Mark Abraham [Tue, 23 Jul 2019 19:46:51 +0000 (21:46 +0200)]
Fix for MSVC+CUDA
MSVC finds it hard to deal with template parameter packs in a few
situations. We don't test with MSVC+CUDA, but a user reports this works in that case.
Change-Id: Id576482facaaf40972ba4fd55b2afcba3113d0e8
Berk Hess [Tue, 14 May 2019 14:17:21 +0000 (16:17 +0200)]
Made gmx disre work with non-consecutively labeled restraints
gmx disre assumed restraint were consecutively labeled starting at 0.
Refs #2953
Change-Id: I7d9c14d43854c88cb1cdec89fc297c64cbea8783
yongwangCPH [Tue, 9 Jul 2019 13:57:59 +0000 (15:57 +0200)]
Solve issue with demux.pl
Changes printout format to resolve discontinuous trajectories
after 100ns simulation length when exchange stride is not a multiple
of 1 ps.
Change-Id: If6bd4d578ba08f9d4fd814b80e69896caf9079eb
Berk Hess [Mon, 29 Jul 2019 11:45:34 +0000 (13:45 +0200)]
Fix segmentation fault with cosine pulling
Both grompp and mdrun would fail with a segmentation fault when
using cosine-weighted COM pulling.
Fixes #3023
Change-Id: I6342a579251d21ba07a42d23ce578ae1e20c3286
David van der Spoel [Mon, 8 Jul 2019 08:24:29 +0000 (09:24 +0100)]
Fixed small bug in gmx anaeig
Poor use of variable names led to a small bug.
Fixes #2972
Change-Id: I244eac13dbaeeb0eac2be6531e579a125f4a66d3
Paul Bauer [Tue, 9 Jul 2019 08:31:45 +0000 (10:31 +0200)]
Fix link to acpype repository
Fix as reported on the user mailing list.
Change-Id: Ifdba6a60857360346653d3c9caaa929094bebae5
Paul Bauer [Mon, 8 Jul 2019 08:57:39 +0000 (10:57 +0200)]
Fix issues found by clang-tidy 7
Same issues as found for the master branch after switching the build
to run on a different machine.
Change-Id: Icf7589eae5ebc77d7974181e4faeea9e9fe8b9d7
Mark Abraham [Tue, 2 Jul 2019 13:19:54 +0000 (15:19 +0200)]
Clarify wording of release notes
A query on gmx-users indicated that the previous wording was confusing
- someone thought it might have meant normal nonbonded interactions
didn't work.
Change-Id: I0481c42ae1667bb5841e9541551dd98f5650c3ae
Paul Bauer [Mon, 1 Jul 2019 09:17:04 +0000 (11:17 +0200)]
Fix bug in gmx xpm2ps
When not providing the name for a library input file the program would
try to create a null string and fail with an assertion failure.
Fixes #3012
Change-Id: Ifd69af5420cdac2f624246aee09f36219b3f6aeb
Szilárd Páll [Thu, 25 Apr 2019 09:16:29 +0000 (11:16 +0200)]
Disable PME GPU on Apple OpenCL
Apple's OpenCL compiler seems to be unable to build a functional clFFT
which leads to a runtime error that aborts the runs rather than falling
back to PME-CPU. Hence this commit disabled PME-GPU on all Apple
platform builds.
Fixes #2941 #2719
Change-Id: I6afd19a56ced2e49d16ab598cd91527e6f73a1db
Paul Bauer [Wed, 12 Jun 2019 07:40:58 +0000 (09:40 +0200)]
Prepare for 2019.4
Reset DOI strings.
Change-Id: I1b5112bda4beb17e0f33276f60b8354b159858f0
Paul Bauer [Wed, 12 Jun 2019 07:36:58 +0000 (09:36 +0200)]
Version 2019.3
Added DOI strings.
Updated regressiontest hash.
Change-Id: If0a3389653dc3594a69886c8a9031af0dc9ddff2
Paul Bauer [Fri, 14 Jun 2019 04:54:44 +0000 (06:54 +0200)]
Merge branch release-2018 into release-2019
Change-Id: I50c1c93898246a8cbb9198227e1e77d483393bab
Paul Bauer [Wed, 12 Jun 2019 13:44:08 +0000 (15:44 +0200)]
Fix qsort not being defined on Apple Clang
Change-Id: Iffcf002d44ef8f6d174886afc67d6926aa8f2faf
Mark Abraham [Wed, 29 May 2019 16:11:02 +0000 (18:11 +0200)]
Initialize all of gmx_domdec_comm_t
Many fields were left uninitizalized when C++ new was used, rather
than snew. All fields are now initialized to zero, false, or nullptr,
in some cases via aggregate initializations of arrays. Moved the
field documentation to the line before the field and its initializer,
which reads better.
