Szilárd Páll [Mon, 30 Jul 2018 16:18:37 +0000 (18:18 +0200)]
Request flushing denorms to zero in OpenCL
This change adds by default the -cl-denorms-are-zero to the flags used
for kernel compilation. This is done to:
- avoid a large performance penalty on AMD Vega with ROCm (which by
default handles denorms on GFX9 or later).
- make the defaults uniform across CUDA and OpenCL.
Fixes #2593
Change-Id: I9e6183c4367b5960e0e21f1dd342d7695acfbc44
Berk Hess [Thu, 16 Aug 2018 11:51:18 +0000 (13:51 +0200)]
Ensure domains are large enough for atom motion
The introduction of the dual pair list has led to larger nstlist
values, which leads to larger atom displacements between domain
decomposition steps. This has made it much more likely that
"atom moved to far" errors appeared at DD and PME redistribution.
Now minimum DD cell size setting correctly takes into account atom
displacement (when there is a reference temperature).
Note that this can significantly increase the minimum DD cell size
for solvent systems and slighlty for systems with large molecules.
Fixes #2614
Change-Id: Ie41131e9eed3ef828928516a6b8ebfb9b5ba2bdb
Berk Hess [Tue, 21 Aug 2018 08:07:22 +0000 (10:07 +0200)]
Fixed mdrun segv with QM/MM ONIOM scheme
Fixes #2617
Change-Id: I097d392ea53aeff589042df5074866e07a0ce5c5
Berk Hess [Thu, 16 Aug 2018 11:45:23 +0000 (13:45 +0200)]
Refactor calc_verlet_buffer_size()
Split of parts, which will be reused, from calc_verlet_buffer_size().
This change is only code motion.
Refs #2614
Change-Id: I9cf68a2661ee10eb991240d2768c077df9f9c0c5
Szilárd Páll [Thu, 19 Jul 2018 13:53:43 +0000 (15:53 +0200)]
Disable single compilation unit with CUDA 9.0
CUDA 9.0 does not support CC 2.x, hence even with the default list of
targeted arch, multiple compilation units an be enabled.
Fixes #2561
Change-Id: I741081da39539f211fad32bda5c1f1dccc4378f9
Berk Hess [Thu, 16 Aug 2018 11:19:55 +0000 (13:19 +0200)]
Fix Verlet buffer estimate with BD
With BD and bd_fric>0, the masses used for estimating the pairlist
buffer based on estimated motion of constrained atoms and virtual
sites were, incorrectly, the actual masses instead of 1.
Fixes #2613
Change-Id: I5378c5f5566ccda28554b5a6c7d7c403228aa794
Berk Hess [Tue, 14 Aug 2018 08:31:24 +0000 (10:31 +0200)]
Fix assertion failure in CG
When the final step coincided with a coordinate output step,
conjugate gradient minimization would exit with an assertion failure
instead of writing confout.gro.
Fixes #2554
Change-Id: I53fffccb5310259132724b83ee452ef01f8ac9c8
Berk Hess [Tue, 14 Aug 2018 08:02:44 +0000 (10:02 +0200)]
Really fix CG with multiple domains
Commit
9232fa9a incorrectly claimed to fix CG with multiple domains.
The change fixes all issues due to the change of the global state
only being available on the master rank.
Note that there is still an issue with writing the final trajectory
frame.
Refs #2554
Change-Id: I1ed3363f722daad9e6aef00d9ded6647acc820f2
Berk Hess [Wed, 15 Aug 2018 14:45:15 +0000 (16:45 +0200)]
Add check for pull group PBC to grompp
Pull groups that use a reference atom for periodic boundary treatment
should have all their atoms well within half the box size of this
reference. When this is not the case, grompp will now issue a warning.
Refs #2397
Change-Id: Ida7004624a470981d9ce22a1ef921daebad83364
Szilárd Páll [Mon, 13 Aug 2018 14:36:38 +0000 (16:36 +0200)]
Improve GPU detection sanity check error message
When the unexpected condition is triggered some extra info on what type
of error has been left behind after a successful detection of a
compatible GPU is now printed to aid with identifying issues.
Refs #2415
Change-Id: I85e0da4c339df8184aa2dec49440ce2d0e83e8bf
Mark Abraham [Tue, 17 Jul 2018 22:49:51 +0000 (00:49 +0200)]
Fix enforced rotation energy output
Its own per-group energy output files were always OK, but normal edr
and log writing didn't work unless pull groups were also active.
Change-Id: I66d3eb1e14b72766c385a69fd35a750b2338343f
Erik Lindahl [Mon, 13 Aug 2018 12:48:26 +0000 (14:48 +0200)]
Fix SIMD anyTrue bug, and add better unit test
The double precision versions could occasionally
miss elements.
Fixes #2588.
