From: Mark Abraham Date: Mon, 16 Nov 2015 10:47:43 +0000 (+0100) Subject: Merge branch release-5-1 X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=545f6d76a58998bb715ff8e672077de5f143b7cb;p=alexxy%2Fgromacs.git Merge branch release-5-1 Conflicts only from version numbers Change-Id: I78235cce0c4fd7bcf4235dd888e1aef739d46001 --- 545f6d76a58998bb715ff8e672077de5f143b7cb diff --cc src/gromacs/timing/walltime_accounting.cpp index 5eeed23c80,0000000000..41317eb5a1 mode 100644,000000..100644 --- a/src/gromacs/timing/walltime_accounting.cpp +++ b/src/gromacs/timing/walltime_accounting.cpp @@@ -1,240 -1,0 +1,243 @@@ +/* + * 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 + +#ifdef HAVE_UNISTD_H +#include +#endif +#ifdef HAVE_SYS_TIME_H +#include +#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() +{ - #if defined HAVE_CLOCK_GETTIME && _POSIX_TIMERS >= 0 ++#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. */ ++ * 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(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(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(t.tv_sec) + 1e-9*t.tv_nsec; + + return seconds; +#else + return gmx_gettime(); +#endif +}