Hi!
Working on Gentoo ebuild for AmberTools I ended up with several
patches which might be useful to include in AmberTools. They will come in
their own messages with descriptions, but in general they are build
system improvements and minor fixes. Though I have to say that
the build system still leaves a lot to be desired.
Probably the biggest highlight here would be fixes for running serial
tests in parallel. Since those tests in general are independent of
each other they can be run concurrently by giving to make option -j
with number of jobs to run at once. On my quad-core machine it reduces
the amount of time needed to run serial tests by more than a half.
These patches were prepared for AmberTools 12 with bugfixes up to 26
applied.
Reinis Danne (8):
AmberTools: Fix buffer overflows in mdgx, nab and ptraj
dsarpack.f: Move into sff to allow build against arpack-ng
nab.c: Don't hardcode CPP path
sqm: Fix OpenMP build
test/nab: Use paths to scripts
AmberTools: Tests should fail when they fail
AmberTools: Fix parallel tests
amber_outputs.py: Format floats in csv output
AmberTools/src/mdgx/Trajectory.c | 2 +-
.../src/mmpbsa_py/MMPBSA_mods/amber_outputs.py | 4 +-
AmberTools/src/nab/database.c | 2 +-
AmberTools/src/nab/nab.c | 4 +-
AmberTools/src/ptraj/trajectory.c | 2 +-
AmberTools/src/sff/Makefile | 2 +-
AmberTools/src/sff/dsarpack.f | 654 +++++++++++++++++++++
AmberTools/src/sqm/qm2_read_nm_and_alloc.F90 | 3 +
AmberTools/src/sqm/qm2_scf.F90 | 5 +-
AmberTools/src/sqm/qmmm_module.F90 | 3 +
AmberTools/test/Makefile | 4 +-
.../01_Generalized_Born/energies.csv.save | 8 +-
AmberTools/test/nab/Makefile | 2 +
AmberTools/test/nab/Run.rism_sp | 2 +-
AmberTools/test/nab/Run.rism_sp2 | 2 +-
AmberTools/test/test_at_serial.sh | 6 +
Makefile | 2 +-
17 files changed, 688 insertions(+), 19 deletions(-)
create mode 100644 AmberTools/src/sff/dsarpack.f
--
1.7.12.4
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Received on Mon Oct 22 2012 - 15:30:04 PDT
