?
Mark
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