Merge release-5-0 into master

Conflicts:
	CMakeLists.txt (version only)
	src/gromacs/fileio/tngio.h (includes only)
	src/gromacs/fileio/tngio_for_tools.h (includes only)
	src/gromacs/gmxlib/gmx_thread_affinity.c
            (took variable rename from 5.0, other changes from master
             kept)
	src/gromacs/gmxpreprocess/hackblock.c (includes only)
	src/gromacs/gmxpreprocess/pdb2top.cpp
            (took 5.0 removal of unused parameter)
	src/gromacs/mdlib/constr.c (includes only)
	src/gromacs/utility/fatalerror.cpp
            (applied similar error message change to basenetwork.cpp)

Change-Id: I7137225e37828a19c4b92aa2ec055e7177aa5676

diff --cc CMakeLists.txt
Simple merge

diff --cc src/external/tng_io/src/lib/md5.c
Simple merge

diff --cc src/gromacs/CMakeLists.txt
Simple merge

diff --cc src/gromacs/essentialdynamics/edsam.c
Simple merge

diff --cc src/gromacs/fft/fft5d.cpp
Simple merge

diff --cc src/gromacs/fileio/CMakeLists.txt
Simple merge

diff --cc src/gromacs/fileio/gmxfio.c
Simple merge

diff --cc src/gromacs/fileio/md5.c
Simple merge

diff --cc src/gromacs/fileio/tngio.cpp
Simple merge

diff --cc src/gromacs/fileio/tngio.h
index 375cd6c7c8eeb1a0baadad41c801d6072aed3040,1f439c537aba1467d33471c63d22032fd114265f..578b8f57edb3bd1c328cade6a75dac4e403987c4
--- 1/src/gromacs/fileio/tngio.h
--- 2/src/gromacs/fileio/tngio.h
+++ b/src/gromacs/fileio/tngio.h
@@@ -36,12 -36,9 +36,12 @@@
  #ifndef GMX_FILEIO_TNGIO_H
  #define GMX_FILEIO_TNGIO_H
  
- #include "external/tng_io/include/tng_io_fwd.h"
 -#include "gromacs/legacyheaders/typedefs.h"
+ #include "tng/tng_io_fwd.h"
  
 +#include "gromacs/legacyheaders/types/inputrec.h"
 +#include "gromacs/math/vectypes.h"
 +#include "gromacs/utility/real.h"
 +
  #ifdef __cplusplus
  extern "C" {
  #endif

diff --cc src/gromacs/fileio/tngio_for_tools.cpp
index 93a3b130a9dd959457480ef7d42a14b921c7f293,1c579a6f81744798b72b727f3771e90fc305a132..f540cbdec1d0c25d5d5614c88ef58b2ab2f2380d
--- 1/src/gromacs/fileio/tngio_for_tools.cpp
--- 2/src/gromacs/fileio/tngio_for_tools.cpp
+++ b/src/gromacs/fileio/tngio_for_tools.cpp
@@@ -44,12 -44,14 +44,12 @@@
  #include "trx.h"
  
  #ifdef GMX_USE_TNG
- #include "../../external/tng_io/include/tng_io.h"
+ #include "tng/tng_io.h"
  #endif
  
 -#include "gromacs/legacyheaders/types/atoms.h"
 -#include "gromacs/legacyheaders/physics.h"
 -#include "gromacs/legacyheaders/gmx_fatal.h"
 -
 +#include "gromacs/math/units.h"
  #include "gromacs/utility/common.h"
 +#include "gromacs/utility/fatalerror.h"
  #include "gromacs/utility/smalloc.h"
  
  void gmx_prepare_tng_writing(const char              *filename,

diff --cc src/gromacs/fileio/tngio_for_tools.h
index 6dbfee17080b28fa1de5f743b32f74aac8d3a64c,f0a31eb250354fce3f5faf692e88e1cdb598760f..c4993a272597c699af2e7447b9246e6040b04d1d
--- 1/src/gromacs/fileio/tngio_for_tools.h
--- 2/src/gromacs/fileio/tngio_for_tools.h
+++ b/src/gromacs/fileio/tngio_for_tools.h
@@@ -35,14 -35,10 +35,14 @@@
  #ifndef GMX_FILEIO_TNGIO_FOR_TOOLS_H
  #define GMX_FILEIO_TNGIO_FOR_TOOLS_H
  
