Merge tag 'v2016.3' into release-2016-fda

cmake/gmxManageSimd.cmake

@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -74,6 +74,11 @@ macro(prepare_power_vsx_toolchain TOOLCHAIN_C_FLAGS_VARIABLE TOOLCHAIN_CXX_FLAGS
             message(FATAL_ERROR "Using VSX SIMD in double precision with GCC requires GCC-4.9 or later.")
         endif()
     endif()
+    if(${CMAKE_CXX_COMPILER_ID} MATCHES "XL" OR ${CMAKE_C_COMPILER_ID} MATCHES "XL")
+        if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "13.1.5" OR CMAKE_C_COMPILER_VERSION VERSION_LESS "13.1.5")
+            message(FATAL_ERROR "Using VSX SIMD requires XL compiler version 13.1.5 or later.")
+        endif()
+    endif()
 endmacro()
 
 # Issue a fatal error with an appropriate message, when the toolchain
@@ -418,7 +423,12 @@ elseif(GMX_SIMD STREQUAL "IBM_VSX")
         SIMD_${GMX_SIMD}_C_FLAGS SIMD_${GMX_SIMD}_CXX_FLAGS
         "-mvsx" "-maltivec -mabi=altivec" "-qarch=auto -qaltivec")
 
-    if(NOT SIMD_${GMX_SIMD}_C_FLAGS OR NOT SIMD_${GMX_SIMD}_CXX_FLAGS)
+    # Usually we check also for the C compiler here, but a C compiler
+    # is not required for SIMD support on this platform. cmake through
+    # at least version 3.7 cannot pass this check with the C compiler
+    # in the latest xlc 13.1.5, but the C++ compiler has different
+    # behaviour and is OK. See Redmine #2102.
+    if(NOT SIMD_${GMX_SIMD}_CXX_FLAGS)
         gmx_give_fatal_error_when_simd_support_not_found("IBM VSX" "disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
     endif()
 
@@ -476,11 +486,16 @@ endif()
 # rather than actual vector data. For now we disable __vectorcall with clang
 # when using the reference build.
 # 
+# xlc 13.1.5 does not seem recognize any attribute, and warns about invalid ones
+# so we avoid searching for any.
+#
 if(NOT DEFINED GMX_SIMD_CALLING_CONVENTION)
     if(GMX_TARGET_BGQ)
         set(CALLCONV_LIST " ")
     elseif(CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND GMX_SIMD STREQUAL "REFERENCE")
         set(CALLCONV_LIST __regcall " ")
+   elseif(CMAKE_CXX_COMPILER_ID MATCHES "XL")
+        set(CALLCONV_LIST " ")
     else()
         set(CALLCONV_LIST __vectorcall __regcall " ")
     endif()

cmake/gmxVersionInfo.cmake

@@ -188,7 +188,7 @@
 # The GROMACS convention is that these are the version number of the next
 # release that is going to be made from this branch.
 set(GMX_VERSION_MAJOR 2016)
-set(GMX_VERSION_PATCH 2)
+set(GMX_VERSION_PATCH 3)
 # The suffix, on the other hand, is used mainly for betas and release
 # candidates, where it signifies the most recent such release from
 # this branch; it will be empty before the first such release, as well
@@ -205,7 +205,7 @@ set(GMX_VERSION_SUFFIX "")
 # code being able to dynamically link with a version of libgromacs
 # that might not work.
 set(LIBRARY_SOVERSION_MAJOR 2)
-set(LIBRARY_SOVERSION_MINOR 2)
+set(LIBRARY_SOVERSION_MINOR 3)
 set(LIBRARY_VERSION ${LIBRARY_SOVERSION_MAJOR}.${LIBRARY_SOVERSION_MINOR}.0)
 
 #####################################################################
@@ -228,7 +228,7 @@ endif()
 
 set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}")
 set(REGRESSIONTEST_BRANCH "refs/heads/release-2016")
-set(REGRESSIONTEST_MD5SUM "e4d24e3c5f28602c2429b3a389121de8" CACHE INTERNAL "MD5 sum of the regressiontests tarball")
+set(REGRESSIONTEST_MD5SUM "bed92d1d9cdca66fbd2efa142b6e0dd3" CACHE INTERNAL "MD5 sum of the regressiontests tarball")
 
 math(EXPR GMX_VERSION_NUMERIC
      "${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")

docs/CMakeLists.txt

@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -120,6 +120,7 @@ if (SPHINX_FOUND)
         user-guide/index.rst
         user-guide/getting-started.rst
         user-guide/flow.rst
+        user-guide/system-preparation.rst
         user-guide/cutoff-schemes.rst
         user-guide/mdrun-features.rst
         user-guide/mdrun-performance.rst

docs/dev-manual/jenkins.rst

@@ -71,9 +71,18 @@ configuration should be more static.
 clang static analysis
 ^^^^^^^^^^^^^^^^^^^^^
 