Change-Id: Ie033a3af0e5de25205533868062716a83f33df3c
Kevin Boyd [Thu, 2 Aug 2018 01:33:19 +0000 (21:33 -0400)]
Fix gmx solvate topology updating
The topology update of gmx solvate was hardcoded to SOL molecules
(and some of the reported quantities also registered HOH and WAT).
Changed to allow updates based on any solvent molecule information.
Also, now allows for updates with multiple solvent molecule types
in the input solvent configuration
Added test case for topology update with multiple solvents
fixes #1929
Change-Id: If506e0f509c8a25cb615fb8d3f15b4dfdb239afa
Paul Bauer [Wed, 25 Jul 2018 14:27:23 +0000 (16:27 +0200)]
Fix -skip option for gmx rms
Made sure request to skip points is honored.
Fixes #2565
Change-Id: I518d3f91861f89426020861d0382f5e689f33ba0
Kevin Boyd [Tue, 31 Jul 2018 01:54:27 +0000 (21:54 -0400)]
Report up to date hwloc version information
The hwloc version in gmx --version and log files had been
taken from HWLOC_API_VERSION in the hwloc header, which is
not always updated to reflect new releases.
Added HWLOC_VERSION to buildinfo.h from cmake, used in place of
HWLOC_API_VERSION
Fixes #2591
Change-Id: I0ed9f1f1ad9b4262fbb966c03c407eeb1edfc3da
Mark Abraham [Wed, 18 Jul 2018 14:50:13 +0000 (16:50 +0200)]
Fix CG with multiple domains
The global state can only be accessed on master rank, so we should set
the flags there and then permit the DD code to propagate the setup of
the cg_p vector.
Fixes #2554
Change-Id: If294bf000eb0266125ecc6c6bf937aac0390e2b8
Szilárd Páll [Mon, 23 Jul 2018 15:06:54 +0000 (17:06 +0200)]
Improve the robustness of the nvcc CMake check
The check to assess whether nvcc is likely functioning as expected is
made more robust by including the build-type specific CUDA_NVCC_FLAGS_*
flags in the test compilation.
Change-Id: I175809809fa436cb887c8b2a1cb48914338e596b
Szilárd Páll [Mon, 23 Jul 2018 13:46:53 +0000 (15:46 +0200)]
Fix nvcc host compiler check triggering
The nvcc host compiler check conditional triggering on the change of the
host compiler binary has not been functional as the check has been
placed after another gmx_check_if_changed() call on the same variable.
This change moves the code that checks the functioning of nvcc and host
compiler to gmxManageNvccConf and refactors the conditionals to reuse
the result of the previously issues check if changed call.
Fixes #2583
Change-Id: I26586aaec394cce93a05774cb4184b3928b560cb
Paul Bauer [Fri, 20 Jul 2018 14:01:36 +0000 (16:01 +0200)]
Fix bfactor output
The fix for the PQR file output caused the files containing bfactors to
be incorrectly written in this format due to a missing check that has
been added.
Fixes #2575
Change-Id: I35c3b99fee81db689df9564c3386edd85e26cbb2
Szilárd Páll [Wed, 25 Jul 2018 14:55:31 +0000 (16:55 +0200)]
Corrections to the user guide mdrun perf section
* Corrected some MPI examples that used the non-suffixed gmx binary;
* Corrected a reference to tMPI threads;
* Added -pmefft to the perf-related options description
Change-Id: I5761e14816ae70efd200bb82cf48641d9d9dad67
Kevin Boyd [Sun, 29 Jul 2018 12:54:04 +0000 (08:54 -0400)]
Fixed syntax error in make_gromos_rtp.py
Didn't affect the resulting rtp if everything else was in order,
just prevented an error message.
Refs #2557
Change-Id: I5289db159b62abde31103841c33d2b90f4a7717e
Mark Abraham [Wed, 18 Jul 2018 05:53:03 +0000 (07:53 +0200)]
Fix pre-submit matrix
Changes in slave configuration for master branch need matching
changes here
Change-Id: I0e1b38ae0de85d02b427d5fb61c0b1068fe43e83
Mark Abraham [Wed, 21 Mar 2018 15:04:44 +0000 (16:04 +0100)]
Updated to prepare for 2018.3 release
Change-Id: I0c33fcbdfcc0010b5a13cbbc5503c6a95df751dc
Mark Abraham [Wed, 13 Jun 2018 00:30:34 +0000 (02:30 +0200)]
Version 2018.2
Updated release notes for some commits that were missing them.
Change-Id: Id9eca559faa981fb762699a34336b6b3d0f58399
Mark Abraham [Wed, 13 Jun 2018 07:24:45 +0000 (09:24 +0200)]
Fix premature reporting of action when GPUs are not detected
The decision about what to do when GPUs could not be detected is a
responsbility taken at a higher level, so the detection handling code
should just report the facts.