 -#include "gromacs/legacyheaders/typedefs.h"
 +#include <stdio.h>
 +
- #include "external/tng_io/include/tng_io_fwd.h"
+ #include "tng/tng_io_fwd.h"
  
 +#include "gromacs/legacyheaders/types/simple.h"
 +#include "gromacs/utility/basedefinitions.h"
 +#include "gromacs/utility/real.h"
 +
  #ifdef __cplusplus
  extern "C" {
  #endif

diff --cc src/gromacs/fileio/tpxio.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_current.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_hbond.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_make_edi.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_pme_error.cpp
Simple merge

diff --cc src/gromacs/gmxana/gmx_tune_pme.c
Simple merge

diff --cc src/gromacs/gmxlib/bondfree.c
Simple merge

diff --cc src/gromacs/gmxlib/checkpoint.cpp
Simple merge

diff --cc src/gromacs/gmxlib/copyrite.cpp
Simple merge

diff --cc src/gromacs/gmxlib/ewald_util.c
Simple merge

diff --cc src/gromacs/gmxlib/gmx_detect_hardware.cpp
Simple merge

diff --cc src/gromacs/gmxlib/gmx_omp_nthreads.c
Simple merge

diff --cc src/gromacs/gmxlib/gmx_thread_affinity.c
index 8814ec410f72b9c3bb89b871ba7bb76d995063a5,90970b6bd29aeb590e2d3bd0686aeb16ba2b11d1..319249506bb52fde70a220f2373667fd154f8275
--- 1/src/gromacs/gmxlib/gmx_thread_affinity.c
--- 2/src/gromacs/gmxlib/gmx_thread_affinity.c
+++ b/src/gromacs/gmxlib/gmx_thread_affinity.c
@@@ -372,11 -369,11 +372,11 @@@ gmx_set_thread_affinity(FIL
   * Note that this will only work on Linux as we use a GNU feature.
   */
  void
 -gmx_check_thread_affinity_set(FILE            gmx_unused *fplog,
 -                              const t_commrec gmx_unused *cr,
 -                              gmx_hw_opt_t    gmx_unused *hw_opt,
 -                              int             gmx_unused  nthreads_hw_avail,
 -                              gmx_bool        gmx_unused  bAfterOpenmpInit)
 +gmx_check_thread_affinity_set(FILE            *fplog,
 +                              const t_commrec *cr,
 +                              gmx_hw_opt_t    *hw_opt,
-                               int  gmx_unused  ncpus,
++                              int  gmx_unused  nthreads_hw_avail,
 +                              gmx_bool         bAfterOpenmpInit)
  {
  #ifdef HAVE_SCHED_GETAFFINITY
      cpu_set_t mask_current;

diff --cc src/gromacs/gmxlib/main.cpp
Simple merge

diff --cc src/gromacs/gmxlib/mvdata.c
Simple merge

diff --cc src/gromacs/gmxlib/network.c
Simple merge

diff --cc src/gromacs/gmxlib/nonbonded/nb_free_energy.c
index bba7805fb74a88edb74174ec5c280092130a7797,2bf8f90e3f8bd8bc60baf5462c60e5cf98e73781..30698281a799775b4de918e0507b0545f41fc972
--- 1/src/gromacs/gmxlib/nonbonded/nb_free_energy.c
--- 2/src/gromacs/gmxlib/nonbonded/nb_free_energy.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_free_energy.c
@@@ -175,8 -177,13 +177,12 @@@ gmx_nb_free_energy_kernel(const t_nblis
      bDoPotential        = kernel_data->flags & GMX_NONBONDED_DO_POTENTIAL;
  