-The exact build sequence and the CMake configuration used is in
-:file:`admin/builds/clang-analysis.py`.  This file also specifies the clang
-version used for the analysis.
+The file :file:`admin/builds/clang-analyzer.py` specifies the exact build
+sequence and the CMake cache variables used for clang static analysis.  This
+file also specifies the clang version used for the analysis, as well as the C++
+compiler used (``clang-static-analyzer-<version>``).
+
+To run the analysis outside Jenkins, you should run both ``cmake`` and ``make``
+under ``scan-build`` command using the same CMake cache variables as in the
+build script. When you do the initial CMake configuration with ``scan-build``,
+it sets the C++ compiler to the analyzer. Note that using ``scan-build`` like
+this will also analyze C code, but Jenkins ignores C code for analysis. This
+can result in extra warnings, which can be suppressed by manually setting
+CMAKE_C_COMPILER to a value other than Clang static analyzer.
 
 cppcheck
 ^^^^^^^^

docs/install-guide/index.rst

@@ -101,10 +101,12 @@ frequently provides the best performance.
 
 You should strive to use the most recent version of your
 compiler. Minimum supported compiler versions are
+
 * GNU (gcc) 4.6
 * Intel (icc) 14
 * LLVM (clang) 3.4
 * Microsoft (MSVC) 2015
+
 Other compilers may work (Cray, Pathscale, older clang) but do
 not offer competitive performance. We recommend against PGI because
 the performance with C++ is very bad.

docs/user-guide/index.rst

@@ -20,6 +20,7 @@ For background on algorithms and implementations, see the
    :maxdepth: 2
 
    getting-started
+   system-preparation
    cutoff-schemes
    mdrun-features
    mdrun-performance

docs/user-guide/mdrun-performance.rst

@@ -709,8 +709,12 @@ Running the OpenCL version of mdrun
 -----------------------------------
 
 The current version works with GCN-based AMD GPUs, and NVIDIA CUDA
-GPUs. Make sure that you have the latest drivers installed. The
-minimum OpenCL version required is |REQUIRED_OPENCL_MIN_VERSION|. See
+GPUs. Make sure that you have the latest drivers installed. For AMD GPUs,
+Mesa version 17.0 or newer with LLVM 4.0 or newer is supported in addition
+to the proprietary driver. For NVIDIA GPUs, using the proprietary driver is
+required as the open source nouveau driver (available in Mesa) does not
+provide the OpenCL support.
+The minimum OpenCL version required is |REQUIRED_OPENCL_MIN_VERSION|. See
 also the :ref:`known limitations <opencl-known-limitations>`.
 