The initializers require another call to snew be replaced with one to
new[].
Fixes #2960
Change-Id: Ide917a47c667a8237519c2f4600bbce48c48f948
Paul Bauer [Tue, 14 May 2019 12:46:05 +0000 (14:46 +0200)]
Fix residue and molecule indexing in selections
The residue and molecule indexing did not account for the global
indices when building blocks from selections.
Also fixed a docs formatting issue noticed while working on the fix.
Fixes #2951
Change-Id: Ifa16f032822f5d96b6ff747333a7aed60b9a414d
Paul Bauer [Wed, 5 Jun 2019 14:04:17 +0000 (16:04 +0200)]
Extend information for gmxcpp syntax error.
Fixes #2911
Change-Id: I6d22c95d32993d5d640bf20031bfdc9c04c99604
Berk Hess [Mon, 13 May 2019 12:39:16 +0000 (14:39 +0200)]
Allow AWH geometry 'direction' to be periodic
When an AWH dimension with pull geometry 'direction' has an interval
length (nearly) matching the periodic unit cell dimension, it is now
made periodic.
Fixes #2946
Change-Id: I9a09b8eb7464e04bd3d72059324bceb590e531f5
Paul Bauer [Mon, 3 Jun 2019 15:30:37 +0000 (17:30 +0200)]
Add check for too many grid points in hbond
Fixes #2962
Change-Id: I61e80f8f254f1b5a0d968af087a87361fe4554ae
Berk Hess [Mon, 10 Jun 2019 09:12:28 +0000 (11:12 +0200)]
Fix gmx wham with angle geometries
Fixes #2609
Change-Id: I36156e1d8bb98499e4357eadc4ca56384da433a5
Berk Hess [Tue, 14 May 2019 09:53:24 +0000 (11:53 +0200)]
Fix reference SIMD memory alignment
Fixes #2952
Change-Id: I86b82c3259986c12c59c0b741df705b4774efe05
Berk Hess [Wed, 15 May 2019 11:43:07 +0000 (13:43 +0200)]
Fix missing intermolecular interactions with DD
When running with domain decomposition, all intermolecular interactions
(when present) were ignored.
Fixes #2953
Change-Id: I98783f4175b40fdfa6ad035323e0897e8caaee5c
Paul Bauer [Mon, 13 May 2019 08:40:23 +0000 (10:40 +0200)]
Version 2018.7
Updated regressiontest hash as usual.
Change-Id: Ibdd47ea72906e7696c67b5e2be6d327bf0d5deae
Berk Hess [Thu, 16 May 2019 07:54:02 +0000 (09:54 +0200)]
Work around gcc 7 avx512 bug
Due to an avx512 loop vectorization bug in gcc 7, many non-bonded
interactions could be ignored when running with more than 16 OpenMP
threads.
Fixes #2762
Change-Id: I3e03fde7114542bbd43069166a6c74937fc0f986
Paul Bauer [Tue, 21 May 2019 08:31:42 +0000 (10:31 +0200)]
Add more info for wrong line endings
Adds some more info for users that encounter preprocessing errors due
to wring line endings.
Change-Id: Id76404befdf598438f1b1fa5da98812cc31e3c5f
Paul Bauer [Tue, 21 May 2019 08:14:36 +0000 (10:14 +0200)]
Fix PQR formatting
Was still broken after the last fix a few months ago.
Fixes #2955
Change-Id: I55b1296918c723654db505d1797114e1358e5aeb
Paul Bauer [Thu, 9 May 2019 14:17:37 +0000 (16:17 +0200)]
Fix membrane embedding
Refactoring forgot to allocate some data, causing a segmentation fault.
More refactoring used wrong data, causing a crash further on.
Even more refactoring lead to invalid memory access.
