anna.marabo...@isa.cnr.it wrote:
Dear Justin,
thank you for your answer. I'm currently using Gromacs version 4.0.7
which was compiled in double precision, therefore I strongly suspect
that this is a problem linked to the old bug. It seems to me that I used
eneconv previously on this machine to concatenate .edr files, but I
cannot be sure. However, before writing you I copied the .edr files on
another machine, which still has Gromacs 4.0.7 installed, but compiled
in single precision, and still I found the same error Segmentation fault.
I don't believe you have a problem related to the bug; it was introduced in the
4.5 series, so 4.0.7 should be unaffected. Since gmxcheck seems to have worked,
that's more evidence that there is no bug. The problem was in the .edr
formating, causing all Gromacs utilities to stop reading double-precision .edr
files.
Concerning the name of the files, when I described the commands in my
previous message I used a "simplified" version of their names in order
to avoid writing the long 2GH9openmod4_pH...blabla, but I checked
several times the names I used and I can assure you that I tried to
concatenate the correct file names. Therefore, the problem is not a
typo. Sorry for not explaining it before.
OK. Literal is always better, and often requires a simple cut and paste from
the terminal, rather than any manual typing at all :)
I made a check wit gmxcheck on 2 files: the .edr and .xtc files from the
MD of 5 ns and the .edr and .xtc files from the MD of 50 ns (started
immediately after the 5ns using tpbconv): these are the results:
Checking file 2GH9openmod4_pH10_5ns.xtc
Reading frame 0 time 0.000
# Atoms 40139
Precision 0.001 (nm)
Last frame 1000 time 5000.000
Item #frames Timestep (ps)
Step 1001 5
Time 1001 5
Lambda 0
Coords 1001 5
Velocities 0
Forces 0
Box 1001 5
Checking energy file 2GH9openmod4_pH10_5ns.edr
Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file
frame: 0 (index 0), t: 0.000
Last energy frame read 50 time 5000.000
Found 51 frames with a timestep of 100 ps.
Checking file 2GH9openmod4_pH10_50ns.xtc
Reading frame 0 time 0.000
# Atoms 40139
Precision 0.001 (nm)
Reading frame 2000 time 10000.000
Item #frames Timestep (ps)
Step 2981 5
Time 2981 5
Lambda 0
Coords 2981 5
Velocities 0
Forces 0
Box 2981 5
Checking energy file 2GH9openmod4_pH10_50ns.edr
Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file
frame: 0 (index 0), t: 0.000
Last energy frame read 149 time 14900.000
Found 150 frames with a timestep of 100 ps.
It seems to me that all is regular; the only strange thing is that both
start at time 0, despite I used tpbconv+mdrun with cpi to continue the
MD after the first 5 ns.
What does the log file tell you regarding the outset of the second job? It
should say that it's starting from a checkpoint, and the first interval written
should have a time of 5000 ps. If not, then the checkpoint file was not
properly used. If both .edr files start at the same point, that could be a
reason for the seg fault, but that's a bit of a guess.
From the gmxcheck output, it appears that your _50ns.edr file does indeed start
from 0 instead of 5000, as you would hope.
I return with my previous question: how can I manage this problem,
especially if I have the version 4.0.7? Do I have to ask administrators
to fix the bug? Do I have to restart all my simulations?
If the "continuation" instead started from t=0, then you don't have to re-do
anything, just don't use the _5ns.* information (.xtc, .edr, etc) since you
basically did that portion of the simulation over. The log files will tell you
what's going on.
