GROMACS 2019.6 release notes
----------------------------
-This version was released on TODO, 2020. These release notes
+This version was released on February 28th, 2020. These release notes
document the changes that have taken place in GROMACS since the
previous 2019.5 version, to fix known issues. It also incorporates all
fixes made in version 2018.8 and earlier, which you can find described
Fixes where mdrun could behave incorrectly
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Actually fix PME forces with FE without perturbed q/LJ
+""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+PME would incorrectly ignore the mesh forces on perturbed atoms when
+no charges or LJ atom types were actually perturbed. Note that this
+is a rather uncommon scenario.
+
+:issue:`2640`
+:issue:`3359`
+
+Avoid overzealous program abort with orientation restraints
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+It could happen that mdrun would abort on checking orientation
+restraints in multiple molecules even though no restraints where
+applied to them.
+
+:issue:`3375`
+
+Calculate Coulomb and LJ reciprocal terms in rerun
+""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Reruns would not calculate Coulomb and LJ reciprocal terms, leading
+to wrong potential energies. This bug only showed up if GROMACS was
+compiled without GPU support.
+
+:issue:`3400`
+
Fixes for ``gmx`` tools
^^^^^^^^^^^^^^^^^^^^^^^
+Added check for inconsistent input of distance restraint labels
+in gmx disre.
+
Fixes that affect portability
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Miscellaneous
^^^^^^^^^^^^^
+Avoid cryptic GPU detection errors when devices are unavailable or out of memory
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+:issue:`3178`
+:issue:`3399`
+
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
+ * Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
* Copyright (c) 2018,2019,2020, 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
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, 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.
vvindex[j] = 0;
}
nat = interaction_function[F_DISRES].nratoms + 1;
+ // Check internal consistency of disres.label
+ // The label for a distance restraint should be at most one larger
+ // than the previous label.
+ int label_old = forceparams[forceatoms[0]].disres.label;
+ for (i = 0; (i < disres->nr); i += nat)
+ {
+ type = forceatoms[i];
+ label = forceparams[type].disres.label;
+ if ((label == label_old) || (label == label_old + 1))
+ {
+ label_old = label;
+ }
+ else
+ {
+ gmx_fatal(FARGS,
+ "Label mismatch in distance restrains. Label for restraint %d is %d, "
+ "expected it to be either %d or %d",
+ i / nat, label, label_old, label_old + 1);
+ }
+ }
+ // Get offset for label index
+ label_old = forceparams[forceatoms[0]].disres.label;
for (i = 0; (i < disres->nr);)
{
type = forceatoms[i];
n = 0;
- label = forceparams[type].disres.label;
+ label = forceparams[type].disres.label - label_old;
if (debug)
{
fprintf(debug, "DISRE: ndr = %d, label = %d i=%d, n =%d\n", ndr, label, i, n);
do
{
n += nat;
- } while (((i + n) < disres->nr) && (forceparams[forceatoms[i + n]].disres.label == label));
+ } while (((i + n) < disres->nr)
+ && (forceparams[forceatoms[i + n]].disres.label == label + label_old));
calc_disres_R_6(nullptr, nullptr, n, &forceatoms[i], x, pbc, fcd, nullptr);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, The GROMACS development team.
+ * Copyright (c) 2017,2018,2019,2020, 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.
/** Dummy kernel used for sanity checking. */
static __global__ void k_dummy_test(void) {}
-static void checkCompiledTargetCompatibility(int deviceId, const cudaDeviceProp& deviceProp)
+static cudaError_t checkCompiledTargetCompatibility(int deviceId, const cudaDeviceProp& deviceProp)
{
cudaFuncAttributes attributes;
cudaError_t stat = cudaFuncGetAttributes(&attributes, k_dummy_test);
if (cudaErrorInvalidDeviceFunction == stat)
{
- gmx_fatal(FARGS,
- "The %s binary does not include support for the CUDA architecture of a "
- "detected GPU: %s, ID #%d (compute capability %d.%d). "
- "By default, GROMACS supports all architectures of compute "
- "capability >= 3.0, so your GPU "
- "might be rare, or some architectures were disabled in the build. "
- "Consult the install guide for how to use the GMX_CUDA_TARGET_SM and "
- "GMX_CUDA_TARGET_COMPUTE CMake variables to add this architecture. "
- "To work around this error, use the CUDA_VISIBLE_DEVICES environment"
- "variable to pass a list of GPUs that excludes the ID %d.",
- gmx::getProgramContext().displayName(), deviceProp.name, deviceId,
- deviceProp.major, deviceProp.minor, deviceId);
- }
-
- CU_RET_ERR(stat, "cudaFuncGetAttributes failed");
+ fprintf(stderr,
+ "\nWARNING: The %s binary does not include support for the CUDA architecture of "
+ "the GPU ID #%d (compute capability %d.%d) detected during detection. "
+ "By default, GROMACS supports all architectures of compute "
+ "capability >= 3.0, so your GPU "
+ "might be rare, or some architectures were disabled in the build. \n"
+ "Consult the install guide for how to use the GMX_CUDA_TARGET_SM and "
+ "GMX_CUDA_TARGET_COMPUTE CMake variables to add this architecture. \n",
+ gmx::getProgramContext().displayName(), deviceId, deviceProp.major, deviceProp.minor);
+ }
+
+ return stat;
}
bool isHostMemoryPinned(const void* h_ptr)
*
* \param[in] dev_id the device ID of the GPU or -1 if the device has already been initialized
* \param[in] dev_prop The device properties structure
- * \returns 0 if the device looks OK
+ * \returns 0 if the device looks OK, -1 if it sanity checks failed, and -2 if the device is busy
*
* TODO: introduce errors codes and handle errors more smoothly.