Clarified some of the intended usage in the documentation
Fixes #2374
Change-Id: I63b569e053dd88d66351640019efc758e91bbdff
Mark Abraham [Wed, 13 Jun 2018 07:09:36 +0000 (09:09 +0200)]
Update top-level README
Included most recent core GROMACS publication
Change-Id: If389c72902831598b7cf0263a7b74e40c8d21f86
Mark Abraham [Wed, 13 Jun 2018 07:39:26 +0000 (09:39 +0200)]
Fixed documentation typo
This version is true to the original text.
Refs #2359
Change-Id: I3c2ab7a30109a397999883d5147346f1244a77f0
Berk Hess [Tue, 20 Mar 2018 13:35:34 +0000 (14:35 +0100)]
Add AWH continuation consistency checking
AWH now checks at checkpoint continuation that the number of
visits/samples matches the update count. This catches unallowed
changes of AWH parameters or the number of walkers.
Change-Id: I3e3325327552f1f6c2f25c61ff8991c06c6fc36a
Mark Abraham [Wed, 21 Mar 2018 09:57:26 +0000 (10:57 +0100)]
More fixes to suit gcc 8 for double build
gcc 7 supports the same syntax, but only gcc 8 requires it.
xl code path untested, because we have no access to a working compiler
Fixes #2421
Change-Id: I8f89af4b066be68e07a286a9fa45b8ded3c925f3
Szilárd Páll [Thu, 29 Mar 2018 12:58:02 +0000 (14:58 +0200)]
Also issue OMP_NUM_THREADS reading note to the log
The note that was meant to inform users that OMP_NUM_THREADS was setting
the number of threads in their run (as this value can be inherited by
the env) has not been logged. It was also printed right after the tpx
reading statues making it hard to notice. Removed stderr output now
that this is no longer required.
This change makes the note easier to notice prepending a newline and
issues it to the log file too.
Refs #2472
Change-Id: I73fc9de5e9d747f9d7a094c6678ffc1547481b94
Viveca Lindahl [Tue, 24 Apr 2018 16:14:15 +0000 (18:14 +0200)]
Changed histogram check interval for multidimensional AWH bias.
The step interval for performing covering checks depended explicitly
on the total number of points in the AWH histogram. The covering
checks themselves however only depends directly on the extent of each
one-dimensional axis. For a multidimensional grid in combination with
relatively few samples to cover the sampling interval (e.g. using
Brownian dynamics), this could lead to a delayed detection of the
covering.
The same step interval was also used for checking for histogram
anomalies, which however only generates warnings and is not integral
to the AWH method itself.
Now the covering check interval is instead determined from the number
of sigmas, the "width" of one sample, required to cover each
dimension. Since there is about 1 point per sigma, the dependency of
the check interval on the number of points is essentially unchanged in
the one-dimensional case. However, this relation is not numerically
exact. Therefore, this change also requires updating reference data
for a regression test to be updated.
The check interval for histogram anomalies is set to be the same as
for the covering, but could in the future be made less frequent.
Added release note.
Fixes #2487
Change-Id: I5af0d48436664d8fdfe8bafa05cde3cdae27e45a
Berk Hess [Thu, 7 Jun 2018 09:14:27 +0000 (11:14 +0200)]
Add fatal error for inconsistent graph
In case a moleculetype consists of multiple monomers connected
by restraints, an inconsistent graph could be generated.
Now a fatal error with explanation is generated for such cases.
Also a fatal error is generated with an inconsistent graph with long
bonds in general.
Fixes #2549
Change-Id: I6fa11fb7cefd74ed077c1fb523a2147c91e0d0fd
Berk Hess [Thu, 7 Jun 2018 12:27:44 +0000 (14:27 +0200)]
Avoid COM removal moving frozen atoms
Fixes #2551
Refs #2542
Change-Id: Ifd7523661248594cce7329dfd86e814b78c9c32c
Berk Hess [Tue, 5 Jun 2018 09:24:16 +0000 (11:24 +0200)]
Remove constraint v correction for frozen atoms
The optimized update routines no longer set the velocities of frozen
dimensions to zero, but the constraint code would still correct
the velocities of frozen dimensions.
Note that the COM correction can still modify velocities of frozen
dimensions, but this is a negligible effect unless there are
systematic COM forces.
Fixes #2542
Change-Id: I4770d9bd7991a021ce173f219eb7310a91eaf10e
Paul Bauer [Fri, 8 Jun 2018 08:32:27 +0000 (10:32 +0200)]
Fix gmx solvate with multiple solvent molecule types
When using a solvent box with multipe solvent molecule types, gmx
solvate would crash due to memory corruption. Fixed by properly freeing
the temporary storage for the atom information.
