Szilard Pall [Thu, 24 Jan 2013 01:27:09 +0000 (02:27 +0100)]
added back cuda.h includes to fix missing CUDA_VERSION
nvcc doesn't define its version identity macro, CUDA_VERSION, by default,
but this needs to be pulled in through cuda.h. Quite weird and
non-standard behavior, but as swithing to legacy kernels and certain
kernel optimizations are broken now, to fix these we need to include
cuda.h.
Change-Id: I4836335e97a287e18e595c160819db2e46a8d798
Mark Abraham [Tue, 22 Jan 2013 18:17:52 +0000 (19:17 +0100)]
Merge "Illegal acceleration defaulted to QPX" into release-4-6
Mark Abraham [Tue, 22 Jan 2013 16:41:00 +0000 (17:41 +0100)]
Merge "Re-licenced FindGROMACS.cmake (was written by me)" into release-4-6
Roland Schulz [Mon, 21 Jan 2013 21:34:35 +0000 (16:34 -0500)]
Illegal acceleration defaulted to QPX
Change-Id: I1bfd9c7bc7bac68944fd912bda84e8bd03af1fbc
Mark Abraham [Tue, 22 Jan 2013 16:40:12 +0000 (17:40 +0100)]
Merge "Fix TOUPPER usage" into release-4-6
Mark Abraham [Tue, 22 Jan 2013 16:39:55 +0000 (17:39 +0100)]
Merge "Updated html manual to 4.6" into release-4-6
Mark Abraham [Tue, 22 Jan 2013 15:31:01 +0000 (16:31 +0100)]
Merge "added missing cleanup of some nbnxn_cuda data" into release-4-6
Roland Schulz [Mon, 21 Jan 2013 21:12:52 +0000 (16:12 -0500)]
Fix TOUPPER usage
The last argument is the variable name, thus it shouldn't be ${..}.
Caused compile error when setting accleration to sse2, because
TOUPPER wasn't done correctly.
Change-Id: I0087a6cf3c9a160862757f561b5782c0ac253df8
Roland Schulz [Sun, 20 Jan 2013 00:51:02 +0000 (19:51 -0500)]
Updated html manual to 4.6
Change-Id: I2d66c41c56a44fddc31bba823a264795c07d078a
Christoph Junghans [Mon, 21 Jan 2013 20:44:02 +0000 (21:44 +0100)]
Merge "Set version info for 4.6.x release series" into release-4-6
Christoph Junghans [Fri, 18 Jan 2013 21:00:56 +0000 (14:00 -0700)]
Re-licenced FindGROMACS.cmake (was written by me)
Change-Id: If6a94c561933cbc6db9d47d5a364f75e7fdf5e13
Roland Schulz [Sat, 19 Jan 2013 06:42:22 +0000 (01:42 -0500)]
Fix AVX double compile error
Introduced by
fa181964de6c9
Note that this change will be included in the 4.6 release, therefore
this commit will effectively be the one that the 4.6 release is made
from instead of the parent.
Change-Id: Ieeede7d15109f2c44fcd2e0ef59eff2944206eab
Mark Abraham [Wed, 16 Jan 2013 01:08:33 +0000 (02:08 +0100)]
Set version info for 4.6.x release series
Change-Id: I31378a7ef5d9b7333aa91f076c2a792072d304f9
Mark Abraham [Wed, 16 Jan 2013 01:06:19 +0000 (02:06 +0100)]
New major release: 4.6
* note -dev gets stripped off by the release manager by hand before
building tarballs
Change-Id: I36fe0b8ec18c7d6f09da852e216fdf6d0a250bb7
Michael Shirts [Wed, 16 Jan 2013 14:03:30 +0000 (09:03 -0500)]
Addendum for expanded ensemble options plus formatting fixes.
Change-Id: I4547fe74064593c939fcb292ccee056b49b292af
Roland Schulz [Fri, 18 Jan 2013 20:25:05 +0000 (15:25 -0500)]
Merge release-4-5-patches into release-4-6
Conflicts:
src/gmxlib/confio.c (whitespace only)
286575f0cd68 commit is not needed and is ignored
by this merge.
