[gmx-users] Re: segmentation fault while running eneconv
anna.marabotti at isa.cnr.it
anna.marabotti at isa.cnr.it
Tue Jan 25 18:04:03 CET 2011
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.
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.
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.
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?
Thank you very much and best regards
Anna
>----------------------------------------------------------------------
>
>Message: 1
>Date: Tue, 25 Jan 2011 09:43:20 -0500
>From: "Justin A. Lemkul" <jalemkul at vt.edu>
>Subject: Re: [gmx-users] segmentation fault while running eneconv
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4D3EE188.7000405 at 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.marabotti at isa.cnr.it <mailto:anna.marabotti at 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
>
>========================================
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