Roland Schulz [Fri, 5 Jun 2015 00:34:38 +0000 (20:34 -0400)]
Fix Wundef warnings
Also fixes a performance bug in gmx_simd_invsqrt_pair_d. Previuosly it
did unnecessary number of iterations because it used an non-existing
preprocessor variable.
Change-Id: Idcdf3872b5a169e8690721bbe83922a4ab280da8
Teemu Murtola [Tue, 23 Jun 2015 06:49:40 +0000 (09:49 +0300)]
Move documentation on tool changes from wiki
Move the text on tool changes from the wiki page to the user guide,
where it is much easier to maintain together with the code changes.
For now, this only contains the 5.0-era changes more or less directly
from the wiki, but I will improve this (as a separate change) once I
have more time.
Change-Id: I4ccea605783de2949221d604e232b36c726dcaa7
Mark Abraham [Thu, 25 Jun 2015 16:57:44 +0000 (18:57 +0200)]
Merge "Merge release-5-0 into master"
Berk Hess [Wed, 4 Mar 2015 21:46:00 +0000 (22:46 +0100)]
Reenabled SIMD kernels without cut-offs
In 4.6 there was a bug that caused incorrect results with group scheme
SIMD kernels with systems without cut-offs. This seems to have been
resolved already in 5.0.
Refs #1249.
Change-Id: I86c2b2ae097769472c1748e6e03a673a58a938eb
Mark Abraham [Thu, 25 Jun 2015 08:47:53 +0000 (10:47 +0200)]
Merge release-5-0 into master
Conflicts:
docs/install-guide/install-guide.md
Applied release-5-0 changes to docs/install-guide/index.rst
docs/manual/install.tex
Applied release-5-0 changes to docs/user-guide/environment-variables.rst
src/gromacs/commandline/cmdlineprogramcontext.cpp
Applied comment from release-5-0
src/gromacs/gmxana/gmx_hbond.c
Removed smooth_tail as in release-5-0
src/gromacs/gmxlib/gmx_detect_hardware.cpp
Removed GMX_MAX_THREADS implementation as in release-5-0
(adjacent changes)
src/gromacs/utility/init.cpp
Combined changes to include statements
src/gromacs/utility/path.cpp
Combined changes to include statements
src/programs/mdrun/mdrun.cpp
Added new please_cite calls from release-5-0 to new call site
in runner.cpp
Change-Id: I5b75b12bb8a49a606b086184017b754477d65068
Mark Abraham [Wed, 24 Jun 2015 21:33:24 +0000 (23:33 +0200)]
Merge release-4-6 into release-5-0
Change-Id: I6cc179f767cc4e0fc1dc3fc0b85428df986c16df
Erik Lindahl [Tue, 23 Jun 2015 20:43:33 +0000 (16:43 -0400)]
Avoid accessing hackblocks for x2top
Previous fixes for generating dihedrals would cause us to access
the hackblock even when using x2top, which we should not do.
Fixes #1711.
Change-Id: Id0ea6d524d80b87fe257c9fd4f1c48c4be828654
Magnus Lundborg [Fri, 27 Mar 2015 11:20:38 +0000 (12:20 +0100)]
Update header when appending to TNG file.
The library now handles updating the size of the headers
by moving the first frame sets to make room (if necessary).
Therefore this is now enabled when appending to a trajectory
from mdrun.
Change-Id: I7334a1b0c251856f30e116b63161f7676055dce1
Berk Hess [Mon, 15 Jun 2015 21:56:26 +0000 (23:56 +0200)]
GPU Ewald table kernel now uses CPU spacing
The tabulated Ewald GPU kernels (only used by default on Fermi),
used a fixed table spacing. Now the same adaptive spacing as on the
CPU is used. With default settings this leads to a coarser table.
Change-Id: I35f0c89e00301ac7e1260b1c0dcc1604300da5aa
Berk Hess [Sun, 21 Jun 2015 06:17:21 +0000 (08:17 +0200)]
Avoid GPU selection with GPU emulation
Change-Id: Iee5949fa11419b0c1344edb6c85ab475baa77719
Berk Hess [Mon, 22 Jun 2015 07:33:29 +0000 (09:33 +0200)]
Minor reformatting of SIMD mismatch message
Added extra newline, removed parentheses.
Change-Id: I2ec3f6d078dfa3b4587213c5ec421d36443a01af
Berk Hess [Mon, 22 Jun 2015 12:03:39 +0000 (14:03 +0200)]
Add sugar to print empty line in printBinaryInformation
The binary information print was missing a prefix and suffix
on an empty line which caused invalid xvg file formatting.
Change-Id: I8faa76502fc44ebd698387e4ab0f85f1473be710
Erik Lindahl [Thu, 18 Jun 2015 16:44:33 +0000 (18:44 +0200)]
Updated physical constants from NIST 2010 CODATA
Minor fixes (usually to the 5-6th decimal), and
more constants have been derived the basic ones instead
of specifying values directly. The units section in
the manual has been updated accordingly.
Fixes #1671.
Change-Id: Ic1d853a4fb6c70c81c3969d3d8ba86f52956ef67
Erik Lindahl [Sun, 21 Jun 2015 13:49:03 +0000 (15:49 +0200)]
Removed buggy -smooth hack in hbond module
As discussed in redmine #1553, this was a hack
added a while ago, but apparently it leads to
segfaults. We should avoid hacks in the first
place, and since nobody has been interested in
fixing it for the last year it's time to kill it.
Fixes #1553.