      rcoulomb            = fr->rcoulomb;
 -    sh_ewald            = fr->ic->sh_ewald;
      rvdw                = fr->rvdw;
      sh_invrc6           = fr->ic->sh_invrc6;
+     sh_lj_ewald         = fr->ic->sh_lj_ewald;
+     ewclj               = fr->ewaldcoeff_lj;
+     ewclj2              = ewclj*ewclj;
+     ewclj6              = ewclj2*ewclj2*ewclj2;
  
      if (fr->coulomb_modifier == eintmodPOTSWITCH)
      {

diff --cc src/gromacs/gmxlib/nrnb.c
Simple merge

diff --cc src/gromacs/gmxlib/orires.c
Simple merge

diff --cc src/gromacs/gmxlib/txtdump.c
Simple merge

diff --cc src/gromacs/gmxpreprocess/gen_ad.c
Simple merge

diff --cc src/gromacs/gmxpreprocess/hackblock.c
index c7919872c1786e63e063223499e88cc63bc7b08f,0e4e1c1cfa988a8723208fb7e5620eda7d03d1f0..0da489f4a2c03b340025e8630579e40eaf1cda54
--- 1/src/gromacs/gmxpreprocess/hackblock.c
--- 2/src/gromacs/gmxpreprocess/hackblock.c
+++ b/src/gromacs/gmxpreprocess/hackblock.c
@@@ -42,7 -42,9 +42,8 @@@
  #include <string.h>
  #include "hackblock.h"
  #include "gromacs/utility/smalloc.h"
 -#include "vec.h"
 -#include "macros.h"
 +#include "gromacs/math/vec.h"
+ #include "names.h"
  
  /* these MUST correspond to the enum in hackblock.h */
  const char *btsNames[ebtsNR] = { "bonds", "angles", "dihedrals", "impropers", "exclusions", "cmap" };

diff --cc src/gromacs/gmxpreprocess/hackblock.h
Simple merge

diff --cc src/gromacs/gmxpreprocess/pdb2top.cpp
Simple merge

diff --cc src/gromacs/gmxpreprocess/pgutil.c
Simple merge

diff --cc src/gromacs/gmxpreprocess/readir.c
Simple merge

diff --cc src/gromacs/legacyheaders/constr.h
Simple merge

diff --cc src/gromacs/legacyheaders/network.h
index f0ae524c17e90888af94adc4c77852e65d7df0d1,8db571ea9c36902f880ea3b13cfa4da5daef71a1..5e5e5f3d855276c3ab6e01a433652d1a97207829
--- 1/src/gromacs/legacyheaders/network.h
--- 2/src/gromacs/legacyheaders/network.h
+++ b/src/gromacs/legacyheaders/network.h
@@@ -116,27 -134,9 +116,27 @@@ void gmx_sumd_sim(int nr, double r[], c
  #define gmx_sum_sim   gmx_sumf_sim
  #endif
  
 +gmx_bool gmx_fexist_master(const char *fname, struct t_commrec *cr);
 +/* Return TRUE when fname exists, FALSE otherwise, bcast from master to others */
 +
 +void
 +gmx_fatal_collective(int f_errno, const char *file, int line,
 +                     const struct t_commrec *cr, struct gmx_domdec_t *dd,
 +                     const char *fmt, ...);
 +/* As gmx_fatal declared in utility/fatalerror.h,
 + * but only the master process prints the error message.
 + * This should only be called one of the following two situations:
 + * 1) On all nodes in cr->mpi_comm_mysim, with cr!=NULL,dd==NULL.
 + * 2) On all nodes in dd->mpi_comm_all,   with cr==NULL,dd!=NULL.
 + * This will call MPI_Finalize instead of MPI_Abort when possible,
 + * This is useful for handling errors in code that is executed identically
 + * for all processes.
 + */
 +
 +/* This doesn't currently work if enabled (needs some header cleanup). */
  #ifdef DEBUG_GMX
  #define debug_gmx() do { FILE *fp = debug ? debug : stderr; \
-                          if (bDebugMode()) { fprintf(fp, "NODEID=%d, %s  %d\n", gmx_mpi_initialized() ? gmx_node_rank() : -1, __FILE__, __LINE__); } fflush(fp); } while (0)
+                          if (bDebugMode()) { fprintf(fp, "rank=%d, %s  %d\n", gmx_mpi_initialized() ? gmx_node_rank() : -1, __FILE__, __LINE__); } fflush(fp); } while (0)
  #else
  #define debug_gmx()
  #endif

diff --cc src/gromacs/legacyheaders/types/inputrec.h
Simple merge

diff --cc src/gromacs/mdlib/constr.c
index 2aa97ffd231ef0fcbc3739a95e9430791313c927,fa8275083dd126e2334755dcbc796210799e48de..d3df9392e44b29be77958f98efe7a6ba0afcd2e3
--- 1/src/gromacs/mdlib/constr.c
--- 2/src/gromacs/mdlib/constr.c
+++ b/src/gromacs/mdlib/constr.c
@@@ -38,7 -38,7 +38,8 @@@
  #include <config.h>
  #endif
  
+ #include <assert.h>
 +#include <stdlib.h>
  
  #include "gromacs/fileio/confio.h"
  #include "types/commrec.h"

