variables:
KUBERNETES_CPU_LIMIT: 8
KUBERNETES_CPU_REQUEST: 4
- KUBERNETES_MEMORY_REQUEST: 8Gi
+ KUBERNETES_MEMORY_REQUEST: 4Gi
+ KUBERNETES_MEMORY_LIMIT: 8Gi
KUBERNETES_EXTENDED_RESOURCE_NAME: ""
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 0
- CACHE_FALLBACK_KEY: "$CI_JOB_NAME-$CI_JOB_STAGE-release-2020"
+ CACHE_FALLBACK_KEY: "$CI_JOB_NAME-$CI_JOB_STAGE-master"
BUILD_DIR: build
INSTALL_DIR: install
CMAKE_GMXAPI_OPTIONS: ""
.rules-element:if-post-merge-acceptance-or-mr-then-always: &if-post-merge-acceptance-or-mr-then-always
if: '$CI_PIPELINE_SOURCE == "merge_request_event" ||
($CI_PIPELINE_SOURCE == "push" &&
- ($CI_COMMIT_REF_NAME == "master" || $CI_COMMIT_REF_NAME == "release-*"))'
- $CI_COMMIT_REF_NAME == "release-2020")'
++ $CI_COMMIT_REF_NAME == "master")'
when: always
# Include job only for post submit push
.rules-element:if-post-merge-acceptance-then-always: &if-post-merge-acceptance-then-always
if: '$CI_PIPELINE_SOURCE == "push" &&
- ($CI_COMMIT_REF_NAME == "master" || $CI_COMMIT_REF_NAME == "release-*")'
- $CI_COMMIT_REF_NAME == "release-2020"'
++ $CI_COMMIT_REF_NAME == "master"'
when: always
# When composing a rule set, note that the first matching rule is applied.
#
# This file is part of the GROMACS molecular simulation package.
#
--# Copyright (c) 2018,2019, by the GROMACS development team, led by
++# 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
# top-level source directory and at http://www.gromacs.org.
src/gromacs/tables/quadraticsplinetable.h: warning: includes "simd.h" unnecessarily
# These are specific to Folding@Home, and easiest to suppress here
- *: warning: includes non-local file as "corewrap.h"
src/gmxpre.h: warning: includes non-local file as "swindirect.h"
-# New external API (see https://redmine.gromacs.org/issues/2586) has some unresolved
+# New external API (see https://gitlab.com/gromacs/gromacs/-/issues/2586) has some unresolved
# conflicts with previous definitions of public API, installed API, and other things
# described or implemented in check-source.py, gmxtree.py, gmxtree.rst, and others
# TODO: resolve definitions, update testing heuristics, and activate policy checks
gmx::serializeKeyValueTree(tree, &serializer);
}
- do_cpt_footer(gmx_fio_getxdr(fp), headerContents.file_version);
-
- /* we really, REALLY, want to make sure to physically write the checkpoint,
- and all the files it depends on, out to disk. Because we've
- opened the checkpoint with gmx_fio_open(), it's in our list
- of open files. */
- ret = gmx_fio_all_output_fsync();
-
- if (ret)
+ // Checkpointing modular simulator
{
- char buf[STRLEN];
- sprintf(buf, "Cannot fsync '%s'; maybe you are out of disk space?", gmx_fio_getname(ret));
-
- if (getenv(GMX_IGNORE_FSYNC_FAILURE_ENV) == nullptr)
- {
- gmx_file(buf);
- }
- else
- {
- gmx_warning("%s", buf);
- }
- }
-
- if (gmx_fio_close(fp) != 0)
- {
- gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
- }
-
- /* we don't move the checkpoint if the user specified they didn't want it,
- or if the fsyncs failed */
-#if !GMX_NO_RENAME
- if (!bNumberAndKeep && !ret)
- {
- if (gmx_fexist(fn))
- {
- /* Rename the previous checkpoint file */
- mpiBarrierBeforeRename(applyMpiBarrierBeforeRename, mpiBarrierCommunicator);
-
- std::strcpy(buf, fn);
- buf[std::strlen(fn) - std::strlen(ftp2ext(fn2ftp(fn))) - 1] = '\0';
- std::strcat(buf, "_prev");
- std::strcat(buf, fn + std::strlen(fn) - std::strlen(ftp2ext(fn2ftp(fn))) - 1);
- if (!GMX_FAHCORE)
- {
- /* we copy here so that if something goes wrong between now and
- * the rename below, there's always a state.cpt.