Change-Id: I94faa3c543bcca4c729753c8b5cdaf5a5775d0ff
Berk Hess [Mon, 22 Jun 2015 14:50:53 +0000 (16:50 +0200)]
Fix g_energy average/RMSD bug
Made g_energy produce correct output for energy files from continued
and appended runs with nstcalcenergy=nstenergy. In that case a count
in the energy file is/was incorrect, but that entry is actually not
necessary for determining the average and RMSD of energy terms. The
RMSD would be NaN and the average would be off in the last decimal.
Fixes #1342.
Change-Id: I82007bfe508023e1c1e17366e10f76bc4470d238
Berk Hess [Sun, 21 Jun 2015 09:02:10 +0000 (11:02 +0200)]
Update launch configuration for physical nodes
OpenMP thread count now prints thread count ranges over ranks.
GPU usage report adds host name with multiple MPI processes.
Change-Id: I9011415957ad5d875d2c215abb0f7f60810c372c
Roland Schulz [Fri, 19 Jun 2015 03:37:16 +0000 (23:37 -0400)]
Fix GMX_ALIGNMENT for MSVC 2012 and 2013
Issue previously identified for 2010 is not fixed
until 2015.
Change-Id: I617ac9524a2e054b325fdc19675fdee0a60370c8
Berk Hess [Thu, 18 Jun 2015 09:42:40 +0000 (11:42 +0200)]
Avoid fp exceptions in pair search debug
Also extended GPU list statistics debug prints.
Change-Id: I8100aac2f3433bf06b3d11c8fedcdd2d3cf5c286
Erik Lindahl [Wed, 17 Jun 2015 06:54:20 +0000 (08:54 +0200)]
Fix compiler warnings in cmake tests
This will not be visible to users, and it won't make it
possible to run cmake with -Werror since lots of internal tests
do not work, but since I fixed a couple of them we might
as well put it in gerrit.
Known remaining issues:
- HAVE_LIBM
Refs #1750.
Change-Id: I734f83f229108e50e2914d455f4032137f924773
Erik Lindahl [Thu, 18 Jun 2015 19:57:11 +0000 (21:57 +0200)]
Use MPI_THREAD_FUNNELED when available
We have never observed any problems with MPI and OpenMP,
but for compliance we should call MPI_Init_thread() and
try to get MPI_THREAD_FUNNELED support level. However,
if that level is not supported we simply call the old
MPI_Init() instead - at least for Gromacs that seems fine.
If we get an error return code we warn the user, but if
MPI_init_thread() still worked we hope for the best and
don't bother the user.
Fixes #1127.
Change-Id: I11b81a65125e32b95255dbb769cf86b835bd62ab
Roland Schulz [Thu, 18 Jun 2015 05:37:23 +0000 (01:37 -0400)]
Fix cmake 3.1 warnings with MSVC
Change-Id: I4c080cd547fdb36695d6d906ea56a1393e4f42aa
Erik Lindahl [Sat, 20 Jun 2015 09:54:26 +0000 (11:54 +0200)]
Fix segfault in random access XTC searching
The XTC random access routine was accessing natoms
in a substructure that could be a null pointer. Fixed
by adding natoms as a separate field in the
high-level status, so we don't depend on frame data.
Fixes #1705.
Change-Id: I88c961b33ae21b16d64ed5d7514a1e0287c89baf
Erik Lindahl [Tue, 16 Jun 2015 22:18:27 +0000 (00:18 +0200)]
Fix argument order error for g_rmsdist
Incorrect argument order to calc_rms() caused
command options to be permuted.
Fixes #1709.
Change-Id: I82042dac463c8bb305ab3d3bc2a122b5409c55ef
Erik Lindahl [Sat, 20 Jun 2015 14:01:46 +0000 (16:01 +0200)]
Fix gro errors with PDB insertion codes
The insertion codes are discarded when converting to GRO files,
which results in adjacent residues with different names but
identical numbers. The reading code has been altered to identify
new residues also when the resname changes; this does not fix
the duplicate numbers (it cannot be fixed in GRO files), but it
will correctly propagate all data so the correct labels can
be recovered by using gmx trjconv with the original PDB file for
the -s argument.
Fixes #1600.
Change-Id: Iaf79f3f9e548e8555d78cb39e869410aa8186029
Berk Hess [Sun, 21 Jun 2015 06:13:37 +0000 (08:13 +0200)]
Replaced hardware threads by logical cores in output
All output (except for debug output) now uses the term logical cores
to report the number of hardware threads.
Add indentation for per node hardware property prints.
Change-Id: I821c8d76ab498b37aa1b510d8a3dd67bb42ffdf9
Szilard Pall [Sat, 20 Jun 2015 23:04:28 +0000 (01:04 +0200)]
fix CPU core oversubscription detection
The detection became non-functional due to unlucky incorrect order in
which the arguments were passed.
Change-Id: Id29ff87e504585f783be742b92a861c06c5e42ac
Erik Lindahl [Fri, 19 Jun 2015 08:02:26 +0000 (10:02 +0200)]
Updated docs for g_gyrate
Added the equations we use for the axis
components.
Fixes #1564.
Change-Id: Ifce17326f738a72386bf24f949e418d2550568b5
Erik Lindahl [Thu, 18 Jun 2015 12:44:14 +0000 (14:44 +0200)]
Fix potential buffer overflow in pdb2gmx
Residue rename database entries were read into 6-char
string variables. We now check and issue fatal errors
if the lengths are above 5 characters.
Fixes #1649.
Change-Id: Id4d88a565b212ef279d400f42b5f2732550eded6
Erik Lindahl [Fri, 19 Jun 2015 08:20:23 +0000 (10:20 +0200)]
Disallow infinite epsilon with PME or GB.
This leads to divide-by-zero errors, and since it just turns off
electrostatics it will be faster to use a plain cutoff, which we
now recommend instead.