Fixes #2550
Change-Id: I68ed6afcd7898eb9de0686b6efeb9ff74174c92b
Berk Hess [Tue, 5 Jun 2018 14:01:01 +0000 (16:01 +0200)]
Fix MPI inconsistency in EM after constraint failure
Fixes issue #2540
Change-Id: Id18c17af82f80917388c11fc776b79bf4966a4ac
Viveca Lindahl [Tue, 5 Jun 2018 20:46:55 +0000 (22:46 +0200)]
Make sure that the value of awh-nsamples-update is allowed
Previously, awh-nsamples-update could be set to zero, leading to
division by zero. Now it results in a fatal error.
Fixes #2489
Change-Id: I65aae5d5c533b9aab7ea9aae3e317e92a926c18c
Erik Lindahl [Fri, 11 May 2018 14:06:59 +0000 (16:06 +0200)]
Use default CMake path variables
Remove our homegrown path variables for binaries, libraries,
manpages and data in favor of the ones documented as part of CMake.
The 'gromacs' part of the data directory has been moved to a separate
GMX_INSTALL_DATASUBDIR variable.
This enables Gromacs-2018 docker builds with multiple different
accelerations installed with different binary/library subdirectories.
Change-Id: I1618428c94ea2cfb90dc1ff5261b26a9307c1a94
Paul Bauer [Tue, 22 May 2018 15:01:20 +0000 (17:01 +0200)]
Fix PQR file output
PQR files from editconf were always written as fixed format PDB files
with just the field information added. As pointed out in the linked
redmine, this can violate the PQR file standard if the field lengths are
too long, even though the file would still be a valid PDB.
This adds a slightly different form of the writeout that has a flexible,
PQR conform format.
Fixes #2511
Change-Id: I626380b642a0214970753da289e9c969ce411ea7
Erik Lindahl [Tue, 5 Jun 2018 09:56:07 +0000 (11:56 +0200)]
Bump GMX_BUILD_OWN_FFTW to 3.3.8 to avoid bugs
FFTW-3.3.8 seems to fix build errors with AVX-512, and
as reported on the FFTW web page it also removes the -ffast-math
flag which results in errors with gcc-8.
Fixes #2541.
Change-Id: Ibe4ef0040986e4b83f92f0bb404c72fa1b5e11ea
Mark Abraham [Mon, 21 May 2018 17:07:25 +0000 (19:07 +0200)]
Fixed enemat when .edr had no matching energy groups
Removed some debug output that obscured both the code and the useful
user-facing warnings.
Used a simpler bool construct to decide whether to issue the warning.
Fixes #2508
Change-Id: Ife56264991e365f8f5ca3b1285caea8033da7584
Mark Abraham [Tue, 27 Mar 2018 19:47:55 +0000 (21:47 +0200)]
Improved docs for gmx mindist -pi
Change-Id: Ia8ba72afd357e4952c5adf7ede3b15ff78ad9fd6
Berk Hess [Mon, 4 Jun 2018 07:29:54 +0000 (09:29 +0200)]
Fix segv in AWH error message
Change-Id: Ie8dee0c11ea0290b5bcbb8ada837a58d00881f03
Paul Bauer [Tue, 29 May 2018 15:04:36 +0000 (17:04 +0200)]
Disallow use of empty box information in solvent files
An empty box information in a solvent file presented to gmx solvate
could case an infinte loop because the current coordinate would always
be incremented by zero. Disallowed by introducing new function that
checks for proper box information.
Fixes #2523
Change-Id: I461509f8aafa2048253faf85ccbe388bbbaf80a7
Aleksei Iupinov [Tue, 22 May 2018 09:05:03 +0000 (11:05 +0200)]
Remove unused results of cudaStreamQuery()
Coincidentally fixes #2509 (Windows + CUDA compilation)
Change-Id: I032c5fab53bf83cf0ea8c0299d8752b10d1f6c0e
Roland Schulz [Mon, 21 May 2018 20:29:41 +0000 (13:29 -0700)]
Fix illegal instruction error on KNL
Fixes #2504
Change-Id: Ie2f55718f98d3dfbf3c312afa5141c77ead77a6d
Berk Hess [Wed, 2 May 2018 14:36:01 +0000 (16:36 +0200)]
Enable SIMD version of update
A bug in setting mdatoms->havePartiallyFrozenAtoms caused the SIMD
version of the leap-frog update to always be deactivated.
Fixes #2497
Change-Id: I670549c95c983cac5033ea6bb71b77561e063223
Berk Hess [Tue, 24 Apr 2018 14:02:09 +0000 (16:02 +0200)]
Fix indexing issue in the pull code
When determining if the COM of pull groups should be computed,
the indexing range of group[] for each pull coordinate is one element
too long. In most cases this element is 0, so in which case it only
lead to extra, useless compute when a cylinder group is used.
Note that for dihedral geometry the extra element is actually dim[0]
in pull coord, which is 0 or 1, which is harmless.