-Justin
Thank you very much and best regards
Anna
----------------------------------------------------------------------
Message: 1
Date: Tue, 25 Jan 2011 09:43:20 -0500
From: "Justin A. Lemkul" <jalem...@vt.edu>
Subject: Re: [gmx-users] segmentation fault while running eneconv
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4d3ee188.7000...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Anna Marabotti wrote:
Dear all,
I launched on my system a first simulation of 5 ns, then I prolonged it
to 50 ns using
tpbconv -s tpr1_5ns.tpr -until 50000 -o tpr2_50ns.tpr
and then
mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt
Since my simulation was interrupted several times, every time I
relaunched it simply doing:
mdrun -s tpr2_50ns.tpr -cpi md2_50ns.cpt -deffnm md2_50ns_2/3/4
At the end of these simulations I obtained the following files:
- md1_5ns.xtc and .edr: files obtained from the first MD of 5 ns long
- md2_50ns.xtc and .edr: files obtained by prolonging the first MD until
50ns
- md2_50ns_2.xtc and .edr: files obtained by restarting the previous
dynamics that was interrupted before 50 ns
- md2_50ns_3.xtc and .edr: same as before
- md2_50ns_4.xtc and .edr: same as before
After all these runs, I want to concatenate all the dynamics in order to
have a single .xtc file md_50ns_tot and a single .edr file
md_50ns_tot.edr. For the first, I used:
trjcat -f md1_5ns.xtc md2_50ns.xtc md2_50ns_2.xtc md2_50ns_3.xtc
md2_50ns_4.xtc -o md_50ns_tot.xtc
and all worked fine: I obtained the output file with no errors (there
are no errors also in the .log files)
On the contrary, when I tried to do the same with eneconv:
eneconv -f md1_5ns.edr md2_50ns.edr md2_50ns_2.edr md2_50ns_3.edr
md2_50ns_4.edr -o md_50ns_tot.edr
I obtained the following output:
Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file
Reading energy frame 1 time 100.000
Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file
Reading energy frame 0 time 0.000
Opened 2GH9openmod4_pH10_50ns_2.part0002.edr as double precision energy file
Reading energy frame 0 time 14900.000
Opened 2GH9openmod4_pH10_50ns_3.part0003.edr as double precision energy file
Reading energy frame 0 time 27800.000
Opened 2GH9openmod4_pH10_50ns_4.part0004.edr as double precision energy file
Reading energy frame 0 time 38800.000
Summary of files and start times used:
File Start time
-----------------------------------------
2GH9openmod4_pH10_5ns.edr 0.000
2GH9openmod4_pH10_50ns.edr 0.000
2GH9openmod4_pH10_50ns_2.part0002.edr 14900.000
2GH9openmod4_pH10_50ns_3.part0003.edr 27800.000
2GH9openmod4_pH10_50ns_4.part0004.edr 38800.000
Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file
Segmentation fault
Looking for some hints in the gmx-users list the only thing I found that
could be similar to my problem is this old message:
http://lists.gromacs.org/pipermail/gmx-users/2007-January/025657.html
What Gromacs version are you using? If it is not 4.5.3, then you're probably
running into a bug regarding double precision .edr files that was fixed some
time ago.
I see in the output error message that the start time for the first two
simulations is the same: could be this one the problem for my system?
However, I did use tpbconv each time to make restarts of my simulations,
I really don't know why the start time is 0.000 in the first two cases.
Well, your commands don't agree with the output of eneconv. The names are
different. Perhaps you've confused what files you think you're using, or
otherwise attempted to append to a file and then gave it a new name. In any
case, gmxcheck is your friend here.
Is there a problem in the results of simulations if these two
simulations have the same start time? Practically, what can I do to
concatenate my .edr files?
Presumably, yes. As long as the .edr files have no internal corruptions (which,
unfortunately, is quite possible if the job frequently went down), then you
should be able to concatenate them. That also depends on the version of Gromacs
you're using, if you're running into the old bug. It's always helpful to state
right up front which version you're using when reporting a problem.
-Justin
Many thanks in advance and best regards
Anna Marabotti
____________________________________________________
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma, 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Email: anna.marabo...@isa.cnr.it <mailto:anna.marabo...@isa.cnr.it>
Skype account: annam1972
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
"When a man with a gun meets a man with a pen, the man with a gun is a
dead man"
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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