[gmx-users] Re: g_energy: Energy names magic number mismatch

[Justin A. Lemkul]

Mikhail Stukan wrote:
> Justin,
> 
> Thanks a lot.
> Concatenation seems to be the only solution, but it works fine. It look like there are some problems with the appending routine on BlueGene.
> 

Please file a bugzilla so this issue gets fixed.

-Justin

> Mikhail
> 
>> 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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