[gmx-users] problem in reading parallel mdrun output

[David van der Spoel]

bharat v. adkar wrote:
> 
> Dear all,
> i'm sorry for confusion in last mail... i wrote that i did gmxcheck, and 
> pasted results of gmxdump...
> here are results from gmxcheck....

I vaguely recall that something is wrong generating tpr files on this 
platform. Maybe you can start by generating a file on another box and 
try to run it on the PowerPC. This point to a problem in the XDR libraries.

As a workaround you can try to use trj and tpb files instead of trr/xtc 
and tpr. These are not platform independent however.
> 
> Checking file traj.trr
> trn version:  -------------------------------------------------------
> Program gmxcheck, VERSION 3.3.1
> Source code file: ../../../../gromacs-3.3.1/src/gmxlib/trnio.c, line: 69
> 
> Fatal error:
> Float size 190909451. Maybe different CPU?
> -------------------------------------------------------
> 
> Checking file traj.xtc
> -------------------------------------------------------
> Program gmxcheck, VERSION 3.3.1
> Source code file: ../../../../gromacs-3.3.1/src/gmxlib/xtcio.c, line: 83
> 
> Fatal error:
> Magic Number Error in XTC file (read 0, should be 1995)
> -------------------------------------------------------
> 
> 
> Checking energy file ener.edr
> -------------------------------------------------------
> Program gmxcheck, VERSION 3.3.1
> Source code file: ../../../../gromacs-3.3.1/src/gmxlib/enxio.c, line: 239
> 
> Fatal error:
> Energy file ener.edr not recognized, maybe different CPU?
> -------------------------------------------------------
> 
> help please...
> 
> bharat
> 
> 
> 
> 
> 
> On Fri, 21 Jul 2006, bharat v. adkar wrote:
> 
>>
>> Dear GMX users,
>>
>> Recently i installed gromacs-3.3.1 on IBM powerpc64 with mpi support.
>> some of the details of the machines are as follows:
>> -------------------------------
>> hostname = cnode39
>> uname -m = ppc64
>> uname -r = 2.6.5-7.139-pseries64
>> uname -s = Linux
>> /bin/arch= ppc64
>> ------------------------------
>>
>> it got installed properly without any error.. i could successfully run 
>> a test mdrun on four nodes. when i tried to gmxcheck of edr, xtc, and 
>> trr files, it gives following errors respectively:
>>
>> gmxcheck -f traj.xtc
>> -------------------------------
>> Program gmxdump, VERSION 3.3.1
>> Source code file: ../../../../gromacs-3.3.1/src/gmxlib/xtcio.c, line: 83
>>
>> Fatal error:
>> Magic Number Error in XTC file (read 0, should be 1995)
>> -------------------------------
>>
>>
>> gmxdump -f traj.trr
>> -------------------------------
>> Program gmxdump, VERSION 3.3.1
>> Source code file: ../../../../gromacs-3.3.1/src/gmxlib/trnio.c, line: 69
>>
>> Fatal error:
>> Float size 190909451. Maybe different CPU?
>> -------------------------------------------------------
>>
>> gmxdump -e ener.edr
>> -------------------------------------------------------
>> Program gmxdump, VERSION 3.3.1
>> Source code file: ../../../../gromacs-3.3.1/src/gmxlib/enxio.c, line: 239
>>
>> Fatal error:
>> Energy file ener.edr not recognized, maybe different CPU?
>> -------------------------------------------------------
>>
>>
>>
>>
>> Any suggestions please....
>>
>> bharat
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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