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Merge branch 'develop' into fix-pair-dump-skip

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This commit is contained in:
Steve Plimpton
2022-09-09 14:32:55 -06:00
parent dee0eda2f0 d4bddd4295
commit ddf97461da
5 changed files with 453 additions and 367 deletions
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17
doc/src/restart.rst
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@ -12,7 +12,7 @@ Syntax
restart N root keyword value ...
restart N file1 file2 keyword value ...
* N = write a restart file every this many timesteps
* N = write a restart file on timesteps which are multipls of N
* N can be a variable (see below)
* root = filename to which timestep # is appended
* file1,file2 = two full filenames, toggle between them when writing file
@ -42,13 +42,14 @@ Description
"""""""""""
Write out a binary restart file with the current state of the
simulation every so many timesteps, in either or both of two modes, as
a run proceeds. A value of 0 means do not write out any restart
files. The two modes are as follows. If one filename is specified, a
series of filenames will be created which include the timestep in the
filename. If two filenames are specified, only 2 restart files will
be created, with those names. LAMMPS will toggle between the 2 names
as it writes successive restart files.
simulation on timesteps which are a multiple of N. A value of N = 0
means do not write out any restart files, which is the default.
Restart files are written in one (or both) of two modes as a run
proceeds. If one filename is specified, a series of filenames will be
created which include the timestep in the filename. If two filenames
are specified, only 2 restart files will be created, with those names.
LAMMPS will toggle between the 2 names as it writes successive restart
files.
Note that you can specify the restart command twice, once with a
single filename and once with two filenames. This would allow you,

21
lib/gpu/geryon/nvd_device.h
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@ -316,6 +316,9 @@ class UCL_Device {
std::vector<CUstream> _cq;
CUdevice _cu_device;
CUcontext _context;
#if GERYON_NVD_PRIMARY_CONTEXT
CUcontext _old_context;
#endif
};
// Grabs the properties for all devices
@ -391,8 +394,14 @@ int UCL_Device::set_platform(const int pid) {
int UCL_Device::set(int num) {
clear();
_device=_properties[num].device_id;
#if GERYON_NVD_PRIMARY_CONTEXT
CU_SAFE_CALL_NS(cuCtxGetCurrent(&_old_context));
CU_SAFE_CALL_NS(cuDeviceGet(&_cu_device,_device));
CUresult err=cuDevicePrimaryCtxRetain(&_context,_cu_device);
#else
CU_SAFE_CALL_NS(cuDeviceGet(&_cu_device,_device));
CUresult err=cuCtxCreate(&_context,0,_cu_device);
#endif
if (err!=CUDA_SUCCESS) {
#ifndef UCL_NO_EXIT
std::cerr << "UCL Error: Could not access accelerator number " << num
@ -401,13 +410,23 @@ int UCL_Device::set(int num) {
#endif
return UCL_ERROR;
}
#if GERYON_NVD_PRIMARY_CONTEXT
if (_context != _old_context) {
CU_SAFE_CALL_NS(cuCtxSetCurrent(_context));
}
#endif
return UCL_SUCCESS;
}
void UCL_Device::clear() {
if (_device>-1) {
for (int i=1; i<num_queues(); i++) pop_command_queue();
cuCtxDestroy(_context);
#if GERYON_NVD_PRIMARY_CONTEXT
CU_SAFE_CALL_NS(cuCtxSetCurrent(_old_context));
CU_SAFE_CALL_NS(cuDevicePrimaryCtxRelease(_cu_device));
#else
cuCtxDestroy(_context));
#endif
}
_device=-1;
}

7
lib/gpu/geryon/nvd_macros.h
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@ -7,6 +7,13 @@
#define CUDA_INT_TYPE size_t
// Use the primary context for GPU access to enable compatibility with tools
// like OpenMPI accessing the GPU through the runtime interface.
// Set to 0 to revert to old behavior
#ifndef GERYON_NVD_PRIMARY_CONTEXT
#define GERYON_NVD_PRIMARY_CONTEXT 1
#endif
#ifdef MPI_GERYON
#include "mpi.h"
#define NVD_GERYON_EXIT do { \