Fixes #2947
Change-Id: I61ad3125102b50c0338e0935a75cd7b1de95bc3f
Berk Hess [Thu, 23 May 2019 08:27:03 +0000 (10:27 +0200)]
Fix SHAKE dH/dlambda contributions
The constraint contributions to dH/dlambda would be incorrect
with more than one SHAKE block.
Refs #2434 abd #2879
Change-Id: I0cb30a9f61893ce57d76bac34e7352fe307efe4e
Mark Abraham [Thu, 16 May 2019 07:17:04 +0000 (09:17 +0200)]
Revert "Fixed dvdlambda for SHAKE + FE"
This broke normal simulations with SHAKE and does not seem
to fix anything with FEP simulations either.
This reverts commit
33093601ff229ed8c8a40e73866a7ff351e8963b.
Fixes #2879
Change-Id: Ib6e9b4fe2b65811e9f64c37e842fd0ed9cdb055c
Paul Bauer [Tue, 21 May 2019 07:57:47 +0000 (09:57 +0200)]
Add check for allocating too many interactions
Also change argument to nbnxn reallocation function from int to
std::size_t to avoid signed integer overflow.
Fixes #2932
Change-Id: I97bdd825ba1e4d81b65b4e4c037f980164c571f2
Mark Abraham [Mon, 20 May 2019 21:28:33 +0000 (23:28 +0200)]
Fix equation typo
Change-Id: Ica8b72f0e423255c410aee3238aadfdc52f4d317
Berk Hess [Mon, 13 May 2019 13:56:19 +0000 (15:56 +0200)]
Correct user guide postion restraint virial
Corrected comment in the user guide note on virial and pressure
with position restraints and refcoord-scaling none or com.
Refs #2942
Change-Id: I3cdb5a01640c388f1c4222b1a43b342ac55fd882
Paul Bauer [Mon, 13 May 2019 08:30:54 +0000 (10:30 +0200)]
Prepare for 2018.7
Also add the release note update for Redmine issue 2845.
Change-Id: I63c6ef4bf4ea2d78741ab3bf77079ea257f1a205
Mark Abraham [Tue, 7 May 2019 07:09:56 +0000 (09:09 +0200)]
Add an example of using an MPI wrapper compiler
A long-time GROMACS user reported not being able to make an MPI build,
and this might help clue people in.
Change-Id: Ie3f442e126561bb5c6e1ae71fee650f2e18c21aa
Berk Hess [Fri, 3 May 2019 13:23:37 +0000 (15:23 +0200)]
Removed non-existent AWH mdp option
Removed non-existent mdp option awh1-dim1-period from user guide.
Fixes #2940
Change-Id: I96c4f1e636e0d171561dcfcf1e17e7f0ce419f8b
Paul Bauer [Thu, 25 Apr 2019 11:50:14 +0000 (13:50 +0200)]
Fix FPE in do_steep
Fixes error when running non-interacting system in steepest decent
minimization.
Fixes #2917
Change-Id: Iaff794ab6c2d41e8c4b3d89feeafae6ae2372ddf
Paul Bauer [Thu, 11 Apr 2019 08:49:50 +0000 (10:49 +0200)]
Prepare for version 2019.3
Reset DOI strings
Change-Id: Iddbafb48832b28eb862a9a7cbe632e9e7a6fdbf7
Paul Bauer [Thu, 11 Apr 2019 08:35:46 +0000 (10:35 +0200)]
Version 2019.2
Set DOI strings.
Updated regressiontest hash.
Change-Id: I87dd50fd154c4f10a04e48be0c4fbe60964395ff
Paul Bauer [Mon, 15 Apr 2019 15:51:57 +0000 (17:51 +0200)]
Fix off-by-one error in gmx cluster
The writing of indices for linking frames to clusters was of by one.
Also fixed naming to refer to indices and not indexes
Fixes #2926
Change-Id: I67d7f8cae56734e425c84460080de8896f6239cb
Berk Hess [Fri, 8 Mar 2019 12:53:04 +0000 (13:53 +0100)]
Make mdrun -nsteps work again.
The mdrun -nsteps option was only functional in some cases,
because it modified ir->nsteps after the checkpoint loading
modified it.
Note that this option is deprecated, but is should either work
or be removed.
