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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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