Change-Id: I7c4aabd918384aadbf6108501023ca77e019d6c1
Roland Schulz [Fri, 18 Jan 2013 05:12:58 +0000 (00:12 -0500)]
Fix typo
Change-Id: Iba23e5cea570b2a283a19290774fe21b0e625cab
Roland Schulz [Fri, 18 Jan 2013 01:07:27 +0000 (20:07 -0500)]
Code beautification with uncrustify
We are going to try to keep our eyeballs from bleeding when we
read prehistoric code from this project while maintaining it.
So we need a point in time where release-4-6 gets beautiful
in tandem with master. That time is now.
At some point we hope to be able to do this automatically so
we can have reviewers concentrate on code quality and not
formatting trivia. But we have to do a whole-of-project
fix first.
Refs #845
Change-Id: I8e99228cc118f75c0831e8297c171fcbbabc8f73
Roland Schulz [Fri, 18 Jan 2013 17:36:17 +0000 (12:36 -0500)]
Add colon after macro to help uncrustify
Without the colon uncrustify adds braces incorrectly
Change-Id: Ib361762c1b252de2b4a274c2be44f1fecb31b7da
Berk Hess [Tue, 15 Jan 2013 09:29:43 +0000 (10:29 +0100)]
thread affinity now uses some topology information
The order of logical cores on x86 is hardware and software dependent.
The cpuid topology reports this and this information is now used.
The mdrun -pinht option is generalized for SMT to -pinstride.
The mdrun -pinoffset option is now in logical (iso phyiscal) cores.
Thread-MPI no longer sets affinity, it's now all done in one place.
The option -pin is now an enum, default auto: only on when using all
cores and when no external affinity has been set.
A big NOTE is printed with auto when no pinning is used.
Option -pin on can now override thread affinity set outside mdrun.
Fixes #1122
All thread affinity code has been moved from runner.c to
gmx_thread_affinity.c.
Updated the mdrun manual for pinning also active without OpenMP.
Change-Id: Ibf0fe5882688de80c223640502c68e6170d4d044
Mark Abraham [Wed, 16 Jan 2013 00:55:31 +0000 (01:55 +0100)]
Fixing copyright issues and code contributors
Added Mark Abraham, Christoph Junghans and
Carsten Kutzner to the list of code contributors,
per discussion with Erik and Berk.
* Now that 2013 is a copyrightable year, we need to
assert that copyright
* No, we can't just say 1995-2013, unless we also say
that every year in the range is a copyrightable year. I'm
not interested in demonstrating after the fact that this is
true for all the years before I was born. So we may as
well start listing explicit years.
Please read "howto (L)GPL" guides before arguing :-)
* Removed erroneous GROMACS copyright statements on
unmodified FindBLAS.cmake,FindLAPACK.cmake,
FindOpenMP.cmake and slightly modified FindGit.cmake
* Note Szilard's uncertainty about the origin of
vectype_ops.cuh and thus its copyright status
* TODO for 4.6.1 deal with material in admin and scripts
References #818
Change-Id: I946200651de7f05c2ff292fcded8f33fca7b356f
Erik Lindahl [Fri, 18 Jan 2013 15:30:39 +0000 (16:30 +0100)]
Merge "remove unnecessary cmake messages" into release-4-6
Erik Lindahl [Fri, 18 Jan 2013 15:09:45 +0000 (16:09 +0100)]
Merge "fix OpenMP detection on Mac OS broken by
a6fee0b" into release-4-6
Roland Schulz [Fri, 18 Jan 2013 06:25:50 +0000 (01:25 -0500)]
Fix reading of g96 title
Change-Id: I5b077ef2f581d704848b658c588636c7510d3c38
Szilard Pall [Fri, 18 Jan 2013 03:50:13 +0000 (04:50 +0100)]
remove unnecessary cmake messages
Unfortunately
f8885a6 slipped in with two debug messages in the compiler
version detection code. This commit removes them so we're back to clean
& silent cmake.
Change-Id: I322183445f75688e3626e8c2382186ce1df1d0a1
Szilárd Páll [Thu, 17 Jan 2013 02:36:08 +0000 (03:36 +0100)]
fix OpenMP detection on Mac OS broken by
a6fee0b
Compiler version check was done before the version got detected. This
code will avoid false positives even if the compiler version is not
available (although for GNUCC it should always be).
Change-Id: I554f13e4b101ae7c9f70674e966065bf9fcf2b27
Mark Abraham [Wed, 16 Jan 2013 00:54:56 +0000 (01:54 +0100)]
Updating the shell completion files
Hope this g_tool -man completion technology still works!