Fixes #2881
Change-Id: Ib611b0e007171f8a351f61f3ecc9b1bda5248486
Berk Hess [Mon, 15 Apr 2019 11:31:31 +0000 (13:31 +0200)]
Update 2019 release notes for issue 2845
We now know that issue reported in 2845 is not actually related to
LJ force switching. So the "fix" in 2019.1 fixes a bug, but the
issue 2845. This is now reported in the release notes for 2019.1
and 2019.2.
Change-Id: I000c518850f970c0f9cc331df22afaa24d9a27bc
Szilárd Páll [Mon, 15 Apr 2019 09:50:35 +0000 (11:50 +0200)]
Add user guide note on AVX512 throttle in GPU runs
Refs #2793
Change-Id: I161f5b92a8a34989ecc1d49410033f9ea8f91164
Berk Hess [Sat, 13 Apr 2019 10:00:06 +0000 (12:00 +0200)]
Fix pdb-related issues
In editconf, if a PDB input was read, chain IDs are known, and should
be written if the output is also PDB. This now works again, after
being broken in commit
8dd3c9ae88004054b3.
This required adding missing tpr support to readConfAndAtoms(), which
also fixes that pdb2gmx, insert-molecules, and solvate could not read
tpr files. Those are the only tools that directly or indirectly called
readConfAndAtoms with a .tpr file.
Fixes #2900
Change-Id: I883777be945023a7e69260b22e76df54477828ee
Berk Hess [Mon, 15 Apr 2019 09:31:19 +0000 (11:31 +0200)]
Disallow pull geometry direction-periodic with AWH
Fixes #2923
Change-Id: Ic309a5598c69e82824d80270466a2de7b00e7d41
Mark Abraham [Tue, 9 Apr 2019 12:51:44 +0000 (14:51 +0200)]
Fix self-consistency tests of hwloc data structures
These relied on assumptions of regularity that have been shown to be
violated in practice. The new tests check that there is a bijective
mapping of logical processors to valid hardware thread descriptors.
Fixes #2921
Change-Id: I31e998b7a2881c05dfb5c7c8b46550489cbdefd6
Mark Abraham [Fri, 12 Apr 2019 16:27:29 +0000 (18:27 +0200)]
Improve warning messages about duplicate definitions
Because the warning is fatal, the wording with "overriding" is
misleading. An override only occurs if the warning is suppressed.
Email on gmx-users made clear that the word "overriding" is not clear
enough for all users to understand that more than one definition was
provided. They do not necessarily know that grompp has already read in
the force field definition. Typically a self-contained molecule .itp
file might override definitions found in the force-field (whether
duplicate or different). In such cases, the user needs to consider
what their intentions are and to express them clearly.
Change-Id: Ie73f1dbe1233d6fd0df41628c770b8f2ad1f1b1b
Mark Abraham [Tue, 9 Apr 2019 12:50:47 +0000 (14:50 +0200)]
Fix typo in AVX512 detection code
Change-Id: I2fb425a1649ac7d06480831016d6c35e7e63ce6f
David van der Spoel [Fri, 29 Mar 2019 12:31:11 +0000 (13:31 +0100)]
Fixed manual for dihedral restraints.
The equations in the manual for dihedral restraints were incorrect
and inconsistent with the code in bonded.cpp.
Change-Id: I335f72cf81990e636366ae75f890df85c5053388
Морозов Дмитрий [Wed, 3 Apr 2019 12:02:21 +0000 (15:02 +0300)]
Fixes bug in l-bfgs.
l-bfgs should now work excatly as it was in 4.6.5,
up-to some numerical precision in forces and energies.
Fixes #2641
Change-Id: I11a85a4241cc933fef94e2095dd8c3cbbb28b01b
Szilárd Páll [Thu, 4 Apr 2019 16:59:20 +0000 (18:59 +0200)]
Revert "Temporarily disable ARM HPC compiler in post-submit"
This reverts commit
2e63850dc17bc9f718344e68cd245c9c96a2256b.
Reason for revert: build slave software issues resolved.
Change-Id: I2a04afeeb51fe0177631c1bf55bed52ea2b0ea63
Paul Bauer [Thu, 28 Feb 2019 09:39:57 +0000 (10:39 +0100)]
Fix segmentation fault with simulated annealing
Fix contributed by Daniel Fragiadakis.
