Mikhail Stukan wrote:
Dear Justin and Berk,
Thank you very much for the hint. Unfortunately, upgrade to 4.5.3 version
doesn't solve the problem, diagnostic is still the same:
==============================
Program g_energy_d, VERSION 4.5.3
Source code file: ../../../src/gmxlib/enxio.c, line: 422
Fatal error:
Energy names magic number mismatch, this is not a GROMACS edr file For
more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
===============================
Do you think there could be any way to overcome this problem apart from running
the job in parts?
Just to clarify, now that you've upgraded to 4.5.3, are you also running the
4.5.3 version of mdrun, and not just analyzing a 4.5.1 .edr file with 4.5.3? I
believe there have been changes to the .edr file format over the course of
development.
There are several things to try to better diagnose what's going on. If file
appending isn't working properly, that would be a major problem. To diagnose:
1. What does gmxcheck tell you about the problematic .edr file?
2. Try running the jobs as separate intervals. Check the integrity of each with
gmxcheck and concatenate them with eneconv. Then use gmxcheck on this manually
concatenated .edr file. If g_energy works on this file, then the problem is in
the appending routines, not the file format.
-Justin
Many thanks in advance,
Mikhail
Dear gromacs users,
I am facing the following problem while running gromacs 4.5.1 at
BlueGene/P supercomputer.
The job is submitted by the following script file:
#!/bin/sh
#
# @ account_no = xxx
# @ job_name = NVT1
# @ job_type = bluegene
# @ output = $(job_name).$(jobid).out
# @ error = $(job_name).$(jobid).err
# @ environment = COPY_ALL;
# @ wall_clock_limit = 24:00:00
# @ notification = always
# @ bg_size = 64
# @ queue ?/mpirun -cwd $PWD -mode VN -np 256 -exe ?/mdrun_bgp_d -args
"-deffnm nvt1 -dds 0.5 -cpi nvt1.cpt -append"
And it is running perfectly fine. I can analyze the data using g_energy
etc. But if after the run is finished I increase the number of time
steps and submit run again or resubmit it after a crash (killed manually
or due to 24 hours wall clock limit), using the same script provided
above, the run itself looks fine, at least .log file looks as it should
but when I try to analyze .edr file with g_energy tool I obtain the
following error message:
-------------------------------------------------------
Program g_energy_d, VERSION 4.5.1
Source code file: ../../../src/gmxlib/enxio.c, line: 409
Fatal error:
Energy names magic number mismatch, this is not a GROMACS edr file For
more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I would really appreciate any hint on this subject.
This was a Gromacs bug in versions 4.5.1 and 4.5.2. Please upgrade to version
4.5.3.
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x
-Justin
Many thanks in advance.
Mikhail.
--
========================================
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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