Change-Id: I4bfd04ee1e0cc050a0690263d1e7e76f560b0372
Szilárd Páll [Wed, 16 Jan 2013 23:57:42 +0000 (00:57 +0100)]
added missing cleanup of some nbnxn_cuda data
While the content of the data structures the pointers in nbnxn_cuda
point to was freed up, the data structures themselves were not.
Change-Id: Icb1c5da9867ee252e2a6dadf7f164d7bb4f41a26
Mark Abraham [Wed, 16 Jan 2013 00:52:42 +0000 (01:52 +0100)]
Gromacs install guide updates.
Change-Id: I6822ef3898abf81f548163386147cbb1a0a01ad0
Mark Abraham [Thu, 17 Jan 2013 22:28:41 +0000 (23:28 +0100)]
Merge "Remove unnecessary ICC flags affecting performance" into release-4-6
Mark Abraham [Thu, 17 Jan 2013 22:26:46 +0000 (23:26 +0100)]
Merge "improved CUDA kernel performance by pre-loading cj" into release-4-6
Christoph Junghans [Thu, 17 Jan 2013 22:22:10 +0000 (23:22 +0100)]
Merge "Added note about make_edi and flooding in ED paragraph" into release-4-6
Christoph Junghans [Thu, 17 Jan 2013 22:21:03 +0000 (23:21 +0100)]
Merge "use the compiler version provided by CMake >=2.8.9" into release-4-6
Roland Schulz [Thu, 17 Jan 2013 22:02:49 +0000 (23:02 +0100)]
Merge "Merge branch 'release-4-5-patches' into release-4-6" into release-4-6
Szilárd Páll [Thu, 17 Jan 2013 22:18:55 +0000 (23:18 +0100)]
Merge changes I930b316c,Iea4283e0,I103648f8 into release-4-6
* changes:
BlueGene/Q installation notes
fixed SD+BD integration slowing down with OpenMP threads
Run regressiontests from build
Roland Schulz [Thu, 17 Jan 2013 09:37:47 +0000 (04:37 -0500)]
Remove unnecessary ICC flags affecting performance
Since we add -msse/../-mavx based on the acceleration we shouldn't
add -mtune=core2 anymore. Especially because it is added later
and takes precedence over the (higher) acceleration flag.
-ip and -funroll-all-loops could also be deleted because they don't
seem to give any significant performance improvement, and might
increase compilation time, but they don't hurt gromacs performance.
In theory it could help to use -xavx instead of -mavx but I can't
measure a difference.
Change-Id: Icd11c40c3cd3ef2ae6ef42f07d5d75c228593f51
Mark Abraham [Thu, 17 Jan 2013 21:10:40 +0000 (22:10 +0100)]
Merge "Fix trjconv -sub with .trr files" into release-4-5-patches
Mark Abraham [Wed, 19 Dec 2012 01:24:31 +0000 (02:24 +0100)]
BlueGene/Q installation notes
Change-Id: I930b316c549dea3ec69ce331bbf9d3dcf0bcd4a9
Mark Abraham [Thu, 17 Jan 2013 18:29:08 +0000 (19:29 +0100)]
Merge branch 'release-4-5-patches' into release-4-6
Conflicts:
src/gmxlib/disre.c
src/kernel/runner.c
src/mdlib/minimize.c
src/tools/gmx_membed.c
Change-Id: I1d5f72a3a9b8468cf478890791bc67d247c1e2c5
Christoph Junghans [Thu, 17 Jan 2013 18:27:01 +0000 (19:27 +0100)]
Merge "note the reason for auto-disabling GPU support in CMake" into release-4-6
Mark Abraham [Thu, 17 Jan 2013 18:13:41 +0000 (19:13 +0100)]
Merge "Added mdp option 'calc-lambda-neighbors'." into release-4-6
Roland Schulz [Thu, 17 Jan 2013 18:03:29 +0000 (19:03 +0100)]
Merge "clarify wording of GPU driver-related notes" into release-4-6
Roland Schulz [Thu, 17 Jan 2013 18:01:52 +0000 (19:01 +0100)]
Merge "Added check for valid wall_atomtype in .mdp" into release-4-5-patches
Mark Abraham [Tue, 15 Jan 2013 16:13:30 +0000 (17:13 +0100)]
Fix trjconv -sub with .trr files
ftp is set from the -o file's extension, which cannot be efTRN,
since that's a place-holder file type for command-line parsing.
