[gmx-developers] cray xt3 port, fio rename, misc fixes

[Axel Kohlmeyer]

hi everybody,

please find attached three patches to the current gromacs
development cvs tree.

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.

-- 
=======================================================================
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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