Paymon Pirzadeh wrote:
Hello all,
A follow up from my previous problems on running the gromacs on glacier
turned out that I had problems in installation. The guide in the manual
was not clear enough. So, I installed the code fine this time, so, I get
errors from 4.0.4 version.
I ran the code
I am running other softwares in parallel on glacier. GROMACS has shown
such problem up to now!
On Thu, 2009-05-28 at 21:52 +0200, p.ya...@fz-juelich.de wrote:
It seems like your nodes cannot communicate.
you might want to check your job-submitting script: does it call mdrun
correctly?
Paymon Pirzadeh wrote:
Hello all,
A follow up from my previous problems on running the gromacs on glacier
turned out that I had problems in installation. The guide in the manual
was not clear enough. So, I installed the code fine this time, so, I get
errors from 4.0.4 version.
I ran the code
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: May 19, 2009 12:36 PM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] gromacs on glacier.westgrid.ca
Dear Tsjerk,
Thanks for your e-mail. The message
Hi,
On Tue, 19 May 2009 14:23:07 -0600, Payman Pirzadeh wrote
Hi Justin,
Following is the script I use. But remember several points:
${MPIRUN} -np $NUM_PROCS -machinefile $PBS_NODEFILE -path
./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d -deffnm npttest
You have a dot before /global/...
Hi Payman,
That is probably not the only grid facility on which Gromacs may be
run and it would be helpful if you could give specifications of it
(WMS software e.g.), which could give you more response. Also, it
would be helpful if you'd be able to give more information regarding
the output. Then
for GROMACS users
Subject: Re: [gmx-users] gromacs on glacier.westgrid.ca
Hi Payman,
That is probably not the only grid facility on which Gromacs may be
run and it would be helpful if you could give specifications of it
(WMS software e.g.), which could give you more response. Also, it
would be helpful
: [gmx-users] gromacs on glacier.westgrid.ca
Hi Payman,
That is probably not the only grid facility on which Gromacs may be
run and it would be helpful if you could give specifications of it
(WMS software e.g.), which could give you more response. Also, it
would be helpful if you'd be able to give
'
Subject: RE: [gmx-users] gromacs on glacier.westgrid.ca
Dear Tsjerk,
Thanks for your e-mail. The message that cluster sends is:
Running on 4 processors.
Starting run at: Sat May 16 17:13:28 PDT 2009
Warning: Command line arguments for program should be given
after the program name. Assuming
-boun...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: May 19, 2009 12:36 PM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] gromacs on glacier.westgrid.ca
Dear Tsjerk,
Thanks for your e-mail. The message that cluster sends is:
Running on 4 processors.
Starting run at: Sat May 16
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