Fixes #1297.
Change-Id: Ia5eba7a1d4bd3b387174c9cb4878a2d65ead2c6c
Erik Lindahl [Fri, 19 Jun 2015 07:29:40 +0000 (09:29 +0200)]
Remove GMX_MAX_MPI_THREADS
This variable has been orpaned for quite a while, and
it's a good example how we introduce bugs by introducing
lots of ways to control the same functionality, and then
we forget to update some of them later. Let's focus on
the command line options as the single way to control
the number of threads in Gromacs.
Fixes #1550.
Change-Id: I37a87125b9dcac36362b561418d787167bb64cec
Erik Lindahl [Fri, 19 Jun 2015 10:16:23 +0000 (12:16 +0200)]
Fix reproducibility bug in fft5d
fft5d has been accessing FFTW directly instead of using the
Gromacs FFT interface, and while doing so the estimate flag was
not correctly set for reproducible runs. For now we have just
fixed it, but this FFTW-specific code should be removed from fft5d,
or we will likely see more fft bugs due to duplicated code paths.
Fixes #1690.
Change-Id: Ib03f7af710ed208d2824f105bd15712d32632cfa
Erik Lindahl [Thu, 18 Jun 2015 17:26:27 +0000 (19:26 +0200)]
Handle multidir/multisim with single argument correctly
Mdrun would only initialize the multi option correctly
with more than one argument, which caused mdrun to fail
in strange ways since it looked for topol.tpr in the
current directory instead.
Fixes #1712.
Change-Id: Ib89860fdff5f8523eee6c2f5a068390b8d4e3c8d
Erik Lindahl [Tue, 16 Jun 2015 22:15:18 +0000 (00:15 +0200)]
Fix incorrect shift with g_density -center
Fixes #1698.
Change-Id: I22be246eded9c1fc6f421f14eb3938584afed0de
Roland Schulz [Thu, 18 Jun 2015 05:58:23 +0000 (01:58 -0400)]
Fix missing include
Didn't compile with MSVC 2013
Change-Id: Ice8af840ba52dc7b6c9fe54c269a641f0ccc3c60
Berk Hess [Mon, 11 Aug 2014 16:11:17 +0000 (18:11 +0200)]
Reduced the cost of the pull communication
With more than 32 ranks, a sub-communicator will be used
for the pull communication. This reduces the pull communication
significantly with small pull groups. With large pull groups the total
simulation performance might not improve much, because ranks
that are not in the sub-communicator will later wait for the pull
ranks during the communication for the constraints.
Added a pull_comm_t struct to separate the data used for communication.
Change-Id: I92b64d098b508b11718ef3ae175b771032ad7be2
Mark Abraham [Wed, 17 Jun 2015 21:16:04 +0000 (23:16 +0200)]
Fix typo in GMX_BUILD_OWN_FFTW message
Change-Id: Ieec8b7d1bccd7e9654a14091e42f5047d441db31
Szilard Pall [Wed, 17 Jun 2015 22:59:57 +0000 (00:59 +0200)]
fix minor CUDA NB kernel performance regression
Commit
f2b9db26 introduced the thread index z component as a stride in
the middle j4 loop. As this index is not a constant but a value
loaded from a special register, this change caused up to a few %
performance loss in the force kernels. This went unnoticed because
some architectures (cc 3.5/5.2) and some compilers (CUDA 7.0) were
barely affected.
Change-Id: I423790e8fb01a35f7234d26ff064dcc555e73c48
Teemu Murtola [Wed, 17 Jun 2015 10:53:54 +0000 (13:53 +0300)]
Minor clean up for refdata.*
- Remove global functions that are no longer necessary. All the state
about the reference data mode is stored internally in refdata.cpp.
These were remnants from an old implementation where the code was
split into multiple .cpp files to support compilation of testutils/
without libxml2 dependencies.
- Make the self-tests for the reference data code not use the source
tree as a location for the transient data they create.
In addition to clarifying the code, these should make it harder to
misuse the constructor intended for self-testing, since it will be
difficult to pass Jenkins if someone tries to use it for other tests.
Change-Id: I204ddadfc224a79c587f0588a4d510b7b8486f9b
Teemu Murtola [Tue, 16 Jun 2015 09:53:02 +0000 (12:53 +0300)]
Improve logic for automatic selection names
If a selection is directly provided from an external index group, the
name of the selection is set to be the name of the group, irrespective
of the exact way the group is selected. The code that did this was a
bit too eager, and used the name of the group that appeared around the
beginning of a more complex selection in some other cases, leading to
confusion.
Make the code only use the name of the group if the group is really used
as-is, and otherwise use the selection text. Add explicit tests for
this behavior.
Change-Id: Ic7fe2626a07cfd3cac3773046ed9f83484ba4368
Berk Hess [Mon, 13 Apr 2015 08:55:04 +0000 (10:55 +0200)]
Refactored pull data structures
Moved the pull work variables into a new pull_t struct.
Only the pull input parameters remain in (renamed) pull_params_t.
For the moment struct pull_t pull_work is still present in t_inputrec.
This should later be moved to a more appropriate place.
Change-Id: I78f6f9736d52514f0327c86e43d4fb2ac88d60cd
Mark Abraham [Fri, 22 May 2015 11:42:21 +0000 (13:42 +0200)]
Stop people installing into the build tree
Several users have tried this and run into problems.
Also patch the install guide so people can find useful information
about using CMAKE_INSTALL_PREFIX
Change-Id: I43b3d9959e0a2fc93dc1d80fb8fb0727cf459f11
Erik Lindahl [Fri, 12 Jun 2015 21:16:07 +0000 (23:16 +0200)]
Fix CUDA version info in NVML application clock warning
Report driver and runtime versions, not the compute capability
of the card (since we already detected the card is recent enough).
Fixes #1706.
Change-Id: Ida8b36203f56dcda20dc367c69dc02586edf40e4
Erik Lindahl [Sat, 13 Jun 2015 08:22:28 +0000 (10:22 +0200)]
Add membrane embedding docs
These were killed by mistake in
86601a237df when the
separate g_membed program was merged into mdrun.
Fixes #1724.
Change-Id: If97dbf13c269e0711cda9798fac03225920c0d6f
Berk Hess [Tue, 16 Jun 2015 18:16:56 +0000 (20:16 +0200)]
Added missing DD cycle counting
Cycle counting was missing for DD repartitioning after replica
exchange or coord swap. Removed DD cycle counting for initial DD.
Moved DD cycle counting into dd_partition_system and added
subract_cycles function with assertion to detect cycle wrapping.
Fixes #1677.
Change-Id: I7f1b19397b36456f1d120dbc0080146a384def5a
Erik Lindahl [Fri, 12 Jun 2015 21:32:56 +0000 (23:32 +0200)]
Updated FFTW recommendations in install-guide.
Both SSE2 and AVX should be used, and there is now
info about the upcoming FFTW-3.3.5 with more SIMD support,
as well as a link to an unofficial prerelease on the gmx site.
Fixes #1696.
Change-Id: I6413d5e0e06c78a3c9f62acbf6fa0bfc1bd0a561
Mark Abraham [Tue, 20 Jan 2015 11:05:31 +0000 (12:05 +0100)]
Move code for managing mdrun -cpi and -append
Prepares for refactoring to simplify and fix this handling. Kept logic
peculiar to handling mdrun command-line options near other such code.
Renamed functions to better suit their roles. Renamed bAppend
variables, in particular to separate the role of "the user asked for
appending" from "whether mdrun is actually going to do appending."
Change-Id: I063138a49d210e92cebe19e290dc6a0e7b72b1cf
Berk Hess [Thu, 7 May 2015 20:28:06 +0000 (22:28 +0200)]
Automated the -gpu_id option
With #PPrank <= #gpu in a node, the GPU id's were already assigned
automatically. Now with #PPrank a multiple of #GPU they are assigned
automatically with GPU sharing.
Change-Id: I59079b542b5703553c3e1b841c47abdc65f64459
Erik Lindahl [Fri, 12 Jun 2015 19:49:27 +0000 (21:49 +0200)]
Fix segfault with timer reset and -nb cpu
Fixes #1710.
Change-Id: I701b8bb6111fd43379997b7af0aedae7a5fe567a
Erik Lindahl [Fri, 12 Jun 2015 20:46:24 +0000 (22:46 +0200)]
Avoid warning about affinity on Blue Gene, reduce warnings
- Blue Gene does not migrate threads, so don't warn about
affinity setting not being available.
- To avoid flooding users with warnings, just use warnings
when it is very likely the user did something incorrect
when setting pinning options, but notes when it might be
a property of the platform, or when it is not severe.
Fixes #1703.
Change-Id: Idaa781959e0997f6737593a8fd9243d6a979a493
Mark Abraham [Thu, 28 May 2015 14:15:29 +0000 (16:15 +0200)]
Fix pairs_nb not recognized as part of moleculetype
Old code gives "unknown directive" error from the default of the
switch statement.
Fixes #1749
Change-Id: I54977f76f82cfdbfd4a7070129aa365d4fe5e188
Mark Abraham [Wed, 18 Mar 2015 08:52:15 +0000 (08:52 +0000)]
Add unit tests for ArrayRef
This fixes mdrun signalling on BG/Q. The templated constructor for
ArrayRef does not work with xlc 12 on BG/Q with array fields of
structs unless the base type has size equal to char. Presumably this
is another example of the way that attributes of struct fields just
get thrown away by compilers.
Changed name of local variable to sig, just in case "signal" clashes
with a preprocessor symbol somewhere...
Some changes to the arrayref.h implementation to make it easier to
write the tests as type-parameterized, by making the factory functions
also appear as members of the corresponding classes, with the same
name for both ArrayRef and ConstArrayRef. While there, remove some
documentation duplication.
Fixes #1701
Change-Id: I6894706b224dc5f3db7893503371107f1ff324d2
Roland Schulz [Tue, 16 Jun 2015 06:15:36 +0000 (02:15 -0400)]
Fix warning in uncrustify
Change-Id: I101a3fcfe4d50191a2237ac0743979a841349cce
Roland Schulz [Tue, 16 Jun 2015 06:29:53 +0000 (02:29 -0400)]
Fix consts in bonded and clincs
- binary constants are not valid C++03
- extra unnecessary bits give warnings with ICC 15
Change-Id: I7645e2c489e6371bfabcbbf460fb3acbda447108
Teemu Murtola [Mon, 15 Jun 2015 15:28:33 +0000 (18:28 +0300)]
Fix broken links from the old flow chart
The program help pages got moved from programs/ to onlinehelp/, but
these explicit links were forgotten.
Change-Id: Ia37f4b20d37f40f727835bca71d9b85f3260502c
Erik Lindahl [Mon, 15 Jun 2015 09:16:49 +0000 (11:16 +0200)]
Fix OS X FFTW build failures introduced 86a772
The two avx/sse options needs to be a list, and
since FFTW always picks gcc by default we need
to disable FFTW AVX regardless of the compiler.
