* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, 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.
#include "gromacs/fileio/tngio.h"
#include "gromacs/fileio/trrio.h"
#include "gromacs/fileio/xtcio.h"
-#include "gromacs/fileio/xvgr.h"
#include "gromacs/math/vec.h"
-#include "gromacs/mdlib/trajectory_writing.h"
+#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdrunutility/handlerestart.h"
#include "gromacs/mdrunutility/multisim.h"
#include "gromacs/mdtypes/awh_history.h"
#include "gromacs/mdtypes/commrec.h"
-#include "gromacs/mdtypes/df_history.h"
#include "gromacs/mdtypes/edsamhistory.h"
#include "gromacs/mdtypes/energyhistory.h"
#include "gromacs/mdtypes/imdoutputprovider.h"
struct gmx_mdoutf
{
- t_fileio* fp_trn;
- t_fileio* fp_xtc;
- gmx_tng_trajectory_t tng;
- gmx_tng_trajectory_t tng_low_prec;
- int x_compression_precision; /* only used by XTC output */
- ener_file_t fp_ene;
- const char* fn_cpt;
- gmx_bool bKeepAndNumCPT;
- int eIntegrator;
- gmx_bool bExpanded;
- int elamstats;
- int simulation_part;
- FILE* fp_dhdl;
- int natoms_global;
- int natoms_x_compressed;
- const SimulationGroups* groups; /* for compressed position writing */
- gmx_wallcycle_t wcycle;
- rvec* f_global;
- gmx::IMDOutputProvider* outputProvider;
- const gmx::MdModulesNotifier* mdModulesNotifier;
- bool simulationsShareState;
- MPI_Comm mastersComm;
+ t_fileio* fp_trn;
+ t_fileio* fp_xtc;
+ gmx_tng_trajectory_t tng;
+ gmx_tng_trajectory_t tng_low_prec;
+ int x_compression_precision; /* only used by XTC output */
+ ener_file_t fp_ene;
+ const char* fn_cpt;
+ gmx_bool bKeepAndNumCPT;
+ IntegrationAlgorithm eIntegrator;
+ gmx_bool bExpanded;
+ LambdaWeightCalculation elamstats;
+ int simulation_part;
+ FILE* fp_dhdl;
+ int natoms_global;
+ int natoms_x_compressed;
+ const SimulationGroups* groups; /* for compressed position writing */
+ gmx_wallcycle* wcycle;
+ rvec* f_global;
+ gmx::IMDOutputProvider* outputProvider;
+ const gmx::MDModulesNotifiers* mdModulesNotifiers;
+ bool simulationsShareState;
+ MPI_Comm mastersComm;
};
-gmx_mdoutf_t init_mdoutf(FILE* fplog,
- int nfile,
- const t_filenm fnm[],
- const gmx::MdrunOptions& mdrunOptions,
- const t_commrec* cr,
- gmx::IMDOutputProvider* outputProvider,
- const gmx::MdModulesNotifier& mdModulesNotifier,
- const t_inputrec* ir,
- const gmx_mtop_t* top_global,
- const gmx_output_env_t* oenv,
- gmx_wallcycle_t wcycle,
- const gmx::StartingBehavior startingBehavior,
- bool simulationsShareState,
- const gmx_multisim_t* ms)
+gmx_mdoutf_t init_mdoutf(FILE* fplog,
+ int nfile,
+ const t_filenm fnm[],
+ const gmx::MdrunOptions& mdrunOptions,
+ const t_commrec* cr,
+ gmx::IMDOutputProvider* outputProvider,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
+ const t_inputrec* ir,
+ const gmx_mtop_t& top_global,
+ const gmx_output_env_t* oenv,
+ gmx_wallcycle* wcycle,
+ const gmx::StartingBehavior startingBehavior,
+ bool simulationsShareState,
+ const gmx_multisim_t* ms)
{
gmx_mdoutf_t of;
const char * appendMode = "a+", *writeMode = "w+", *filemode;
gmx_tng_open(filename, filemode[0], &of->tng_low_prec);
if (filemode[0] == 'w')
{
- gmx_tng_prepare_low_prec_writing(of->tng_low_prec, top_global, ir);
+ gmx_tng_prepare_low_prec_writing(of->tng_low_prec, &top_global, ir);
}
bCiteTng = TRUE;
break;
gmx_tng_open(filename, filemode[0], &of->tng);
if (filemode[0] == 'w')
{
- gmx_tng_prepare_md_writing(of->tng, top_global, ir);