No release note, since this did not affect results, it could only
cause a minor performance loss with cylinder pulling.
Fixes #2486
Change-Id: Ie5785181fbe28d8db57e37c58553ae3835e657b7
Paul Bauer [Tue, 17 Apr 2018 15:48:54 +0000 (17:48 +0200)]
Remove obsolete variable prec gro file output
It seems like the help message for the -ndec option in trjconv has never
been updated to indicate that gro files can no longer be written with
flexible precision. This has been fixed now.
Change-Id: Ia514bf48f6a25f13911524211a703d49b3bc307a
Aleksei Iupinov [Tue, 27 Mar 2018 20:30:43 +0000 (22:30 +0200)]
Prevent OpenCL timing memory leak
Fixes #2470
Change-Id: I4917de697bee7df98da0037e9165e52e660f83a0
Mark Abraham [Thu, 29 Mar 2018 12:22:26 +0000 (14:22 +0200)]
Remove leftover mention of twin-range scheme
Also fixed a broken symref to a version number that should
never have been a symref
Change-Id: Id1b10614106748de6ff114ade4b542ac7581f4cf
Berk Hess [Tue, 3 Apr 2018 08:00:15 +0000 (10:00 +0200)]
Change warninp filenm to std::string
This prevent buffer overflows with long filenames.
Fixes #2465
Change-Id: Ifcd264a6b33929f6b369d543c83c16d5378db937
Mark Abraham [Tue, 27 Mar 2018 19:39:34 +0000 (21:39 +0200)]
Clarified mdp options relating to bonds
Change-Id: Iffcaaaf1fc6c707c8f644da18cf03e28d2137557
Mark Abraham [Tue, 20 Mar 2018 07:39:37 +0000 (08:39 +0100)]
More gcc-8 fixes for POWER
Fixes #2421
Change-Id: I43c13df3a217d0f2154dca0ef215efd9cd27474a
Mark Abraham [Wed, 21 Mar 2018 15:04:44 +0000 (16:04 +0100)]
Updated to prepare for 2018.2 release
Change-Id: I1c72e8a3ac1b6b2e29b39c2d52bad5b87a884912
Mark Abraham [Fri, 23 Feb 2018 13:20:17 +0000 (14:20 +0100)]
Version 2018.1
Change-Id: I3285c77fc557c1a6f34796c4bfb4843846b0d8a5
Mark Abraham [Wed, 21 Mar 2018 11:07:16 +0000 (12:07 +0100)]
Merge "Merge branch release-2016 into release-2018" into release-2018
Mark Abraham [Tue, 27 Feb 2018 16:10:15 +0000 (17:10 +0100)]
Update release notes for 2018.1
Change-Id: Ia60d523647e1915856ae3b00a0cb9eacd939fc56
Mark Abraham [Tue, 20 Mar 2018 22:17:51 +0000 (23:17 +0100)]
Merge branch release-2016 into release-2018
Conflict in pre-submit matrix, kept 2018 content that already
has the same logical change made.
Change-Id: I40b2db8d149388bed07471fcdb8082b0fc92b9b5
Vedran Miletić [Tue, 20 Mar 2018 11:27:45 +0000 (12:27 +0100)]
Document matrix_convert function in PBC
The brief documentation was in place, but the documentation of the
function parameters was missing. This patch adds it and also fixes
incorrect Doxygen syntax at pbc_dx_d.
Change-Id: Ic897911bf4b8866bb7c4dc3aea982493cc03874c
Berk Hess [Tue, 20 Mar 2018 12:19:01 +0000 (13:19 +0100)]
Fix gmx dump AWH formatting issue
A comma was missing in the list of AWH checkpoint entry string
which caused the naming to be messed up in the gmx dump output.
Change-Id: I85d0722236f3f9559c1117fdcee39766d04b424d
Mark Abraham [Tue, 20 Mar 2018 11:50:17 +0000 (12:50 +0100)]
Update use of gpu_id in Jenkins
We plan to remove one of the GPUs from the slave that had three, so we
need to update the testing configurations. The new configuration might
balance load a little better.
Refs #2408, #2410
Change-Id: I3b5d9c8702c021f0676ea3ca12f9e7f1d3317ed1
Berk Hess [Mon, 19 Mar 2018 13:33:47 +0000 (14:33 +0100)]
Disallow single simulation with multisim
To avoid many untested code paths, we, at least temporarily,
disable a single simulation with mdrun -multisim and -multidir.
Refs #2448
Change-Id: I9befdb677f3c77bcc6dc0c77abc3478f0b83ba8d
Mark Abraham [Tue, 20 Mar 2018 11:51:56 +0000 (12:51 +0100)]
Update use of gpu_id in Jenkins
We plan to remove one of the GPUs from the slave that had three, so we
need to update the testing configurations. The new configuration might
balance load a little better.
