We are running SUSE Linux
It's best to keep all of this on the mailing list in case it becomes
useful to somebody else.
jayant james wrote:
Hi!
thanks for your mail. I have never used pull code before and so I am a
bit apprehensive but I do accept your suggestion and I am working on
that. By the wat what is the OS that you are using? Is it Suse or Fedora?
Thanks
Jayant James
On Thu, Jun 25, 2009 at 4:31 PM, Chris Neale <chris.ne...@utoronto.ca
<mailto:chris.ne...@utoronto.ca>> wrote:
Let me re-emphasize that the pull code may be a good solution for you.
As per your request, I currently use the following without any
problems:
fftw 3.1.2
gromacs 3.3.1 or 4.0.4
openmpi 1.2.6
Be especially aware that openmpi 1.3.0 and 1.3.1 are broken, as I
posted here:
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040844.html
To be clear, I have never experienced any openmpi-based problems
with any version of gromacs 4 and openmpi 1.2.6.
I posted the original notice of our problems with openmpi (1.2.1)
that were solved by using lam here.
http://www.mail-archive.com/gmx-users@gromacs.org/msg08257.html
Chris
jayant james wrote:
Hi!
thanks for your mail. Could you please share what OS and
versions of fftw, openmpi and gmx you are currently using.
Thanks you
JJ
On Thu, Jun 25, 2009 at 12:28 PM, <chris.ne...@utoronto.ca
<mailto:chris.ne...@utoronto.ca>
<mailto:chris.ne...@utoronto.ca
<mailto:chris.ne...@utoronto.ca>>> wrote:
Why not use the pull code? If you haev to use distance
restraints,
then try LAM mpi with your pd run. We had similar error
messages
with vanilla .mdp files using openmpi with large and complex
systems that went away when we switched to LAM MPI. Our
problems
disappeared in gmx 4 so we went back to openmpi for all
systems as
that mdrun_mpi version is faster in our hands.
I admit, there is no good reason why LAM would work and openMPI
would not, but I have seen it happen before so it's worth a
shot.
-- original message--
The energy minimization went on without any problem on 4
processors but the
problem occurs when I perform the MD run. Also, I did not
get any
error
message with relevance to LINCS etc...
JJ
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--
Jayasundar Jayant James
www.chick.com/reading/tracts/0096/0096_01.asp
<http://www.chick.com/reading/tracts/0096/0096_01.asp>
<http://www.chick.com/reading/tracts/0096/0096_01.asp>)
--
Jayasundar Jayant James
www.chick.com/reading/tracts/0096/0096_01.asp
<http://www.chick.com/reading/tracts/0096/0096_01.asp>)
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