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Add dump cfg/zstd

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This commit is contained in:
Richard Berger
2020-08-31 14:20:52 -04:00
parent a922355e19
commit 99b83333c9
4 changed files with 384 additions and 0 deletions
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190
src/COMPRESS/dump_cfg_zstd.cpp Normal file
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "dump_cfg_zstd.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "update.h"
#include "force.h"
#include <cstring>
#include <fmt/format.h>
using namespace LAMMPS_NS;
#define UNWRAPEXPAND 10.0
DumpCFGZstd::DumpCFGZstd(LAMMPS *lmp, int narg, char **arg) :
DumpCFG(lmp, narg, arg)
{
if (!compressed)
error->all(FLERR,"Dump cfg/zstd only writes compressed files");
}
/* ---------------------------------------------------------------------- */
DumpCFGZstd::~DumpCFGZstd()
{
}
/* ----------------------------------------------------------------------
generic opening of a dump file
ASCII or binary or zstdipped
some derived classes override this function
------------------------------------------------------------------------- */
void DumpCFGZstd::openfile()
{
// single file, already opened, so just return
if (singlefile_opened) return;
if (multifile == 0) singlefile_opened = 1;
// if one file per timestep, replace '*' with current timestep
char *filecurrent = filename;
if (multiproc) filecurrent = multiname;
if (multifile) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
if (maxfiles > 0) {
if (numfiles < maxfiles) {
nameslist[numfiles] = new char[strlen(filecurrent)+1];
strcpy(nameslist[numfiles],filecurrent);
++numfiles;
} else {
remove(nameslist[fileidx]);
delete[] nameslist[fileidx];
nameslist[fileidx] = new char[strlen(filecurrent)+1];
strcpy(nameslist[fileidx],filecurrent);
fileidx = (fileidx + 1) % maxfiles;
}
}
}
// each proc with filewriter = 1 opens a file
if (filewriter) {
if (append_flag) {
error->one(FLERR, "dump cfg/zstd currently doesn't support append");
}
try {
writer.open(filecurrent);
} catch (FileWriterException & e) {
error->one(FLERR, e.what());
}
}
// delete string with timestep replaced
if (multifile) delete [] filecurrent;
}
/* ---------------------------------------------------------------------- */
void DumpCFGZstd::write_header(bigint n)
{
// set scale factor used by AtomEye for CFG viz
// default = 1.0
// for peridynamics, set to pre-computed PD scale factor
// so PD particles mimic C atoms
// for unwrapped coords, set to UNWRAPEXPAND (10.0)
// so molecules are not split across periodic box boundaries
double scale = 1.0;
if (atom->peri_flag) scale = atom->pdscale;
else if (unwrapflag == 1) scale = UNWRAPEXPAND;
std::string header = fmt::format("Number of particles = {}\n", n);
header += fmt::format("A = {0:g} Angstrom (basic length-scale)\n", scale);
header += fmt::format("H0(1,1) = {0:g} A\n",domain->xprd);
header += fmt::format("H0(1,2) = 0 A \n");
header += fmt::format("H0(1,3) = 0 A \n");
header += fmt::format("H0(2,1) = {0:g} A \n",domain->xy);
header += fmt::format("H0(2,2) = {0:g} A\n",domain->yprd);
header += fmt::format("H0(2,3) = 0 A \n");
header += fmt::format("H0(3,1) = {0:g} A \n",domain->xz);
header += fmt::format("H0(3,2) = {0:g} A \n",domain->yz);
header += fmt::format("H0(3,3) = {0:g} A\n",domain->zprd);
header += fmt::format(".NO_VELOCITY.\n");
header += fmt::format("entry_count = {}\n",nfield-2);
for (int i = 0; i < nfield-5; i++)
header += fmt::format("auxiliary[{}] = {}\n",i,auxname[i]);
writer.write(header.c_str(), header.length());
}
/* ---------------------------------------------------------------------- */
void DumpCFGZstd::write_data(int n, double *mybuf)
{
writer.write(mybuf, n);
}
/* ---------------------------------------------------------------------- */
void DumpCFGZstd::write()
{
DumpCFG::write();
if (filewriter) {
if (multifile) {
writer.close();
} else {
if (flush_flag && writer.isopen()) {
writer.flush();
}
}
}
}
/* ---------------------------------------------------------------------- */
int DumpCFGZstd::modify_param(int narg, char **arg)
{
int consumed = DumpCFG::modify_param(narg, arg);
if(consumed == 0) {
try {
if (strcmp(arg[0],"checksum") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) writer.setChecksum(true);
else if (strcmp(arg[1],"no") == 0) writer.setChecksum(false);
else error->all(FLERR,"Illegal dump_modify command");
return 2;
} else if (strcmp(arg[0],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
int compression_level = force->inumeric(FLERR,arg[1]);
writer.setCompressionLevel(compression_level);
return 2;
}
} catch (FileWriterException & e) {
error->one(FLERR, e.what());
}
}
return consumed;
}