Refs #2408, #2410
Change-Id: Ie253ef07998cf45c5fc2e118a5394f0817e66f75
Aleksei Iupinov [Thu, 1 Mar 2018 22:32:03 +0000 (23:32 +0100)]
Clarify the mdrun GPU options docs
Refs #2359
Change-Id: If112077a59f875ffb1c689b2ac67dad7cdf2adb9
Mark Abraham [Fri, 16 Mar 2018 21:21:48 +0000 (22:21 +0100)]
Fix VSX SIMD with gcc 8
gcc 8 apparently generates different code for the former GROMACS
code, which seems buggy. See
https://bugzilla.redhat.com/show_bug.cgi?id=
1556989#c3
and https://gcc.gnu.org/bugzilla/show_bug.cgi?id=84907
Fixes #2421
Change-Id: I31492cd582b785cdfb42e8b999a165a7339ce4be
Berk Hess [Fri, 16 Mar 2018 10:00:41 +0000 (11:00 +0100)]
Correct PMF sign error in AWH bias sharing
Recent commit
229c8f63 was though to fix a sign error in
the calculation of the deconvolution of the AWH PMF when sharing
the bias over multiple simulations, but this sign was misplaced.
Fixes #2439
Change-Id: I67ec06ff4d832a857467b58b362f9f6f88671aa8
Berk Hess [Thu, 15 Mar 2018 17:09:55 +0000 (18:09 +0100)]
Fix recent mdrun signaling bug
Recent commit
e4deba12 accidentally negated the locality condition
for signaling checkpoint and termination in mdrun.
Fixes #2457
Change-Id: I1b7a4c26637766a44cad2581c9c9ec420aa4ab6e
Berk Hess [Thu, 15 Mar 2018 10:25:50 +0000 (11:25 +0100)]
Fix virial with external pull potential and MPI
When using an external pull potential with domain decomposition,
currently this is only used by AWH, the virial contribution would
be multiplied with the number of MPI ranks.
Fixes #2455
Change-Id: I61452fb9eca6e68fea3256cc25b39033a9c5d8e7
Berk Hess [Wed, 14 Mar 2018 10:59:53 +0000 (11:59 +0100)]
Improve inter-simulation signaling
Use a single boolean for controlling inter-simulation signaling.
This would have prevented issue #2447.
Introduce an inter-simulating signaling frequency. This both
simplifies the code and significantly reduces communiation overhead
for many simulations and/or many ranks per simulation.
Correct the terminimation step print with replica exchange.
Refs #2440 and #2447
Change-Id: I8ed50c5b11564d9a967bcacb15c4fcd3be05caea
Berk Hess [Wed, 14 Mar 2018 08:32:23 +0000 (09:32 +0100)]
Fix mdrun signalling with AWH bias sharing
The recent commit
717fd5b8, which should have fixed issue #2440,
disabled checkpointing and termination by disabled signalling
between AWH runs that share a bias.
Fixes #2447
Refs #2440
Change-Id: Ic80ea07cfa1bde1b31fa9d660f00492b794b000f
Berk Hess [Mon, 12 Mar 2018 15:54:04 +0000 (16:54 +0100)]
Fix COM pulling with external potential with #ranks>32
With more than 32 PP-ranks, the pull code could use only a subset
of the PP-ranks. This change forces all ranks to do pulling when
external potentials are present (currently only used by AWH).
Fixes #2441
Change-Id: I8501024b7961600ec79f3707e239ddf25525aa79
Berk Hess [Tue, 13 Mar 2018 13:59:19 +0000 (14:59 +0100)]
Fix pull bug with geometry=direction-periodic
When doing COM pulling with geometry direction-periodic,
the reference location needs to be used to compute the current
distance. This reference was taken from the previous step instead
of the current. In practice this only caused issues at restarts
when the distance was more than half the box length.
Fixes #2446
Change-Id: Ie0c0341ad8c6ce1e78951270cab27ecaf95d65eb
Berk Hess [Tue, 13 Mar 2018 13:18:45 +0000 (14:18 +0100)]
Add AWH fixes to release notes
Change-Id: I17531da77495367b0e62b4e0b0e912bbd16659f9
Berk Hess [Mon, 12 Mar 2018 15:43:53 +0000 (16:43 +0100)]
Fix AWH ensemble checkpointing
AWH multi-runs with shared bias could terminate at different steps
leading to checkpointing from which continuation was impossible.
Fixes #2440.
Change-Id: I728c6aea9d030fcfad04efc6082309dafe3408bd
Berk Hess [Mon, 12 Mar 2018 20:36:07 +0000 (21:36 +0100)]
Fix AWH deconvolution when sharing a bias
When sharing an AWH bias over multiple simulations, the PMF output
was garbage due to a missing minus sign in the reduction.
