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

[David van der Spoel]

Dongsheng Zhang wrote:
> Thank you, David. I try it as:
> 
> 
> mpirun -np 2  n1 /home/brasilia/dong/mdrun_mpi_MC  -replex 500 -reseed
> -1 -s replica -v >& zevel 
> 
> It gives me the same error message: Can not open file: replica.tpr
> 
was mdrun compiled with MPI? are you sure the second copy of mdrun is in 
the right directory? try it from your home directory

> Any other suggestions?
> 
> Thanks!
> 
> 
> Dongsheng
> 
> 
> On Thu, 2006-05-04 at 20:17 +0200, David van der Spoel wrote:
>> 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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