- * If renames are atomic (such as in POSIX systems),
- * this copying should be unneccesary.
- */
- gmx_file_copy(fn, buf, FALSE);
- /* We don't really care if this fails:
- * there's already a new checkpoint.
- */
- }
- else
- {
- gmx_file_rename(fn, buf);
- }
- }
-
- /* Rename the checkpoint file from the temporary to the final name */
- mpiBarrierBeforeRename(applyMpiBarrierBeforeRename, mpiBarrierCommunicator);
-
- if (gmx_file_rename(fntemp, fn) != 0)
- {
- gmx_file("Cannot rename checkpoint file; maybe you are out of disk space?");
- }
+ gmx::FileIOXdrSerializer serializer(fp);
+ modularSimulatorCheckpointData->serialize(&serializer);
}
-#endif /* GMX_NO_RENAME */
-
- sfree(fntemp);
+ do_cpt_footer(gmx_fio_getxdr(fp), headerContents.file_version);
+ #if GMX_FAHCORE
+ /* Always FAH checkpoint immediately after a Gromacs checkpoint.
+ *
+ * Note that it is critical that we save a FAH checkpoint directly
+ * after writing a Gromacs checkpoint. If the program dies, either
+ * by the machine powering off suddenly or the process being,
+ * killed, FAH can recover files that have only appended data by
+ * truncating them to the last recorded length. The Gromacs
+ * checkpoint does not just append data, it is fully rewritten each
+ * time so a crash between moving the new Gromacs checkpoint file in
+ * to place and writing a FAH checkpoint is not recoverable. Thus
+ * the time between these operations must be kept as short a
+ * possible.
+ */
+ fcCheckpoint();
+ #endif
}
static void check_int(FILE* fplog, const char* type, int p, int f, gmx_bool* mm)
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/sysinfo.h"
+ #include "architecture.h"
+
//! Constant used to help minimize preprocessed code
-static const bool bGPUBinary = GMX_GPU != GMX_GPU_NONE;
+static constexpr bool bGPUBinary = (GMX_GPU != 0);
/*! \internal \brief
* Returns the GPU information text, one GPU per line.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
++ * 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
* top-level source directory and at http://www.gromacs.org.
// getenv results are ignored when clearly they are used.
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wunused-result"
- devFlags.enableGpuBufferOps = (getenv("GMX_USE_GPU_BUFFER_OPS") != nullptr)
- && (GMX_GPU == GMX_GPU_CUDA) && useGpuForNonbonded;
+
+ devFlags.enableGpuBufferOps =
+ GMX_GPU_CUDA && useGpuForNonbonded && (getenv("GMX_USE_GPU_BUFFER_OPS") != nullptr);
+ devFlags.enableGpuHaloExchange = GMX_GPU_CUDA && GMX_THREAD_MPI && getenv("GMX_GPU_DD_COMMS") != nullptr;
- devFlags.forceGpuUpdateDefault = (getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") != nullptr);
+ devFlags.forceGpuUpdateDefault = (getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") != nullptr) || GMX_FAHCORE;
- devFlags.enableGpuHaloExchange =
- (getenv("GMX_GPU_DD_COMMS") != nullptr && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA));
devFlags.enableGpuPmePPComm =
- (getenv("GMX_GPU_PME_PP_COMMS") != nullptr && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA));
+ GMX_GPU_CUDA && GMX_THREAD_MPI && getenv("GMX_GPU_PME_PP_COMMS") != nullptr;
+
#pragma GCC diagnostic pop
if (devFlags.enableGpuBufferOps)
* So the PME-only nodes (if present) will also initialize
* the distance restraints.
