Roland Schulz [Wed, 25 Jul 2012 23:27:56 +0000 (01:27 +0200)]
Merge "cmake: allow switch between single and double" into release-4-6
Roland Schulz [Wed, 25 Jul 2012 23:24:54 +0000 (01:24 +0200)]
Merge "fix a segfault in sse_mask_init" into release-4-6
Roland Schulz [Tue, 24 Jul 2012 11:44:07 +0000 (07:44 -0400)]
Fix installation rules for man pages: don't install gromacs.7.cmakein
8c87e60 added gromacs.7.cmakein and didn't add an exclusion rule.
Change to CPackInit.cmake: Removing wrong (incorrect path) and unnessary file in message.
Change-Id: I8fe7436b8164d80ad6db64eb54dc81424cd44e4a
Roland Schulz [Tue, 24 Jul 2012 11:26:07 +0000 (07:26 -0400)]
Add default root folder to cpack archives
Fixes that source archives had no root folder. If non-default
root folder for binary archives is wanted, this still can be
achived by:
cmake -DGMX_INSTALL_PREFIX={path}/ -DCPACK_INCLUDE_TOPLEVEL_DIRECTORY=0
Fixes #977
Change-Id: Iaf42afd3617873e5c1e5e7cb7c327986efa20fcd
Mark Abraham [Tue, 24 Jul 2012 00:16:27 +0000 (10:16 +1000)]
Clean up of environment variables
In particular, reduce ambiguous usage of "force".
Refs #974
Change-Id: Ia6178ce3392f66451341dd7a4af98312f9e72c0f
Christoph Junghans [Thu, 19 Jul 2012 22:34:54 +0000 (16:34 -0600)]
cmake: allow switch between single and double
* only use FFTW_INCLUDE_DIR and FFTW_LIBRARY if user set them
* otherwise do not initialize them
* description will still show up in ccmake as advanced
* fixes #971 (linking error when switching without "make rebuild_cache")
Change-Id: Idfce7d912c3d432f48fd3a7021c8c04d6311569b
Berk Hess [Tue, 17 Jul 2012 16:50:24 +0000 (10:50 -0600)]
fix a segfault in sse_mask_init
* work array was unaligned in some cases
* fixes #970
Change-Id: I1b474019bf93e6ef6f7cc935aa3f73f2597a91a8
Christoph Junghans [Mon, 16 Jul 2012 15:26:35 +0000 (17:26 +0200)]
Merge "Removed commas from gmx_hbond OpenMP constructs." into release-4-6
Christoph Junghans [Mon, 16 Jul 2012 15:25:35 +0000 (17:25 +0200)]
Merge "Enforced rotation: PBC/restart fix" into release-4-6
Roland Schulz [Wed, 11 Jul 2012 19:31:33 +0000 (15:31 -0400)]
Take first description if programs.txt has more than one entry
26bd5f7ac took the last description of programs.txt. I wasn't
aware at the time that programs.txt can have more than one
description for one program. I think this is not a particularly
good to allow more than one description, and then somewhat
arbitrary take the first one. But this is how mknroff.pl behaved
and I don't want to change more then needed at this point.
Change-Id: Ia4fba1b1a66baab8b409fbb3932ee099cec80298
David van der Spoel [Sun, 15 Jul 2012 12:44:04 +0000 (14:44 +0200)]
Merge "Autogenerate gromacs.7 from programs.txt" into release-4-6
Roland Schulz [Tue, 10 Jul 2012 16:49:32 +0000 (12:49 -0400)]
Adding missing entries in programs.txt
Change-Id: I323524d32f07409c02de6066a24e73fb8a966481
Teemu Murtola [Sun, 15 Jul 2012 09:44:39 +0000 (12:44 +0300)]
Removed commas from gmx_hbond OpenMP constructs.
Commas between clauses within #pragma omp caused compilation to fail
with some compilers (e.g., gcc 4.2 on OS X 10.5), even with OpenMP
disabled.
Change-Id: I089d67a6442a745faa3bf5e3be1c779855725a67
Roland Schulz [Fri, 13 Jul 2012 13:04:58 +0000 (09:04 -0400)]
Merge release-4.5-patches into HEAD
Conflicts:
src/mdlib/mdebin.c
src/mdlib/minimize.c
src/tools/gmx_hbond.c
src/tools/gmx_tune_pme.c
Change-Id: I114f1ab4d58c9ccca0261e8588b61c39feaae874
Roland Schulz [Tue, 10 Jul 2012 16:32:05 +0000 (12:32 -0400)]
Adding missing entries in programs.txt
Change-Id: I3b7879fc93d9b3a7c5eed5f14825331a12589b25
Roland Schulz [Tue, 10 Jul 2012 07:28:24 +0000 (03:28 -0400)]
Use relative rpath to support relocatable binary packages
Change-Id: I7ec8707acf021b0f168691014fb0ba2f68ae29a6
Roland Schulz [Sun, 8 Jul 2012 16:56:05 +0000 (12:56 -0400)]
Allow usage of relative install paths
Relative install paths is recommended(*) and required by some
cpack generators (e.g. NSIS). Using relative install paths should
always work, but to take no risks the absolute install paths are
still the default.
*) http://www.cmake.org/pipermail/cmake/2008-May/021663.html
Change-Id: Ie656d5fcfa62f9c7e0fee605c90251084a421a72
Christoph Junghans [Mon, 9 Jul 2012 23:44:01 +0000 (01:44 +0200)]
Merge "Fixed bug in sfactor.c that makes g_rdf -sq give wrong results." into release-4-5-patches
Jochen Hub [Mon, 9 Jul 2012 19:46:02 +0000 (21:46 +0200)]
Fixed bug in sfactor.c that makes g_rdf -sq give wrong results.
The number of neutrons is not any more in sfactor.dat, but the
respective sscanf line in sfactor.c has still a placeholder for it.
Consequently, the Cromer-Mann parameter were read incorrectly.
I left the element n (for number of neurons) in gmx_structurefactors_t
for now, but the variable is at present not used.
Fixes Bug #919
Change-Id: I20a78b0b1cf4bf2271ba0ce8c785d900502d7656
Teemu Murtola [Fri, 22 Jun 2012 06:25:59 +0000 (09:25 +0300)]
Fix memory error with complex boolean selections.
Backported from
dd3a102.
Conflicts:
src/gmxlib/selection/compiler.c
Fixes #968.
Change-Id: If92b5b1eb8cf6b3acb510ba43f64fc82b63ab82a
Roland Schulz [Sat, 7 Jul 2012 03:25:08 +0000 (23:25 -0400)]
Autogenerate gromacs.7 from programs.txt
Change-Id: I958906dc9967155bccd3f43e5a6882632a829951
Carsten Kutzner [Fri, 15 Jun 2012 12:43:35 +0000 (14:43 +0200)]
Enforced rotation: PBC/restart fix
... for rot groups consisting of >1 molecule. This commit fixes a problem with checkpoint-restarts
when using a rotation group consisting of more than a single molecule.
Change-Id: I7378047b5cd0909b864a62200ded747682f627a1
Erik Marklund [Fri, 6 Jul 2012 07:32:32 +0000 (09:32 +0200)]
Bugfix for the segfault that occurs with g_hbond -hbm -contact.
Fixes #967
Change-Id: I23968ca45683b5867f919bf32e588058bd391c67
Roland Schulz [Thu, 5 Jul 2012 23:08:41 +0000 (19:08 -0400)]
Don't prevent GMX_PREFER_STATIC_LIBS with BUILD_SHARED_LIBS
In general it seems better to not overwrite the user requested
settings unless the settings are not possible.
In this case the combination makes sense for binary packages.
Static external libraries make them easier to distribute and
shared gromacs libraries make them much smaller.
Change-Id: Icb9c4dfa2e7d211ab6bd2efcb2f2437504a87cfe
Roland Schulz [Wed, 4 Jul 2012 01:55:29 +0000 (21:55 -0400)]
Build man-pages instead of distributing them in the source
One less thing to do manual for releasing the code. And thus
avoiding to accidental releasing which old version of man-pages.
Writing copyright notice to stderr for all programs (was inconsistent)
and caused copyright notice to be displayed during build.
The CPack source package continues to contain the man pages pre-build.
CPack verifies that they are genenerated before building the source
package.
Added .isreposource to distinquish code obtained from git from code
downloaded as CPack source package.
Related to #645, #854, #735
Fixes #878
Change-Id: I7d7145fb99d3f1991d0f3992ca4f3ea20668dd9a
Christoph Junghans [Thu, 5 Jul 2012 19:45:36 +0000 (21:45 +0200)]
Merge "Don't rerun checks and be quiet 2nd time cmake is run" into release-4-6
Christoph Junghans [Thu, 5 Jul 2012 19:42:15 +0000 (21:42 +0200)]
Merge "Allow also FindMPI for cmake<2.8.5" into release-4-6
Christoph Junghans [Thu, 5 Jul 2012 19:26:41 +0000 (21:26 +0200)]
Merge "Finalized and extended Szilard's openMP cleanup of gmx_hbond.c:" into release-4-6
Roland Schulz [Tue, 26 Jun 2012 19:23:38 +0000 (15:23 -0400)]
Don't rerun checks and be quiet 2nd time cmake is run
Change-Id: I86f8cb4dfb73898e74d320ae8ef3676e62ebde51
Erik Marklund [Thu, 28 Jun 2012 19:02:00 +0000 (21:02 +0200)]
Finalized and extended Szilard's openMP cleanup of gmx_hbond.c:
* Changed HAVE_OPENMP into GMX_OPENMP
* Fixed incorrect use of OpenMP API functions
* Made variables shared by default in parallel sections
This also avoids problems with stderr being a macro in certain
implementations, which caused compilation errors on some systems
when stderr occurs explicitly in pragmas.
* Protected a block where reallocation of hbdata occurs with a critical section
* Cleaned out some output that was commented out anyway.
* Removed redundant preprocessor directives
Change-Id: I452ab2e873434086e6bc616d9d24a8d890147220
Roland Schulz [Wed, 4 Jul 2012 05:18:46 +0000 (07:18 +0200)]
Merge "Add FindGROMACS.cmake to template's CMakeLists.txt" into release-4-6
Roland Schulz [Wed, 4 Jul 2012 05:16:56 +0000 (07:16 +0200)]
Merge "Fixed bug in free energy calculation for Morse potentials" into release-4-6
Berk Hess [Mon, 2 Jul 2012 17:08:41 +0000 (19:08 +0200)]
set default for rcoulomb, rvdw and rlist to -1
To avoid users using the default values and to force them to think
about the cut-offs, all default values are now -1.
This also avoids grompp notes with the new Verlet scheme,
where the rlist value can be generated automatically.
Change-Id: I99bc7eee76953d06767f9c9916d1c9289badf74f
Elton Carvalho [Thu, 28 Jun 2012 15:13:03 +0000 (17:13 +0200)]
Fixed L-BFGS trajectory output.
This bug made mdrun ignore nstxout and nstfout when running l_bfgs.
When calling write_traj, MDOF_X|MDOF_F was given as mdof_flags to write
the trajetory, thus ignoring do_x and do_f evaluated on the previous
lines.
Fixes #905.
Change-Id: Id3ff7b090efd23fd28d8c27ea99992d1647f1ed6
Szilárd Páll [Tue, 3 Jul 2012 09:35:35 +0000 (11:35 +0200)]
Merge "Minor formatting and consistency changes to txtdump.c" into release-4-6
Christoph Junghans [Mon, 2 Jul 2012 20:20:10 +0000 (14:20 -0600)]
Do not print disabled pressures and virials
* For some methods pressure and virial calculation is disabled
* md.bVir and md.bPress was added in
*
d870cd31bee97e277f48ba982da85303bce98611
* At this point only AdResS has md.bVir=md.bPress=FALSE
Change-Id: I6abe24a5c286d20dcf554831ade9540674df9d77
David van der Spoel [Sat, 30 Jun 2012 13:18:31 +0000 (15:18 +0200)]
Fixed bug in free energy calculation for Morse potentials
Introduced recently when FEP was added to the Morse potential.
Change-Id: I90edfd13835637c872af31f2c7abf900ce8a8e5f
Christoph Junghans [Fri, 29 Jun 2012 20:18:17 +0000 (14:18 -0600)]
Add FindGROMACS.cmake to template's CMakeLists.txt
Change-Id: Id5adec8aa057f1d56021b06aaedd35dab108ead7
Michael Shirts [Fri, 29 Jun 2012 17:35:59 +0000 (11:35 -0600)]
Minor formatting and consistency changes to txtdump.c
Change-Id: I2992a927ccf49b407fa985eb2283c37818bbd2a5
Michael Shirts [Fri, 29 Jun 2012 17:28:37 +0000 (11:28 -0600)]
Corrected checkpoint version issues with free energy changes.
Change-Id: If9494aa0bdbd6f83cc2a8a57a5c7e399aaa787f4
Sebastian Fritsch [Fri, 29 Jun 2012 10:05:18 +0000 (12:05 +0200)]
Merge "Fixed adress kernel for double precision" into release-4-6
Christoph Junghans [Thu, 28 Jun 2012 17:27:58 +0000 (11:27 -0600)]
Fixed adress kernel for double precision
Change-Id: I5145ced14d59f7186dd8ef47fe6877fe00cbd94b
Roland Schulz [Thu, 28 Jun 2012 16:29:02 +0000 (12:29 -0400)]
Allow also FindMPI for cmake<2.8.5
Using FindMPI instead of mpi-wrapper makes it easier to compile
with CUDA. While FindMPI of cmake<2.8.5 is unreliable it depends
on the OS whether it works. With this change FindMPI is attemted
if no mpi wrapper is used and if it fails, mpi-wrapper or cmake
upgrade is recommended.
Change-Id: I20c0ac3958724feecaaef5c20279d340ecca4b1a
Christoph Junghans [Thu, 28 Jun 2012 16:22:44 +0000 (18:22 +0200)]
Merge "Fix MPI build for MPI library without mpi wrapper" into release-4-6
Roland Schulz [Wed, 27 Jun 2012 07:31:12 +0000 (03:31 -0400)]
Fix MPI build for MPI library without mpi wrapper
Some MPI library (e.g. MPICH and OpenMPI on Windows) don't
contain any MPI wrappers and thus
417d0afff broke the support for
those MPI libraries.
This change uses the FindMPI module if the compiler is not a
mpi wrapper and cmake >= 2.8.5. Requiring mpi wrappers for
cmake < 2.8.5 avoids reintroducing the problems of #851.
To avoid any confusion of different behavior with older and newer
versions of cmake, all documentation should recommend the mpi wrapper
approach, which works for all versions. The FindMPI approach should
only be discussed for advanced users (to support e.g. Windows).
As a side effect this change makes it more convinient to use with
cmake>=2.8.5. No need to speciy mpi wrapper and less problems with
nvcc.
Fixes #958
Change-Id: Ic53d8125c5a58edc6789fe16f2b710e7e2568d4f
Szilard Pall [Tue, 26 Jun 2012 11:30:59 +0000 (13:30 +0200)]
fixes typo gmx_omp introduced by
697bcdc
Also removes an unnecessary include and replaces a few remaining
HAVE_OPENMP-s with GMX_OPENMP.
Change-Id: I8a92a5f1849d170951719b29b17e0ec6134ee556
Roland Schulz [Tue, 26 Jun 2012 18:50:55 +0000 (14:50 -0400)]
Fix that rerunning cmake gives the same result as 1st run
- SetBuildInformation: strip was missing for 3 of 6 CPU_* variables
Not sure why this caused only for the first run an extra newline.
Extra newline doesn't change the build but causes unnessray
complete rebuild.
- IsFinite: The cached value of whether one of the 3 isfinite
function was found wasn't set the 2nd time. Thus after reruninng
cmake the isfinite function wasn't used anymore.
Change-Id: I988763e6b26cc5bae62c4da66cc7b30f2f93c128
Roland Schulz [Tue, 26 Jun 2012 01:32:58 +0000 (03:32 +0200)]
Merge "Fix gmx_fatal for serial compilation" into release-4-6
Szilard Pall [Fri, 15 Jun 2012 15:03:41 +0000 (17:03 +0200)]
introduce gmx_omp wrapper for the OpenMP API
The gmx_omp_* OpenMP API wrappers should be used instead of directly
calling OpenMP functions. Therefore, gmx_omp.h should be included
instead of omp.h so OpenMP API functions don't need #ifdef-ing.
Additionally, moved GMX_OPENMP from command-line define to config.h.
Change-Id: If30f433946fef908c26a29f1bff3671580e90629
Berk Hess [Mon, 25 Jun 2012 09:39:03 +0000 (11:39 +0200)]
fixed segv/hang with EM and foreign lambda values
Energy minimization with nstcalcenergy=-1, foreign lambda values
and no separate dhdl.xvg output file called malloc with negative count.
Fixes #962
Change-Id: I3d6b636ddba80fc2ae400590c48642c217325293
Berk Hess [Mon, 25 Jun 2012 08:03:11 +0000 (10:03 +0200)]
added check for log fp!=NULL when disabling acceleration
Change-Id: I79d16574b6c4cb039afa01240e7d3aa816b3f337
Christoph Junghans [Sun, 24 Jun 2012 20:26:37 +0000 (22:26 +0200)]
Merge "Remove MPI define for FAH" into release-4-6
Michael Shirts [Sun, 24 Jun 2012 17:27:15 +0000 (19:27 +0200)]
Merge "Fix mdp_opt formatting of expanded ensemble" into release-4-6
Roland Schulz [Sun, 24 Jun 2012 15:07:04 +0000 (11:07 -0400)]
Fix mdp_opt formatting of expanded ensemble
Was introduced with
c7a82654f2e. Broke the build of the manual
because dl tag wasn't closed.
Change-Id: I86afd4a2bdc638fb910cb0afa827b3f56447bb36
Roland Schulz [Sun, 24 Jun 2012 05:11:58 +0000 (01:11 -0400)]
Remove MPI define for FAH
FAH will use with 4.6 the standard GMX_MPI define instead of MPI.
This removes problems with C++ compile.
This fixes #849 and is related to #853.
Change-Id: I63bfc14400cda096350aba9a94a676e9c0952d56
Roland Schulz [Thu, 21 Jun 2012 16:28:36 +0000 (12:28 -0400)]
Fix illegal usage of MPI_Comm_create
Bug was introduced by
8cd25f0d45567
Illegal to call MPI_Comm_create with different group arguments
Change-Id: Ia70f81862fa50b03ab127e8796226369f6732942
Christoph Junghans [Fri, 22 Jun 2012 21:04:20 +0000 (23:04 +0200)]
Merge "Simple patch for openmm_wrapper.cpp" into release-4-6
Erik Lindahl [Thu, 21 Jun 2012 09:38:12 +0000 (11:38 +0200)]
Fixed gcc inline assembly issue with PIC and older gcc compilers
Some gcc versions had problems with the recently introduced inline
assembly for cpuid (clobbering of ebx register), and since we used
a slightly different inline assembly instruction test in cmake we
did not detect it properly. This patch both makes the inline asm
itself much more portable, and we also test with exactly the same
instruction in cmake so we don't set the flag for supporting inline
asm unless we know this instruction works.
Change-Id: Ib479e2706024abb5e3f66d0249291ce55f1257b1
David van der Spoel [Thu, 21 Jun 2012 16:14:33 +0000 (18:14 +0200)]
Fixes #961 - Shake reports wrong error
The constraint index reported by shake was off by 1.
Change-Id: I6f4d0c013b30f5963fb312b41fb87e90e6314619
Roland Schulz [Thu, 14 Jun 2012 23:16:06 +0000 (19:16 -0400)]
Fix gmx_fatal for serial compilation
With neither GMX_MPI nor GMX_THREAD_MPI gmx_fatal
called gmx_abort which called gmx_fatal.
Change-Id: Id18c3bc94f19a8008fa2aaa8335c221f115fcd8b
Erik Marklund [Wed, 20 Jun 2012 11:23:12 +0000 (13:23 +0200)]
Correct normalization for HB-contact c-correlation.
Fixes #960
Change-Id: I391dd84fd38e784ac6c311dd913284de47d6a93d
Mark Abraham [Tue, 19 Jun 2012 23:12:18 +0000 (01:12 +0200)]
Merge "Fixes #882 - looping bug in trxio.c" into release-4-5-patches
Christoph Junghans [Tue, 19 Jun 2012 22:46:12 +0000 (00:46 +0200)]
Merge "Quiet linker on BlueGene" into release-4-5-patches
Christoph Junghans [Mon, 18 Jun 2012 21:32:22 +0000 (23:32 +0200)]
Merge "Fix g_lie counting last frame twice" into release-4-5-patches
Martin Hoefling [Wed, 13 Jun 2012 12:29:24 +0000 (14:29 +0200)]
gmx_dyecoupl: check selected groups from user
check if the user accidentally selected the same group twice. Abort
with error, since this will not produce any meaningful results.
Change-Id: Iace69c473e5f1b815e35d20a39845533297ad208
Erik Lindahl [Mon, 28 May 2012 18:54:17 +0000 (20:54 +0200)]
New CPU detection & AVX/SSE code, removed raw assembly files.
Removed all raw assembly files and deprecated altivec support.
Removed support for NASM and other assemblers, and replaced
previous SSE detection code with a new module using CPUID instead.
Added detection for SSE2, SSE4.1, AVX 128-bit with FMA, and AVX 256-bit.
Added Cmake detection of build platform based on CPUID, and output this
to the log file. The executables now compare the compile-time platform
and selected acceleration with the run-time platform and most suitable
acceleration and warns the user if they do not match. The compiler
detection code has also been reordered slightly to produce more readable
warnings when OpenMP is not available, and correctly disable pragma
warnings.
Added intrinsics code and math functions for SSE2, SSE4.1, AVX128/256
both in single and double precision. All math functions and permutation
code have been tested & verified. Single precision math functions are
correct apart from the least significant bit, and double precision has
roughly twice the accuracy.
This has forced me to temporarily disable the SSE & Fortran acceleration.
SSE will be added back soon based on new intrinsics-only kernels currently
in testing, and we will test if Fortran still makes sense then.
Finally, the patch includes a modification to gmx_rmsdist where
a regression issue was introduced recently by using sqrtf() for
the norm function. This caused the intel compiler to produce slightly
different results at high optimization leves, which got evident here.
Closes #926 - Raw assembly code has been removed.
Refs #923 - Old kernels removed, new will be added shortly.
Fixes #914 - Cmake now does architecture-speficic optimization.
Fixes #912, #913
Fixes #857 - We detect rdtscp support with CPUID and use it if possible.
Fixes #750
Closes #537, #574 - Altivec is now deprecated.
Change-Id: Icfca5a940762f8d82ae67b59c65b2d2ac683256d
David van der Spoel [Fri, 15 Jun 2012 11:47:07 +0000 (13:47 +0200)]
Fixes #882 - looping bug in trxio.c
This led to infinite output files in the case of a corrupt
input file.
Change-Id: I25d61752d901012e9ce5e6adae1679c2ef99467a
Justin Lemkul [Thu, 7 Jun 2012 00:11:26 +0000 (20:11 -0400)]
Simple patch for openmm_wrapper.cpp
The naming of several variables is changed to be consistent with the
latest free energy changes. Allows mdrun-gpu to be compiled, which
otherwise fails (as reported on gmx-developers).
Change-Id: I497ba07ee6883ef78d23022450f6c3d971b2127e
Mark Abraham [Tue, 5 Jun 2012 04:08:29 +0000 (14:08 +1000)]
Quiet linker on BlueGene
Change-Id: Ib105a93ca233c763d3b6caf3c3c636a673078986
Erik Marklund [Fri, 8 Jun 2012 23:36:53 +0000 (01:36 +0200)]
Makes g_hbond -contact work
Fixes #955
Change-Id: I5d421d5f2e25d3801497efccb291425f90480a8c
Mark Abraham [Fri, 15 Jun 2012 07:46:26 +0000 (17:46 +1000)]
Fix g_lie counting last frame twice
Change-Id: Ia1c37e79843cd0e10d5e8444d004c7aca9cce87a
Christoph Junghans [Fri, 15 Jun 2012 00:16:37 +0000 (02:16 +0200)]
Merge "Work around failure of endianness testing on BlueGene" into release-4-5-patches
Roland Schulz [Thu, 14 Jun 2012 14:14:49 +0000 (16:14 +0200)]
Merge "Made mdrun more verbose about PME split" into release-4-5-patches
Carsten Kutzner [Thu, 24 May 2012 13:18:11 +0000 (15:18 +0200)]
Small fix for g_tune_pme
Change-Id: I12fd2e48dc409f87b270f1ddaaaf2d1a83683fd1
Christoph Junghans [Fri, 8 Jun 2012 15:45:24 +0000 (17:45 +0200)]
Merge "Added more suggested strategies to error message" into release-4-5-patches
Mark Abraham [Wed, 6 Jun 2012 11:52:41 +0000 (21:52 +1000)]
Work around failure of endianness testing on BlueGene
Refs #944
Change-Id: I4bbfe9865800bbe4e407a88cdecec6678d56f3b4
Mark Abraham [Wed, 6 Jun 2012 10:15:58 +0000 (20:15 +1000)]
Fix endian test functionality
Code for big-endian systems was silently failing with CMake. This
patch brings CMake and autotools into agreement.
Partial fix of #944
Change-Id: I1f14938fd23e926e05397977963fbf968f0406e0
Michael Shirts [Tue, 17 Jan 2012 14:51:13 +0000 (09:51 -0500)]
Merging in free energy, exp. ensemble, & andersen t-control to 4.6
Conflicts:
src/gmxlib/mvdata.c
src/gmxlib/txtdump.c
src/kernel/readir.c
src/mdlib/sim_util.c
src/tools/gmx_membed.c
include/mdrun.h
src/kernel/md.c
src/kernel/md_openmm.c
src/kernel/md_openmm.h
src/kernel/runner.c
src/mdlib/minimize.c
src/mdlib/tpi.c
src/tools/gmx_membed.c
src/kernel/md.c
Change-Id: Ide69a8dbfb96072d5c55d0a051dc9db788cbe144
Mark Abraham [Mon, 4 Jun 2012 07:34:49 +0000 (17:34 +1000)]
Added more suggested strategies to error message
Change-Id: I4a68ea06697890175bb03e900664dd9bb886305c
Roland Schulz [Fri, 1 Jun 2012 06:24:10 +0000 (02:24 -0400)]
Merge release-4-5-patches into release-4-6
Changes in 4.5 for removed lines/files in 4.6:
Makefile.am
include/domdec.h
include/domdec_network.h
Trivial conflict:
include/types/commrec.h
Fixed GMX_THREADS into GMX_THREAD_MPI for those added in 4.5 in:
include/mdrun.h
src/gmxlib/shift_util.c
src/mdlib/gmx_fft_fftw3.c
Change-Id: Id37bfbbacc945a7cf184fa21313c05e2680e1fba
Christoph Junghans [Fri, 1 Jun 2012 06:04:28 +0000 (08:04 +0200)]
Merge "Use External BLAS/LAPACK by default" into release-4-6
Christoph Junghans [Fri, 1 Jun 2012 05:35:50 +0000 (07:35 +0200)]
Merge "Replace our fftpack version with Numpy's version" into release-4-5-patches
Roland Schulz [Sun, 27 May 2012 18:07:30 +0000 (14:07 -0400)]
Replace our fftpack version with Numpy's version
Fixes incorrect results for vectors with length of multiples of 12
Fixes #946
Change-Id: I9a110de7334cbb96a72d0ced73ade4d55f665fee
Mark Abraham [Thu, 31 May 2012 11:26:20 +0000 (21:26 +1000)]
Made mdrun more verbose about PME split
Change-Id: Ieda0ba5dcf08260cf94ad9aefd8937e067f2c6e2
Teemu Murtola [Wed, 30 May 2012 04:18:10 +0000 (07:18 +0300)]
Fix use after free in g_anaeig projection code.
PBC removal structure was deleted immediately after it was initialized,
and used afterwards.
Change-Id: I6126967b34e8de289370dede79cc50a9924ac34d
Sander Pronk [Tue, 22 May 2012 15:46:37 +0000 (17:46 +0200)]
Removed dependency on windows.h through commrec.h, domdec.h.
Change-Id: If40506b521a4b4690506465a3f421dab93bc9ce6
Christoph Junghans [Tue, 29 May 2012 16:26:52 +0000 (18:26 +0200)]
Merge "Revised g_tune_pme" into release-4-6
Christoph Junghans [Mon, 28 May 2012 23:25:59 +0000 (01:25 +0200)]
Merge "Continuing to fix threading on Cygwin" into release-4-5-patches
Roland Schulz [Sun, 27 May 2012 19:26:24 +0000 (15:26 -0400)]
Fix editconf real-bool misusage
Bool variable was declared as real. Caused invalid stack read
in double precision. Could have caused wrong value to be printed
for argument display but couldn't have caused wrong behavior.
Found with AddressSanitizer
Change-Id: I32553b1a898fb3a7f072ae177518dd63fad56dde
David van der Spoel [Sun, 27 May 2012 08:49:56 +0000 (10:49 +0200)]
Merge "added explicit sqrtf to the float version of norm" into release-4-6
Roland Schulz [Sun, 27 May 2012 02:51:05 +0000 (22:51 -0400)]
Fix Clang 3.1 warning
grid_spacing is an integer and thus it was always set to 0
Change-Id: Id10bccdadef8f2630631d638e94bd27d78774536
Mark Abraham [Fri, 25 May 2012 09:45:09 +0000 (19:45 +1000)]
Continuing to fix threading on Cygwin
Fixes #833
Change-Id: I5d577a149ad18b295559f6d87c24dc42bffd281e
Roland Schulz [Mon, 21 May 2012 18:21:23 +0000 (14:21 -0400)]
Make load_vmd_library static
Was already used only within the same file
Change-Id: I43276424d51021bc8247c04a3c3647f7fc1565f7
Roland Schulz [Thu, 17 May 2012 22:23:25 +0000 (18:23 -0400)]
Made all vmdio headers private
- Made vmdio struct in trx a pointer
- No need for vmdio to be in the public API
Change-Id: Ic142a6900d0cbc803e8c24139efbfbc072b46c22
Roland Schulz [Fri, 25 May 2012 14:47:21 +0000 (16:47 +0200)]
Merge "fixed [dd] and [TT] typos in documentation of mdrun and gmx_sans" into release-4-6
David van der Spoel [Fri, 25 May 2012 14:26:50 +0000 (16:26 +0200)]
Merge "grompp now retains the order of bonds converted to constraints" into release-4-6
Martin Hoefling [Fri, 25 May 2012 10:09:07 +0000 (12:09 +0200)]
fixed [dd] and [TT] typos in documentation of mdrun and gmx_sans
Change-Id: Ia51f67b2b056f66072875d2c7a366ae4685bf9d4
Christoph Junghans [Fri, 25 May 2012 07:17:48 +0000 (09:17 +0200)]
Merge "Fix that sigaction mask wasn't zeroed" into release-4-6
Berk Hess [Wed, 23 May 2012 16:23:12 +0000 (18:23 +0200)]
now mdrun always initializes MPI
MPI was only initialized with more than one process. This required
checks everywhere. Now MPI is also initialized with one process.
Change-Id: I4d0f543d5c1ae5a6136a0ba34f0f83ac27604b14
Teemu Murtola [Thu, 24 May 2012 17:02:36 +0000 (19:02 +0200)]
Merge "Code cleanup to avoid name collisions" into release-4-6