Fixes #2871
Change-Id: I237d49f9996eb2ae869d59e4c39a6c2d33c9ece7
Szilárd Páll [Mon, 1 Apr 2019 19:51:32 +0000 (21:51 +0200)]
Temporarily disable ARM HPC compiler in post-submit
Change-Id: I27a6699109e5d7ce3576200a3a977b7a63a305aa
Szilárd Páll [Mon, 25 Feb 2019 15:29:57 +0000 (16:29 +0100)]
Better document GMX_OPENMP_MAX_THREADS
Change-Id: I2c44f8b2331d69fde5fa242b5e53132813a2cb31
Roland Schulz [Tue, 26 Mar 2019 00:24:39 +0000 (17:24 -0700)]
Fix UB vector usage
Fixes a buffer overflow for c_simdBestPairAlignment=2.
Found with _LIBCPP_DEBUG=1.
Change-Id: Ib21ca875244673b27748a01373e7fc10252a7c44
Mark Abraham [Tue, 19 Mar 2019 09:23:18 +0000 (10:23 +0100)]
Prevented FFTW build errors with clang and AVX-512
FFTW hard-codes the inclusion of files that does not work with its
AVX-512 flags when using thee clang compiler, so in this case
GROMACS should compile without AVX-512 support.
Updated release notes, but didn't update the install guide for this
niche case.
Fixes #2892
Change-Id: Ida18fad66e654511937d51ee58f42440de2a321d
Mark Abraham [Wed, 13 Mar 2019 08:59:27 +0000 (09:59 +0100)]
Provide reminder of which nvcc is in use
FindCUDA.cmake + the user might have combined to find an unexpected
nvcc, so we help everyone help themselves by outputting it here,
particularly if they report problems on the users list.
Change-Id: Ic951fa219c9133760a3c97ad2a92d65d64f03bfb
Paul Bauer [Tue, 12 Mar 2019 10:27:58 +0000 (11:27 +0100)]
Fix formatting error in user guide reference
Change-Id: I02a25bb81f9c30ee7ddf7ed6f3757cb494ac4f06
Berk Hess [Thu, 7 Mar 2019 17:41:25 +0000 (18:41 +0100)]
Add grompp warning with use of GROMOS FF
Replaced GROMOS-based simulation database entry with similar
OPLS-based one, since our test systems should not trigger warnings
unless that is the intent of the test.
Refs #2884
Change-Id: I55afcf7ea5b423fa27792acebe09ea520b475974
Roland Schulz [Fri, 8 Mar 2019 15:52:29 +0000 (07:52 -0800)]
Fix ICC warnings
Change-Id: I5170eacf9ac7590d2d72dbb1dac3316a1b2e8ab0
Paul Bauer [Sun, 24 Feb 2019 06:44:49 +0000 (07:44 +0100)]
Add error when manual cannot be built
Added error message informing the user why a manual build is not
possible if Sphinx is not installed.
Change-Id: I74765960ea5f5f642771e75ac349cf2b55d360a9
Szilárd Páll [Tue, 9 Oct 2018 00:56:23 +0000 (02:56 +0200)]
Relax OpenCL gather kernel barrier on AMD
Not needed on arch with >32 execution width.
Refs #2519
Change-Id: I4c8f2cff405cd3044bd60b99f01bcdd918dc5d0e
Jukka Maatta [Wed, 27 Feb 2019 15:03:52 +0000 (17:03 +0200)]
Make OpenCL dummyKernel to require a input parameter
This is a tentative fix for OpenCL error with mdrun on MacOS.
MacOS seems to require that kernel functions have at least one parameter.
Otherwise clBuildProgram fails with error -11.
Here dummyKernel takes an empty pointer in the definition.
We then pass an empty pointer to dummyKernel with clSetKernelArg.
Fixes #2865
Change-Id: Ib7c08eeeb2ec6d8a43bfe703cf1b273819a45a29
Mark Abraham [Tue, 26 Feb 2019 21:41:26 +0000 (13:41 -0800)]
Keep niche CMake variables as advanced
Change-Id: I99781749d9f4f481f7943a27c415af6b5c4ef5bc
Mark Abraham [Tue, 26 Feb 2019 22:38:21 +0000 (14:38 -0800)]
Add new line to trjconv notice to users
This line can be the final terminal output, and it looks ugly to give
the user a prompt on the same line.