The error text clearly indicates that .trr (== efTRR) should
work, but of course we have no tests for anything.
Added comment that other trajectory types could work here,
but can't be tested at this time.
Fixes #1118
Change-Id: I118b9b1c25fa7c0640c27e584400dfc64853e67f
Berk Hess [Thu, 17 Jan 2013 09:01:11 +0000 (10:01 +0100)]
fixed SD+BD integration slowing down with OpenMP threads
The SD and BD integrators would integrate on all OpenMP threads,
making the integration much slower instead of faster.
It is not clear if the results could be affected by this bug.
Fixes #1121
Change-Id: Iea4283e0470b72f6f927cb49503ac91d65025647
Roland Schulz [Sat, 22 Dec 2012 21:47:50 +0000 (16:47 -0500)]
Run regressiontests from build
If either REGRESSIONTEST_PATH or REGRESSIONTEST_DOWNLOAD is set,
the regressiontests are run as ctests. The later option auto-
downloads the regressiontest repo.
The "check" target builds and runs tests in one step.
The "gmxtests" target builds tests.
If neither variable is set by the user, the commit doesn't change
the prior behavior (no messsages). Running the new target "check"
without either variable set, prints a warnings.
This commit also removes the prior pseudo test of running
"mdrun -h".
Change-Id: I103648f8a87891727a70775b19449fc269002a1c
Berk Hess [Sat, 12 Jan 2013 21:41:15 +0000 (22:41 +0100)]
improved CUDA kernel performance by pre-loading cj
Change-Id: Ic725a82d550e2ecffd4d32edd2c44205aef99b8d
Sander Pronk [Tue, 15 Jan 2013 12:19:23 +0000 (13:19 +0100)]
Added mdp option 'calc-lambda-neighbors'.
Added an option 'calc-lambda-neighbors' to limit the number of free
energy delta H evaluations and output operations: this value sets the
amount of neighboring lambda points to calculate and print the energy
for. If it's 1, it will only calculate directly adjacent lambda points'
energies (if it's -1, it will calculate all points). This tremendously
cuts down the number of (expensive) energy calculations done without
impacting the results for most users
Note that this commit only limits the number of outputs, not the number
of calculations. That is left for a later commit.
Change-Id: I10590dd1a2036b529946da86b414c2561d14bda1
Sander Pronk [Thu, 10 Jan 2013 22:35:28 +0000 (23:35 +0100)]
Fixes to free energy code, output & g_bar compatibility.
- Fixes to the handling of the new free energy input options, so that
input are more stringently checked and common errors are caught.
- Fixed g_bar so it can deal with output from mdrun (in dhdl.xvg and
ener.edr input)
- Free energy output is now backward compatible with g_bar if 4.5-style
settings are used
- Some mdp option documentation clarifications.
This fixes issue #1090
Still left to do:
- g_energy -odh relies on an ugly hack to get the xvg headers for free
energy
output to work. That needs to be fixed so ener.edr can be interpreted
independently from the associated tpr file.
- The mdp documentation could use some more improvements.
Change-Id: I6198f935a94b7341d8dd85444e348ea8a55621ad
Carsten Kutzner [Thu, 17 Jan 2013 12:39:35 +0000 (13:39 +0100)]
Added note about make_edi and flooding in ED paragraph
Change-Id: I735c75194aeaa76570d211e51665ec89cfc3ef82
Szilárd Páll [Thu, 17 Jan 2013 05:43:53 +0000 (06:43 +0100)]
use the compiler version provided by CMake >=2.8.9
With CMake <2.8.9 we still use our slightly naive compiler version
detection code, but from 2.8.9 CMake provides a compiler version
variable which should be more robust and portable, so we will use that
instead.
Change-Id: I3cefa227c4962d9a2fae06af2c5b2a0d22ef30c4
Szilárd Páll [Wed, 16 Jan 2013 20:27:42 +0000 (21:27 +0100)]
note the reason for auto-disabling GPU support in CMake
As the status message on unsuccesful CUDA detection has been muted, the
user is left clueless about why do we disable GPU support at configure
time. Extended the status message to note that this happens because no
compatible CUDA was found.
Some minor status message and code comment tweaks were also done.
Change-Id: Icfba7b56546997cd38952ceff2b7914c9f5b2d67
Szilárd Páll [Thu, 17 Jan 2013 03:01:35 +0000 (04:01 +0100)]
clarify wording of GPU driver-related notes
After getting the ill-documented return value of cudaDriverGetVersion
clarified with NVIDIA driver engineers, the notes and warnings have been
clarified and now refer to driver API version 5.0.
Change-Id: I66cda563cd6753e5337ac0ed28264a3941627a03
Mark Abraham [Mon, 14 Jan 2013 00:47:02 +0000 (01:47 +0100)]
Finally move OpenMM to contrib
I've paid lip service to attempting to leave the build functional.
There's a few places GMX_OPENMM still has to appear in the main code,
because of how CMake works and how badly GROMACS libraries work. I'm
prepared to fix obvious major issues anyone spots. I'm proposing not
to do any testing of whether the build works, since the 4.5 build is
still available. If later on someone wants both OpenMM and some
feature in 4.6 they can ask then for help fixing the damage here.
Fixes #1079, for certain values of "fixes" :-)
Change-Id: Ic27b8c3bdc1255cc3edb01bcfa11f47d6a03b44d
Roland Schulz [Tue, 15 Jan 2013 22:29:49 +0000 (17:29 -0500)]
Fix confusing gmx_header_config.h include
Easy to forget gmx_header_config.h because
historically only config.h is needed and
in master only config.h is needed, too.
Hid a bug in gmx_cpuid.c which didn't
do anything on Windows because the proper
define wasn't set.
Also fixes the compiler warnings in gmx_cpuid.c
Change-Id: I0ad9ca77bfe05551bdde82ab4e92b180c1e5963b
Szilard Pall [Fri, 11 Jan 2013 06:11:55 +0000 (07:11 +0100)]
don't use polling with new driver
With the 304.xx (API v5.0) drivers the cudaStreamSynchronize overhead
has been substantially reduced, so with these there is no need to switch
to polling. Additionally, with GPUs oversubscribed the polling has been
shown to be unstable, so this case is now detected and switch to polling
is not done.
Also corrected some warning/note printing layout.
Change-Id: I32a7ecda42de31f825a6341c81f04ca0b97c0d4a
Christoph Junghans [Tue, 25 Dec 2012 00:28:29 +0000 (17:28 -0700)]
clean up fortran name mangling
* centralize name mangling for easy change
* mangling is set to GNU's default mangling
* don't expose internal blas/lapack/arpack headers
Change-Id: I5a2a6298808cbb43e6aea0f06397ee0f0102685f
Berk Hess [Fri, 11 Jan 2013 13:59:31 +0000 (14:59 +0100)]
fixed nbnxn hybrid mode with OpenMP
Fixes #1100
Change-Id: I2f3c95f698852ab496a648a04555c0e9ecb57463
Berk Hess [Mon, 14 Jan 2013 09:19:25 +0000 (10:19 +0100)]
made PME load balancing + DD DLB more efficient
The DD dynamic load balancing is now limited, such that the fastest
timed PME load balancing cut-off setting can always be used.
Fixes #1089
Change-Id: I3216dfd5a8b2b0676eee5519e08cf36e06047251
Carsten Kutzner [Mon, 14 Jan 2013 16:12:45 +0000 (17:12 +0100)]
Made g_tune_pme work correctly again with thread-MPI mdrun
Up to now, g_tune_pme would put the -nt switch on the mdrun command
line to ask for thread-MPI processes. Due to changes in mdrun, this
now leads to the fact that all runs with separate PME nodes exit
because the number of MPI threads must be explicitly specified with
the -ntmpi switch. Now the g_tune_pme -nt option is renamed to -ntmpi.
The remaining changes are only minor code cleanup / formatting things
plus getting rid of unused variables.
Change-Id: I7518799ef593d78d1cce1496852f0241e6d01755
Roland Schulz [Mon, 14 Jan 2013 06:38:05 +0000 (01:38 -0500)]
Don't cache ${FFTW}_HAVE_(SIMD|AVX)
The error message was incorrect if the library was changed. E.g.
if the library wasn't found on the first try and then (e.g. with
CMAKE_PREFIX_PATH) was found on the 2nd try. Could have been
resolved by using FORCE when setting variables, but that would
have defeated the purpose of allowing the user to overwrite
the value for future versions which might be misidentified.
Any solution which lets the user to overwrite but still works
correctly if the library changes would be difficult. Given that
it is only for displaying a warning message, it is not worth
making it much more complicated.
