The latest CVS checkout of Amber 8 compiles with MPICH2 on yellowtail
(SGI_ALTIX) with no problems (ifort v8.0). It appears to run ok. I haven't
tried out any benchmarks yet.
If you want to try it out the installations are in:
/usr/people/rcw/Amber-MPICH_2_Testing
You need to add the following lines to your .cshrc file:
setenv PATH /usr/people/rcw/Amber-MPICH_2_Testing/MPICH2/install/bin:$PATH
setenv MPICH_HOME /usr/people/rcw/Amber-MPICH_2/Testing/MPICH/install
You also need to create a file in your home directory called .mpd.conf
which
contains:
secretword=xxxxxx
Where xxxxx is a secret word known only to you. Chmod 600 this file so
only
you can read it.
MPICH2 now uses a demon calle mpd for job control. It reads the host list
from mpd.conf (so you need to modify your run script to write the
$PBS_NODEFILE to mpd.conf. E.g yellowtail
Then execute:
mpdboot mpd.conf
Then you can run sander with:
mpirun -np 4 /usr/people/rcw/Amber-MPICH_2_Testing/amber8/exe/sander
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
> -----Original Message-----
> From: owner-amber-developers.scripps.edu
> [mailto:owner-amber-developers.scripps.edu] On Behalf Of David A. Case
> Sent: 17 September 2004 09:31
> To: amber-developers.scripps.edu
> Subject: amber-developers: [lusk.mcs.anl.gov: new release of MPICH2]
>
> If anyone wants to play with this, let us know what you find....dac
>
> ----- Forwarded message from Rusty Lusk <lusk.mcs.anl.gov> -----
>
> Date: Fri, 17 Sep 2004 08:33:55 -0500 (CDT)
> To: mpi-users.mcs.anl.gov
> Subject: new release of MPICH2
> From: Rusty Lusk <lusk.mcs.anl.gov>
>
> A new release of MPICH2 is now available from the web site
>
> http://www.mcs.anl.gov/mpi/mpich2
>
> This has nearly all MPI-2 functionality. Details can be found in the
> RELEASE-NOTES file in the distribution.
>
> This is release 0.971. (We are saving the number 1.0 for when
> absolutely all of the complete MPI-2 Standard is fully implemented.)
> For Linux and Windows clusters, this MPICH is more robust and
> higher-performning than any versions of MPICH-1, the current
> version of
> which is 1.2.6.
>
> Regards,
> The MPICH team
>
> ----- End forwarded message -----
>
Received on Wed Apr 05 2006 - 23:50:00 PDT
