hillclimber 0.1.6__cp314-cp314t-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl

plumed/_lib/lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/taskassignment/decidegpuusage.cpp

@@ -0,0 +1,886 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright 2015- The GROMACS Authors
+ * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
+ * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
+ *
+ * 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
+ * https://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 https://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out https://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief Defines functionality for deciding whether tasks will run on GPUs.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_taskassignment
+ */
+
+#include "gmxpre.h"
+
+#include "gromacs/taskassignment/decidegpuusage.h"
+
+#include "config.h"
+
+#include <cstdlib>
+#include <cstring>
+
+#include <algorithm>
+#include <string>
+
+#include "gromacs/ewald/pme.h"
+#include "gromacs/hardware/cpuinfo.h"
+#include "gromacs/hardware/detecthardware.h"
+#include "gromacs/hardware/hardwaretopology.h"
+#include "gromacs/hardware/hw_info.h"
+#include "gromacs/listed_forces/listed_forces_gpu.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
+#include "gromacs/mdlib/update_constrain_gpu.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/taskassignment/taskassignment.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/baseversion.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/logger.h"
+#include "gromacs/utility/message_string_collector.h"
+#include "gromacs/utility/stringutil.h"
+
+
+namespace gmx
+{
+
+namespace
+{
+
+//! Helper variable to localise the text of an often repeated message.
+const char* const g_specifyEverythingFormatString =
+        "When you use mdrun -gputasks, %s must be set to non-default "
+        "values, so that the device IDs can be interpreted correctly."
+#if GMX_GPU
+        " If you simply want to restrict which GPUs are used, then it is "
+        "better to use mdrun -gpu_id. Otherwise, setting the "
+#    if GMX_GPU_CUDA
+        "CUDA_VISIBLE_DEVICES"
+#    elif GMX_GPU_OPENCL
+        // Technically there is no portable way to do this offered by the
+        // OpenCL standard, but the only current relevant case for GROMACS
+        // is AMD OpenCL, which offers this variable.
+        "GPU_DEVICE_ORDINAL"
+#    elif GMX_GPU_SYCL && GMX_SYCL_DPCPP
+        // https://github.com/intel/llvm/blob/sycl/sycl/doc/EnvironmentVariables.md
+        "SYCL_DEVICE_FILTER"
+#    elif GMX_GPU_SYCL && GMX_SYCL_HIPSYCL
+        // Not true if we use hipSYCL over CUDA or IntelLLVM, but in that case the user probably
+        // knows what they are doing.
+        // https://rocmdocs.amd.com/en/latest/Other_Solutions/Other-Solutions.html#hip-environment-variables
+        "HIP_VISIBLE_DEVICES"
+#    else
+#        error "Unreachable branch"
+#    endif
+        " environment variable in your bash profile or job "
+        "script may be more convenient."
+#endif
+        ;
+
+} // namespace
+
+// The conditions below must be in sync with getSkipMessagesIfNecessary check in src/programs/mdrun/tests/pmetest.cpp
+constexpr bool c_gpuBuildSyclWithoutGpuFft =
+        // NOLINTNEXTLINE(misc-redundant-expression)
+        (GMX_GPU_SYCL != 0) && (GMX_GPU_FFT_MKL == 0) && (GMX_GPU_FFT_ROCFFT == 0)
+        && (GMX_GPU_FFT_VKFFT == 0) && (GMX_GPU_FFT_DBFFT == 0); // NOLINT(misc-redundant-expression)
+
+bool decideWhetherToUseGpusForNonbondedWithThreadMpi(const TaskTarget        nonbondedTarget,
+                                                     const bool              haveAvailableDevices,
+                                                     const std::vector<int>& userGpuTaskAssignment,
+                                                     const EmulateGpuNonbonded emulateGpuNonbonded,
+                                                     const bool buildSupportsNonbondedOnGpu,
+                                                     const bool nonbondedOnGpuIsUseful,
+                                                     const int  numRanksPerSimulation)
+{
+    // First, exclude all cases where we can't run NB on GPUs.
+    if (nonbondedTarget == TaskTarget::Cpu || emulateGpuNonbonded == EmulateGpuNonbonded::Yes
+        || !nonbondedOnGpuIsUseful || !buildSupportsNonbondedOnGpu)
+    {
+        // If the user required NB on GPUs, we issue an error later.