Note that this only affected the PMF output, not the sampling.
Fixes #2439
Change-Id: I688cda045f5e757e58b392d64384705b3ac73a17
Szilárd Páll [Mon, 12 Mar 2018 23:23:07 +0000 (00:23 +0100)]
Fix clang 6.0 with CUDA 9.0
This enables clang 6.0 CUDA build for sm_70 and works around an issue
which seems to affect sm_37 support.
Fixes #2443
Change-Id: Ib9c52e4a3a8ac1e05e851c8166eec4a6b5df4825
Mark Abraham [Fri, 23 Feb 2018 12:20:56 +0000 (13:20 +0100)]
Test gcc-6 and cuda-9.0
Change-Id: Iba9436d9629a404290eb02d897b8d48f2a77b5ee
Berk Hess [Wed, 7 Mar 2018 12:48:42 +0000 (13:48 +0100)]
Correct pdb2gmx -missing option
The help text for the pdb2gmx -missing option only mentioned
missing atoms, but when atoms are missing also bonded interactions
will be missing. Now bonds are mentioned in the help text.
Since -missing allows for missing bonds, it now also allows for
dangling bonds at termini (which can actually be useful in special
cases).
Change-Id: I8d7215691ffc7dbb49f41964af9639c01355d775
Szilárd Páll [Tue, 6 Mar 2018 18:10:55 +0000 (19:10 +0100)]
Extend "Finding out how to run mdrun better" section
Change-Id: I76c75504ef505e2547861015eb20d6d6b1f31383
Mark Abraham [Fri, 2 Mar 2018 10:22:42 +0000 (11:22 +0100)]
Fixed dvdlambda for SHAKE + FE
Garbage values have been accumulated to dvdlambda whenever SHAKE was
used.
Refactoring in
513813b514 removed the lam variable. Previously, it was
used as a temporary iteration variable over SHAKE blocks, but that
refactoring to use the main variable changed the logic of the
following loop.
Fixes #2434
Change-Id: Ia9642f50358ab31ec98f8317f7a1dcda8622a9f1
Berk Hess [Mon, 5 Mar 2018 15:34:38 +0000 (16:34 +0100)]
Make multi-atom TPI reproducible
Test particle insertion of molecules of more than one atom called
a rotate function with multiple random calls in the arguments. This
lead to non-reproducible results, at least when switching compiler,
since the language does not define the argument evaluation order.
Note that this issue did not affect physical correctness.
Change-Id: I9ab07566878f381f11284d813d9077fa90e68866
Viveca Lindahl [Mon, 5 Mar 2018 18:31:20 +0000 (19:31 +0100)]
Add checks for non-null log file pointer in AWH
Mdp-option 'awh1-equilibrate-histogram=yes' and certain run setups could
lead to a segmentation fault due to fplog being null.
Fixes #2436
Change-Id: I0110325a8624c9d434af5eeeccace29814d40f2d
Berk Hess [Wed, 28 Feb 2018 13:09:33 +0000 (14:09 +0100)]
Work around gcc bug with group kernel tables
The LJ-only interaction tables for the group kernels were incorrectly
copied with the combination of gcc-6, AVX and -O3.
Since this bug replaced -1/(6 r^6), 1/(12 r^-12) by 1/r,-1/(6 r^6)
for odd table indices, this could not cause silent errors.
Fixes #2424
Change-Id: I021d4f2fe81bd635e6f02686118d661af8c444a6
Szilárd Páll [Fri, 2 Mar 2018 16:58:41 +0000 (17:58 +0100)]
Add to the contributor section
Change-Id: I1642f1ca247cf0e11781af4848b74e3d0ebd5082
Berk Hess [Thu, 1 Mar 2018 20:58:32 +0000 (21:58 +0100)]
Fix AWH bias-sharing with parallel simulation
Sharing the AWH bias over multiple simulations only worked when
each simulation was running on a single MPI rank. Now parallel
simulations also work.
Fixes #2433.
Change-Id: I71f9069a31b033151c772aac84c9912d91b213a1
Berk Hess [Fri, 23 Feb 2018 14:22:50 +0000 (15:22 +0100)]
Detect AMD SMT topology
On AMD Zen the cpuinfo code detected hyperthreading but put all
threads on different cores in the topology. Now the correct
topology is detected using extended APIC.
Also disabled topology detection for non-AMD, non-x2APIC x86.
Fixes #2388
Change-Id: I194f3e09e669c20d1d62355a36be062e6cce264e
Berk Hess [Thu, 1 Mar 2018 08:30:55 +0000 (09:30 +0100)]
Fix mdrun multisim with separate PME ranks
When running multiple simulations using separate PME ranks,
mdrun would call MPI_Barrier with MPI_COMM_NULL on some ranks.
Note: no new release note needed, since this fixes a fix.