diff --cc src/gromacs/mdlib/domdec.c
Simple merge

diff --cc src/gromacs/mdlib/domdec_con.c
Simple merge

diff --cc src/gromacs/mdlib/domdec_setup.c
Simple merge

diff --cc src/gromacs/mdlib/force.c
Simple merge

diff --cc src/gromacs/mdlib/forcerec.c
Simple merge

diff --cc src/gromacs/mdlib/mdebin.c
Simple merge

diff --cc src/gromacs/mdlib/mdebin_bar.c
Simple merge

diff --cc src/gromacs/mdlib/minimize.c
Simple merge

diff --cc src/gromacs/mdlib/nbnxn_atomdata.c
Simple merge

diff --cc src/gromacs/mdlib/nbnxn_search.c
Simple merge

diff --cc src/gromacs/mdlib/pme.c
Simple merge

diff --cc src/gromacs/mdlib/pme_pp.c
Simple merge

diff --cc src/gromacs/mdlib/qmmm.c
Simple merge

diff --cc src/gromacs/mdlib/shellfc.c
Simple merge

diff --cc src/gromacs/mdlib/sim_util.c
Simple merge

diff --cc src/gromacs/mdlib/tables.c
Simple merge

diff --cc src/gromacs/mdlib/update.c
Simple merge

diff --cc src/gromacs/selection/evaluate.cpp
Simple merge

diff --cc src/gromacs/selection/params.cpp
Simple merge

diff --cc src/gromacs/selection/parsetree.cpp
Simple merge

diff --cc src/gromacs/selection/parsetree.h
Simple merge

diff --cc src/gromacs/selection/selectioncollection.cpp
Simple merge

diff --cc src/gromacs/selection/selelem.h
Simple merge

diff --cc src/gromacs/selection/tests/selectioncollection.cpp
Simple merge

diff --cc src/gromacs/swap/swapcoords.c
Simple merge

diff --cc src/gromacs/timing/wallcycle.c
Simple merge

diff --cc src/gromacs/tools/compare.c
Simple merge

diff --cc src/gromacs/utility/basenetwork.cpp
index 8e74d6bf82da1c18ee0590abcdf385a8a58f18d5,0000000000000000000000000000000000000000..adc27e7c8ddf38ea5a6d004fcfe53bc9d9522f66
mode 100644,000000..100644
--- 1/src/gromacs/utility/basenetwork.cpp
--- /dev/null
+++ b/src/gromacs/utility/basenetwork.cpp
@@@ -1,254 -1,0 +1,254 @@@
-         std::fprintf(stderr, "Halting parallel program %s on node %d out of %d\n",
 +/*
 + * This file is part of the GROMACS molecular simulation package.
 + *
 + * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 + * Copyright (c) 2001-2004, The GROMACS development team.
 + * Copyright (c) 2013,2014, 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.
 + *
 + * GROMACS is free software; you can redistribute it and/or
 + * modify it under the terms of the GNU Lesser General Public License
 + * as published by the Free Software Foundation; either version 2.1
 + * of the License, or (at your option) any later version.
 + *
 + * GROMACS is distributed in the hope that it will be useful,
 + * but WITHOUT ANY WARRANTY; without even the implied warranty of
 + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 + * Lesser General Public License for more details.
 + *
 + * You should have received a copy of the GNU Lesser General Public
 + * License along with GROMACS; if not, see
 + * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 + *
 + * If you want to redistribute modifications to GROMACS, please
 + * consider that scientific software is very special. Version
 + * control is crucial - bugs must be traceable. We will be happy to
 + * consider code for inclusion in the official distribution, but
 + * derived work must not be called official GROMACS. Details are found
 + * in the README & COPYING files - if they are missing, get the
 + * official version at http://www.gromacs.org.
 + *
 + * To help us fund GROMACS development, we humbly ask that you cite
 + * the research papers on the package. Check out http://www.gromacs.org.
 + */
 +#include "basenetwork.h"
 +
 +#include "config.h"
 +
 +#include <cctype>
 +#include <cstdio>
 +#include <cstdlib>
 +#include <cstring>
 +
 +#include <algorithm>
 +#include <exception>
 +
 +#ifdef HAVE_UNISTD_H
 +#include <unistd.h>
 +#endif
 +
 +#include "gromacs/utility/cstringutil.h"
 +#include "gromacs/utility/fatalerror.h"
 +#include "gromacs/utility/gmxmpi.h"
 +#include "gromacs/utility/programcontext.h"
 +
 +int gmx_gethostname(char *name, size_t len)
 +{
 +    if (len < 8)
 +    {
 +        gmx_incons("gmx_gethostname called with len<8");
 +    }
 +#if defined(HAVE_UNISTD_H) && !defined(__native_client__)
 +    if (gethostname(name, len-1) != 0)
 +    {
 +        std::strncpy(name, "unknown", 8);
 +        return -1;
 +    }
 +    return 0;
 +#else
 +    std::strncpy(name, "unknown", 8);
 +    return -1;
 +#endif
 +}
 +
 +gmx_bool gmx_mpi_initialized(void)
 +{
 +#ifndef GMX_MPI
 +    return 0;
 +#else
 +    int n;
 +    MPI_Initialized(&n);
 +
 +    return n;
 +#endif
 +}
 +
 +int gmx_node_num(void)
 +{
 +#ifndef GMX_MPI
 +    return 1;
 +#else
 +    int i;
 +    (void) MPI_Comm_size(MPI_COMM_WORLD, &i);
 +    return i;
 +#endif
 +}
 +
 +int gmx_node_rank(void)
 +{
 +#ifndef GMX_MPI
 +    return 0;
 +#else
 +    int i;
 +    (void) MPI_Comm_rank(MPI_COMM_WORLD, &i);
 +    return i;
