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 comput
Dear Tom,
Thank you for your reply. Unfortunately, mpirun is not available. I can
only find mdrun_mpi which is related with mpi.
Best wishes!
Dongsheng
On Tue, 2006-03-21 at 21:02 -0500, Tom Joseph wrote:
> Certainly you should consult your documentation, but one possibility is:
>
> mpiru
Certainly you should consult your documentation, but one possibility is:
mpirun -np 8 mdrun_mpi -np 8 -s pr -o pr -c after_pr -e pr -g pr -v -
N 8
--Tom
On Mar 21, 2006, at 6:48 PM, Erik Lindahl wrote:
mdrun_mpi -np 8 mdrun -np 8 -s pr -o pr -c after_pr -e pr -g pr -
v -N 8
This won't
Dear Erik,
Thank you very much for your help. When I check command under ../bin
directory, I only find mdrun_mpi (which is related mpi), not mpirun. I
have tried mpirun (because I find some people used mpirun in the mailing
list), the computer complained "mpirun not found".
Could you please tell
mdrun_mpi -np 8 mdrun -np 8 -s pr -o pr -c after_pr -e pr -g pr -v
-N 8
This won't work. You should start mdrun_mpi, using the program
(mpirun or something) specified by your MPI library. There is no
standard for this, so consult the documentation for your MPI
implementation.
Cheers,
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 at
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 superco
Dongsheng Zhang wrote:
Dear David,
Thank you very much for your quick reply. The machine is IBM. Then,
could you please tell me how to fix it? Thanks again.
you optimized it for e.g. power2 processor and run it on power4. You may
have to recompile everything except mdrun without optimization. C
Dear David,
Thank you very much for your quick reply. The machine is IBM. Then,
could you please tell me how to fix it? Thanks again.
Best Wishes!
Dongsheng
On Tue, 2006-03-21 at 17:00 +0100, David van der Spoel wrote:
> Dongsheng Zhang wrote:
> > Dear All,
> >
> > I want to use gromacs in res
Dongsheng Zhang wrote:
Dear All,
I want to use gromacs in research computing center in my school. When I
used pdb2gmx as
pdb2gmx -f Ace5AlaNac -o Ace5AlaNac -p Ace5AlaNac -ignh -ter
it gave me an error message as follows,
illegal instruction (core dumped)
what kind of computer? this kind of s
Dear All,
I want to use gromacs in research computing center in my school. When I
used pdb2gmx as
pdb2gmx -f Ace5AlaNac -o Ace5AlaNac -p Ace5AlaNac -ignh -ter
it gave me an error message as follows,
illegal instruction (core dumped)
Could anyone give me a clue what is wrong? Thank you in advance
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.
We've got about as much chance of gu
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
___
gmx
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