+ gmx_tng_prepare_md_writing(of->tng, &top_global, ir);
}
bCiteTng = TRUE;
break;
}
of->fn_cpt = opt2fn("-cpo", nfile, fnm);
- if ((ir->efep != efepNO || ir->bSimTemp) && ir->fepvals->nstdhdl > 0
- && (ir->fepvals->separate_dhdl_file == esepdhdlfileYES) && EI_DYNAMICS(ir->eI))
+ if ((ir->efep != FreeEnergyPerturbationType::No || ir->bSimTemp) && ir->fepvals->nstdhdl > 0
+ && (ir->fepvals->separate_dhdl_file == SeparateDhdlFile::Yes) && EI_DYNAMICS(ir->eI))
{
if (restartWithAppending)
{
}
outputProvider->initOutput(fplog, nfile, fnm, restartWithAppending, oenv);
- of->mdModulesNotifier = &mdModulesNotifier;
+ of->mdModulesNotifiers = &mdModulesNotifiers;
/* Set up atom counts so they can be passed to actual
trajectory-writing routines later. Also, XTC writing needs
to know what (and how many) atoms might be in the XTC
groups, and how to look up later which ones they are. */
- of->natoms_global = top_global->natoms;
- of->groups = &top_global->groups;
+ of->natoms_global = top_global.natoms;
+ of->groups = &top_global.groups;
of->natoms_x_compressed = 0;
- for (i = 0; (i < top_global->natoms); i++)
+ for (i = 0; (i < top_global.natoms); i++)
{
if (getGroupType(*of->groups, SimulationAtomGroupType::CompressedPositionOutput, i) == 0)
{
}
}
- if (ir->nstfout && DOMAINDECOMP(cr))
+ if (ir->nstfout && haveDDAtomOrdering(*cr))
{
- snew(of->f_global, top_global->natoms);
+ snew(of->f_global, top_global.natoms);
}
}
return of->fp_dhdl;
}
-gmx_wallcycle_t mdoutf_get_wcycle(gmx_mdoutf_t of)
+gmx_wallcycle* mdoutf_get_wcycle(gmx_mdoutf_t of)
{
return of->wcycle;
}
const t_commrec* cr,
ivec domdecCells,
int nppnodes,
- int eIntegrator,
+ IntegrationAlgorithm eIntegrator,
int simulation_part,
gmx_bool bExpanded,
- int elamstats,
+ LambdaWeightCalculation elamstats,
int64_t step,
double t,
t_state* state,
ObservablesHistory* observablesHistory,
- const gmx::MdModulesNotifier& mdModulesNotifier,
+ const gmx::MDModulesNotifiers& mdModulesNotifiers,
gmx::WriteCheckpointDataHolder* modularSimulatorCheckpointData,
bool applyMpiBarrierBeforeRename,
MPI_Comm mpiBarrierCommunicator)
char buf[1024], suffix[5 + STEPSTRSIZE], sbuf[STEPSTRSIZE];
t_fileio* ret;
- if (DOMAINDECOMP(cr))
+ if (haveDDAtomOrdering(*cr))
{
npmenodes = cr->npmenodes;
}
int nED = (edsamhist ? edsamhist->nED : 0);
swaphistory_t* swaphist = observablesHistory->swapHistory.get();
- int eSwapCoords = (swaphist ? swaphist->eSwapCoords : eswapNO);
+ SwapType eSwapCoords = (swaphist ? swaphist->eSwapCoords : SwapType::No);
- CheckpointHeaderContents headerContents = { 0,
+ CheckpointHeaderContents headerContents = { CheckPointVersion::UnknownVersion0,
{ 0 },
{ 0 },
{ 0 },
std::strcpy(headerContents.version, gmx_version());
std::strcpy(headerContents.fprog, gmx::getProgramContext().fullBinaryPath());
std::strcpy(headerContents.ftime, timebuf.c_str());
- if (DOMAINDECOMP(cr))
+ if (haveDDAtomOrdering(*cr))
{
copy_ivec(domdecCells, headerContents.dd_nc);
}
- write_checkpoint_data(fp, headerContents, bExpanded, elamstats, state, observablesHistory,
- mdModulesNotifier, &outputfiles, modularSimulatorCheckpointData);
+ write_checkpoint_data(fp,
+ headerContents,
+ bExpanded,
+ elamstats,
+ state,
+ observablesHistory,
+ mdModulesNotifiers,
+ &outputfiles,
+ modularSimulatorCheckpointData);
/* 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
#if !GMX_NO_RENAME
if (!bNumberAndKeep && !ret)
{
+ // Add a barrier before renaming to reduce chance to get out of sync (#2440)
+ // Note: Checkpoint might only exist on some ranks, so put barrier before if clause (#3919)
+ mpiBarrierBeforeRename(applyMpiBarrierBeforeRename, mpiBarrierCommunicator);
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");
/* Rename the checkpoint file from the temporary to the final name */
mpiBarrierBeforeRename(applyMpiBarrierBeforeRename, mpiBarrierCommunicator);
- if (gmx_file_rename(fntemp, fn) != 0)
+ try
+ {
+ gmx_file_rename(fntemp, fn);
+ }
+ catch (gmx::FileIOError const&)
{
- gmx_file("Cannot rename checkpoint file; maybe you are out of disk space?");
+ // In this case we can be more helpful than the generic message from gmx_file_rename
+ GMX_THROW(gmx::FileIOError(
+ "Cannot rename checkpoint file; maybe you are out of disk space?"));
}
}
#endif /* GMX_NO_RENAME */
sfree(fntemp);
#if GMX_FAHCORE
- /*code for alternate checkpointing scheme. moved from top of loop over
- steps */
- fcRequestCheckPoint();
- if (fcCheckPointParallel(cr->nodeid, NULL, 0) == 0)
- {
- gmx_fatal(3, __FILE__, __LINE__, "Checkpoint error on step %d\n", step);
- }
+ /* 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 as
+ * possible.
+ */
+ fcCheckpoint();
#endif /* end GMX_FAHCORE block */
}
* checkpoint files getting out of sync.
*/
ivec one_ivec = { 1, 1, 1 };
- write_checkpoint(of->fn_cpt, of->bKeepAndNumCPT, fplog, cr,
- DOMAINDECOMP(cr) ? cr->dd->numCells : one_ivec,
- DOMAINDECOMP(cr) ? cr->dd->nnodes : cr->nnodes, of->eIntegrator,
- of->simulation_part, of->bExpanded, of->elamstats, step, t, state_global,
- observablesHistory, *(of->mdModulesNotifier), modularSimulatorCheckpointData,
- of->simulationsShareState, of->mastersComm);
+ write_checkpoint(of->fn_cpt,
+ of->bKeepAndNumCPT,
+ fplog,
+ cr,
+ haveDDAtomOrdering(*cr) ? cr->dd->numCells : one_ivec,
+ haveDDAtomOrdering(*cr) ? cr->dd->nnodes : cr->nnodes,
+ of->eIntegrator,
+ of->simulation_part,
+ of->bExpanded,
+ of->elamstats,
+ step,
+ t,
+ state_global,
+ observablesHistory,
+ *(of->mdModulesNotifiers),
+ modularSimulatorCheckpointData,
+ of->simulationsShareState,
+ of->mastersComm);
}
void mdoutf_write_to_trajectory_files(FILE* fplog,
{
const rvec* f_global;
- if (DOMAINDECOMP(cr))
+ if (haveDDAtomOrdering(*cr))
{
if (mdof_flags & MDOF_CPT)
{
if (mdof_flags & (MDOF_X | MDOF_X_COMPRESSED))
{
auto globalXRef = MASTER(cr) ? state_global->x : gmx::ArrayRef<gmx::RVec>();
- dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
- state_local->cg_gl, state_local->x, globalXRef);
+ dd_collect_vec(cr->dd,
+ state_local->ddp_count,
+ state_local->ddp_count_cg_gl,
+ state_local->cg_gl,
+ state_local->x,
+ globalXRef);
}
if (mdof_flags & MDOF_V)
{
auto globalVRef = MASTER(cr) ? state_global->v : gmx::ArrayRef<gmx::RVec>();
- dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
- state_local->cg_gl, state_local->v, globalVRef);
+ dd_collect_vec(cr->dd,
+ state_local->ddp_count,
+ state_local->ddp_count_cg_gl,
+ state_local->cg_gl,
+ state_local->v,
+ globalVRef);
}
}
f_global = of->f_global;
if (mdof_flags & MDOF_F)
{
- dd_collect_vec(
- cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl, f_local,
- gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(of->f_global), f_local.size()));
+ auto globalFRef = MASTER(cr) ? gmx::arrayRefFromArray(
+ reinterpret_cast<gmx::RVec*>(of->f_global), of->natoms_global)
+ : gmx::ArrayRef<gmx::RVec>();
