[gmx-developers] cray xt3 port, fio rename, misc fixes
David van der Spoel
spoel at xray.bmc.uu.se
Wed Aug 30 11:52:30 CEST 2006
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!
> 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.
> contains a fix for a typo in a comment and fixes a segfault
> at the end of jobs that do _not_ use domain decomposition.
> 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.
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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
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