Change-Id: Ie82d7cc85de0715d5f2dd7a6198af079575fe891
Erik Lindahl [Tue, 12 May 2015 07:07:58 +0000 (09:07 +0200)]
Fixed SIMD detection and flags common for IBM archs
At some point the entire SIMD detection code in
CMake had been turned off for all platforms except
x86, likely because it caused problems when cross-
compiling for BG/Q. This fixes it to avoid executing
a binary when cross-compiling, but re-enables the
automatic detection on all other non-x86 platforms.
Second, the IBM compilers are buggy _without_ -O3
for SIMD code, so we now add high optimization for
xlc by default. When using CUDA, we avoid propagating
CFLAGS since that causes problems with VSX "vector",
but we add the -O3 optimization level to nvcc.
Finally, at high optimization level xlc produces
incorrect sign for tan(0) when it is converted to
float. We fix this by using tanf() when the compiler
is xlc.
Change-Id: Ia4cb627e5c65b84fee87815fcb5f5c220f34c2f3
Rossen Apostolov [Tue, 3 Mar 2015 13:47:17 +0000 (14:47 +0100)]
Building own fftw now uses version 3.3.4
Uses --enable-avx when GMX_SIMD is also AVX-based (and not on Mac with
GCC, where the build runs into issues with which assembler to use).
Change-Id: I47bc33655970ba8fc4c005de00bad3c5cb06e763
Berk Hess [Wed, 22 Apr 2015 09:42:57 +0000 (11:42 +0200)]
Refactored mdrun resource division
The functions concerned with divided MPI/thread resources have been
moved from runner.cpp to the new file resource-division.cpp.
Set min_atoms_per_mpi_rank to 1 for NM and TPI to avoid compiler
warning and for NM on systems of a few atoms.
Change-Id: I94f770c47b4b5ca03de8f5a29a165631796204ad
Berk Hess [Wed, 29 Apr 2015 10:13:00 +0000 (12:13 +0200)]
Hardware reporting now covers all nodes
The CPU and GPU hardware reporting and checking were only printed
for the node(s) of the master rank(s) of each simulation.
Now the most important CPU and GPU information is reduced over
MPI_COMM_WORLD. These results are printed and checks/warnings are
now based on this.
Because this is now system wide, the printing is moved up to directly
after the detection and GPU info is printed together with CPU info.
The Gromacs reference printing is moved to after hardware printing.
Refs #1643.
Change-Id: I974871c9a293a922dd1db9dcf633d485f62996ae
Mark Abraham [Fri, 12 Jun 2015 13:17:44 +0000 (15:17 +0200)]
Fix commandline test data
There was a recent change to the output routines, with a pending
commit of other code whose new reference data still used the old
output routines. Regenerated that data.
Change-Id: Ic25d10b74b70733b8aeb271a293d5580c745ca5d
Teemu Murtola [Thu, 23 Apr 2015 10:31:22 +0000 (13:31 +0300)]
Update help output
Various changes to console help output (and some to man output) based on
feedback in #1687:
- People seem to prefer a centered startup header with some ASCII art,
so made the first output line just like that (except if running with
-quiet), and center the list of authors.
- Always start the option description at a new line.
- Give more space to various parts of the option list so that they are
more likely to align up.
- Split the file listing based on input/output type. This causes,
e.g., some logically related options (e.g., -cpi and -cpo) to get
separated in the output, but this seems to be the preferred approach.
- Add formatting to the synopsis on man pages (similar to how the
options appeared in the 4.6-era man pages, except that reasonable
line wrapping is still there).
Clean up the design for formatting the options list; now the actual
formatting code is better encapsulated in HelpWriterContext.
The user-visible scope of this change is limited to changing behavior
that changed between 4.6 and 5.0. Thus, the changes here should be
sufficient to close #1687.
Change-Id: I349fd9021472f064f5797441090a3f3864868280
Magnus Lundborg [Fri, 12 Jun 2015 11:12:24 +0000 (13:12 +0200)]
TNG version 1.7.6
Fixed bug with reading and writing TNG compressed blocks
on big endian platforms.
Fixed compiler warning about potentially uninitialized values.
Fixes #1725.
Change-Id: I92062492116fa3044c3d1d0d0f920cfe42d21cbe
Teemu Murtola [Fri, 5 Jun 2015 19:25:13 +0000 (22:25 +0300)]
Improve uncrustify Jenkins builds
Add a script to wrap uncrustify.sh for Jenkins, and make it produce
additional text files that can more easily be used for further
processing in Jenkins.
Change-Id: I3c25760eec4c37a07a7889f471eb5b61f9932a9c
Teemu Murtola [Fri, 5 Jun 2015 11:20:41 +0000 (14:20 +0300)]
Initial docs for Jenkins integration
Add basic documentation for (some) of the Jenkins builds from the
perspective of how they interact with the build system. This part
cannot change without changes in the build system and so can be
documented in the same repository as the build system. And the
developer guide is a place where people would (hopefully) first look for
this kind of information. Links can be provided to more documentation
on Jenkins usage and other configuration (e.g., on the wiki), once that
stabilizes.
Related to #1731.
Change-Id: I87e180d12a77c692ac4594b6c062fb6ca150aa5d
Teemu Murtola [Fri, 22 May 2015 05:43:18 +0000 (08:43 +0300)]
Initial build system documentation in dev guide
Add some documentation for the build system from the developer
perspective. The documentation is far from complete, but should provide
a scaffold into which more documentation can be added, and should
already document parts that may not be familiar for everyone.
Explicit TODO items listed are not intended to be addressed in this
change.
Change-Id: I85094549d28ffeaf7063b472e2873ea6396ea897
Teemu Murtola [Fri, 5 Jun 2015 10:47:50 +0000 (13:47 +0300)]
Improve Jenkins docs build
- Use GMX_COMPACT_DOXYGEN=ON for per-patch set builds to save disk space
and some running time.
