Move some mdrun code out of gmxlib/

[gromacs.git] / src / gromacs / mdrunutility / threadaffinity.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 2012,2013,2014,2015, 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.
 *
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 * as published by the Free Software Foundation; either version 2.1
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 */
#include "gmxpre.h"

#include "threadaffinity.h"

#include "config.h"

#include <cerrno>
#include <cstdio>
#include <cstring>

#ifdef HAVE_SCHED_AFFINITY
#  include <sched.h>
#  include <sys/syscall.h>
#endif

#include "thread_mpi/threads.h"

#include "gromacs/gmxlib/gmx_omp_nthreads.h"
#include "gromacs/gmxlib/md_logging.h"
#include "gromacs/hardware/hardwaretopology.h"
#include "gromacs/hardware/hw_info.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxomp.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/smalloc.h"


static int
get_thread_affinity_layout(FILE *fplog,
                           const t_commrec *cr,
                           const gmx_hw_info_t * hwinfo,
                           int   threads,
                           int pin_offset, int * pin_stride,
                           int **localityOrder)
{
    int                          hwThreads;
    int                          hwThreadsPerCore = 0;
    bool                         bPickPinStride;
    bool                         haveTopology;

    const gmx::HardwareTopology &hwTop = *hwinfo->hardwareTopology;

    haveTopology = (hwTop.supportLevel() >= gmx::HardwareTopology::SupportLevel::Basic);

    if (pin_offset < 0)
    {
        gmx_fatal(FARGS, "Negative thread pinning offset requested");
    }
    if (*pin_stride < 0)
    {
        gmx_fatal(FARGS, "Negative thread pinning stride requested");
    }

    if (haveTopology)
    {
        hwThreads           = hwTop.machine().logicalProcessorCount;
        // Just use the value for the first core
        hwThreadsPerCore    = hwTop.machine().sockets[0].cores[0].hwThreads.size();
        snew(*localityOrder, hwThreads);
        int i = 0;
        for (auto &s : hwTop.machine().sockets)
        {
            for (auto &c : s.cores)
            {
                for (auto &t : c.hwThreads)
                {
                    (*localityOrder)[i++] = t.logicalProcessorId;
                }
            }
        }
    }
    else
    {
        /* topology information not available or invalid, ignore it */
        hwThreads       = hwinfo->nthreads_hw_avail;
        *localityOrder  = NULL;

        if (hwThreads <= 0)
        {
            /* We don't know anything about the hardware, don't pin */
            md_print_warn(cr, fplog,
                          "NOTE: No information on available cores, thread pinning disabled.");

            return -1;
        }
    }

    if (threads > hwThreads)
    {
        /* We are oversubscribing, don't pin */
        md_print_warn(NULL, fplog,
                      "NOTE: Oversubscribing the CPU, will not pin threads");

        return -1;
    }

    if (pin_offset + threads > hwThreads)
    {
        /* We are oversubscribing, don't pin */
        md_print_warn(NULL, fplog,
                      "WARNING: Requested offset too large for available cores, thread pinning disabled.");

        return -1;
    }


    /* do we need to choose the pinning stride? */
    bPickPinStride = (*pin_stride == 0);

    if (bPickPinStride)
    {
        if (haveTopology && pin_offset + threads*hwThreadsPerCore <= hwThreads)
        {
            /* Put one thread on each physical core */
            *pin_stride = hwThreadsPerCore;
        }
        else
        {
            /* We don't know if we have SMT, and if we do, we don't know
             * if hw threads in the same physical core are consecutive.
             * Without SMT the pinning layout should not matter too much.
             * so we assume a consecutive layout and maximally spread out"
             * the threads at equal threads per core.
             * Note that IBM is the major non-x86 case with cpuid support
             * and probably threads are already pinned by the queuing system,
             * so we wouldn't end up here in the first place.
             */
            *pin_stride = (hwThreads - pin_offset)/threads;
        }
    }
    else
    {
        /* Check the placement of the thread with the largest index to make sure
         * that the offset & stride doesn't cause pinning beyond the last hardware thread. */
        if (pin_offset + (threads-1)*(*pin_stride) >= hwThreads)
        {
            /* We are oversubscribing, don't pin */
            md_print_warn(NULL, fplog,
                          "WARNING: Requested stride too large for available cores, thread pinning disabled.");

            return -1;
        }
    }

    if (fplog != NULL)
    {
        fprintf(fplog, "Pinning threads with a%s logical core stride of %d\n",
                bPickPinStride ? "n auto-selected" : " user-specified",
                *pin_stride);
    }

    return 0;
}

/* Set CPU affinity. Can be important for performance.
   On some systems (e.g. Cray) CPU Affinity is set by default.
   But default assigning doesn't work (well) with only some ranks
   having threads. This causes very low performance.
   External tools have cumbersome syntax for setting affinity
   in the case that only some ranks have threads.
   Thus it is important that GROMACS sets the affinity internally
   if only PME is using threads.
 */
void
gmx_set_thread_affinity(FILE                *fplog,
                        const t_commrec     *cr,
                        const gmx_hw_opt_t  *hw_opt,
                        const gmx_hw_info_t *hwinfo)
{
    int        nth_affinity_set, thread0_id_node,
               nthread_local, nthread_node;
    int        offset;
    int *      localityOrder = nullptr;
    int        rc;

    if (hw_opt->thread_affinity == threadaffOFF)
    {
        /* Nothing to do */
        return;
    }

    /* If the tMPI thread affinity setting is not supported encourage the user
     * to report it as it's either a bug or an exotic platform which we might
     * want to support. */
    if (tMPI_Thread_setaffinity_support() != TMPI_SETAFFINITY_SUPPORT_YES)
    {
        /* we know Mac OS & BlueGene do not support setting thread affinity, so there's
           no point in warning the user in that case. In any other case
           the user might be able to do something about it. */
#if !defined(__APPLE__) && !defined(__bg__)
        md_print_warn(NULL, fplog,
                      "NOTE: Cannot set thread affinities on the current platform.");
#endif  /* __APPLE__ */
        return;
    }

    /* threads on this MPI process or TMPI thread */
    if (cr->duty & DUTY_PP)
    {
        nthread_local = gmx_omp_nthreads_get(emntNonbonded);
    }
    else
    {
        nthread_local = gmx_omp_nthreads_get(emntPME);
    }

    /* map the current process to cores */
    thread0_id_node = 0;
    nthread_node    = nthread_local;
#ifdef GMX_MPI
    if (PAR(cr) || MULTISIM(cr))
    {
        /* We need to determine a scan of the thread counts in this
         * compute node.
         */
        MPI_Comm comm_intra;

        MPI_Comm_split(MPI_COMM_WORLD,
                       gmx_physicalnode_id_hash(), cr->rank_intranode,
                       &comm_intra);
        MPI_Scan(&nthread_local, &thread0_id_node, 1, MPI_INT, MPI_SUM, comm_intra);
        /* MPI_Scan is inclusive, but here we need exclusive */
        thread0_id_node -= nthread_local;
        /* Get the total number of threads on this physical node */
        MPI_Allreduce(&nthread_local, &nthread_node, 1, MPI_INT, MPI_SUM, comm_intra);
        MPI_Comm_free(&comm_intra);
    }
#endif

    if (hw_opt->thread_affinity == threadaffAUTO &&
        nthread_node != hwinfo->nthreads_hw_avail)
    {
        if (nthread_node > 1 && nthread_node < hwinfo->nthreads_hw_avail)
        {
            md_print_warn(cr, fplog,
                          "NOTE: The number of threads is not equal to the number of (logical) cores\n"
                          "      and the -pin option is set to auto: will not pin thread to cores.\n"
                          "      This can lead to significant performance degradation.\n"
                          "      Consider using -pin on (and -pinoffset in case you run multiple jobs).\n");
        }

        return;
    }

    offset = 0;
    if (hw_opt->core_pinning_offset != 0)
    {
        offset = hw_opt->core_pinning_offset;
        md_print_info(cr, fplog, "Applying core pinning offset %d\n", offset);
    }

    int core_pinning_stride = hw_opt->core_pinning_stride;
    rc = get_thread_affinity_layout(fplog, cr, hwinfo,
                                    nthread_node,
                                    offset, &core_pinning_stride,
                                    &localityOrder);
    gmx::scoped_guard_sfree localityOrderGuard(localityOrder);

    if (rc != 0)
    {
        /* Incompatible layout, don't pin, warning was already issued */
        return;
    }

    /* Set the per-thread affinity. In order to be able to check the success
     * of affinity settings, we will set nth_affinity_set to 1 on threads
     * where the affinity setting succeded and to 0 where it failed.
     * Reducing these 0/1 values over the threads will give the total number
     * of threads on which we succeeded.
     */

    // To avoid warnings from the static analyzer we initialize nth_affinity_set
    // to zero outside the OpenMP block, and then add to it inside the block.
    // The value will still always be 0 or 1 from each thread.
    nth_affinity_set = 0;
#pragma omp parallel num_threads(nthread_local) reduction(+:nth_affinity_set)
    {
        try
        {
            int      thread_id, thread_id_node;
            int      index, core;
            gmx_bool setaffinity_ret;

            thread_id      = gmx_omp_get_thread_num();
            thread_id_node = thread0_id_node + thread_id;
            index          = offset + thread_id_node*core_pinning_stride;
            if (localityOrder != nullptr)
            {
                core = localityOrder[index];
            }
            else
            {
                core = index;
            }

            setaffinity_ret = tMPI_Thread_setaffinity_single(tMPI_Thread_self(), core);

            /* store the per-thread success-values of the setaffinity */
            nth_affinity_set += (setaffinity_ret == 0);

            if (debug)
            {
                fprintf(debug, "On rank %2d, thread %2d, index %2d, core %2d the affinity setting returned %d\n",
                        cr->nodeid, gmx_omp_get_thread_num(), index, core, setaffinity_ret);
            }
        }
        GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
    }

    if (nth_affinity_set > nthread_local)
    {
        char msg[STRLEN];

        sprintf(msg, "Looks like we have set affinity for more threads than "
                "we have (%d > %d)!\n", nth_affinity_set, nthread_local);
        gmx_incons(msg);
    }
    else
    {
        /* check & warn if some threads failed to set their affinities */
        if (nth_affinity_set != nthread_local)
        {
            char sbuf1[STRLEN], sbuf2[STRLEN];

            /* sbuf1 contains rank info, while sbuf2 OpenMP thread info */
            sbuf1[0] = sbuf2[0] = '\0';
            /* Only add rank info if we have more than one rank. */
            if (cr->nnodes > 1)
            {
#ifdef GMX_MPI
#ifdef GMX_THREAD_MPI
                sprintf(sbuf1, "In tMPI thread #%d: ", cr->nodeid);
#else           /* GMX_LIB_MPI */
                sprintf(sbuf1, "In MPI process #%d: ", cr->nodeid);
#endif
#endif          /* GMX_MPI */
            }

            if (nthread_local > 1)
            {
                sprintf(sbuf2, "for %d/%d thread%s ",
                        nthread_local - nth_affinity_set, nthread_local,
                        nthread_local > 1 ? "s" : "");
            }

            md_print_warn(NULL, fplog,
                          "NOTE: %sAffinity setting %sfailed. This can cause performance degradation.\n"
                          "      If you think your settings are correct, ask on the gmx-users list.",
                          sbuf1, sbuf2);
        }
    }
    return;
}

/* Check the process affinity mask and if it is found to be non-zero,
 * will honor it and disable mdrun internal affinity setting.
 * Note that this will only work on Linux as we use a GNU feature.
 */
void
gmx_check_thread_affinity_set(FILE            *fplog,
                              const t_commrec *cr,
                              gmx_hw_opt_t    *hw_opt,
                              int  gmx_unused  nthreads_hw_avail,
                              gmx_bool         bAfterOpenmpInit)
{
    GMX_RELEASE_ASSERT(hw_opt, "hw_opt must be a non-NULL pointer");

    if (!bAfterOpenmpInit)
    {
        /* 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 later
         */
        if (hw_opt->thread_affinity != threadaffOFF)
        {
            char *message;
            if (!gmx_omp_check_thread_affinity(&message))
            {
                /* TODO: with -pin auto we should only warn when using all cores */
                md_print_warn(cr, fplog, "%s", message);
                sfree(message);
                hw_opt->thread_affinity = threadaffOFF;
            }
        }

        /* With thread-MPI this is needed as pinning might get turned off,
         * which needs to be known before starting thread-MPI.
         * With thread-MPI hw_opt is processed here on the master rank
         * and passed to the other ranks later, so we only do this on master.
         */
        if (!SIMMASTER(cr))
        {
            return;
        }
#ifndef GMX_THREAD_MPI
        return;
#endif
    }

#ifdef HAVE_SCHED_AFFINITY
    int       ret;
    cpu_set_t mask_current;

    if (hw_opt->thread_affinity == threadaffOFF)
    {
        /* internal affinity setting is off, don't bother checking process affinity */
        return;
    }

    CPU_ZERO(&mask_current);
    if ((ret = sched_getaffinity(0, sizeof(cpu_set_t), &mask_current)) != 0)
    {
        /* failed to query affinity mask, will just return */
        if (debug)
        {
            fprintf(debug, "Failed to query affinity mask (error %d)", ret);
        }
        return;
    }

    /* Before proceeding with the actual check, make sure that the number of
     * detected CPUs is >= the CPUs in the current set.
     * We need to check for CPU_COUNT as it was added only in glibc 2.6. */
#ifdef CPU_COUNT
    if (nthreads_hw_avail < CPU_COUNT(&mask_current))
    {
        if (debug)
        {
            fprintf(debug, "%d hardware threads detected, but %d was returned by CPU_COUNT",
                    nthreads_hw_avail, CPU_COUNT(&mask_current));
        }
        return;
    }
#endif /* CPU_COUNT */

    gmx_bool bAllSet = TRUE;
    for (int i = 0; (i < nthreads_hw_avail && i < CPU_SETSIZE); i++)
    {
        bAllSet = bAllSet && (CPU_ISSET(i, &mask_current) != 0);
    }

#ifdef GMX_LIB_MPI
    gmx_bool  bAllSet_All;

    MPI_Allreduce(&bAllSet, &bAllSet_All, 1, MPI_INT, MPI_LAND, MPI_COMM_WORLD);
    bAllSet = bAllSet_All;
#endif

    if (!bAllSet)
    {
        if (hw_opt->thread_affinity == threadaffAUTO)
        {
            if (!bAfterOpenmpInit)
            {
                md_print_warn(cr, fplog,
                              "Non-default thread affinity set, disabling internal thread affinity");
            }
            else
            {
                md_print_warn(cr, fplog,
                              "Non-default thread affinity set probably by the OpenMP library,\n"
                              "disabling internal thread affinity");
            }
            hw_opt->thread_affinity = threadaffOFF;
        }
        else
        {
            /* Only warn once, at the last check (bAfterOpenmpInit==TRUE) */
            if (bAfterOpenmpInit)
            {
                md_print_warn(cr, fplog,
                              "Overriding thread affinity set outside %s\n",
                              gmx::getProgramContext().displayName());
            }
        }

        if (debug)
        {
            fprintf(debug, "Non-default affinity mask found\n");
        }
    }
    else
    {
        if (debug)
        {
            fprintf(debug, "Default affinity mask found\n");
        }
    }
#endif /* HAVE_SCHED_AFFINITY */
}