59
src/COMPRESS/dump_cfg_zstd.h Normal file
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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef DUMP_CLASS
DumpStyle(cfg/zstd,DumpCFGZstd)
#else
#ifndef LMP_DUMP_CFG_ZSTD_H
#define LMP_DUMP_CFG_ZSTD_H
#include "dump_cfg.h"
#include "zstd_file_writer.h"
namespace LAMMPS_NS {
class DumpCFGZstd : public DumpCFG {
public:
DumpCFGZstd(class LAMMPS *, int, char **);
virtual ~DumpCFGZstd();
protected:
ZstdFileWriter writer;
virtual void openfile();
virtual void write_header(bigint);
virtual void write_data(int, double *);
virtual void write();
virtual int modify_param(int, char **);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Dump cfg/zstd only writes compressed files
The dump cfg/zstd output file name must have a .zstd suffix.
E: Cannot open dump file
Self-explanatory.
*/

6
unittest/formats/CMakeLists.txt
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@ -64,6 +64,12 @@ if (PKG_COMPRESS)
add_test(NAME DumpCustomZstd COMMAND test_dump_custom_zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
set_tests_properties(DumpCustomZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
set_tests_properties(DumpCustomZstd PROPERTIES ENVIRONMENT "ZSTD_BINARY=${ZSTD_BINARY}")
add_executable(test_dump_cfg_zstd test_dump_cfg_zstd.cpp)
target_link_libraries(test_dump_cfg_zstd PRIVATE lammps GTest::GMock GTest::GTest)
add_test(NAME DumpCfgZstd COMMAND test_dump_cfg_zstd WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
set_tests_properties(DumpCfgZstd PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
set_tests_properties(DumpCfgZstd PROPERTIES ENVIRONMENT "ZSTD_BINARY=${ZSTD_BINARY}")
endif()
endif()

129
unittest/formats/test_dump_cfg_zstd.cpp Normal file
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "gtest/gtest.h"
#include "gmock/gmock.h"
#include "fmt/format.h"
#include "utils.h"
#include "../testing/core.h"
#include "../testing/systems/melt.h"
#include "../testing/utils.h"
char * ZSTD_BINARY = nullptr;
using ::testing::Eq;
class DumpCfgZstdTest : public MeltTest {
std::string dump_style = "cfg";
public:
void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, std::string compression_style,
std::string fields, std::string dump_modify_options, int ntimesteps) {
if (!verbose) ::testing::internal::CaptureStdout();
command(fmt::format("dump id0 all {} 1 {} {}", dump_style, text_file, fields));
command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_file, fields));
if (!dump_modify_options.empty()) {
command(fmt::format("dump_modify id0 {}", dump_modify_options));
command(fmt::format("dump_modify id1 {}", dump_modify_options));
}
command(fmt::format("run {}", ntimesteps));
if (!verbose) ::testing::internal::GetCapturedStdout();
}
std::string convert_compressed_to_text(std::string compressed_file) {
if (!verbose) ::testing::internal::CaptureStdout();
std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.'));
std::string cmdline = fmt::format("{} -d -c {} > {}", ZSTD_BINARY, compressed_file, converted_file);
system(cmdline.c_str());
if (!verbose) ::testing::internal::GetCapturedStdout();
return converted_file;
}
};
TEST_F(DumpCfgZstdTest, compressed_run0)
{
if(!ZSTD_BINARY) GTEST_SKIP();
auto text_files = "dump_cfg_zstd_text_run*.melt.cfg";
auto compressed_files = "dump_cfg_zstd_compressed_run*.melt.cfg.zst";
auto text_file = "dump_cfg_zstd_text_run0.melt.cfg";
auto compressed_file = "dump_cfg_zstd_compressed_run0.melt.cfg.zst";
auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz";
generate_text_and_compressed_dump(text_files, compressed_files, "cfg/gz", fields, "", 0);
TearDown();
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(compressed_file);
auto converted_file = convert_compressed_to_text(compressed_file);
ASSERT_FILE_EXISTS(converted_file);
ASSERT_FILE_EQUAL(text_file, converted_file);
delete_file(text_file);
delete_file(compressed_file);
delete_file(converted_file);
}
TEST_F(DumpCfgZstdTest, compressed_unwrap_run0)
{
if(!ZSTD_BINARY) GTEST_SKIP();
auto text_files = "dump_cfg_unwrap_zstd_text_run*.melt.cfg";
auto compressed_files = "dump_cfg_unwrap_zstd_compressed_run*.melt.cfg.zst";
auto text_file = "dump_cfg_unwrap_zstd_text_run0.melt.cfg";
auto compressed_file = "dump_cfg_unwrap_zstd_compressed_run0.melt.cfg.zst";
auto fields = "mass type xsu ysu zsu id proc procp1 x y z ix iy iz vx vy vz fx fy fz";
generate_text_and_compressed_dump(text_files, compressed_files, "cfg/zstd", fields, "", 0);
TearDown();
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(compressed_file);
auto converted_file = convert_compressed_to_text(compressed_file);
ASSERT_FILE_EXISTS(converted_file);
ASSERT_FILE_EQUAL(text_file, converted_file);
delete_file(text_file);
delete_file(compressed_file);
delete_file(converted_file);
}
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);
::testing::InitGoogleMock(&argc, argv);
// handle arguments passed via environment variable
if (const char *var = getenv("TEST_ARGS")) {
std::vector<std::string> env = utils::split_words(var);
for (auto arg : env) {
if (arg == "-v") {
verbose = true;
}
}
}
ZSTD_BINARY = getenv("ZSTD_BINARY");
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
int rv = RUN_ALL_TESTS();
MPI_Finalize();
return rv;
}