[gmx-users] GROMACS on Bluegene

[Roland Schulz]

Mathias has updated the wiki:
http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene


On Wed, Nov 12, 2008 at 11:57 AM, Suman Chakrabarty <
suman at sscu.iisc.ernet.in> wrote:

> I am interested in this as well, since I am planning to compile
> version 4.0.2 in Blue Gene within a few days (once I get hold of my
> account!).
>
>
> --
> Suman Chakrabarty.
>
>
> On Wed, Nov 12, 2008 at 8:21 PM, Mike Hanby <mhanby at uab.edu> wrote:
> > Has there been any further discussion about fixing the issues discussed
> > below regarding Blue Gene?
> >
> > -----Original Message-----
> > From: gmx-users-bounces at gromacs.org
> > [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
> > Sent: Thursday, October 16, 2008 10:43 PM
> > To: Gromacs Users
> > Subject: [gmx-users] GROMACS on Bluegene
> >
> > Hi,
> >
> > I can see GROMACS 4.0 has inner loops apparently optimized for BlueGene,
> >
> > however the distribution is incomplete. At least the files
> >
> > interaction.h
> > nb_kernel_w3_bluegene.h
> > nb_kernel_w3w3_bluegene.h
> > nb_kernel_w4_bluegene.h
> > nb_kernel_w4w4_bluegene.h
> > nb_kernel_gen_bluegene.h
> >
> > are missing from src/gmxlib/nonbonded/nb_kernel_bluegene in the official
> >
> > distribution.
> >
> > Further, src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_bluegene.h
> > contains the contents of file
> > src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.h which
> > obviously won't work.
> >
> > Further, GROMACS configure won't work out-of-the-box on this platform
> > (see also
> > http://www.gromacs.org/pipermail/gmx-users/2008-October/037179.html and
> > discussions on this list months back). Since I can see in the source
> > code that Mathias Puetz at IBM has done (at least some of) the
> > development work here, then I suggest that IBM may like to provide some
> > official build instructions. I have my own black magic that makes
> > configure work on my machine, and I'm prepared to make that available
> > off-list to interested parties, but I don't know how portable it will be
> >
> > between Bluegene installations. A better solution should be available if
> >
> > one of the GROMACS developers can approach the IBM people for us,
> > please.
> >
> > Mark
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> > --
> > This message has been scanned for viruses and
> > dangerous content by MailScanner, and is
> > believed to be clean.
> >
> >
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081112/74d23656/attachment.html>