[gmx-users] problem in reading parallel mdrun output

[Erik Lindahl]

Hi,

The error David mentions concerned big-endian 64-bit platforms with  
sizeof(long)>sizeof(int).

http://bugzilla.gromacs.org/show_bug.cgi?id=55

I fixed it in both CVS branches a couple of months ago - you can find  
patches through the link above.

Cheers,

Erik

On Jul 24, 2006, at 8:37 PM, bharat v. adkar wrote:

>
> Thanx David...
>
> It's working with trj and ene files though tpb is not working and i  
> faced no problem with tpr generated on the same system also...
> as you said, even these files cannot be read on other platforms :(
>
> bharat
>
>
>
>
> On Sun, 23 Jul 2006, David van der Spoel wrote:
>
>> 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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>>
>>
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