Change-Id: I0b6c5a204ee0114ef9de9337491a14457917f9d7
Erik Lindahl [Sun, 13 Jan 2013 19:21:05 +0000 (11:21 -0800)]
Fixed GB interactions for release-4-6
Release-4-6 was not using the correct GB kernels,
but the non-GB electrostatics cutoff kernel. In addition,
the accelerated kernels unrolled more than a factor 2 had
a bug that caused a small error in the forces. Both these
issues have been fixed, and the GB results now match
release-4.5.
Note: The GB _radius_ calculations are still only done
in C, but the accelerated options will be re-enabled in
a pending patch (separated for clarity).
Fixes #1096.
Change-Id: I40151b9a9f1920006bfe9a39a8719698a824bfac
fix
Change-Id: I45630252d6a9c05a7f3695a7e6d07dcd13e0a25c
Berk Hess [Thu, 10 Jan 2013 17:59:27 +0000 (18:59 +0100)]
split off pick_nbnxn_resource from nbnxn_pick_nbnxn
Fixes #1049
Change-Id: Iadf46f40676551b9b58d0d3da5bdca0f94d4a3fb
Mark Abraham [Fri, 11 Jan 2013 17:06:33 +0000 (18:06 +0100)]
Quiet stderr output, particularly for multi-simulations
* removed printing of DD info to stderr
* printed multi-simulation information only once in places where
repetition is clearly redundant (Some repetition remains,
but only from each simulation master.)
* add option to not print result of multi-simulation check
if it passed, so that we don't have to print things to
stderr/stdout just because the .log file is not yet open
* printing of diagnostics about the number of MPI
processes present when mdrun starts only goes (once) to
each debug file, and not to stderr
* reduced printing of diagnostics about the number of OpenMP
threads; now goes to stderr only on SIMMASTER, or
once to each debug file
* clarified errors and informational messages about selecting
the number of OpenMP threads
Fixes #1078, refs #1083
Change-Id: If782259bcd62ddd9be325393930080b70c5cfb4e
Michael Shirts [Sun, 13 Jan 2013 17:20:57 +0000 (12:20 -0500)]
fixes issues with pressure control and infrequent evaluation
Fixes a bug when pressure control in md-vv when nstcalcenergy is not a
multiple of nstpcouple or nsttcouple. This bug results in boxes slowly
expanding to unphysical sizes because the virial is
neglected in the second half of the md-vv calculation.
Also discovered that as part of the bug, global energies were being communicated
where they did not need to be when nstpcouple and nsttcouple are > 1 in the case
of md-vv, so redid some of the iteration counting and global communication to fix
this all together. In the process, this simplified some of the interation counting.
Change-Id: I3f77ba361fc88e03ccdfdde1b0be388ea46a8683
Christoph Junghans [Tue, 15 Jan 2013 22:33:18 +0000 (15:33 -0700)]
Remove debug statment
* left from I1c2a27f6fc1162cf8999c65ff6173121109cfbad
Change-Id: If520406444a810bf2810f68cf97a4a1bbf8141de
Mark Abraham [Tue, 15 Jan 2013 17:09:31 +0000 (18:09 +0100)]
Added check for valid wall_atomtype in .mdp
Otherwise, mdrun would dump core when the garbage got dereferenced.
Note that this does not need to be merged into release-4-6, because
c7a82654 already fixes it.
Fixes #700
Change-Id: I39f440595f7b112d4f01b5e32218ec45a2a97370
Roland Schulz [Tue, 15 Jan 2013 20:53:25 +0000 (15:53 -0500)]
Fix missing replacement/typo
Change-Id: Ia2b1c7a2aa222134c5d6847539d0f4287a3510a3
Mark Abraham [Tue, 15 Jan 2013 18:53:29 +0000 (19:53 +0100)]
Merge "Hid nbnxn kernel names behind a lookup function" into release-4-6
Christoph Junghans [Tue, 15 Jan 2013 17:36:06 +0000 (18:36 +0100)]
Merge "Added fatal error for constraints + L-BFGS minimizer" into release-4-5-patches
Christoph Junghans [Tue, 15 Jan 2013 17:35:19 +0000 (18:35 +0100)]
Merge "disable OpenMP with all OS X gcc 4.2-based compilers" into release-4-6
Sander Pronk [Tue, 15 Jan 2013 17:16:51 +0000 (18:16 +0100)]
Merge "Continuation of documentation for expanded ensemble." into release-4-6
Mark Abraham [Mon, 14 Jan 2013 22:48:20 +0000 (23:48 +0100)]
Velocity-verlet integrators and v-rescale are broken
Added fatal error and suggestion to upgrade GROMACS version.