+ dd_collect_vec(cr->dd,
+ state_local->ddp_count,
+ state_local->ddp_count_cg_gl,
+ state_local->cg_gl,
+ f_local,
+ globalFRef);
}
}
else
{
if (mdof_flags & MDOF_CPT)
{
- mdoutf_write_checkpoint(of, fplog, cr, step, t, state_global, observablesHistory,
- modularSimulatorCheckpointData);
+ mdoutf_write_checkpoint(
+ of, fplog, cr, step, t, state_global, observablesHistory, modularSimulatorCheckpointData);
}
if (mdof_flags & (MDOF_X | MDOF_V | MDOF_F))
if (of->fp_trn)
{
- gmx_trr_write_frame(of->fp_trn, step, t, state_local->lambda[efptFEP],
- state_local->box, natoms, x, v, f);
+ gmx_trr_write_frame(of->fp_trn,
+ step,
+ t,
+ state_local->lambda[FreeEnergyPerturbationCouplingType::Fep],
+ state_local->box,
+ natoms,
+ x,
+ v,
+ f);
if (gmx_fio_flush(of->fp_trn) != 0)
{
gmx_file("Cannot write trajectory; maybe you are out of disk space?");
velocities and forces to it. */
else if (of->tng)
{
- gmx_fwrite_tng(of->tng, FALSE, step, t, state_local->lambda[efptFEP],
- state_local->box, natoms, x, v, f);
+ gmx_fwrite_tng(of->tng,
+ FALSE,
+ step,
+ t,
+ state_local->lambda[FreeEnergyPerturbationCouplingType::Fep],
+ state_local->box,
+ natoms,
+ x,
+ v,
+ f);
}
/* If only a TNG file is open for compressed coordinate output (no uncompressed
coordinate output) also write forces and velocities to it. */
else if (of->tng_low_prec)
{
- gmx_fwrite_tng(of->tng_low_prec, FALSE, step, t, state_local->lambda[efptFEP],
- state_local->box, natoms, x, v, f);
+ gmx_fwrite_tng(of->tng_low_prec,
+ FALSE,
+ step,
+ t,
+ state_local->lambda[FreeEnergyPerturbationCouplingType::Fep],
+ state_local->box,
+ natoms,
+ x,
+ v,
+ f);
}
}
if (mdof_flags & MDOF_X_COMPRESSED)
}
}
}
- if (write_xtc(of->fp_xtc, of->natoms_x_compressed, step, t, state_local->box, xxtc,
- of->x_compression_precision)
+ if (write_xtc(of->fp_xtc, of->natoms_x_compressed, step, t, state_local->box, xxtc, of->x_compression_precision)
== 0)
{
gmx_fatal(FARGS,
"simulation with major instabilities resulting in coordinates "
"that are NaN or too large to be represented in the XTC format.\n");
}
- gmx_fwrite_tng(of->tng_low_prec, TRUE, step, t, state_local->lambda[efptFEP],
- state_local->box, of->natoms_x_compressed, xxtc, nullptr, nullptr);
+ gmx_fwrite_tng(of->tng_low_prec,
+ TRUE,
+ step,
+ t,
+ state_local->lambda[FreeEnergyPerturbationCouplingType::Fep],
+ state_local->box,
+ of->natoms_x_compressed,
+ xxtc,
+ nullptr,
+ nullptr);
if (of->natoms_x_compressed != of->natoms_global)
{
sfree(xxtc);
}
if (mdof_flags & MDOF_LAMBDA)
{
- lambda = state_local->lambda[efptFEP];
+ lambda = state_local->lambda[FreeEnergyPerturbationCouplingType::Fep];
}
gmx_fwrite_tng(of->tng, FALSE, step, t, lambda, box, natoms, nullptr, nullptr, nullptr);
}
}
if (mdof_flags & MDOF_LAMBDA_COMPRESSED)
{
- lambda = state_local->lambda[efptFEP];
+ lambda = state_local->lambda[FreeEnergyPerturbationCouplingType::Fep];
}
- gmx_fwrite_tng(of->tng_low_prec, FALSE, step, t, lambda, box, natoms, nullptr,
- nullptr, nullptr);
+ gmx_fwrite_tng(of->tng_low_prec, FALSE, step, t, lambda, box, natoms, nullptr, nullptr, nullptr);
}
}
{
if (of->tng || of->tng_low_prec)
{
- wallcycle_start(of->wcycle, ewcTRAJ);
+ wallcycle_start(of->wcycle, WallCycleCounter::Traj);
gmx_tng_close(&of->tng);
gmx_tng_close(&of->tng_low_prec);
- wallcycle_stop(of->wcycle, ewcTRAJ);
+ wallcycle_stop(of->wcycle, WallCycleCounter::Traj);
}
}
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