diff --git a/src/COMPRESS/dump_cfg_zstd.cpp b/src/COMPRESS/dump_cfg_zstd.cpp new file mode 100644 index 0000000000..ac746df431 --- /dev/null +++ b/src/COMPRESS/dump_cfg_zstd.cpp @@ -0,0 +1,190 @@ +/* ---------------------------------------------------------------------- + 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 +#include + +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; +} diff --git a/src/COMPRESS/dump_cfg_zstd.h b/src/COMPRESS/dump_cfg_zstd.h new file mode 100644 index 0000000000..71e06b0529 --- /dev/null +++ b/src/COMPRESS/dump_cfg_zstd.h @@ -0,0 +1,59 @@ +/* -*- 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. + +*/ diff --git a/unittest/formats/CMakeLists.txt b/unittest/formats/CMakeLists.txt index cacbfb83af..8a07bee0e8 100644 --- a/unittest/formats/CMakeLists.txt +++ b/unittest/formats/CMakeLists.txt @@ -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() diff --git a/unittest/formats/test_dump_cfg_zstd.cpp b/unittest/formats/test_dump_cfg_zstd.cpp new file mode 100644 index 0000000000..9ac84577cb --- /dev/null +++ b/unittest/formats/test_dump_cfg_zstd.cpp @@ -0,0 +1,129 @@ +/* ---------------------------------------------------------------------- + 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 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; +}