*/
- snew(fcd, 1);
/* This needs to be called before read_checkpoint to extend the state */
- init_disres(fplog, &mtop, inputrec, cr, ms, fcd, globalState.get(), replExParams.exchangeInterval > 0);
+ t_disresdata* disresdata;
+ snew(disresdata, 1);
+ init_disres(fplog, &mtop, inputrec.get(), DisResRunMode::MDRun,
+ MASTER(cr) ? DDRole::Master : DDRole::Agent,
+ PAR(cr) ? NumRanks::Multiple : NumRanks::Single, cr->mpi_comm_mysim, ms, disresdata,
+ globalState.get(), replExParams.exchangeInterval > 0);
- init_orires(fplog, &mtop, inputrec, cr, ms, globalState.get(), &(fcd->orires));
+ t_oriresdata* oriresdata;
+ snew(oriresdata, 1);
+ init_orires(fplog, &mtop, inputrec.get(), cr, ms, globalState.get(), oriresdata);
- auto deform = prepareBoxDeformation(globalState->box, cr, *inputrec);
+ auto deform = prepareBoxDeformation(
+ globalState != nullptr ? globalState->box : box, MASTER(cr) ? DDRole::Master : DDRole::Agent,
+ PAR(cr) ? NumRanks::Multiple : NumRanks::Single, cr->mpi_comm_mygroup, *inputrec);
+ #if GMX_FAHCORE
+ /* We have to remember the generation's first step before reading checkpoint.
+ This way, we can report to the F@H core both the generation's first step
+ and the restored first step, thus making it able to distinguish between
+ an interruption/resume and start of the n-th generation simulation.
+ Having this information, the F@H core can correctly calculate and report
+ the progress.
+ */
+ int gen_first_step = 0;
+ if (MASTER(cr))
+ {
+ gen_first_step = inputrec->init_step;
+ }
+ #endif
+
ObservablesHistory observablesHistory = {};
+ auto modularSimulatorCheckpointData = std::make_unique<ReadCheckpointDataHolder>();
if (startingBehavior != StartingBehavior::NewSimulation)
{
/* Check if checkpoint file exists before doing continuation.
*
* 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) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
++ * 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
* top-level source directory and at http://www.gromacs.org.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2011,2014,2015,2016,2018,2019,2020, by the GROMACS development team, led by
++ * Copyright (c) 2011,2014,2015,2016,2018, The GROMACS development team.
+ * Copyright (c) 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.
*
* 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) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
++ * 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
* top-level source directory and at http://www.gromacs.org.
*
* 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) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
++ * 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
* top-level source directory and at http://www.gromacs.org.
# ifdef gmx_ffclose
# undef gmx_ffclose
# endif
- # if (!HAVE_PIPES && !defined(__native_client__))
+ #endif
+ #if (!HAVE_PIPES && !defined(__native_client__))
-static FILE* popen(const char* nm, const char* mode)
+static FILE* popen(const char* /* nm */, const char* /* mode */)
{
gmx_impl("Sorry no pipes...");
int fn;
/* get the file number */
- # if HAVE_FILENO
+ #if HAVE_FILENO
fn = fileno(fp);
- # elif HAVE__FILENO
+ #elif HAVE__FILENO
fn = _fileno(fp);
- # else
+ #else
+ GMX_UNUSED_VALUE(fp);
fn = -1;
- # endif
+ #endif
/* do the actual fsync */
if (fn >= 0)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2018,2019,2020, by the GROMACS development team, led by
++ * Copyright (c) 2013,2014,2015,2016,2018, The GROMACS development team.
+ * Copyright (c) 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.
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
++# To avoid running into test timeouts, some end-to-end tests of mdrun
++# functionality are split off. This can be rearranged in future as we
++# see fit.
set(testname "MdrunTests")
set(exename "mdrun-test")
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff