Thanks a lot for your reply Dr. Hess.
As you expected, the -nt 1 option in the mdrun fix the problem in
4.5-beta version. Actually, the problem there was not a "segmentation
fault" warning appearing in the output, it just got stop in an
apparently random behavior. With 4.0.7 version that I have compiled from
source I still have the same "Segmentation fault" problem. I tried with
a trajectory generated with the same compiled version but it still fails.
Anyway, I guess it can be due to a mistake during my compilation since
this feature had no such failure reports in the mailing list, and in
preliminary tries, it seems that the results for the tpi calculation in
4.0.7 and 4.5beta versions are similar. Concretely, I am trying to use a
modification of the tpi program similar to the slab-tpi proposed by
Robert Vacha
(http://lists.gromacs.org/pipermail/gmx-developers/2008-December/002931.html)
but, for practical reasons the partition of the box is performed
specifying the number of slices in which the box is partitioned
(nslices) and in which partition the particle are inserted (islice). For
that I just modified tpi.c (line 431) to:
x_init[ZZ] = (gmx_rng_uniform_real(tpi_rand) + islice -
1)*state->box[ZZ][ZZ]/nslices;
where nslice and islice are correctly passed to the program though
unused mdp parameters in tpi calculations (nstxtcout and nstenergy). I
applied it for the study of a lipid bilayer and as a results I expected
a nice simmetrical curve for <mu> vs. Z-positions (similar to the ones
in J. Phys. Chem. B 2007, 111, 12748-12755) but I got rough irregular
curves and partition dependent (the shape depends on nslices). I am
using pseudo-NPT ensemble (Berendsen coupling) in the production step
and nsteps=10000 nstlist=100 for tpi insertion. I tried to use different
versions to investigation why the results are not the expected ones. But
maybe there is something wrong in the modification (for exmaple, I think
that there might be some issues since the box size and subsequently the
partitions are being modified during the trajectory). Does someone have
any idea about that?
Thank you.
Javier
Date: Mon, 16 Aug 2010 11:49:21 +0200
From: Berk Hess<g...@hotmail.com>
Subject: RE: [gmx-users] tpi segmentation fault
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
Message-ID:<col113-w26902708ba85122a825a338e...@phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I don't understand why 4.0.7 gives a segv.
But 4.5-beta probably gives a segv because of a parallel problem.
Could you try 4.5-beta with the mdrun option -nt 1
and report back?
Thanks,
Berk
Date: Fri, 13 Aug 2010 18:35:55 +0200
From:j...@um.es
To:gmx-users@gromacs.org
Subject: [gmx-users] tpi segmentation fault
Hi all.
I am trying to perform a tpi (test particle insertion) calculation on a
trajectory generated with mpi_mdrun (gromacs 4.0.7, run in a Beowulf
cluster of Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz). I am using
tpi integrator in the mdp file and the following command:
$ grompp -f tpi.mdp -c 32hoa_128dmpcwrun.gro -n index_tpi.ndx -p
topol_tpi.top
$ mdrun -rerun 32hoa_128dmpcwrun.trr -g tpi.log
I tried different versions of gromcas and for 4.0.X I got a segmentation
fault getting the message:
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000 Segmentation fault
using a compiled version with "config --prefix
/home/cerezo/Programs/gromacs4.07" + "make" + "make install". However,
it works when I used a precompiled version (got with apt-get, I have
kubuntu). So I guess that it may be due to a mistake during the
compilation. In addition, other integrators (i.e. md, steep) work
correctly with the version I've compiled. My system is and Intel(R)
Core(TM)2 Quad CPU Q8400 @ 2.66GHz. Is there any trick I could try
in the compilation?
I also tried gromacs-4.5-betaX and it works but sometimes (apparently
randomly) the calculation gets stops (as if it had entered in an
infinite loop) after reading the last frame.
Thanks for your attention!
Javier
--
Javier CEREZO BASTIDA
Estudiante de Doctorado
---------------------
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434
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Javier CEREZO BASTIDA
Estudiante de Doctorado
---------------------
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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