 Devices from the AMD GCN architectures (all series) and NVIDIA Fermi

docs/user-guide/system-preparation.rst

@@ -0,0 +1,130 @@
+System preparation
+==================
+
+.. toctree::
+   :hidden:
+
+There are many ways to prepare a simulation system to run with
+|Gromacs|. These often vary with the kind of scientific question being
+considered, or the model physics involved. A protein-ligand atomistic
+free-energy simulation might need a multi-state topology, while a
+coarse-grained simulation might need to manage defaults that suit
+systems with higher density.
+
+Steps to consider
+-----------------
+
+The following general guidance should help with planning successful
+simulations. Some stages are optional for some kinds of simulations.
+
+1. Clearly identify the property or phenomena of interest to be
+   studied by performing the simulation. Do not continue further until
+   you are clear on this! Do not run your simulation and then seek to
+   work out how to use it to test your hypothesis, because it may be
+   unsuitable, or the required information was not saved.
+
+2. Select the appropriate tools to be able to perform the simulation
+   and observe the property or phenomena of interest. It is important
+   to read and familiarize yourself with publications by other
+   researchers on similar systems. Choices of tools include:
+
+   - software with which to perform the simulation (consideration of
+     force field may influence this decision)
+
+   - the force field, which describes how the particles within the
+     system interact with each other. Select one that is appropriate
+     for the system being studied and the property or phenomena of
+     interest. This is a very important and non-trivial step! Consider
+     now how you will analyze your simulation data to make your
+     observations.
+
+3. Obtain or generate the initial coordinate file for each molecule to
+   be placed within the system. Many different software packages are
+   able to build molecular structures and assemble them into suitable
+   configurations.
+
+4. Generate the raw starting structure for the system by placing the
+   molecules within the coordinate file as appropriate. Molecules may
+   be specifically placed or arranged randomly. Several non-|Gromacs|
+   tools are useful here; within |Gromacs| :ref:`gmx solvate`,
+   :ref:`gmx insert-molecules` and :ref:`gmx genconf` solve frequent
+   problems.
+
+5. Obtain or generate the topology file for the system, using (for
+   example) :ref:`gmx pdb2gmx`, :ref:`gmx x2top`, `SwissParam
+   <http://swissparam.ch/>`_ (for CHARMM forcefield), `PRODRG
+   <http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg>`_ (for GROMOS96
+   43A1), `Automated Topology Builder
+   <http://compbio.biosci.uq.edu.au/atb/>`_ (for GROMOS96 53A6),
+   `MKTOP <http://www.aribeiro.net.br/mktop>`_ (for OPLS/AA) or your
+   favourite text editor in concert with chapter 5 of the |Gromacs|
+   `Reference Manual`_. For the AMBER force fields, `antechamber
+   <http://amber.scripps.edu/antechamber/antechamber.html>`_ or
+   `acpype <https://code.google.com/archive/p/acpype/>`_ might be
+   appropriate.
+
+6. Describe a simulation box (e.g. using :ref:`gmx editconf`) whose
+   size is appropriate for the eventual density you would like, fill
+   it with solvent (e.g. using :ref:`gmx solvate`), and add any
+   counter-ions needed to neutralize the system (e.g. using :ref:`gmx
+   grompp` and :ref:`gmx insert-molecules`). In these steps you may
+   need to edit your topology file to stay current with your
+   coordinate file.
+
+7. Run an energy minimization on the system (using :ref:`gmx grompp`
+   and :ref:`gmx mdrun`). This is required to sort out any bad
+   starting structures caused during generation of the system, which
+   may cause the production simulation to crash. It may be necessary
+   also to minimize your solute structure in vacuo before introducing
+   solvent molecules (or your lipid bilayer or whatever else). You
+   should consider using flexible water models and not using bond
+   constraints or frozen groups. The use of position restraints and/or
+   distance restraints should be evaluated carefully.
+
+8. Select the appropriate simulation parameters for the equilibration
+   simulation (defined in .mdp file). You need to choose simulation
+   parameters that are consistent with how force field was
+   derived. You may need to simulate at NVT with position restraints
+   on your solvent and/or solute to get the temperature almost right,
+   then relax to NPT to fix the density (which should be done with
+   Berendsen until after the density is stabilized, before a further
+   switch to a barostat that produces the correct ensemble), then move
+   further (if needed) to reach your production simulation ensemble
+   (e.g. NVT, NVE). If you have problems here with the system `blowing
+   up <http://www.gromacs.org/Documentation/Terminology/Blowing_Up>`_,
+   consider using the suggestions on that page, e.g. position
+   restraints on solutes, or not using bond constraints, or using
+   smaller integration timesteps, or several gentler heating stage(s).
+
+9. Run the equilibration simulation for sufficient time so that the
+   system relaxes sufficiently in the target ensemble to allow the
+   production run to be commenced (using :ref:`gmx grompp` and
+   :ref:`gmx mdrun`, then :ref:`gmx energy` and `trajectory
+   visualization tools
+   <http://www.gromacs.org/Documentation/How-tos/Trajectory_Visualization>`_).
+
+10. Select the appropriate simulation parameters for the production
+    simulation (defined in .mdp file). In particular, be careful not
+    to re-generate the velocities. You still need to be consistent
+    with how the force field was derived and how to measure the
+    property or phenomena of interest.
+
+.. _Reference Manual: `gmx-manual`_
+
+Tips and tricks
+---------------
+
+Database files
+^^^^^^^^^^^^^^
+
+The ``share/top`` directory of a |Gromacs| installation contains
+numerous plain-text helper files with the ``.dat`` file extension.
+Some of the command-line tools (see :doc:`cmdline`) refer to these,
+and each tool documents which files it uses, and how they are used.
+
+If you need to modify these files (e.g. to introduce new atom types
+with VDW radii into ``vdwradii.dat``), you can copy the file from your
+installation directory into your working directory, and the |Gromacs|
+tools will automatically load the copy from your working directory
+rather than the standard one. To suppress all the standard
+definitions, use an empty file in the working directory.