Change-Id: Ie3830ba9a86979ab60094271894ebd1651aa6f34
Berk Hess [Tue, 26 Feb 2019 14:07:18 +0000 (15:07 +0100)]
Correct grompp index file error message
Change-Id: I6b59c6d7e1d3a33054836f16d879d40e109eb8ee
Paul Bauer [Wed, 20 Feb 2019 10:09:13 +0000 (11:09 +0100)]
Version 2018.6
Added release notes for one change.
Updated regresiiontest hash.
Change-Id: Ifa207f9b270e835ba8c942e87e1fe156e6d204e0
Berk Hess [Wed, 13 Feb 2019 08:55:35 +0000 (09:55 +0100)]
Fix mass Delta H double counting
With separate mass lambda parameters, the perturbed mass contribution
to Delta H (not dH/dlambda) was double counted. This was due to an
incorrect fix for issue #2703 for missing Delta H contribution.
Refs #2703
Fixes #2849
Change-Id: I1349260e1e90a17a6b7dbe0d239d9474dcfa928c
Berk Hess [Thu, 31 Jan 2019 21:47:53 +0000 (22:47 +0100)]
Fix incorrect LJ repulsion force switching on GPUs
When using a CUDA or OpenCL GPU, the coefficient for the second order
term for the LJ repulsion in the force (not energy) switching function,
called 'A' in the manual, had the wrong sign in both the force-only
kernels and the force+energy kernels.
Note that the dispersion force switching was correct.
Cherry picked from 2019
Fixes #2845
Change-Id: Ib5c250a1f370d4c0a4fd652bf6efa03e70e18748
Paul Bauer [Fri, 15 Feb 2019 14:00:29 +0000 (15:00 +0100)]
Fix release notes formatting
Change-Id: Icea8712088068c14dbfcb20e403dd68f9aa11227
Paul Bauer [Wed, 13 Feb 2019 12:54:24 +0000 (13:54 +0100)]
Prepare for 2019.2
Reset doi strings.
Change-Id: I497ce4e5afe3a0f776dfba107e45d74bc51d4cc8
Szilárd Páll [Thu, 7 Feb 2019 13:12:17 +0000 (14:12 +0100)]
Disable instruction fusion on Power8
The -mpower8-fusion flag seems to be the source of incorrect code; not
confirmed, but likely a codegen issue that also affects Power9 with the
similar flag used.
Fixes #2747 #2746 #2734
Change-Id: I56f50e54db47f4fe30c42488f4c4f79ac474518a
Paul Bauer [Sat, 9 Feb 2019 12:34:53 +0000 (13:34 +0100)]
Change icc-18 to no-hwloc
Made to avoid issue with hwloc installation on bs-nix1310.
Change-Id: I824aa9b64db86814df10328141dbd0fd47470e02
Paul Bauer [Wed, 13 Feb 2019 12:49:51 +0000 (13:49 +0100)]
Version 2019.1
Updated regression test hash.
Set DOI strings.
Change-Id: If56a4e81c853af49ebe6a908bb9cc8883d24a7bc
Mark Abraham [Thu, 14 Feb 2019 16:01:25 +0000 (17:01 +0100)]
Improved diagnostics when PME cannot run on GPUs
Fixes #2789, #2823
Change-Id: Iff7609a3774c11329d36bd8557b741a4d29f7c5a
Paul Bauer [Thu, 14 Feb 2019 15:38:09 +0000 (16:38 +0100)]
Fix tune_pme
There was an issue with the file option for the tpr file being empty
that caused a segmentation fault.
Fixes #2827
Change-Id: I2702898d071d6e9325fa2e7ebb223b9043b7109e
Berk Hess [Wed, 13 Feb 2019 08:55:35 +0000 (09:55 +0100)]
Fix mass Delta H double counting
With separate mass lambda parameters, the perturbed mass contribution
to Delta H (not dH/dlambda) was double counted. This was due to an
incorrect fix for issue #2703 for missing Delta H contribution.
Refs #2703
Fixes #2849
Change-Id: I1349260e1e90a17a6b7dbe0d239d9474dcfa928c
Szilárd Páll [Fri, 15 Feb 2019 01:09:39 +0000 (02:09 +0100)]
Extend performance considerations on bonded offload
Refs #2793
Change-Id: I4a8ae8554cf2aad540eb4eb485898f8cabeb3966
Mark Abraham [Tue, 29 Jan 2019 11:56:31 +0000 (12:56 +0100)]
Fix use of selections referring to index groups
Selections that refer only to groups in an index file do not require a
topology file. This (and other behaviours) was inadvertently broken
by the wrong implementation of the default constructor, because that
constructor is used in setting up the analysis environment.
