Merge release-5-0 into master

Conflicts:
- src/gromacs/legacyheaders/types/simple.h
  moved changes into src/gromacs/utility/real.h
- src/gromacs/gmxlib/network.c &
  src/gromacs/utility/basenetwork.cpp
  changes to network.c partially applied to itself
  and paritally to basenetwork.
- src/gromacs/legacyheaders/network.h (trivial)
- src/programs/mdrun/md.cpp (trivial)

Change-Id: Iaeae5bcc691a3fa84978ee261ceb4a5d2aeb4f62

diff --cc CMakeLists.txt
Simple merge

diff --cc src/contrib/do_shift.c
Simple merge

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

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

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

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

diff --cc src/gromacs/gmxana/gmx_make_ndx.c
index 3e48c99a264628710de5ffb8ea09286ef045fbaa,686ee49aaa59611fee725941e93d7eeb7159aac9..7bdccbefff8c4cf25f7fbfa4eecc912779abbf97
--- 1/src/gromacs/gmxana/gmx_make_ndx.c
--- 2/src/gromacs/gmxana/gmx_make_ndx.c
+++ b/src/gromacs/gmxana/gmx_make_ndx.c
@@@ -41,21 -41,25 +41,24 @@@
  #include <ctype.h>
  #include <string.h>
  
 -#include "sysstuff.h"
 -#include "gromacs/fileio/futil.h"
 +#include "gromacs/utility/futil.h"
  #include "macros.h"
 -#include "gromacs/utility/cstringutil.h"
 -#include "gromacs/commandline/pargs.h"
  #include "gromacs/fileio/confio.h"
  #include "typedefs.h"
 -#include "index.h"
 -#include "gromacs/utility/smalloc.h"
 -#include "vec.h"
 -#include "index.h"
 +#include "gromacs/topology/index.h"
 +#include "gromacs/math/vec.h"
  
 -#include "gromacs/legacyheaders/gmx_fatal.h"
 +#include "gromacs/commandline/pargs.h"
 +#include "gromacs/topology/block.h"
 +#include "gromacs/utility/cstringutil.h"
 +#include "gromacs/utility/fatalerror.h"
 +#include "gromacs/utility/smalloc.h"
  
- #define MAXNAMES 30
- #define NAME_LEN 30
+ /* It's not nice to have size limits, but we should not spend more time
+  * on this ancient tool, but instead use the new selection library.
+  */
+ #define MAXNAMES 1024
+ #define NAME_LEN 1024
  
  gmx_bool bCase = FALSE;
  

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

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

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

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

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

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

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

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

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

diff --cc src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
Simple merge

diff --cc src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
Simple merge

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

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

diff --cc src/gromacs/utility/basenetwork.cpp
index d4adc345a8dfb72cca9202d837921d272b2d4c80,0000000000000000000000000000000000000000..8e74d6bf82da1c18ee0590abcdf385a8a58f18d5
mode 100644,000000..100644
--- 1/src/gromacs/utility/basenetwork.cpp
--- /dev/null
+++ b/src/gromacs/utility/basenetwork.cpp
@@@ -1,270 -1,0 +1,254 @@@
- #if defined GMX_LIB_MPI && defined GMX_TARGET_BGQ
- #include <spi/include/kernel/location.h>
- #endif
- 
- int gmx_physicalnode_id_hash(void)
 +/*
 + * 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
 +}
 +
- int gmx_hostname_num()
- {
- #ifndef GMX_MPI
-     return 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.
-      */
-     return 0;
- #else
-     int  resultlen, hostnum, i, j;
-     char mpi_hostname[MPI_MAX_PROCESSOR_NAME], hostnum_str[MPI_MAX_PROCESSOR_NAME];
++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;
 +}
 +
-     MPI_Get_processor_name(mpi_hostname, &resultlen);
- #ifdef GMX_TARGET_BGQ
++#if defined GMX_LIB_MPI && defined GMX_TARGET_BGQ
++#include <spi/include/kernel/location.h>
 +
- #else
-     /* This procedure can only differentiate nodes with host names
-      * that end on unique numbers.
-      */
-     i = 0;
-     j = 0;
-     /* Only parse the host name up to the first dot */
-     while (i < resultlen && mpi_hostname[i] != '.')
-     {
-         if (std::isdigit(mpi_hostname[i]))
-         {
-             hostnum_str[j++] = mpi_hostname[i];
-         }
-         i++;
-     }
-     hostnum_str[j] = '\0';
-     if (j == 0)
-     {
-         hostnum = 0;
-     }
-     else
-     {
-         /* Use only the last 9 decimals, so we don't overflow an int */
-         hostnum = std::strtol(hostnum_str + std::max(0, j-9), NULL, 10);
-     }
- #endif
++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;
-         std::fprintf(debug, "In gmx_hostname_num: hostname '%s', hostnum %d\n",
-                      mpi_hostname, hostnum);
- #ifdef GMX_TARGET_BGQ
 +
 +    if (debug)
 +    {
- #endif
 +        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 node %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/gromacs/utility/fatalerror.cpp
Simple merge

diff --cc src/gromacs/utility/futil.cpp
Simple merge

diff --cc src/gromacs/utility/real.h
index 03141a25a7cf34474f8ac566acd2a4a0e1a0cba6,0000000000000000000000000000000000000000..a8fb5a52deec970017af31f1f15437b9bc0fccb8
mode 100644,000000..100644
--- 1/src/gromacs/utility/real.h
--- /dev/null
+++ b/src/gromacs/utility/real.h
@@@ -1,115 -1,0 +1,115 @@@
- #define GMX_DOUBLE_EPS   1.11022302E-16
 +/*
 + * 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.
 + */
 +/*! \file
 + * \brief
 + * Declares `real` and related constants.
 + *
 + * \inpublicapi
 + * \ingroup module_utility
 + */
 +#ifndef GMX_UTILITY_REAL_H
 +#define GMX_UTILITY_REAL_H
 +
 +/*! \brief Double precision accuracy */
- #define GMX_DOUBLE_MAX   1.79769312E+308
++#define GMX_DOUBLE_EPS   2.2204460492503131e-16
 +
 +/*! \brief Maximum double precision value - reduced 1 unit in last digit for MSVC */
- #define GMX_DOUBLE_MIN   2.22507386E-308
++#define GMX_DOUBLE_MAX   1.7976931348623157e+308
 +
 +/*! \brief Minimum double precision value */
- #define GMX_FLOAT_EPS    5.96046448E-08
++#define GMX_DOUBLE_MIN   2.2250738585072014e-308
 +
 +/*! \brief Single precision accuracy */
- #define GMX_FLOAT_MAX    3.40282346E+38
++#define GMX_FLOAT_EPS    1.19209290e-07F
 +
 +/*! \brief Maximum single precision value - reduced 1 unit in last digit for MSVC */
- #define GMX_FLOAT_MIN    1.17549435E-38
++#define GMX_FLOAT_MAX    3.40282346E+38F
 +
 +/*! \brief Minimum single precision value */
++#define GMX_FLOAT_MIN    1.175494351E-38F
 +
 +
 +/*! \typedef real
 + * \brief Precision-dependent \Gromacs floating-point type.
 + */
 +/*! \def HAVE_REAL
 + * \brief Used to check whether `real` is already defined.
 + */
 +/*! \def GMX_MPI_REAL
 + * \brief MPI data type for `real`.
 + */
 +/*! \def GMX_REAL_EPS
 + * \brief Accuracy for `real`.
 + */
 +/*! \def GMX_REAL_MIN
 + * \brief Smallest non-zero value for `real`.
 + */
 +/*! \def GMX_REAL_MAX
 + * \brief Largest finite value for `real`.
 + */
 +/*! \def gmx_real_fullprecision_pfmt
 + * \brief Format string for full `real` precision.
 + */
 +#ifdef GMX_DOUBLE
 +
 +#ifndef HAVE_REAL
 +typedef double      real;
 +#define HAVE_REAL
 +#endif
 +
 +#define GMX_MPI_REAL    MPI_DOUBLE
 +#define GMX_REAL_EPS    GMX_DOUBLE_EPS
 +#define GMX_REAL_MIN    GMX_DOUBLE_MIN
 +#define GMX_REAL_MAX    GMX_DOUBLE_MAX
 +#define gmx_real_fullprecision_pfmt "%21.14e"
 +
 +#else /* GMX_DOUBLE */
 +
 +#ifndef HAVE_REAL
 +typedef float           real;
 +#define HAVE_REAL
 +#endif
 +
 +#define GMX_MPI_REAL    MPI_FLOAT
 +#define GMX_REAL_EPS    GMX_FLOAT_EPS
 +#define GMX_REAL_MIN    GMX_FLOAT_MIN
 +#define GMX_REAL_MAX    GMX_FLOAT_MAX
 +#define gmx_real_fullprecision_pfmt "%14.7e"
 +
 +#endif /* GMX_DOUBLE */
 +
 +#endif

diff --cc src/programs/mdrun/md.cpp
index 88c78dc9be381fbf3cde0db6ae2127b585800d4f,b7dab3cf200677fa778e29ec6b4e3906ce302b8e..c8b4db19d5d8f3208ff92c3acd520d3f11e4effb
--- 1/src/programs/mdrun/md.cpp
--- 2/src/programs/mdrun/md.c
+++ b/src/programs/mdrun/md.cpp
@@@ -189,8 -189,10 +189,8 @@@ double do_md(FILE *fplog, t_commrec *cr
      gmx_ekindata_t   *ekind, *ekind_save;
      gmx_shellfc_t     shellfc;
      int               count, nconverged = 0;
 -    real              timestep   = 0;
 -    double            tcount     = 0;
 -    gmx_bool          bConverged = TRUE, bOK, bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
 -    gmx_bool          bAppend;
 +    double            tcount                 = 0;
-     gmx_bool          bConverged             = TRUE, bOK, bSumEkinhOld, bExchanged, bNeedRepartition;
++    gmx_bool          bConverged             = TRUE, bOK, bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
      gmx_bool          bResetCountersHalfMaxH = FALSE;
      gmx_bool          bVV, bIterativeCase, bFirstIterate, bTemp, bPres, bTrotter;
      gmx_bool          bUpdateDoLR;

diff --cc src/programs/view/logo.cpp
Simple merge

diff --cc src/programs/view/x11.cpp
Simple merge