+        return false;
+    }
+
+    // We now know that NB on GPUs makes sense, if we have any.
+
+    if (!userGpuTaskAssignment.empty())
+    {
+        // Specifying -gputasks requires specifying everything.
+        if (nonbondedTarget == TaskTarget::Auto || numRanksPerSimulation < 1)
+        {
+            GMX_THROW(InconsistentInputError(formatString(
+                    g_specifyEverythingFormatString, GMX_THREAD_MPI ? "-nb and -ntmpi" : "-nb")));
+        }
+        return true;
+    }
+
+    if (nonbondedTarget == TaskTarget::Gpu)
+    {
+        return true;
+    }
+
+    // Because this is thread-MPI, we already know about the GPUs that
+    // all potential ranks can use, and can use that in a global
+    // decision that will later be consistent.
+    // If we get here, then the user permitted or required GPUs.
+    return haveAvailableDevices;
+}
+
+static bool decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget)
+{
+    const bool useCpuFft = (pmeFftTarget == TaskTarget::Cpu)
+                           || (pmeFftTarget == TaskTarget::Auto && c_gpuBuildSyclWithoutGpuFft);
+    return !useCpuFft;
+}
+
+static bool canUseGpusForPme(const bool        useGpuForNonbonded,
+                             const TaskTarget  pmeTarget,
+                             const TaskTarget  pmeFftTarget,
+                             const t_inputrec& inputrec,
+                             std::string*      errorMessage)
+{
+    if (pmeTarget == TaskTarget::Cpu)
+    {
+        return false;
+    }
+
+    std::string                 tempString;
+    gmx::MessageStringCollector errorReasons;
+    // Before changing the prefix string, make sure that it is not searched for in regression tests.
+    errorReasons.startContext("Cannot compute PME interactions on a GPU, because:");
+    errorReasons.appendIf(!useGpuForNonbonded, "Nonbonded interactions must also run on GPUs.");
+    errorReasons.appendIf(!pme_gpu_supports_build(&tempString), tempString);
+    errorReasons.appendIf(!pme_gpu_supports_input(inputrec, &tempString), tempString);
+    if (!decideWhetherToUseGpusForPmeFft(pmeFftTarget))
+    {
+        // We need to do FFT on CPU, so we check whether we are able to use PME Mixed mode.
+        errorReasons.appendIf(!pme_gpu_mixed_mode_supports_input(inputrec, &tempString), tempString);
+    }
+    errorReasons.finishContext();
+
+    if (errorReasons.isEmpty())
+    {
+        return true;
+    }
+    else
+    {
+        if (pmeTarget == TaskTarget::Gpu && errorMessage != nullptr)
+        {
+            *errorMessage = errorReasons.toString();
+        }
+        return false;
+    }
+}
+
+bool decideWhetherToUseGpusForPmeWithThreadMpi(const bool              useGpuForNonbonded,
+                                               const TaskTarget        pmeTarget,
+                                               const TaskTarget        pmeFftTarget,
+                                               const int               numDevicesToUse,
+                                               const std::vector<int>& userGpuTaskAssignment,
+                                               const t_inputrec&       inputrec,
+                                               const int               numRanksPerSimulation,
+                                               const int               numPmeRanksPerSimulation)
+{
+    // First, exclude all cases where we can't run PME on GPUs.
+    if (!canUseGpusForPme(useGpuForNonbonded, pmeTarget, pmeFftTarget, inputrec, nullptr))
+    {
+        // PME can't run on a GPU. If the user required that, we issue an error later.
+        return false;
+    }
+
+    // We now know that PME on GPUs might make sense, if we have any.
+
+    if (pmeTarget == TaskTarget::Gpu)
+    {
+        if ((numRanksPerSimulation > 1) && (numPmeRanksPerSimulation < 0))
+        {
+            GMX_THROW(NotImplementedError(
+                    "PME tasks were required to run on GPUs with multiple ranks "
+                    "but the -npme option was not specified. "
+                    "A non-negative value must be specified for -npme."));
+        }
+    }
+
+    if (!userGpuTaskAssignment.empty())
+    {
+        // Follow the user's choice of GPU task assignment, if we
+        // can. Checking that their IDs are for compatible GPUs comes
+        // later.
