[gmx-users] REMD in one nodes with two processors

[David van der Spoel]

Dongsheng Zhang wrote:
> Dear David,
> 
> I had tried mpirun before, it didn't work either. the command was:
> mpirun -np 2 n1 /home/brasilia/dong/mdrun_mpi_MC  -replex 500 -reseed -1
> -multi -s replica -deffnm replica -N 2 -v >& zevel

remove the -N 2 -multi -deffnm replica options and try again.


> 
>  Because the two processors are in one node, so I changed my command to
> ( and go to the local node n1 to submit the job):
> 
> /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi -s
> replica -deffnm replica -N 2 -v >& zevel
> 
> Could you please tell me if there is any way to check if the program can
> recognize -multi option?
> 
> Thank you!
> 
> 
> Dongsheng
> 
> 
> 
> On Thu, 2006-05-04 at 19:13 +0200, David van der Spoel wrote:
>> Dongsheng Zhang wrote:
>>> Marcus,
>>>
>>> Thank you for your suggestion. I try it. The computer gives me the same
>>> error message. The problem is that the program always looks for
>>> replica.tpr instead of replica0.tpr and replica1.tpr. I don't know why.
>>>
>> use mpirun
>> search mailinglist
>>> Best wishes!
>>>
>>>
>>> Dongsheng
>>>
>>>
>>> On Thu, 2006-05-04 at 18:38 +0200, Marcus Kubitzki wrote:
>>>> If you use the -deffnm option, you do not need -s, b/c it is
>>>> already accounted for with the -deffnm.
>>>> Marcus
>>>>
>>>> Dongsheng Zhang wrote:
>>>>> David,
>>>>>
>>>>> Thank you for your reply. I have provided replica0.tpr and replica1.tpr,
>>>>> but the program looks for replica.tpr. It surprises me.
>>>>>
>>>>> I have also tried to run 
>>>>>
>>>>> /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi -s
>>>>> replica0  replica1 -deffnm replica -N 2 -v >& zevel 
>>>>>  It doesn't work either (complains only one replica: Nothing to exchange
>>>>> with only one replica). it seems the program does not recognize the
>>>>> -multi option. 
>>>>>
>>>>>
>>>>> Best wishes!
>>>>>
>>>>>
>>>>> Dongsheng
>>>>>
>>>>>
>>>>> On Thu, 2006-05-04 at 18:11 +0200, David van der Spoel wrote:
>>>>>
>>>>>> Dongsheng Zhang wrote:
>>>>>>
>>>>>>> Dear gmx users,
>>>>>>>
>>>>>>> I have trouble to run REMD on one node with two processors. The command
>>>>>>> I used is
>>>>>>> /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi -s
>>>>>>> replica -deffnm replica -N 2 -v >& zevel
>>>>>>>
>>>>>>> the error message is:
>>>>>>>
>>>>>>> Can not open file:
>>>>>>> replica.tpr
>>>>>> you need replica0 and replica1.tpr
>>>>>>
>>>>>>> This error message looks strange to me. Because I have used -multi, the
>>>>>>> program should look for replica0.tpr and replica1.tpr. Could anyone
>>>>>>> point out what's wrong in my command?
>>>>>>>
>>>>>>>
>>>>>>> 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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