21
src/output.cpp
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@ -237,11 +237,9 @@ void Output::setup(int memflag)
last_dump[idump] = ntimestep;
}
// calculate timestep and/or time for next dump
// set next_dump and next_time_dump, 0 arg for setup()
// only do this if dump written or dump has not been written yet
// calculate timestep or time for next dump
// set next_dump and next_time_dump
if (writeflag || last_dump[idump] < 0)
calculate_next_dump(SETUP,idump,ntimestep);
// if dump not written now, use addstep_compute_all()
@ -268,11 +266,11 @@ void Output::setup(int memflag)
if (restart_flag && update->restrict_output == 0) {
if (restart_flag_single) {
if (restart_every_single)
if (restart_every_single) {
next_restart_single =
(ntimestep/restart_every_single)*restart_every_single +
restart_every_single;
else {
} else {
auto nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_single));
if (nextrestart <= ntimestep)
@ -365,7 +363,7 @@ void Output::setup(int memflag)
modify->clearstep_compute();
// perform dump
// reset next_dump and next_time_dump, 1 arg for write()
// set next_dump and next_time_dump
dump[idump]->write();
last_dump[idump] = ntimestep;
@ -388,7 +386,6 @@ void Output::setup(int memflag)
if (next_restart == ntimestep) {
if (next_restart_single == ntimestep) {
std::string file = restart1;
std::size_t found = file.find('*');
if (found != std::string::npos)
@ -407,6 +404,7 @@ void Output::setup(int memflag)
modify->addstep_compute(next_restart_single);
}
}
if (next_restart_double == ntimestep) {
if (last_restart != ntimestep) {
if (restart_toggle == 0) {
@ -417,6 +415,7 @@ void Output::setup(int memflag)
restart_toggle = 0;
}
}
if (restart_every_double) next_restart_double += restart_every_double;
else {
modify->clearstep_compute();
@ -489,8 +488,9 @@ void Output::calculate_next_dump(int which, int idump, bigint ntimestep)
if (every_dump[idump]) {
// which = SETUP: nextdump = next multiple of every_dump
// which = WRITE: increment nextdump by every_dump
// which = SETUP: next_dump = next multiple of every_dump
// which = WRITE: increment next_dump by every_dump
// current step is already multiple of every_dump
if (which == SETUP)
next_dump[idump] = (ntimestep/every_dump[idump])*every_dump[idump] + every_dump[idump];
@ -728,7 +728,6 @@ void Output::reset_dt()
next = MIN(next,next_thermo);
}
/* ----------------------------------------------------------------------
add a Dump to list of Dumps
------------------------------------------------------------------------- */

60
unittest/formats/test_dump_atom.cpp
View File

@ -699,6 +699,66 @@ TEST_F(DumpAtomTest, binary_write_dump)
delete_file(dump_file);
}
TEST_F(DumpAtomTest, frequency)
{
auto dump_file = dump_filename("frequency");
BEGIN_HIDE_OUTPUT();
command("dump id all atom 5 " + dump_file);
command("run 15 post no");
command("run 12 post no");
END_HIDE_OUTPUT();
// NOTE: must reset to current timestep (27) to avoid unexpected issues with following
TEST_FAILURE(".*ERROR: Cannot reset timestep with active dump - must undump first.*",
command("reset_timestep 27"););
BEGIN_HIDE_OUTPUT();
command("run 3 post no");
command("undump id");
command("reset_timestep 5");
command("dump id all atom 10 " + dump_file);
command("dump_modify id append yes");
command("run 20 post no");
command("undump id");
END_HIDE_OUTPUT();
std::vector<std::string> expected, values;
values = extract_items(dump_file, "TIMESTEP");
expected = {"0", "5", "10", "15", "20", "25", "30", "10", "20"};
ASSERT_EQ(values.size(), expected.size());
for (int i = 0; i < expected.size(); ++i)
ASSERT_THAT(values[i], Eq(expected[i]));
BEGIN_HIDE_OUTPUT();
command("reset_timestep 10");
command("dump id all atom 10 " + dump_file);
command("run 20 post no");
command("undump id");
END_HIDE_OUTPUT();
values = extract_items(dump_file, "TIMESTEP");
expected = {"10", "20", "30"};
ASSERT_EQ(values.size(), expected.size());
for (int i = 0; i < expected.size(); ++i)
ASSERT_THAT(values[i], Eq(expected[i]));
BEGIN_HIDE_OUTPUT();
command("reset_timestep 0");
command("dump id all atom 10 " + dump_file);
command("minimize 0.0 0.0 15 30");
command("run 20 post no");
command("undump id");
END_HIDE_OUTPUT();
values = extract_items(dump_file, "TIMESTEP");
expected = {"0", "10", "15", "20", "30"};
ASSERT_EQ(values.size(), expected.size());
for (int i = 0; i < expected.size(); ++i)
ASSERT_THAT(values[i], Eq(expected[i]));
delete_file(dump_file);
}
//-------------------------------------------------------------------------------------------------
// dump_modify
//-------------------------------------------------------------------------------------------------