The default constructor of TopologyInformation should establish the
intended invariant, namely that until a topology is loaded, topology
getters should return nullptr.
Fixed that constructor, and fixed the unit test that verifies that
behaviour. Since that test was added at the same time as a change to
the implementation of TopologyInformation in commit
264458c9, the
broken invariant wasn't noticed.
Added a test also to gmx rdf that verifies that the selection
behaviour is fixed.
Fixes #2847
Change-Id: I2149616e0248c6d5cdd5657a8292d2c3346614b9
Mark Abraham [Wed, 13 Feb 2019 14:24:04 +0000 (15:24 +0100)]
Revert changes to implementation of insert-molecules and solvate
This is a partial reversion of
5181f8d1, which made an inappropriate
dependency from preparation tools to TopologyInformation, which is
intended for analysis tools. This is needed in order to fix some
actual analysis tools that were broken by related changes to
TopologyInformation.
Unfortunately in
5181f8d1 readConformation was replaced with
TopologyInformation, and the former is no longer available. Instead,
readConfAndTopology is used in the same way that it was originally
used to implement readConformation. So the behaviour is reverted
even though the code looks different.
Refs #2847, #1862
Change-Id: I6e4900eea38b5c2e1b85b0d48427dabe26b09f9d
Mark Abraham [Wed, 13 Feb 2019 17:44:26 +0000 (18:44 +0100)]
Improved electric-field docs
Change-Id: Ib1c6aa260f54a3933b1d80e375dc6ee007317473
Szilárd Páll [Thu, 7 Feb 2019 13:12:17 +0000 (14:12 +0100)]
Disable instruction fusion on Power8
The -mpower8-fusion flag seems to be the source of incorrect code; not
confirmed, but likely a codegen issue that also affects Power9 with the
similar flag used.
Fixes #2747 #2746 #2734
Change-Id: I56f50e54db47f4fe30c42488f4c4f79ac474518a
Paul Bauer [Tue, 5 Feb 2019 14:55:55 +0000 (15:55 +0100)]
Move simulated tempering default setting
Setting the default value for the simulated tempering when nstexpanded
was not specified in the mdp file was done before the values for the
temperature coupling are known. Moved this to a new location where the
value is known instead.
Added message to user in this case.
Refs #2754
Change-Id: I194829d5a817019da6d63a075e0dd7f4af8a4735
Berk Hess [Fri, 8 Feb 2019 09:57:48 +0000 (10:57 +0100)]
Disallow rerun with perturbed masses or constraints
Since rerun no longer integrates, free-energy contributions due to
changing masses and constraints are no longer computed. Now rerun
exits with a fatal error when such a system is provided.
Fixes #2849
Change-Id: Ic1550fce22f68c573b52d6895e1e61398b671e51
Szilárd Páll [Sun, 6 Jan 2019 10:51:26 +0000 (11:51 +0100)]
Require a 64-bit platform for OpenCL
GROMACS requires a 64-bit OpenCL implementation as the PME code assumes
8-byte size cl_mem. Therefore, we require a 64-bit platform,
where pointers and therefore cl_mem will be of the assumed size.
Fixes #2821
Change-Id: I5fa60419a948e2cfdb344e7611b197550f866262
Berk Hess [Wed, 6 Feb 2019 12:39:55 +0000 (13:39 +0100)]
Fix segfault with EM, DD and group scheme
Resetting to an old DD state during EM would leave the cg sorting array
used with the group scheme in an invalid state. This could cause
out of bounds vector access one DD step after rejecting an EM step.
When merging this into master branch, prefer to change to use ssize
rather than the static_cast.
Fixes #2813
Change-Id: I7f13b46d7ff5352ce41838b813c46f2e90c93b1c
Berk Hess [Thu, 31 Jan 2019 21:47:53 +0000 (22:47 +0100)]
Fix incorrect LJ repulsion force switching on GPUs
When using a CUDA or OpenCL GPU, the coefficient for the second order
term for the LJ repulsion in the force (not energy) switching function,
called 'A' in the manual, had the wrong sign in both the force-only
kernels and the force+energy kernels.
Note that the dispersion force switching was correct.