*/
}
}
+ cu_err = checkCompiledTargetCompatibility(dev_id, dev_prop);
+ // Avoid triggering an error if GPU devices are in exclusive or prohibited mode;
+ // it is enough to check for cudaErrorDevicesUnavailable only here because
+ // if we encounter it that will happen in cudaFuncGetAttributes in the above function.
+ if (cu_err == cudaErrorDevicesUnavailable)
+ {
+ return -2;
+ }
+ else if (cu_err != cudaSuccess)
+ {
+ return -1;
+ }
+
/* try to execute a dummy kernel */
- checkCompiledTargetCompatibility(dev_id, dev_prop);
+ try
+ {
+ KernelLaunchConfig config;
+ config.blockSize[0] = 512;
+ const auto dummyArguments = prepareGpuKernelArguments(k_dummy_test, config);
+ launchGpuKernel(k_dummy_test, config, nullptr, "Dummy kernel", dummyArguments);
+ }
+ catch (gmx::GromacsException& ex)
+ {
+ // launchGpuKernel error is not fatal and should continue with marking the device bad
+ fprintf(stderr,
+ "Error occurred while running dummy kernel sanity check on device #%d:\n %s\n", id,
+ formatExceptionMessageToString(ex).c_str());
+ return -1;
+ }
- KernelLaunchConfig config;
- config.blockSize[0] = 512;
- const auto dummyArguments = prepareGpuKernelArguments(k_dummy_test, config);
- launchGpuKernel(k_dummy_test, config, nullptr, "Dummy kernel", dummyArguments);
if (cudaDeviceSynchronize() != cudaSuccess)
{
return -1;
* the dummy test kernel fails to execute with a "device busy message" we
* should appropriately report that the device is busy instead of insane.
*/
- if (do_sanity_checks(deviceId, deviceProp) != 0)
+ const int checkResult = do_sanity_checks(deviceId, deviceProp);
+ switch (checkResult)
{
- return egpuInsane;
+ case 0: return egpuCompatible;
+ case -1: return egpuInsane;
+ case -2: return egpuUnavailable;
+ default:
+ GMX_RELEASE_ASSERT(false, "Invalid do_sanity_checks() return value");
+ return egpuCompatible;
}
-
- return egpuCompatible;
}
bool isGpuDetectionFunctional(std::string* errorMessage)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020, 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.
// move to a single place in gpu_utils.
/* Names of the GPU detection/check results (see e_gpu_detect_res_t in hw_info.h). */
const char* const gpu_detect_res_str[egpuNR] = {
- "compatible", "nonexistent", "incompatible",
- "incompatible (please recompile with GMX_OPENCL_NB_CLUSTER_SIZE=4)", "insane"
+ "compatible", "nonexistent",
+ "incompatible", "incompatible (please recompile with GMX_OPENCL_NB_CLUSTER_SIZE=4)",
+ "insane", "unavailable"
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018,2019,2020, 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.
*
* The egpuInsane value means that during the sanity checks an error
* occurred that indicates malfunctioning of the device, driver, or
- * incompatible driver/runtime. */
+ * incompatible driver/runtime.
+ * eGpuUnavailable indicates that CUDA devices are busy or unavailable
+ * typically due to use of cudaComputeModeExclusive, cudaComputeModeProhibited modes.
+ */
typedef enum
{
egpuCompatible = 0,
egpuIncompatible,
egpuIncompatibleClusterSize,
egpuInsane,
+ egpuUnavailable,
egpuNR
} e_gpu_detect_res_t;
*/
#include "gmxpre.h"
-#include "config.h"
-
#include <cinttypes>
#include <cmath>
#include <cstdio>
}
force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
- | (GMX_GPU ? GMX_FORCE_VIRIAL : 0) | // TODO: Get rid of this once #2649 is solved
+ | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 and #3400 are solved
GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
if (shellfc)
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff