Merge branch release-5-1

Conflicts only from version numbers

Change-Id: I78235cce0c4fd7bcf4235dd888e1aef739d46001

diff --cc cmake/gmxVersionInfo.cmake
Simple merge

diff --cc src/gromacs/mdlib/clincs.cpp
Simple merge

diff --cc src/gromacs/timing/walltime_accounting.cpp
index 5eeed23c80f8e4f07b9e78166c41684d0499e3f4,0000000000000000000000000000000000000000..41317eb5a1a381b4aff925f0462d3304e97952e8
mode 100644,000000..100644
--- 1/src/gromacs/timing/walltime_accounting.cpp
--- /dev/null
+++ b/src/gromacs/timing/walltime_accounting.cpp
@@@ -1,240 -1,0 +1,243 @@@
- #if defined HAVE_CLOCK_GETTIME && _POSIX_TIMERS >= 0
 +/*
 + * This file is part of the GROMACS molecular simulation package.
 + *
 + * Copyright (c) 2013, The GROMACS development team.
 + * Copyright (c) 2013,2014,2015, 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 "gmxpre.h"
 +
 +#include "walltime_accounting.h"
 +
 +#include "config.h"
 +
 +#include <ctime>
 +
 +#ifdef HAVE_UNISTD_H
 +#include <unistd.h>
 +#endif
 +#ifdef HAVE_SYS_TIME_H
 +#include <sys/time.h>
 +#endif
 +
 +#include "gromacs/utility/basedefinitions.h"
 +#include "gromacs/utility/smalloc.h"
 +
 +/* TODO in future: convert gmx_walltime_accounting to a class,
 + * resolve who should have responsibility for recording the number of
 + * steps done, consider whether parts of finish_time, print_perf,
 + * wallcycle_print belong in this module.
 + *
 + * If/when any kind of task parallelism is implemented (even OpenMP
 + * regions simultaneously assigned to different tasks), consider
 + * whether this data structure (and/or cycle counters) should be
 + * maintained on a per-OpenMP-thread basis. */
 +
 +/*! \brief Manages caching wall-clock time measurements for
 + * simulations */
 +typedef struct gmx_walltime_accounting {
 +    //! Seconds since the epoch recorded at the start of the simulation
 +    double          start_time_stamp;
 +    //! Seconds since the epoch recorded at the start of the simulation for this thread
 +    double          start_time_stamp_per_thread;
 +    //! Total seconds elapsed over the simulation
 +    double          elapsed_time;
 +    //! Total seconds elapsed over the simulation running this thread
 +    double          elapsed_time_over_all_threads;
 +    /*! \brief Number of OpenMP threads that will be launched by this
 +     * MPI rank.
 +     *
 +     * This is used to scale elapsed_time_over_all_threads so
 +     * that any combination of real MPI, thread MPI and OpenMP (even
 +     * mdrun -ntomp_pme) processes/threads would (when run at maximum
 +     * efficiency) return values such that the sum of
 +     * elapsed_time_over_all_threads over all threads was constant
 +     * with respect to parallelism implementation. */
 +    int             numOpenMPThreads;
 +    //! Set by integrators to report the amount of work they did
 +    gmx_int64_t     nsteps_done;
 +} t_gmx_walltime_accounting;
 +
 +/*! \brief Calls system timing routines (e.g. clock_gettime) to get
 + * the (fractional) number of seconds elapsed since the epoch when
 + * this thread was executing.
 + *
 + * This can be used to measure system load. This can be unreliable if
 + * threads migrate between sockets. If thread-specific timers are not
 + * supported by the OS (e.g. if the OS is not POSIX-compliant), this
 + * function is implemented by gmx_gettime. */
 +static double gmx_gettime_per_thread();
 +
 +// TODO In principle, all this should get protected by checks that
 +// walltime_accounting is not null. In practice, that NULL condition
 +// does not happen, and future refactoring will likely enforce it by
 +// having the gmx_walltime_accounting_t object be owned by the runner
 +// object. When these become member functions, existence will be
 +// guaranteed.
 +
 +gmx_walltime_accounting_t
 +walltime_accounting_init(int numOpenMPThreads)
 +{
 +    gmx_walltime_accounting_t walltime_accounting;
 +
 +    snew(walltime_accounting, 1);
 +    walltime_accounting->start_time_stamp            = 0;
 +    walltime_accounting->start_time_stamp_per_thread = 0;
 +    walltime_accounting->elapsed_time                = 0;
 +    walltime_accounting->nsteps_done                 = 0;
 +    walltime_accounting->numOpenMPThreads            = numOpenMPThreads;
 +
 +    return walltime_accounting;
 +}
 +
 +void
 +walltime_accounting_destroy(gmx_walltime_accounting_t walltime_accounting)
 +{
 +    sfree(walltime_accounting);
 +}
 +
 +void
 +walltime_accounting_start(gmx_walltime_accounting_t walltime_accounting)
 +{
 +    walltime_accounting->start_time_stamp            = gmx_gettime();
 +    walltime_accounting->start_time_stamp_per_thread = gmx_gettime_per_thread();
 +    walltime_accounting->elapsed_time                = 0;
 +    walltime_accounting->nsteps_done                 = 0;
 +}
 +
 +void
 +walltime_accounting_end(gmx_walltime_accounting_t walltime_accounting)
 +{
 +    double now, now_per_thread;
 +
 +    now            = gmx_gettime();
 +    now_per_thread = gmx_gettime_per_thread();
 +
 +    walltime_accounting->elapsed_time                  = now - walltime_accounting->start_time_stamp;
 +    walltime_accounting->elapsed_time_over_all_threads = now_per_thread - walltime_accounting->start_time_stamp_per_thread;
 +    /* For thread-MPI, the per-thread CPU timer makes this just
 +     * work. For OpenMP threads, the per-thread CPU timer measurement
 +     * needs to be multiplied by the number of OpenMP threads used,
 +     * under the current assumption that all regions ever opened
 +     * within a process are of the same size, and each thread should
 +     * keep one core busy.
 +     */
 +    walltime_accounting->elapsed_time_over_all_threads *= walltime_accounting->numOpenMPThreads;
 +}
 +
 +double
 +walltime_accounting_get_current_elapsed_time(gmx_walltime_accounting_t walltime_accounting)
 +{
 +    return gmx_gettime() - walltime_accounting->start_time_stamp;
 +}
 +
 +double
 +walltime_accounting_get_elapsed_time(gmx_walltime_accounting_t walltime_accounting)
 +{
 +    return walltime_accounting->elapsed_time;
 +}
 +
 +double
 +walltime_accounting_get_elapsed_time_over_all_threads(gmx_walltime_accounting_t walltime_accounting)
 +{
 +    return walltime_accounting->elapsed_time_over_all_threads;
 +}
 +
 +double
 +walltime_accounting_get_start_time_stamp(gmx_walltime_accounting_t walltime_accounting)
 +{
 +    return walltime_accounting->start_time_stamp;
 +}
 +
 +gmx_int64_t
 +walltime_accounting_get_nsteps_done(gmx_walltime_accounting_t walltime_accounting)
 +{
 +    return walltime_accounting->nsteps_done;
 +}
 +
 +void
 +walltime_accounting_set_nsteps_done(gmx_walltime_accounting_t   walltime_accounting,
 +                                    gmx_int64_t                 nsteps_done)
 +{
 +    walltime_accounting->nsteps_done = nsteps_done;
 +}
 +
 +double
 +gmx_gettime()
 +{
-      * implementation. */
++#if defined HAVE_CLOCK_GETTIME && _POSIX_TIMERS >= 0 && !(defined __bgq__ && defined __clang__)
 +    /* Mac and Windows do not support this. For added fun, Windows
 +     * defines _POSIX_TIMERS without actually providing the
++     * implementation. The BlueGene/Q CNK only supports gettimeofday,
++     * and bgclang doesn't provide a fully functional implementation
++     * for clock_gettime (unlike xlc). */
 +    struct timespec t;
 +    double          seconds;
 +
 +    clock_gettime(CLOCK_REALTIME, &t);
 +    seconds = static_cast<double>(t.tv_sec) + 1e-9*t.tv_nsec;
 +
 +    return seconds;
 +#elif defined HAVE_GETTIMEOFDAY
 +    // Note that gettimeofday() is deprecated by POSIX, but since Mac
 +    // and Windows do not yet support POSIX, we are still stuck.
++    // Also, this is the only supported API call on Bluegene/Q.
 +    struct timeval t;
 +    double         seconds;
 +
 +    gettimeofday(&t, NULL);
 +    seconds = static_cast<double>(t.tv_sec) + 1e-6*t.tv_usec;
 +
 +    return seconds;
 +#else
 +    double  seconds;
 +
 +    seconds = time(NULL);
 +
 +    return seconds;
 +#endif
 +}
 +
 +static double
 +gmx_gettime_per_thread()
 +{
 +#if defined HAVE_CLOCK_GETTIME && _POSIX_THREAD_CPUTIME >= 0
 +    struct timespec t;
 +    double          seconds;
 +
 +    clock_gettime(CLOCK_THREAD_CPUTIME_ID, &t);
 +    seconds = static_cast<double>(t.tv_sec) + 1e-9*t.tv_nsec;
 +
 +    return seconds;
 +#else
 +    return gmx_gettime();
 +#endif
 +}