[gmx-developers] cray xt3 port, fio rename, misc fixes
akohlmey at cmm.chem.upenn.edu
Fri Sep 1 22:48:06 CEST 2006
On 8/30/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Axel Kohlmeyer wrote:
> > hi everybody,
> > please find attached three patches to the current gromacs
> > development cvs tree.
> I have implemented your patches in the cvs tree, and fixed all
> compilation errors and warnings.
> Note that I did not test any of the code!
well, i got so carried away in testing on non-cray machines,
that i actually overlooked two typos on the cray.
under normal circumstances, you would compile and
run those programs in serial mode without the cray
catamount settings, so this should not even matter,
but for the sake of completeness, the attached patch
should be applied as well.
> > gmx-fio-rename.diff:
> > renames all fio_XXX functions to gmx_fio_XXX as needed
> > for static linkage with PGI runtime libs. not all renames are
> > needed, but for the sake of consistency i changed all functions.
> > gmx-misc-fixes.diff:
> > contains a fix for a typo in a comment and fixes a segfault
> > at the end of jobs that do _not_ use domain decomposition.
> > gmx-cray-xt3-port.diff:
> > contains the port of gromacs to the cray xt3 architecture.
> > a few remarks about that. this machine uses two different
> > kernels on the head nodes and the compute nodes with otherwise
> > identical hardware. this means, that the serial compile is
> > like on a normal (opteron CPU), in fact you can copy and
> > use serial binaries from other machines, but for parallel
> > compilation, you have to 'cross-compile' using a different
> > libc adapted to the compute nodes which is linked statically
> > into the binary. the modified configure.ac script should take
> > care of that. the compute nodes have a very restricted
> > kernel (similar to BG/L) without support of sockets,
> > subprocesses, userids, shared libraries, no /proc etc.
> > the more generic features (no nice, no call system)
> > i wrapped into more generic defines GMX_NO_XXX.
> > then there is GMX_BROKEN_CALLOC which is a
> > special story: the default malloc in the special libc for
> > the compute nodes has a bad performance for many
> > small allocations, so there is also libgmalloc as a remedy,
> > but the one shipped with the current versions has a
> > broken callloc (it does not zero out all elements) which
> > explained the 'memory corruption' that shawn and i
> > reported earlier. luckily this can be easily fixed using
> > malloc and memset (i am still puzzled why cray is
> > not able to correct that). the rest are changes particular
> > for the cray xt3 architecture and thus wrapped into
> > GMX_CRAY_XT3 defines.
> > please let me know ASAP if you're not happy with any
> > of these changes, so i can fix them before i'll be working
> > on implementing the changes for our project.
> > enjoy,
> > axel.
> > ------------------------------------------------------------------------
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> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> gmx-developers mailing list
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Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.
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