- Build also the man and install-guide targets, which were previously
missing.
- Make the build fail if it actually fails, and unstable if it just
produces warnings.
- Make the end of the console output contain some useful information on
what exactly failed. This gets put into unsuccessful-reason.log,
which can be used by Jenkins to show as the reason of the build
failure when it reports back to Gerrit.
- Add options to the script to make it more convenient to test.
Fix some issues found in man page generation and in handling of
GMX_COMPACT_DOXYGEN.
Change-Id: Ice7622d7760c3dbd74f7b5b25700482d0a08e06b
Teemu Murtola [Mon, 11 May 2015 10:52:27 +0000 (13:52 +0300)]
Extend source layout description in dev guide
Move the contents of codelayout.rst into overview.rst (some parts to
naming.rst), and organize and extend it for better readability.
This should now provide quite a comprehensive overview of the layout of
the Gromacs repository.
Change-Id: Ib9045c5572a072dacb5f22a64f0af48385307677
Mark Abraham [Thu, 11 Jun 2015 20:46:57 +0000 (22:46 +0200)]
Merge "Merge branch release-4-6 into release-5-0" into release-5-0
Mark Abraham [Tue, 9 Jun 2015 14:37:43 +0000 (16:37 +0200)]
Handle timing better in Jenkins
Sometimes we get floating-point exceptions in Jenkins when timers get
strange values and e.g. the code divides by zero. Added several checks
for such behaviour, including a new early exit from the timing routine
when a non-positive number of CPU cycles were counted. Removed a
recently added check that is now redundant because of the early exit.
Added several assertions about numbers of threads and ranks, which
might help reducing future mysterious FP exceptions if things are
broken elsewhere.
Fixes #1677
Change-Id: I532e164fc13e91f5f109dd63bb99c1569bdc70cd
Teemu Murtola [Fri, 22 May 2015 13:39:48 +0000 (16:39 +0300)]
Script for Jenkins documentation build
Move the script to do the documentation build from Jenkins to the
repository to reduce coupling. There is hardly any content in the
script that would need to change if something in Jenkins changes (and
those few details can easily be passed into the script), but a lot that
needs to be changed whenever the build system for the documentation is
refined.
For now, the contents are essentially the same as in the Jenkins job
configuration for Documentation_Gerrit_master or
Documentation_Nightly_master. Having a script in the same repository as
the build system makes it easier to evolve the script and the build
system in sync without enforcing rebases for every change in Gerrit.
Change-Id: If5eda21c94bc7d4707d4716d4f54b2be3ae898cf
Mark Abraham [Mon, 25 May 2015 08:39:09 +0000 (10:39 +0200)]
Clean up vsite interaction clean-up code
Lists of atom indices in interactions were being copied simply so that
they could be compared later. Instead, use a pointer to the original
data. This code has caused issues with multiple compiler versions and
checkers, concerned about initialization state or possible over-run,
and the best fix is to stop copying data unnecessarily.
Some general grompp checks were skipped for F_VSITEN, those are now
activated. The clean-up might have done incorrect memory access when
both normal vsites and F_VSITEN were present in the same molecule,
this is now fixed, but interactions with F_VSITEN are not removed.
Added new assertions to keep compilers happy that the logic of the use
of vsnral and first_atoms is sound.
Removed an old assertion that was added to satisfy an earlier version
of gcc.
Noted several TODOs for future clean up.
Change-Id: Ia7a6b2310640d1c1ca73ff3223269339d595c67d
Mark Abraham [Thu, 28 May 2015 14:34:47 +0000 (16:34 +0200)]
Document limitations of trjconv -dump
Change-Id: I336791a2eeb84a773de1ea96b8e36a42ac3fc66e
Teemu Murtola [Wed, 13 May 2015 18:11:03 +0000 (21:11 +0300)]
Misc. improvements to docs build system
- Get rid of GMX_BUILD_WEBPAGE. It did not disable any user-visible
detection, but only affected what build rules were generated, and none
of those affected the default 'all' target. Now the webpage target is
always created, and any informative messages that were previously
given during CMake time with GMX_BUILD_WEBPAGE=ON are now given when
the user tries to build the target.
- For all the documentation custom targets, create a dummy target that
gives a message to the user when building if the tools required to
build that target are not available.
- Reduce the required dependencies for the 'webpage' target. If some
non-essential parts cannot be built, just give a message to the user
and build the remaining parts with some broken links.
These should make the build system easier to document and to understand
from the user's perspective.
Change-Id: Ib65e3348b88b1e0461f1f69ba1218f09d376a6dc
Mark Abraham [Tue, 9 Jun 2015 12:41:38 +0000 (14:41 +0200)]
Merge branch release-4-6 into release-5-0
Conflicts:
src/gromacs/gmxlib/copyrite.cpp
New citations in release-5-0 branch adjacent to incoming
ones; kept all citations
src/programs/mdrun/mdrun.cpp
New please_cite calls next to a line removed in release-5-0;
retained the calls.
Change-Id: I463a598e32ffa82ebdd66211feba84635bc962b5
Teemu Murtola [Tue, 5 May 2015 10:55:23 +0000 (13:55 +0300)]
Add description of relocatable binaries
Add some explanation of the current implementation for relocatable
binaries to the developer guide. This was requested in some Gerrit
comment quite some time ago, so hopefully it will be helpful.
Change-Id: I6216306900ab138d24f34e8c2b472c06430d1003
Teemu Murtola [Wed, 3 Jun 2015 19:17:20 +0000 (22:17 +0300)]
Resolve one TODO for command line help tests
Make [PROGRAM] replacement respect the binary name passed to
CommandLineModuleManager, giving the tests full control over the help
output.
There are complications making this work nicely in the selection help
(requires some effort in propagating the information), so change the
wording there for now to avoid this tag. Can be revisited at a later
time if/when the help writing context is more uniform for different
cases that can trigger the selection help ('gmx help ...' vs. 'help ...'
in the selection prompt).
Change-Id: I93e7dd8279d3730d38122c212174e533420859b9
Teemu Murtola [Wed, 3 Jun 2015 10:54:56 +0000 (13:54 +0300)]
Improve user guide text for command line interface
- Restructure the tools.rst to have all the content on a single page.
- Correct inaccuracies in the information about common options and
general behavior, and extend the text to cover more cases.
- Include the list of common options on the HTML pages (somewhat ugly
still).
- Restructure the Sphinx input for easier management and
understandability: all pages generated from the gmx binary is now
under onlinehelp/, and all rst fragments (whether generated or not)
are under fragments/ to make it easy to apply the same rules to all of
them.
Change-Id: I2d55281bfba7dc781afcc2b09a9fef843730de5f
Szilard Pall [Tue, 2 Jun 2015 16:59:43 +0000 (18:59 +0200)]
add last two GROMACS paper citations
The 4.5 paper was only in the README file but not printed to the log
while the last (de-facto 4.6) LNCS paper was not mentioned anywhere.
Change-Id: I95e947564957ded0b7f76cb82c3fe4f69c72f85f
Erik Lindahl [Sat, 6 Jun 2015 11:06:42 +0000 (13:06 +0200)]
Fix out-of-range integer literals for threefry
The 64-bit literals need to have LL suffixes, or
xlc will warn about out-of-range literals and generate
code that fails the unit test. There was also a
single 64-bit literal in the implementation. Other
compilers appear to have handled this correctly,
so it is unlikely to have caused any user bug.
Refs #1725.
Change-Id: I575b6c12ace14973d4fae1edc81836686a2ff9d5
Szilard Pall [Tue, 21 Apr 2015 16:57:25 +0000 (18:57 +0200)]
Optimize atomic accumulation in CUDA NB kernel
As a result of this reorganization of the reduction, the final atomic
accumulation of the three force components can happen on three threads
concurrently. As this can be serviced by the hardware in a single
instruction, the optimization improves overall performance by a few %.
This also results in fewer shuffle operations.
Change-Id: I29519469b1e1848c026ee5b7a32256440031dbce
Roland Schulz [Tue, 26 May 2015 18:21:40 +0000 (11:21 -0700)]
Use stat to check that paths are equivalent
Replaces the previous approach of comparing path as string.
The previous approach didn't work reliable on case insenstive filesystems
or with symlinks.
Change-Id: Iee11c172db89b98a26b3592be2f285110a85a632
Roland Schulz [Fri, 5 Jun 2015 18:15:33 +0000 (14:15 -0400)]
Merge release-5-0 into master
Conflicts:
src/gromacs/gmxlib/rbin.c
(added also ICC16)
src/gromacs/mdlib/tpi.cpp
(gmx_simd_check_and_reset_overflow was removed already
in master branch, so no changes needed here)
src/programs/mdrun/runner.cpp
(adjacent additions)
Change-Id: I85d92bce71ebeb6e38ac63bb61c3931d5bb54c16
Roland Schulz [Sat, 30 May 2015 07:46:07 +0000 (03:46 -0400)]
Reenable lincs/bonded SIMD for ICC on Windows
It was accidentally disabled when disabling MSVC because ICC
also has _MSC_VER defined.
Change-Id: I7733b4af74a12dd0997ed22e86f2cdf459f08aba
Mark Abraham [Thu, 4 Jun 2015 11:32:32 +0000 (13:32 +0200)]
Remove gmx_simd_check_and_reset_overflow
We think this can only be implemented on x86, was only used for TPI,
and protected against an issue Berk can't reproduce. Thus best
removed.
Refs #1740
Change-Id: Ia8ca50b67683dab5a0e5e4a8b8485946edfd922a
Berk Hess [Tue, 19 May 2015 09:10:06 +0000 (11:10 +0200)]
Don't use PME ranks with GPUs and -npme=-1
The code disabling the automated PME rank choice with GPUs was
accidentally moved after init_domain_decomposition. This caused
PME ranks to be set up, but later a fatal_error occured for
inconsistent PP rank and GPU counts.
Refs #1374.
Change-Id: I5f6bcc90fecac7f63b332b8f1acca7368b5f71bc
Mark Abraham [Mon, 18 May 2015 12:36:37 +0000 (14:36 +0200)]
Fix naming from "Gromacs" to "GROMACS"
A bunch of user-facing names used the wrong name, so improved the
consistency there.
Fixing naming within source-code comments is not targeted here.
There's one or two fixes in the Doxygen comments, but that's not
targeted here. In particular, many references to "Gromacs" are in the
SIMD module, which would be silly to bump right now, since there are
lots of patches in Gerrit possibly affected.
Change-Id: I83f1414bffa322dbe2756dc4e5902342ac5fa2a5
Erik Lindahl [Sun, 22 Feb 2015 12:00:07 +0000 (13:00 +0100)]
More new quotes
Change-Id: I582cc4b025bd4f18f358134d11980d90cd66f363
Teemu Murtola [Sun, 31 May 2015 03:21:40 +0000 (06:21 +0300)]
Fix potential FPE in selection tests
Always initialize dynamic evaluation results to zero during the static
analysis pass. The old code tried to do that, but missed a few cases
where the same expression was evaluated more than once. Even during
static analysis, some dynamic arithmetic expressions are actually
evaluated, which could lead to FPE if the memory was uninitialized, even
though the results of the evaluation were never used.
Part of #1677.
Change-Id: I0cf73eb656d58f7ad08f6e12705c6d8a273adf84
Teemu Murtola [Tue, 2 Jun 2015 10:26:30 +0000 (13:26 +0300)]
Refactor rst parsing for console output
Move code from helpwritercontext.cpp into a separate class in
rstparser.*, and structure it more cleanly. The logic is mostly the
same as earlier, but the new structure also makes it easier to fix
some issues. In particular, since the code now first identifies what
the next paragraph is, and uses a separate loop to format it, it is much
easier to adapt the formatting to the contents of the paragraph.
Add comments for the complicated paragraph parsing logic.
To support this change, make TextLineWrapper not produce whitespace-only
lines if requested to indent an empty line.
Add tests for fixed/enhanced functionality.
Change-Id: I690dcf1578780d5fb0016d41da1e67dca96bd08c
Teemu Murtola [Sat, 30 May 2015 06:24:31 +0000 (09:24 +0300)]
Replace gromacs.7 man page with gmx.1
The description is the same, and the command list is there, but other
content is omitted. Useful parts can be added back later, when it is
clearer what we want to include here. Also, the man page now contains a
synopsis and common options for the gmx binary, as is suitable for
gmx.1.
Part of #1437.
Change-Id: I4dbdf542dd2b8a0a7a2e734eebdf13d68483842e
Teemu Murtola [Fri, 29 May 2015 10:10:11 +0000 (13:10 +0300)]
Document current help formatting
Add basic Doxygen documentation for the onlinehelp module. Most
notably, this describes the markup used for the in-source comments,
including the latest developments that allow bullet lists, enumerated
lists, and some titles.
Change-Id: I25be2bcd4c590356d4af0fa5671bbeddcd1afe1f
Teemu Murtola [Wed, 27 May 2015 10:12:35 +0000 (13:12 +0300)]
Basic support for titles within tool help
Preserve reStructuredText title formatting within tool help texts when
printing to console. For now, manual care is needed to properly nest
the sections in the rst help export (which means that the first
subsection needs to use an underline of ^'s). This allows removal of
all remaining [BR] tags, improving the HTML help.
Remove extra indentation from gmx wham bullet lists; they result in
unnecessary indentation in the HTML output that looks bad.
Fix formatting of the known issues bullet list by just using the
existing formatting engine, now that bullet lists are properly
supported.
Change-Id: I38a4f442f590515dde724c0cf60f0a862dc9cde7
Teemu Murtola [Wed, 27 May 2015 09:41:13 +0000 (12:41 +0300)]
Support rst tables in tool help texts
Make it possible to use reStructuredTables in the help texts for tools,
and replace some [BR] tags in gmx energy help with a proper table. The
formatting in the HTML help is greatly improved.
Change-Id: Ib25f7366d3196ba10fbc6cbcd09a0edd8dd3daf5
Roland Schulz [Fri, 29 May 2015 20:06:43 +0000 (16:06 -0400)]
Use stack buffer for LINCS&bonded gather/scatter
Fixes #1726
Change-Id: Idd57adc02c8fc05529a50e75f3017475b476a90f
Rossen Apostolov [Tue, 9 Sep 2014 12:38:33 +0000 (14:38 +0200)]
Converted random module to C++.
Removed ununsed variables. Changed gmx_rng_cycle_* functions
to use uint64 instead of int64. Fixed uninitialized return variable.
Change-Id: I41ba38f21a0560da1080c8f51bcb36c311783c89
Roland Schulz [Thu, 5 Feb 2015 06:28:51 +0000 (01:28 -0500)]
Work-around for ICC 15 on Phi
Change-Id: Id72e6fb124974f0d8572a1715bc1f25e536f7c69
Teemu Murtola [Sun, 24 May 2015 03:33:08 +0000 (06:33 +0300)]
Improve lists in user guide for selections
- Support enumerated list formatting in console output to make it
possible to use reStructuredText enumerated lists in help texts.
- Make the keyword list use a bullet list for the keyword groups,
providing some visual structure for the HTML output. The extra stars
do not hurt in the console output, either, but changed the extra help
indicator to be a + instead of * to reduce confusion with these other
stars.
Change-Id: I4d5063d4f117a31ea31d8d78cd799dfbd0f1eac8
Teemu Murtola [Sat, 23 May 2015 03:57:09 +0000 (06:57 +0300)]
Additional selection examples
Add some examples with explicit tool references, in particular for how
to use selections with tools that require pairs of atoms (gmx distance
and vector options of gmx gangle).
Add examples to explain the difference between the various
center-of-mass keywords.
Fix old note about default index groups with selection tools
(defselections.dat is not currently used).
Change-Id: Ic9e723e6dd2f46f8f0f5a7e1c4127994577acc3e
Berk Hess [Fri, 6 Mar 2015 11:32:24 +0000 (12:32 +0100)]
Refactoring of PME load balancing
Moved all the higher level PME load balancing management code from
md.cpp to pme-load-balancing.c.
Change-Id: Ic9f4be7373ccaa40b3867af6facce66b873efab3
Mark Abraham [Mon, 25 May 2015 15:43:45 +0000 (17:43 +0200)]
Fix warnings from GCC 5
Removed unnecessary ddata array from PME-spread spline
calculation. That might even be a useful optimization, for really bad
compilers. Moved declarations into the appropriate loops, so that
analyzers can work better here.
Added several other assertions to keep the code analyzers happy.
Reorganized implementation of get_vsite_masses to get cam declared and
used in a way that keeps analyzers happier. Removed a now useless
assert on j >= 1.
Change-Id: I9c5113f7e4013c629fca87614af4b74e249ee27a