Fixes #2845
Change-Id: Ib5c250a1f370d4c0a4fd652bf6efa03e70e18748
Mark Abraham [Wed, 30 Jan 2019 12:30:19 +0000 (13:30 +0100)]
Merge remote branch release-2018 into release-2019
Change-Id: Ie5a4add2fe010bc94c00418a728f01d3aac6cb9d
Szilárd Páll [Tue, 29 Jan 2019 14:49:18 +0000 (15:49 +0100)]
Fix double-increment of GPU NB launch subcounter
Only increment once per nonbonded task per step.
Fixes #2837
Change-Id: Ic68bf1af184f895f2fb769b026855fd3d48fa849
Mark Abraham [Wed, 30 Jan 2019 08:23:04 +0000 (09:23 +0100)]
Fix release notes issue links
The space means sphinx can't recognize the construct
Change-Id: I8c25114a1f45a7744345e2e8bc6862fdd4568f5f
Mark Abraham [Wed, 30 Jan 2019 08:20:31 +0000 (09:20 +0100)]
Fix release notes issue links
The space means sphinx can't recognize the construct
Change-Id: Ia0b96e8a1ecd24e2bac97d7bc9f176abbe30abc9
Teemu Murtola [Tue, 29 Jan 2019 07:05:44 +0000 (08:05 +0100)]
Avoid warnings with Apple Clang
The logic for -Wno-missing-prototypes for group kernels left the
warning enabled for Apple Clang, making it impossible to compile
the code with -Werror.
Change-Id: Ib9a0e23bd47f8cc1dd8f656aae49ba27bbf9b28b
Mark Abraham [Thu, 10 Jan 2019 09:14:40 +0000 (10:14 +0100)]
Stop trying to check nvcc on Windows
The execute_process() call used in this check is not constructed to
work on Windows, so we should not run it there.
Refs #1616
Change-Id: I2103b78203f71d3f68b54898dd03c8fe0eb0fa4c
Roland Schulz [Thu, 24 Jan 2019 23:42:55 +0000 (15:42 -0800)]
Work-around for ICC bug in simd-tests
Only affects test harnest so isn't critical but confuses users
with false positive unit test.
Change-Id: Ida7f8f1dbc8da32bb960d5fa3550531a94cc2dab
Paul Bauer [Wed, 23 Jan 2019 14:37:15 +0000 (15:37 +0100)]
Change gcov to run on bs-mic
Final change needed to decommission bs-mac.
Change-Id: Iaf0011906fae672b83af1d3631f8d698a0d9f52d
Roland Schulz [Wed, 23 Jan 2019 17:22:37 +0000 (09:22 -0800)]
Merge release-2018 into release-2019
Change-Id: Ifb898eb777bc2986d600cdbf190203dda3f441ec
Paul Bauer [Wed, 23 Jan 2019 14:37:15 +0000 (15:37 +0100)]
Change gcov to run on bs-mic
Final change needed to decommission bs-mac.
Change-Id: Iaf0011906fae672b83af1d3631f8d698a0d9f52d
Berk Hess [Wed, 23 Jan 2019 09:29:55 +0000 (10:29 +0100)]
Fix error with 2D/3D DLB
With 2D or 3D dynamic domain decomposition with dynamic load balancing,
mdrun would exit with a fatal error when a cell size was limited.
This bug was introduced in commit
49367d45.
Fixes #2830
Change-Id: If36fcc2ddbb45c0855c78a2767b1d8562584b76f
Paul Bauer [Mon, 21 Jan 2019 08:47:44 +0000 (09:47 +0100)]
Prepare for 2018.6
Change-Id: Ie71adbecb99819aae1ba87c6f886d44a97958165
Paul Bauer [Mon, 21 Jan 2019 08:10:11 +0000 (09:10 +0100)]
Version 2018.5
Added release notes for commits that missed them.
Updated regressiontest hash.
Change-Id: I335988ed2b9c7a371e76dda7f7272eb30fe71a03
Christoph Junghans [Thu, 3 Jan 2019 10:39:04 +0000 (03:39 -0700)]
gmxManageLmfit.cmake: enforce usage of 7.0
LMFIT_FOUND will also be true for version lower than 7.0, so we
need to check the version explicitly in gmxManageLmfit.cmake.
Change-Id: Ia3ae12b3a74d2b567432f5ef18a77c13b19cdb85