+
+        // Specifying -gputasks requires specifying everything.
+        if (pmeTarget == TaskTarget::Auto || numRanksPerSimulation < 1)
+        {
+            GMX_THROW(InconsistentInputError(
+                    formatString(g_specifyEverythingFormatString, "all of -nb, -pme, and -ntmpi")));
+        }
+
+        // PME on GPUs is only supported in a single case
+        if (pmeTarget == TaskTarget::Gpu)
+        {
+            if (((numRanksPerSimulation > 1) && (numPmeRanksPerSimulation == 0))
+                || (numPmeRanksPerSimulation > 1))
+            {
+                GMX_THROW(InconsistentInputError(
+                        "When you run mdrun -pme gpu -gputasks, you must supply a PME-enabled .tpr "
+                        "file and use a single PME rank."));
+            }
+            return true;
+        }
+
+        // pmeTarget == TaskTarget::Auto
+        return numRanksPerSimulation == 1;
+    }
+
+    // Because this is thread-MPI, we already know about the GPUs that
+    // all potential ranks can use, and can use that in a global
+    // decision that will later be consistent.
+
+    if (pmeTarget == TaskTarget::Gpu)
+    {
+        if (((numRanksPerSimulation > 1) && (numPmeRanksPerSimulation == 0))
+            || (numPmeRanksPerSimulation > 1))
+        {
+            GMX_THROW(NotImplementedError(
+                    "PME tasks were required to run on GPUs, but that is not implemented with "
+                    "more than one PME rank. Use a single rank simulation, or a separate PME rank, "
+                    "or permit PME tasks to be assigned to the CPU."));
+        }
+        return true;
+    }
+
+    if (numRanksPerSimulation == 1)
+    {
+        // PME can run well on a GPU shared with NB, and we permit
+        // mdrun to default to try that.
+        return numDevicesToUse > 0;
+    }
+
+    if (numPmeRanksPerSimulation == 1)
+    {
+        // We have a single separate PME rank, that can use a GPU
+        return numDevicesToUse > 0;
+    }
+
+    if (numRanksPerSimulation < 1)
+    {
+        // Full automated mode for thread-MPI (the default). PME can
+        // run well on a GPU shared with NB, and we permit mdrun to
+        // default to it if there is only one GPU available.
+        return (numDevicesToUse == 1);
+    }
+
+    // Not enough support for PME on GPUs for anything else
+    return false;
+}
+
+bool decideWhetherToUseGpusForNonbonded(const TaskTarget          nonbondedTarget,
+                                        const std::vector<int>&   userGpuTaskAssignment,
+                                        const EmulateGpuNonbonded emulateGpuNonbonded,
+                                        const bool                buildSupportsNonbondedOnGpu,
+                                        const bool                nonbondedOnGpuIsUseful,
+                                        const bool                gpusWereDetected)
+{
+    if (nonbondedTarget == TaskTarget::Cpu)
+    {
+        if (!userGpuTaskAssignment.empty())
+        {
+            GMX_THROW(InconsistentInputError(
+                    "A GPU task assignment was specified, but nonbonded interactions were "
+                    "assigned to the CPU. Make no more than one of these choices."));
+        }
+
+        return false;
+    }
+
+    if (!buildSupportsNonbondedOnGpu && nonbondedTarget == TaskTarget::Gpu)
+    {
+        GMX_THROW(InconsistentInputError(
+                "Nonbonded interactions on the GPU were requested with -nb gpu, "
+                "but the GROMACS binary has been built without GPU support. "
+                "Either run without selecting GPU options, or recompile GROMACS "
+                "with GPU support enabled"));
+    }
+
+    // TODO refactor all these TaskTarget::Gpu checks into one place?
+    // e.g. use a subfunction that handles only the cases where
+    // TaskTargets are not Cpu?
+    if (emulateGpuNonbonded == EmulateGpuNonbonded::Yes)
+    {
+        if (nonbondedTarget == TaskTarget::Gpu)
+        {
+            GMX_THROW(InconsistentInputError(
+                    "Nonbonded interactions on the GPU were required, which is inconsistent "
+                    "with choosing emulation. Make no more than one of these choices."));
+        }
+        if (!userGpuTaskAssignment.empty())
+        {
+            GMX_THROW(
+                    InconsistentInputError("GPU ID usage was specified, as was GPU emulation. Make "
+                                           "no more than one of these choices."));
+        }
+
+        return false;
+    }
+
+    if (!nonbondedOnGpuIsUseful)
+    {
+        if (nonbondedTarget == TaskTarget::Gpu)
+        {
+            GMX_THROW(InconsistentInputError(
+                    "Nonbonded interactions on the GPU were required, but not supported for these "
+                    "simulation settings. Change your settings, or do not require using GPUs."));
+        }
+
+        return false;
+    }
+
+    if (!userGpuTaskAssignment.empty())
+    {
+        // Specifying -gputasks requires specifying everything.
+        if (nonbondedTarget == TaskTarget::Auto)
+        {
+            GMX_THROW(InconsistentInputError(formatString(
+                    g_specifyEverythingFormatString, GMX_THREAD_MPI ? "-nb and -ntmpi" : "-nb")));
+        }
+
+        return true;
+    }
+
+    if (nonbondedTarget == TaskTarget::Gpu)
+    {
+        // We still don't know whether it is an error if no GPUs are found
+        // because we don't know the duty of this rank, yet. For example,
+        // a node with only PME ranks and -pme cpu is OK if there are not
+        // GPUs.
+        return true;
+    }
+
+    // If we get here, then the user permitted GPUs, which we should
+    // use for nonbonded interactions.
+    return buildSupportsNonbondedOnGpu && gpusWereDetected;
+}
+
+bool decideWhetherToUseGpusForPme(const bool              useGpuForNonbonded,
+                                  const TaskTarget        pmeTarget,
+                                  const TaskTarget        pmeFftTarget,
+                                  const std::vector<int>& userGpuTaskAssignment,
+                                  const t_inputrec&       inputrec,
+                                  const int               numRanksPerSimulation,
+                                  const int               numPmeRanksPerSimulation,
+                                  const bool              gpusWereDetected)
+{
+    std::string message;
+    if (!canUseGpusForPme(useGpuForNonbonded, pmeTarget, pmeFftTarget, inputrec, &message))
+    {
+        if (!message.empty())
+        {
+            GMX_THROW(InconsistentInputError(message));
+        }
+        return false;
+    }
+
+    if (pmeTarget == TaskTarget::Cpu)
+    {
+        if (!userGpuTaskAssignment.empty())
+        {
+            GMX_THROW(InconsistentInputError(
+                    "A GPU task assignment was specified, but PME interactions were "
+                    "assigned to the CPU. Make no more than one of these choices."));
+        }
+
+        return false;
+    }
+
+    if (pmeTarget == TaskTarget::Gpu)
+    {
+        if ((numRanksPerSimulation > 1) && (numPmeRanksPerSimulation < 0))
+        {
+            GMX_THROW(NotImplementedError(
+                    "PME tasks were required to run on GPUs with multiple ranks "
+                    "but the -npme option was not specified. "
+                    "A non-negative value must be specified for -npme."));
+        }
+    }
+
+    if (!userGpuTaskAssignment.empty())
+    {
+        // Specifying -gputasks requires specifying everything.
+        if (pmeTarget == TaskTarget::Auto)
+        {
+            GMX_THROW(InconsistentInputError(
+                    formatString(g_specifyEverythingFormatString,
+                                 GMX_THREAD_MPI ? "all of -nb, -pme, and -ntmpi" : "-nb and -pme")));
+        }
+
+        return true;
+    }
+
+    // We still don't know whether it is an error if no GPUs are found
+    // because we don't know the duty of this rank, yet. For example,
+    // a node with only PME ranks and -pme cpu is OK if there are not
+    // GPUs.
+
+    if (pmeTarget == TaskTarget::Gpu)
+    {
+        return true;
+    }
+
+    // If we get here, then the user permitted GPUs.
+    if (numRanksPerSimulation == 1)
+    {
+        // PME can run well on a single GPU shared with NB when there
+        // is one rank, so we permit mdrun to try that if we have
+        // detected GPUs.
+        return gpusWereDetected;
+    }
+
+    if (numPmeRanksPerSimulation == 1)
+    {
+        // We have a single separate PME rank, that can use a GPU
+        return gpusWereDetected;
+    }
+
+    // Not enough support for PME on GPUs for anything else
+    return false;
+}
+
+
+PmeRunMode determinePmeRunMode(const bool useGpuForPme, const TaskTarget& pmeFftTarget, const t_inputrec& inputrec)
+{
+    if (!usingPme(inputrec.coulombtype) && !usingLJPme(inputrec.vdwtype))
+    {
+        return PmeRunMode::None;
+    }
+
+    if (useGpuForPme)
+    {
+        if (c_gpuBuildSyclWithoutGpuFft && pmeFftTarget == TaskTarget::Gpu)
+        {
+            gmx_fatal(FARGS,
+                      "GROMACS is built without SYCL GPU FFT library. Please do not use -pmefft "
+                      "gpu.");
+        }
+        if (!decideWhetherToUseGpusForPmeFft(pmeFftTarget))
+        {
+            return PmeRunMode::Mixed;
+        }
+        else
+        {
+            return PmeRunMode::GPU;
+        }
+    }
+    else
+    {
+        if (pmeFftTarget == TaskTarget::Gpu)
+        {
+            gmx_fatal(FARGS,
+                      "Assigning FFTs to GPU requires PME to be assigned to GPU as well. With PME "
+                      "on CPU you should not be using -pmefft.");
+        }
+        return PmeRunMode::CPU;
+    }
+}
+
+bool decideWhetherToUseGpusForBonded(bool              useGpuForNonbonded,
+                                     bool              useGpuForPme,
+                                     TaskTarget        bondedTarget,
+                                     const t_inputrec& inputrec,
+                                     const gmx_mtop_t& mtop,
+                                     int               numPmeRanksPerSimulation,
+                                     bool              gpusWereDetected)
+{
+    if (bondedTarget == TaskTarget::Cpu)
+    {
+        return false;
+    }
+
+    std::string errorMessage;
+
+    if (!buildSupportsListedForcesGpu(&errorMessage))
+    {
+        if (bondedTarget == TaskTarget::Gpu)
+        {
+            GMX_THROW(InconsistentInputError(errorMessage.c_str()));
+        }
+
+        return false;
+    }
+
+    if (!inputSupportsListedForcesGpu(inputrec, mtop, &errorMessage))
+    {
+        if (bondedTarget == TaskTarget::Gpu)
+        {
+            GMX_THROW(InconsistentInputError(errorMessage.c_str()));
+        }
+
+        return false;
+    }
+
+    if (!useGpuForNonbonded)
+    {
+        if (bondedTarget == TaskTarget::Gpu)
+        {
+            GMX_THROW(InconsistentInputError(
+                    "Bonded interactions on the GPU were required, but this requires that "
+                    "short-ranged non-bonded interactions are also run on the GPU. Change "
+                    "your settings, or do not require using GPUs."));
+        }
+
+        return false;
+    }
+
+    // TODO If the bonded kernels do not get fused, then performance
+    // overheads might suggest alternative choices here.
+
+    if (bondedTarget == TaskTarget::Gpu)
+    {
+        // We still don't know whether it is an error if no GPUs are
+        // found.
+        return true;
+    }
+
+    // If we get here, then the user permitted GPUs, which we should
+    // use for bonded interactions if any were detected and the CPU
+    // is busy, for which we currently only check PME or Ewald.
+    // (It would be better to dynamically assign bondeds based on timings)
+    // Note that here we assume that the auto setting of PME ranks will not
+    // choose separate PME ranks when nonBonded are assigned to the GPU.
+    bool usingOurCpuForPmeOrEwald = (usingLJPme(inputrec.vdwtype)
+                                     || (usingPmeOrEwald(inputrec.coulombtype) && !useGpuForPme
+                                         && numPmeRanksPerSimulation <= 0));
+
+    return gpusWereDetected && usingOurCpuForPmeOrEwald;
+}
+
+bool decideWhetherToUseGpuForUpdate(const bool           isDomainDecomposition,
+                                    const bool           useUpdateGroups,
+                                    const PmeRunMode     pmeRunMode,
+                                    const bool           havePmeOnlyRank,
+                                    const bool           useGpuForNonbonded,
+                                    const TaskTarget     updateTarget,
+                                    const bool           gpusWereDetected,
+                                    const t_inputrec&    inputrec,
+                                    const gmx_mtop_t&    mtop,
+                                    const bool           useEssentialDynamics,
+                                    const bool           doOrientationRestraints,
+                                    const bool           haveFrozenAtoms,
+                                    const bool           useModularSimulator,
+                                    const bool           doRerun,
+                                    const bool           usePlumed, /* PLUMED */
+                                    const gmx::MDLogger& mdlog)
+{
+
+    // '-update cpu' overrides the environment variable, '-update auto' does not
+    const bool forceCpuUpdateDefault = getenv("GMX_FORCE_UPDATE_DEFAULT_CPU") != nullptr;
+
+    if (forceCpuUpdateDefault)
+    {
+        GMX_LOG(mdlog.warning)
+                .asParagraph()
+                .appendTextFormatted(
+                        "This run will default to '-update cpu' as requested by the "
+                        "GMX_FORCE_UPDATE_CPU environment variable.");
+    }
+
+
+    if (updateTarget == TaskTarget::Cpu || (updateTarget == TaskTarget::Auto && forceCpuUpdateDefault))
+    {
+        return false;
+    }
+
+    const bool hasAnyConstraints      = gmx_mtop_interaction_count(mtop, IF_CONSTRAINT) > 0;
+    const bool pmeSpreadGatherUsesCpu = (pmeRunMode == PmeRunMode::CPU);
+
+    std::string errorMessage;
+    // Flag to set if we do not want to log the error with `-update auto` (e.g., for non-GPU build)
+    bool silenceWarningMessageWithUpdateAuto = forceCpuUpdateDefault;
+
+    if (isDomainDecomposition)
+    {
+        if (hasAnyConstraints && !useUpdateGroups)
+        {
+            errorMessage +=
+                    "Domain decomposition is only supported with constraints when update "
+                    "groups "
+                    "are used. This means constraining all bonds is not supported, except for "
+                    "small molecules, and box sizes close to half the pair-list cutoff are not "
+                    "supported.\n ";
+        }
+    }
+
+    if (havePmeOnlyRank)
+    {
+        if (pmeSpreadGatherUsesCpu)
+        {
+            errorMessage += "With separate PME rank(s), PME must run on the GPU.\n";
+        }
+    }
+
+    if (inputrec.useMts)
+    {
+        errorMessage += "Multiple time stepping is not supported.\n";
+    }
+
+    if (inputrec.eConstrAlg == ConstraintAlgorithm::Shake && hasAnyConstraints
+        && gmx_mtop_ftype_count(mtop, F_CONSTR) > 0)
+    {
+        errorMessage += "SHAKE constraints are not supported.\n";
+    }
+    // Using the GPU-version of update if:
+    // 1. PME is on the GPU (there should be a copy of coordinates on GPU for PME spread) or inactive, or
+    // 2. Non-bonded interactions are on the GPU.
+    if ((pmeRunMode == PmeRunMode::CPU || pmeRunMode == PmeRunMode::None) && !useGpuForNonbonded)
+    {
+        errorMessage +=
+                "Either PME or short-ranged non-bonded interaction tasks must run on the GPU.\n";
+        silenceWarningMessageWithUpdateAuto = true;
+    }
+    if (!gpusWereDetected)
+    {
+        errorMessage += "Compatible GPUs must have been found.\n";
+        silenceWarningMessageWithUpdateAuto = true;
+    }
+    if (!(GMX_GPU_CUDA || GMX_GPU_SYCL))
+    {
+        errorMessage += "Only CUDA and SYCL builds are supported.\n";
+        // Silence clang-analyzer deadcode.DeadStores warning about ignoring the previous assignments
+        GMX_UNUSED_VALUE(silenceWarningMessageWithUpdateAuto);
+        silenceWarningMessageWithUpdateAuto = true;
+    }
+    if (inputrec.eI != IntegrationAlgorithm::MD)
+    {
+        errorMessage += "Only the md integrator is supported.\n";
+    }
+    if (inputrec.etc == TemperatureCoupling::NoseHoover)
+    {
+        errorMessage += "Nose-Hoover temperature coupling is not supported.\n";
+    }
+    if (!(inputrec.pressureCouplingOptions.epc == PressureCoupling::No
+          || inputrec.pressureCouplingOptions.epc == PressureCoupling::ParrinelloRahman
+          || inputrec.pressureCouplingOptions.epc == PressureCoupling::Berendsen
+          || inputrec.pressureCouplingOptions.epc == PressureCoupling::CRescale))
+    {
+        errorMessage +=
+                "Only Parrinello-Rahman, Berendsen, and C-rescale pressure coupling are "
+                "supported.\n";
+    }
+    if (inputrec.cos_accel != 0 || inputrec.useConstantAcceleration)
+    {
+        errorMessage += "Acceleration is not supported.\n";
+    }
+    if (usingPmeOrEwald(inputrec.coulombtype) && inputrec.epsilon_surface != 0)
+    {
+        // The graph is needed, but not supported
+        errorMessage += "Ewald surface correction is not supported.\n";
+    }
+    if (gmx_mtop_interaction_count(mtop, IF_VSITE) > 0)
+    {
+        errorMessage += "Virtual sites are not supported.\n";
+    }
+    if (useEssentialDynamics)
+    {
+        errorMessage += "Essential dynamics is not supported.\n";
+    }
+    if (inputrec.bPull && pull_have_constraint(*inputrec.pull))
+    {
+        errorMessage += "Constraints pulling is not supported.\n";
+    }
+    if (doOrientationRestraints)
+    {
+        // The graph is needed, but not supported
+        errorMessage += "Orientation restraints are not supported.\n";
+    }
+    if (inputrec.efep != FreeEnergyPerturbationType::No
+        && (haveFepPerturbedMasses(mtop) || havePerturbedConstraints(mtop)))
+    {
+        errorMessage += "Free energy perturbation for mass and constraints are not supported.\n";
+    }
+    const auto particleTypes = gmx_mtop_particletype_count(mtop);
+    if (particleTypes[ParticleType::Shell] > 0)
+    {
+        errorMessage += "Shells are not supported.\n";
+    }
+    if (inputrec.eSwapCoords != SwapType::No)
+    {
+        errorMessage += "Swapping the coordinates is not supported.\n";
+    }
+    if (useModularSimulator)
+    {
+        errorMessage += "The modular simulator is not supported.\n";
+    }
+    if (doRerun)
+    {
+        errorMessage += "Re-run is not supported.\n";
+    }
+    /* PLUMED */
+    if (usePlumed)
+    {
+        errorMessage += "PLUMED is not supported.\n";
+    }
+    /* PLUMED */
+    // TODO: F_CONSTRNC is only unsupported, because isNumCoupledConstraintsSupported()
+    // does not support it, the actual CUDA LINCS code does support it
+    if (gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0)
+    {
+        errorMessage += "Non-connecting constraints are not supported\n";
+    }
+    if (!UpdateConstrainGpu::isNumCoupledConstraintsSupported(mtop))
+    {
+        errorMessage +=
+                "The number of coupled constraints is higher than supported in the GPU LINCS "
+                "code.\n";
+    }
+    if (hasAnyConstraints && !UpdateConstrainGpu::areConstraintsSupported())
+    {
+        errorMessage += "Chosen GPU implementation does not support constraints.\n";
+    }
+    if (haveFrozenAtoms)
+    {
+        // There is a known bug with frozen atoms and GPU update, see Issue #3920.
+        errorMessage += "Frozen atoms not supported.\n";
+    }
+
+    if (!errorMessage.empty())
+    {
+        if (updateTarget == TaskTarget::Auto && !silenceWarningMessageWithUpdateAuto)
+        {
+            GMX_LOG(mdlog.info)
+                    .asParagraph()
+                    .appendText(
+                            "Update task can not run on the GPU, because the following "
+                            "condition(s) were not satisfied:");
+            GMX_LOG(mdlog.info).asParagraph().appendText(errorMessage.c_str());
+        }
+        else if (updateTarget == TaskTarget::Gpu)
+        {
+            std::string prefix = gmx::formatString(
+                    "Update task on the GPU was required,\n"
+                    "but the following condition(s) were not satisfied:\n");
+            GMX_THROW(InconsistentInputError((prefix + errorMessage).c_str()));
+        }
+        return false;
+    }
+
+    return (updateTarget == TaskTarget::Gpu
+            || (updateTarget == TaskTarget::Auto && !forceCpuUpdateDefault));
+}
+
+bool decideWhetherDirectGpuCommunicationCanBeUsed(const DevelopmentFeatureFlags& devFlags,
+                                                  bool                           haveMts,
+                                                  bool                           haveSwapCoords,
+                                                  const gmx::MDLogger&           mdlog)
+{
+    const bool buildSupportsDirectGpuComm = (GMX_GPU_CUDA || GMX_GPU_SYCL) && GMX_MPI;
+    if (!buildSupportsDirectGpuComm)
+    {
+        return false;
+    }
+
+    // Direct GPU communication is presently turned off due to insufficient testing
+    const bool enableDirectGpuComm = (getenv("GMX_ENABLE_DIRECT_GPU_COMM") != nullptr)
+                                     || (getenv("GMX_GPU_DD_COMMS") != nullptr)
+                                     || (getenv("GMX_GPU_PME_PP_COMMS") != nullptr);
+
+    if (GMX_THREAD_MPI && GMX_GPU_SYCL && enableDirectGpuComm)
+    {
+        GMX_LOG(mdlog.warning)
+                .asParagraph()
+                .appendTextFormatted(
+                        "GMX_ENABLE_DIRECT_GPU_COMM environment variable detected, "
+                        "but SYCL does not support direct communications with threadMPI.");
+    }
+
+    // Now check those flags that may cause, from the user perspective, an unexpected
+    // fallback to CPU halo, and report accordingly
+    gmx::MessageStringCollector errorReasons;
+    errorReasons.startContext("GPU direct communication can not be activated because:");
+    errorReasons.appendIf(haveMts, "MTS is not supported.");
+    errorReasons.appendIf(haveSwapCoords, "Swap-coords is not supported.");
+    errorReasons.finishContext();
+
+    if (!errorReasons.isEmpty())
+    {
+        GMX_LOG(mdlog.warning).asParagraph().appendText(errorReasons.toString());
+    }
+
+    bool runUsesCompatibleFeatures = errorReasons.isEmpty();
+
+    bool runAndGpuSupportDirectGpuComm = (runUsesCompatibleFeatures && enableDirectGpuComm);
+
+    // Thread-MPI case on by default, can be disabled with env var.
+    bool canUseDirectGpuCommWithThreadMpi =
+            (runAndGpuSupportDirectGpuComm && GMX_THREAD_MPI && !GMX_GPU_SYCL);
+    // GPU-aware MPI case off by default, can be enabled with dev flag
+    // Note: GMX_DISABLE_DIRECT_GPU_COMM already taken into account in devFlags.enableDirectGpuCommWithMpi
+    bool canUseDirectGpuCommWithMpi = (runAndGpuSupportDirectGpuComm && GMX_LIB_MPI
+                                       && devFlags.canUseGpuAwareMpi && enableDirectGpuComm);
+
+    return canUseDirectGpuCommWithThreadMpi || canUseDirectGpuCommWithMpi;
+}
+
+bool decideWhetherToUseGpuForHalo(bool                 havePPDomainDecomposition,
+                                  bool                 useGpuForNonbonded,
+                                  bool                 canUseDirectGpuComm,
+                                  bool                 useModularSimulator,
+                                  bool                 doRerun,
+                                  bool                 haveEnergyMinimization,
+                                  const gmx::MDLogger& mdlog)
+{
+    if (!canUseDirectGpuComm || !havePPDomainDecomposition || !useGpuForNonbonded)
+    {
+        // return false without warning
+        return false;
+    }
+
+    // Now check those flags that may cause, from the user perspective, an unexpected
+    // fallback to CPU halo, and report accordingly
+    gmx::MessageStringCollector errorReasons;
+    errorReasons.startContext("GPU halo exchange will not be activated because:");
+    errorReasons.appendIf(useModularSimulator, "Modular simulator runs are not supported.");
+    errorReasons.appendIf(doRerun, "Re-runs are not supported.");
+    errorReasons.appendIf(haveEnergyMinimization, "Energy minimization is not supported.");
+    errorReasons.finishContext();
+
+    if (!errorReasons.isEmpty())
+    {
+        GMX_LOG(mdlog.warning).asParagraph().appendText(errorReasons.toString());
+    }
+
+    return errorReasons.isEmpty();
+}
+
+} // namespace gmx