[gmx-users] pdb2gmx illegal instruction

[David van der Spoel]

Dongsheng Zhang wrote:
> Dear Erik,
> 
> Thank you very much for your reply. I have fixed the problem with
> David's helps. Now I am struggling with parallel running with gromacs.
> 
> I use 
> grompp -np 8 -sort -shuffle -f pr -o pr -c after_em -p AceAla5ac to get
> pr.tpr
> 
> When I submitted a job to the computing center by using the attached
> script file, I got the following error message:
> 
> Fatal error:
> run input file pr.tpr was made for 8 nodes,
>              while mdrun_mpi expected it to be for 1 nodes.
> 
> my script file is:
> 
> #PBS -S /bin/ksh -q sp_short
> . /etc/profile
> module load gromacs
> cd  $PBS_O_WORKDIR
> ### CPU number
> #PBS -l nodes=8:ppn=1
> ###Job name
> #PBS -N test
> mdrun_mpi -np 8 mdrun -np 8 -s pr -o pr -c after_pr -e pr -g pr  -v -N 8
> 
> Could you please tell me what's wrong? Thanks!

check your system for info on starting mpi programs. ask your sysadmin.

> 
> 
> Dongsheng
> 
> 
> On Tue, 2006-03-21 at 23:18 +0100, Erik Lindahl wrote:
>> Hi,
>>
>> Sounds like the binary was compiled (and optimized for) one machine,  
>> but run another. Give us some info both about the command you ran and  
>> how Gromacs was compiled/installed.
>>
>> Cheers,
>>
>> Erik
>>
>> On Mar 21, 2006, at 6:11 AM, Dongsheng Zhang wrote:
>>
>>> Dear All,
>>>
>>> I want to run gromacs in supercomputer center at my school. When I  
>>> used
>>> pdb2gmx, it gave me an error message as follows:
>>> illegal instruction (core dumped out)
>>>
>>> Could anyone give a clue what's happening? Thank you in advance.
>>>
>>>
>>> Dongsheng
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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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