 +#endif
 +}
 +
 +static int mpi_hostname_hash(void)
 +{
 +    int hash_int;
 +
 +#ifndef GMX_LIB_MPI
 +    /* We have a single physical node */
 +    hash_int = 0;
 +#else
 +    int  resultlen;
 +    char mpi_hostname[MPI_MAX_PROCESSOR_NAME];
 +
 +    /* This procedure can only differentiate nodes with different names.
 +     * Architectures where different physical nodes have identical names,
 +     * such as IBM Blue Gene, should use an architecture specific solution.
 +     */
 +    MPI_Get_processor_name(mpi_hostname, &resultlen);
 +
 +    /* The string hash function returns an unsigned int. We cast to an int.
 +     * Negative numbers are converted to positive by setting the sign bit to 0.
 +     * This makes the hash one bit smaller.
 +     * A 63-bit hash (with 64-bit int) should be enough for unique node hashes,
 +     * even on a million node machine. 31 bits might not be enough though!
 +     */
 +    hash_int =
 +        (int)gmx_string_fullhash_func(mpi_hostname, gmx_string_hash_init);
 +    if (hash_int < 0)
 +    {
 +        hash_int -= INT_MIN;
 +    }
 +#endif
 +
 +    return hash_int;
 +}
 +
 +#if defined GMX_LIB_MPI && defined GMX_TARGET_BGQ
 +#include <spi/include/kernel/location.h>
 +
 +static int bgq_nodenum(void)
 +{
 +    int           hostnum;
 +    Personality_t personality;
 +    Kernel_GetPersonality(&personality, sizeof(personality));
 +    /* Each MPI rank has a unique coordinate in a 6-dimensional space
 +       (A,B,C,D,E,T), with dimensions A-E corresponding to different
 +       physical nodes, and T within each node. Each node has sixteen
 +       physical cores, each of which can have up to four hardware
 +       threads, so 0 <= T <= 63 (but the maximum value of T depends on
 +       the confituration of ranks and OpenMP threads per
 +       node). However, T is irrelevant for computing a suitable return
 +       value for gmx_hostname_num().
 +     */
 +    hostnum  = personality.Network_Config.Acoord;
 +    hostnum *= personality.Network_Config.Bnodes;
 +    hostnum += personality.Network_Config.Bcoord;
 +    hostnum *= personality.Network_Config.Cnodes;
 +    hostnum += personality.Network_Config.Ccoord;
 +    hostnum *= personality.Network_Config.Dnodes;
 +    hostnum += personality.Network_Config.Dcoord;
 +    hostnum *= personality.Network_Config.Enodes;
 +    hostnum += personality.Network_Config.Ecoord;
 +
 +    if (debug)
 +    {
 +        std::fprintf(debug,
 +                     "Torus ID A: %d / %d B: %d / %d C: %d / %d D: %d / %d E: %d / %d\n"
 +                     "Node ID T: %d / %d core: %d / %d hardware thread: %d / %d\n",
 +                     personality.Network_Config.Acoord,
 +                     personality.Network_Config.Anodes,
 +                     personality.Network_Config.Bcoord,
 +                     personality.Network_Config.Bnodes,
 +                     personality.Network_Config.Ccoord,
 +                     personality.Network_Config.Cnodes,
 +                     personality.Network_Config.Dcoord,
 +                     personality.Network_Config.Dnodes,
 +                     personality.Network_Config.Ecoord,
 +                     personality.Network_Config.Enodes,
 +                     Kernel_ProcessorCoreID(),
 +                     16,
 +                     Kernel_ProcessorID(),
 +                     64,
 +                     Kernel_ProcessorThreadID(),
 +                     4);
 +    }
 +    return hostnum;
 +}
 +#endif
 +
 +int gmx_physicalnode_id_hash(void)
 +{
 +    int hash;
 +
 +#ifndef GMX_MPI
 +    hash = 0;
 +#else
 +#ifdef GMX_THREAD_MPI
 +    /* thread-MPI currently puts the thread number in the process name,
 +     * we might want to change this, as this is inconsistent with what
 +     * most MPI implementations would do when running on a single node.
 +     */
 +    hash = 0;
 +#else
 +#ifdef GMX_TARGET_BGQ
 +    hash = bgq_nodenum();
 +#else
 +    hash = mpi_hostname_hash();
 +#endif
 +#endif
 +#endif
 +
 +    if (debug)
 +    {
 +        fprintf(debug, "In gmx_physicalnode_id_hash: hash %d\n", hash);
 +    }
 +
 +    return hash;
 +}
 +
 +#ifdef GMX_LIB_MPI
 +void gmx_abort(int errorno)
 +{
 +    const char *programName = "GROMACS";
 +    try
 +    {
 +        programName = gmx::getProgramContext().displayName();
 +    }
 +    catch (const std::exception &)
 +    {
 +    }
 +    const int nnodes   = gmx_node_num();
 +    const int noderank = gmx_node_rank();
 +    if (nnodes > 1)
 +    {
++        std::fprintf(stderr, "Halting parallel program %s on rank %d out of %d\n",
 +                     programName, noderank, nnodes);
 +    }
 +    else
 +    {
 +        std::fprintf(stderr, "Halting program %s\n", programName);
 +    }
 +
 +    MPI_Abort(MPI_COMM_WORLD, errorno);
 +    std::exit(errorno);
 +}
 +#endif

diff --cc src/programs/mdrun/mdrun.cpp
Simple merge

diff --cc src/programs/mdrun/pme_loadbal.c
Simple merge

diff --cc src/programs/mdrun/runner.cpp
index 603f24470354e8ff8f1b1a10852c69c1b533185c,923f0f654461ddd943684299ef919dfc18229d4f..85a2d17991d301bafce2149a26b8617fdd3f1ddb
--- 1/src/programs/mdrun/runner.cpp
--- 2/src/programs/mdrun/runner.c
+++ b/src/programs/mdrun/runner.cpp
@@@ -1206,8 -1210,23 +1206,16 @@@ int mdrunner(gmx_hw_opt_t *hw_opt
                            "      Verlet cut-off scheme.\n");
  #endif
          }
+ 
+         if (inputrec->eI == eiSD2)
+         {
+             md_print_warn(cr, fplog, "The stochastic dynamics integrator %s is deprecated, since\n"
+                           "it is slower than integrator %s and is slightly less accurate\n"
+                           "with constraints. Use the %s integrator.",
+                           ei_names[inputrec->eI], ei_names[eiSD1], ei_names[eiSD1]);
+         }
      }
  
 -    /* Check for externally set OpenMP affinity and turn off internal
 -     * pinning if any is found. We need to do this check early to tell
 -     * thread-MPI whether it should do pinning when spawning threads.
 -     * TODO: the above no longer holds, we should move these checks down
 -     */
 -    gmx_omp_check_thread_affinity(fplog, cr, hw_opt);
 -
      /* Check and update the hardware options for internal consistency */
      check_and_update_hw_opt_1(hw_opt, SIMMASTER(cr));
  

diff --cc tests/CppCheck.cmake
index 8ca224cb9d9250cd9627441b1e409d0c0456b68a,9d4a3d52eea87c8c01698bb68ecab161639120be..7e2581c235487e32a2de2ef16f6989dd29529f40
--- 1/tests/CppCheck.cmake
--- 2/tests/CppCheck.cmake
+++ b/tests/CppCheck.cmake
@@@ -70,12 -68,12 +70,13 @@@ if (CPPCHECK_EXECUTABLE AND UNIX
          set(_outputopt --xml)
      endif()
      set(_common_flags
 -        --enable=style -DLINUX
 +        --enable=style -DLINUX -DHAVE_UNISTD_H
          -I src/gromacs/legacyheaders -I src
          -I src/external/thread_mpi/include
+         -I src/external/tng_io/include
          -I ${CMAKE_BINARY_DIR}/src -I ${CMAKE_BINARY_DIR}/src/gromacs/utility
          --quiet
 +        --inline-suppr
          ${_outputopt})
      set(_c_flags
          --suppress=variableScope