src/contrib/fftw/CMakeLists.txt

@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -73,7 +73,12 @@ elseif(${GMX_SIMD} MATCHES "^(AVX)")
     # Support for --enable-avx2 was only added in 3.3.5, but
     # configuring with it is at worst a warning, even on an earlier
     # version.
+if((CMAKE_COMPILER_IS_GNUCC AND (C_COMPILER_VERSION VERSION_GREATER 4.9 OR CXX_COMPILER_VERSION VERSION_GREATER 4.9)) OR
+   (CMAKE_C_COMPILER_ID MATCHES "Clang" AND (C_COMPILER_VERSION VERSION_GREATER 3.9 OR CXX_COMPILER_VERSION VERSION_GREATER 3.9)))
     set(_fftw_simd_support_level --enable-sse2;--enable-avx;--enable-avx2;--enable-avx512)
+elseif()
+    set(_fftw_simd_support_level --enable-sse2;--enable-avx;--enable-avx2)
+endif()
 elseif(${GMX_SIMD} MATCHES "^(VSX)")
     set(_fftw_simd_support_level --enable-vsx)
 endif()

src/gromacs/gmxana/gmx_do_dssp.cpp

@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -423,8 +423,8 @@ void analyse_ss(const char *outfile, t_matrix *mat, const char *ss_string,
     }
     fprintf(fp, "\n");
 
-    /* now print percentages */
-    fprintf(fp, "%-8s %5.2f", "# SS %", total_count / static_cast<real>(mat->nx * mat->ny));
+    /* now print probabilities */
+    fprintf(fp, "%-8s %5.2f", "# SS pr.", total_count / static_cast<real>(mat->nx * mat->ny));
     for (s = 0; s < static_cast<size_t>(mat->nmap); s++)
     {
         fprintf(fp, " %5.2f", total[s] / static_cast<real>(mat->nx * mat->ny));

src/gromacs/gmxana/gmx_mindist.cpp

@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -413,15 +413,16 @@ void dist_plot(const char *fn, const char *afile, const char *dfile,
         sprintf(buf, "%simum Distance", bMin ? "Min" : "Max");
         respertime = xvgropen(rfile, buf, output_env_get_time_label(oenv), "Distance (nm)", oenv);
         xvgr_legend(respertime, ng-1, (const char**)leg, oenv);
-        if (bPrintResName)
+        if (bPrintResName && output_env_get_print_xvgr_codes(oenv) )
         {
             fprintf(respertime, "# ");
+
+            for (j = 0; j < nres; j++)
+            {
+                fprintf(respertime, "%s%d ", *(atoms->resinfo[atoms->atom[index[0][residue[j]]].resind].name), atoms->atom[index[0][residue[j]]].resind);
+            }
+            fprintf(respertime, "\n");
         }
-        for (j = 0; j < nres; j++)
-        {
-            fprintf(respertime, "%s%d ", *(atoms->resinfo[atoms->atom[index[0][residue[j]]].resind].name), atoms->atom[index[0][residue[j]]].resind);
-        }
-        fprintf(respertime, "\n");
 
     }
 

src/gromacs/gmxana/gmx_traj.cpp

@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -461,7 +461,7 @@ static void write_pdb_bfac(const char *fname, const char *xname,
             svmul(scale, sum[index[i]], sum[index[i]]);
         }
 
-        fp = xvgropen(xname, title, "Atom", "", oenv);
+        fp = xvgropen(xname, title, "Atom", "Spatial component", oenv);
         for (i = 0; i < isize; i++)
         {
             fprintf(fp, "%-5d  %10.3f  %10.3f  %10.3f\n", 1+i,

src/gromacs/gmxana/gmx_trjconv.cpp

@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -665,10 +665,6 @@ int gmx_trjconv(int argc, char *argv[])
         "   results if you in fact have a cluster. Luckily that can be checked",
         "   afterwards using a trajectory viewer. Note also that if your molecules",
         "   are broken this will not work either.",
-        "",
-        "   The separate option [TT]-clustercenter[tt] can be used to specify an",
-        "   approximate center for the cluster. This is useful e.g. if you have",
-        "   two big vesicles, and you want to maintain their relative positions.",
         " * [TT]whole[tt] only makes broken molecules whole.",
         "",