Refs #2403
Fixes #2431
Fixes #2432
Change-Id: I7fe96a15b5030dea3e093d12850f89f00ccc9f48
Mark Abraham [Fri, 23 Feb 2018 14:15:46 +0000 (15:15 +0100)]
Fix GPU utils test
We should only attempt device-side work when we have compatible GPUs.
Fixes #2405 for CUDA
Change-Id: Idc28c7e89a5f08ee1d19943e3663385f2b23ff44
Mark Abraham [Fri, 23 Feb 2018 10:45:56 +0000 (11:45 +0100)]
Permit define .mdp field to assign values
It is intended that the "define" .mdp field can set preprocessor
variables to values, but this got broken in some clean up. Added a
test to cover it.
Fixes #2392
Change-Id: I16a3705a0d59a912a8eb7bfad0b472f12d2dc377
Mark Abraham [Tue, 9 Jan 2018 13:41:38 +0000 (14:41 +0100)]
Organize for recording 2016-era release notes and add them
This hierarchical organization will make it easy for us to present to
users that there were two maintained release series at the time of
writing, while making available links to the releases notes of
unmaintained series, and having a straightforward path for migrating
the 2016 folder to the older folder and updating the appropriate
links.
In master branch, we will have stub .rst files in
docs/release-notes/major/ that we can fill out as functionality
changes, and movev to docs/release-notes/2019/major when we
make the release-2019 branch.
Changes to release notes in release branches will merge naturally.
Later, we can make sure that tarballs can have a useful plain-text
version built into them via sphinx also.
Change-Id: Ie35f90a616cb89727f5a9600389fdf228ecd03cb
Berk Hess [Wed, 21 Feb 2018 22:02:32 +0000 (23:02 +0100)]
Fix md integrator with Nose-Hoover coupling
When applying NH T-coupling at an MD step and no PR P-coupling,
the md integrator could apply pressure scaling with an uninitialized
or outdated PR scaling matrix.
Fixes #2418
Change-Id: I835db72776e7782ac044807961bb899e4f8c6c7b
Szilárd Páll [Wed, 21 Feb 2018 00:12:59 +0000 (01:12 +0100)]
Switch pre-submit CUDA 8.0 test to 9.0
Noted in TODO to add a CUDA 9.1 + gcc 6 config.
Change-Id: I1e9e1a0bcd99237167335f475d65791f6059dbb3
Szilárd Páll [Fri, 16 Feb 2018 18:48:46 +0000 (19:48 +0100)]
Avoid aborting mdrun when GPU sanity check detects errors
A release assertion was added which assumed that the GPU
compatibility/sanity checks return with a clean CUDA API state.
Consequently, any run that encountered a non-success return value from
the CUDA API would abort the run instead of continuing the run without
using the GPU in question.
This change adds code to handle and issue a note on the error
encountered as well as ensures that the CUDA API error state cleared
at the return of the GPU detection.
Fixes #2415
Change-Id: I5d7ed59ef8e4052a75b51c9a526b8dcb465ff611
Mark Abraham [Fri, 16 Feb 2018 17:09:01 +0000 (18:09 +0100)]
Merge branch release-2016 into release-2018
Change-Id: If1c8c37bbfc44ae383999b828d1dfea4cf67d1ea
Mark Abraham [Fri, 16 Feb 2018 15:06:21 +0000 (16:06 +0100)]
Bumped patch version for next release
Change-Id: I174548b1be5261aea861ec29d550ee323ce3702e
Berk Hess [Wed, 7 Feb 2018 10:03:46 +0000 (11:03 +0100)]
Correct multisim MPI barrier
An MPI barrier used with multisim was called on incorrect ranks
and a barrier was missing.
Fixes #2403
Change-Id: I06a66167afc8dca9cdd4ca9b4f9a806984a6ec7a
Aleksei Iupinov [Thu, 15 Feb 2018 12:27:48 +0000 (13:27 +0100)]
Fix PME for large systems with Fermi GPUs
PME spread/gather CUDA kernel scheduling did not account for
compute capability limitations. Realistically this has only
caused it to fail on CC 2.x with input systems larger than
2^18 ~= 262k atoms. This is now fixed for all CUDA architectures.
Fixes #2409
Change-Id: I59295b5d53a341d08a221aebb52e1db9f1e80107
Mark Abraham [Fri, 16 Feb 2018 07:41:28 +0000 (08:41 +0100)]
Version 2016.5
Change-Id: I7dd31f2deea884f3075555547c4f3691bd4adae3
Aleksei Iupinov [Thu, 15 Feb 2018 14:19:33 +0000 (15:19 +0100)]
Add the missing comma in the quote
This was printed as:
GROMACS reminds you: "It's just B I O L O G Y, can't you see?Joe Jackson" ((null))
Change-Id: I69e86ecda8930fffeeab3a54f2f015339fd9b345