Fixes #1000
Change-Id: I22653fafdfd0fb2f1fa772fbd95bc55fcf072d8c
Michael Shirts [Mon, 14 Jan 2013 02:19:18 +0000 (21:19 -0500)]
Continuation of documentation for expanded ensemble.
With a few other corrections here and there.
Change-Id: Ic7ebefc8e959a50f2bba917fe90cbef4b44ab2fd
Szilárd Páll [Tue, 15 Jan 2013 01:27:10 +0000 (17:27 -0800)]
disable OpenMP with all OS X gcc 4.2-based compilers
Although gcc 4.2 should have OpenMP support, the gcc 4.2.1-based
compilers on Mac OS X (defaults in 10.6.x) all claim to support OpenMP,
but generates segfaulting code.
This change reworks the llvm-specific check and moves it out from the
C/CXX flag generation module.
This compiler is the default on many BSD os-es, but as no other gcc
4.2.x has been tested yet (to my knowledge), for now the limitation is
introduced only for the Mac OS X and gcc 4.2.x.
Refs #900
Change-Id: I1c2a27f6fc1162cf8999c65ff6173121109cfbad
Mark Abraham [Mon, 14 Jan 2013 23:36:53 +0000 (00:36 +0100)]
Added fatal error for constraints + L-BFGS minimizer
Refs #1053
Change-Id: I0fd609918927883fc9ec20d0599a48e396d81d94
Mark Abraham [Mon, 14 Jan 2013 22:04:20 +0000 (23:04 +0100)]
Hid nbnxn kernel names behind a lookup function
Keeps clang syntax checking in master branch quiet - otherwise
it complains about unused variables. See discussion in
Change-Id: I753f701d74b8d4533e74cede19712b030bf97ca6
Change-Id: Id73ef041d7d3c9443be4992dc18f28ac09f499e9
Carsten Kutzner [Fri, 11 Jan 2013 16:58:48 +0000 (17:58 +0100)]
Essential dynamics output file now in .xvg format
No need to run a parser script on sam.edo anymore!
Change-Id: I37fcc7018482f31a25f5b6ba1bde7f22ccf0c31f
David van der Spoel [Mon, 14 Jan 2013 19:16:59 +0000 (20:16 +0100)]
Merge "Fixing trjconv -sub" into release-4-5-patches
David van der Spoel [Mon, 14 Jan 2013 19:04:48 +0000 (20:04 +0100)]
Merge "Noting that and why gmxdump -s -sys is broken" into release-4-5-patches
Roland Schulz [Sun, 13 Jan 2013 23:42:52 +0000 (00:42 +0100)]
Merge "Fixes for md-vv and rerun" into release-4-6
Roland Schulz [Sun, 13 Jan 2013 23:42:36 +0000 (00:42 +0100)]
Merge "fixed resetting states with parallel Verlet scheme" into release-4-6
Mark Abraham [Sun, 13 Jan 2013 18:57:36 +0000 (05:57 +1100)]
Updated code checks with distance restraints
Ensemble-averaged distance restraints require -multi, and it is
also reasonable to do REMD with distance restraints, which also
requires -multi. So checks for the ensemble-averaging case need
to be more sensitive to their context.
In fact, ensemble-averaging is probably functional only with PD and
one processor per system, since that was probably all that was
available when it was built.
Fixes #613, refs #1117
Change-Id: Ia6f1bb4eb82eab3c7c249638cd3a5a5d1f707132
Mark Abraham [Wed, 3 Oct 2012 13:19:32 +0000 (23:19 +1000)]
Fixing trjconv -sub
The process of making code thread safe broke this.
Change-Id: Ie6617c00e52b09ea0eade2dcb0ae998e8ebf3cc4
Roland Schulz [Wed, 28 Nov 2012 00:23:28 +0000 (19:23 -0500)]
Proper fix for copyrite cuda dependence
Change-Id: I3d3329dcdfde86b954854aff7c83b518b8c49c2d
Michael Shirts [Tue, 1 Jan 2013 04:19:27 +0000 (23:19 -0500)]
Fixes for md-vv and rerun
Implements several fixes for md-vv and mdrun -rerun.
* Dispersion is correctly added.
* COM motion is removed only on the second half of the timestep.
* Now can do md-vv rerun with multiple threads.
* Now gives exact kinetic energy reruns for everything except MTTK, where the iterative algorithm
makes exact kinetic energy impossible when nstpcouple == 1.
* Eliminated an extranaous variable in anderdsen temperature control since I had to move that code anyway.
Change-Id: I1c2a5a9c3da549baa0ef25601bc623a3e39bff84
Berk Hess [Fri, 11 Jan 2013 16:55:23 +0000 (17:55 +0100)]
fixed resetting states with parallel Verlet scheme
The simulation state might need to be reset with e.g. REMD
or energy minimization. With the Verlet scheme in parallel
the contents of one outdated array was used, leading to gmx_fatal.
Fixes #1024
Change-Id: I24d07ea7dfd41e9689dd083cafbf778a7c8033fd
Christoph Junghans [Sun, 13 Jan 2013 21:52:27 +0000 (22:52 +0100)]
Merge "Remove unused bfunc.h." into release-4-6
Mark Abraham [Sun, 13 Jan 2013 21:23:37 +0000 (22:23 +0100)]
Noting that and why gmxdump -s -sys is broken
Not worth fixing. You could pass a boolean from gmxdump
into the set_posres_params to avoid executing the
problematic line, but that would hit a lot of
other code paths that also call gmx_mtop_to_t_topology.
Refs #635
Change-Id: I308e59287dc578b95ea67c313867df3e75047fa4
Christoph Junghans [Sun, 13 Jan 2013 18:37:12 +0000 (19:37 +0100)]
Merge "Clarified some comments & warnings about thread pinning" into release-4-6
Christoph Junghans [Sun, 13 Jan 2013 18:33:30 +0000 (19:33 +0100)]
Merge "Manage BlueGene/Q configuration" into release-4-6
Christoph Junghans [Sun, 13 Jan 2013 18:32:33 +0000 (19:32 +0100)]
Merge "Re-organize BlueGene toolchain files" into release-4-6
Christoph Junghans [Sun, 13 Jan 2013 18:32:24 +0000 (19:32 +0100)]
Merge "Changed defaults for building shared libraries" into release-4-6
Mark Abraham [Fri, 11 Jan 2013 18:13:44 +0000 (19:13 +0100)]
Clarified some comments & warnings about thread pinning
Change-Id: I0c0382e2d6a93b5ea5531d07e9002e20ed16ef5d
Roland Schulz [Sun, 13 Jan 2013 16:48:27 +0000 (17:48 +0100)]
Merge "prepared the nbnxn code for non-x86 SIMD" into release-4-6
Mark Abraham [Tue, 18 Dec 2012 23:37:16 +0000 (00:37 +0100)]
Manage BlueGene/Q configuration
* add toolchain
* set up to use IBM QPX accelerated kernels
* check the compiler will compile the kernels
Refs #1064
Change-Id: I97ad3c3c96c4c3b0c59318c181f66972ebd9a903
Mark Abraham [Tue, 18 Dec 2012 23:19:38 +0000 (00:19 +0100)]
Re-organize BlueGene toolchain files
Rename /L and /P toolchain files. Add /Q files from
http://www.cmake.org/Bug/view.php?id=13512
Refs #1064
Change-Id: I7492737be936e59dce6217c41986316b88ec1e06
Mark Abraham [Wed, 9 Jan 2013 15:29:50 +0000 (16:29 +0100)]
Changed defaults for building shared libraries
Some platforms have reasons for preferring shared or static
libraries and we should nudge the user in the right direction
if we can.
Also, the logic for detecting external shared vs static libraries
was conflated with the settings for building shared libraries. This
needed to be separated so there was a place where specific
toolchains could manage options settings correctly for their
contexts.
Change-Id: I76ed873f2ff5d8aba11c454dea497e5f329111af
Mark Abraham [Sun, 13 Jan 2013 15:06:11 +0000 (16:06 +0100)]
Merge "Added basic CPU topology information to cpuid code" into release-4-6
Teemu Murtola [Sun, 13 Jan 2013 11:55:01 +0000 (13:55 +0200)]
Remove unused bfunc.h.
In addition to being unused, it also contains a non-terminated comment.
Related to #845 (uncrustify doesn't like the comment).
Change-Id: I662d2ecde5e58b6babc211010d4364b27e58c564