diff --git a/src/COMPRESS/dump_local_gz.cpp b/src/COMPRESS/dump_local_gz.cpp index e8065a848a..a0a39b51e0 100644 --- a/src/COMPRESS/dump_local_gz.cpp +++ b/src/COMPRESS/dump_local_gz.cpp @@ -11,24 +11,18 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "dump_local_gz.h" #include "domain.h" +#include "dump_local_gz.h" #include "error.h" #include "update.h" - #include - using namespace LAMMPS_NS; DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) : DumpLocal(lmp, narg, arg) { - gzFp = nullptr; - - compression_level = Z_BEST_COMPRESSION; - if (!compressed) error->all(FLERR,"Dump local/gz only writes compressed files"); } @@ -38,12 +32,8 @@ DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) : DumpLocalGZ::~DumpLocalGZ() { - if (gzFp) gzclose(gzFp); - gzFp = nullptr; - fp = nullptr; } - /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or gzipped @@ -93,17 +83,12 @@ void DumpLocalGZ::openfile() // each proc with filewriter = 1 opens a file if (filewriter) { - std::string mode; - if (append_flag) { - mode = fmt::format("ab{}", compression_level); - } else { - mode = fmt::format("wb{}", compression_level); + try { + writer.open(filecurrent, append_flag); + } catch (FileWriterException &e) { + error->one(FLERR, e.what()); } - - gzFp = gzopen(filecurrent, mode.c_str()); - - if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file"); - } else gzFp = nullptr; + } // delete string with timestep replaced @@ -112,29 +97,34 @@ void DumpLocalGZ::openfile() void DumpLocalGZ::write_header(bigint ndump) { + std::string header; + if ((multiproc) || (!multiproc && me == 0)) { if (unit_flag && !unit_count) { ++unit_count; - gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style); + header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style); } - if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time()); - gzprintf(gzFp,"ITEM: TIMESTEP\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); - gzprintf(gzFp,"ITEM: NUMBER OF %s\n",label); - gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); - if (domain->triclinic) { - gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz); - } else { - gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxxlo,boxxhi); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxylo,boxyhi); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxzlo,boxzhi); + if (time_flag) { + header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); } - gzprintf(gzFp,"ITEM: %s %s\n",label,columns); + + header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep); + header += fmt::format("ITEM: NUMBER OF {}\n{}\n", label, ndump); + if (domain->triclinic == 0) { + header += fmt::format("ITEM: BOX BOUNDS {}\n", boundstr); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxxlo, boxxhi); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxylo, boxyhi); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxzlo, boxzhi); + } else { + header += fmt::format("ITEM: BOX BOUNDS xy xz yz {}\n", boundstr); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxxlo, boxxhi, boxxy); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxylo, boxyhi, boxxz); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxzlo, boxzhi, boxyz); + } + header += fmt::format("ITEM: {} {}\n", label, columns); + + writer.write(header.c_str(), header.length()); } } @@ -143,19 +133,28 @@ void DumpLocalGZ::write_header(bigint ndump) void DumpLocalGZ::write_data(int n, double *mybuf) { if (buffer_flag == 1) { - gzwrite(gzFp,mybuf,sizeof(char)*n); - + writer.write(mybuf, sizeof(char)*n); } else { - int i,j; + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; int m = 0; - for (i = 0; i < n; i++) { - for (j = 0; j < size_one; j++) { - if (vtype[j] == INT) - gzprintf(gzFp,vformat[j],static_cast (mybuf[m])); - else gzprintf(gzFp,vformat[j],mybuf[m]); + for (int i = 0; i < n; i++) { + for (int j = 0; j < size_one; j++) { + int written = 0; + if (vtype[j] == Dump::INT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } else { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + } + + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump local/gz output"); + } m++; } - gzprintf(gzFp,"\n"); + writer.write("\n", 1); } } } @@ -167,11 +166,11 @@ void DumpLocalGZ::write() DumpLocal::write(); if (filewriter) { if (multifile) { - gzclose(gzFp); - gzFp = nullptr; + writer.close(); } else { - if (flush_flag) - gzflush(gzFp,Z_SYNC_FLUSH); + if (flush_flag && writer.isopen()) { + writer.flush(); + } } } } @@ -182,14 +181,15 @@ int DumpLocalGZ::modify_param(int narg, char **arg) { int consumed = DumpLocal::modify_param(narg, arg); if (consumed == 0) { - if (strcmp(arg[0],"compression_level") == 0) { - if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); - int min_level = Z_DEFAULT_COMPRESSION; - int max_level = Z_BEST_COMPRESSION; - compression_level = utils::inumeric(FLERR, arg[1], false, lmp); - if (compression_level < min_level || compression_level > max_level) - error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level)); - return 2; + try { + if (strcmp(arg[0],"compression_level") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + int compression_level = utils::inumeric(FLERR, arg[1], false, lmp); + writer.setCompressionLevel(compression_level); + return 2; + } + } catch (FileWriterException &e) { + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/src/COMPRESS/dump_local_gz.h b/src/COMPRESS/dump_local_gz.h index b3f7c7dcf8..7feb6a8945 100644 --- a/src/COMPRESS/dump_local_gz.h +++ b/src/COMPRESS/dump_local_gz.h @@ -21,7 +21,7 @@ DumpStyle(local/gz,DumpLocalGZ) #define LMP_DUMP_LOCAL_GZ_H #include "dump_local.h" -#include +#include "gz_file_writer.h" namespace LAMMPS_NS { @@ -31,8 +31,7 @@ class DumpLocalGZ : public DumpLocal { virtual ~DumpLocalGZ(); protected: - int compression_level; - gzFile gzFp; // file pointer for the compressed output stream + GzFileWriter writer; virtual void openfile(); virtual void write_header(bigint); diff --git a/src/COMPRESS/dump_local_zstd.cpp b/src/COMPRESS/dump_local_zstd.cpp index d26555d282..a4303f3b25 100644 --- a/src/COMPRESS/dump_local_zstd.cpp +++ b/src/COMPRESS/dump_local_zstd.cpp @@ -17,15 +17,13 @@ #ifdef LAMMPS_ZSTD -#include "dump_local_zstd.h" #include "domain.h" +#include "dump_local_zstd.h" #include "error.h" #include "update.h" - #include - using namespace LAMMPS_NS; DumpLocalZstd::DumpLocalZstd(LAMMPS *lmp, int narg, char **arg) : @@ -42,7 +40,6 @@ DumpLocalZstd::~DumpLocalZstd() { } - /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or gzipped @@ -145,7 +142,31 @@ void DumpLocalZstd::write_header(bigint ndump) void DumpLocalZstd::write_data(int n, double *mybuf) { - writer.write(mybuf, sizeof(char)*n); + if (buffer_flag == 1) { + writer.write(mybuf, sizeof(char)*n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < size_one; j++) { + int written = 0; + if (vtype[j] == Dump::INT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } else { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + } + + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump local/gz output"); + } + m++; + } + writer.write("\n", 1); + } + } } /* ---------------------------------------------------------------------- */ @@ -184,7 +205,7 @@ int DumpLocalZstd::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, e.what()); + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/unittest/formats/test_dump_local.cpp b/unittest/formats/test_dump_local.cpp index fb38ca08ad..b122d71849 100644 --- a/unittest/formats/test_dump_local.cpp +++ b/unittest/formats/test_dump_local.cpp @@ -93,6 +93,18 @@ TEST_F(DumpLocalTest, run0) delete_file(dump_file); } +TEST_F(DumpLocalTest, label_run0) +{ + auto dump_file = "dump_local_label_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "label ELEMENTS", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + ASSERT_THAT(lines[2], Eq("ITEM: NUMBER OF ELEMENTS")); + ASSERT_THAT(lines[8], Eq("ITEM: ELEMENTS index c_comp[1] ")); + delete_file(dump_file); +} + TEST_F(DumpLocalTest, format_line_run0) { auto dump_file = "dump_local_format_line_run0.melt"; @@ -170,6 +182,60 @@ TEST_F(DumpLocalTest, no_buffer_run0) delete_file(dump_file); } +TEST_F(DumpLocalTest, with_units_run0) +{ + auto dump_file = "dump_with_units_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "units yes", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + ASSERT_EQ(lines.size(), 875); + + ASSERT_THAT(lines[0], Eq("ITEM: UNITS")); + ASSERT_THAT(lines[1], Eq("lj")); + + ASSERT_THAT(lines[2], Eq("ITEM: TIMESTEP")); + ASSERT_EQ(std::stoi(lines[3]), 0); + + ASSERT_THAT(lines[4], Eq("ITEM: NUMBER OF ENTRIES")); + ASSERT_EQ(std::stoi(lines[5]), 864); +} + +TEST_F(DumpLocalTest, with_time_run0) +{ + auto dump_file = "dump_with_time_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "time yes", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + ASSERT_EQ(lines.size(), 875); + + ASSERT_THAT(lines[0], Eq("ITEM: TIME")); + ASSERT_THAT(std::stof(lines[1]), 0.0); + + ASSERT_THAT(lines[2], Eq("ITEM: TIMESTEP")); + ASSERT_EQ(std::stoi(lines[3]), 0); + + ASSERT_THAT(lines[4], Eq("ITEM: NUMBER OF ENTRIES")); + ASSERT_EQ(std::stoi(lines[5]), 864); +} + +TEST_F(DumpLocalTest, triclinic_run0) +{ + auto dump_file = "dump_local_triclinic_run0.melt"; + enable_triclinic(); + generate_dump(dump_file, "index c_comp[1]", "", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + + ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS xy xz yz pp pp pp")); + ASSERT_EQ(utils::split_words(lines[5]).size(), 3); + ASSERT_EQ(utils::split_words(lines[6]).size(), 3); + ASSERT_EQ(utils::split_words(lines[7]).size(), 3); + delete_file(dump_file); +} + int main(int argc, char **argv) { MPI_Init(&argc, &argv); diff --git a/unittest/formats/test_dump_local_compressed.cpp b/unittest/formats/test_dump_local_compressed.cpp index 95656071fc..cd217354af 100644 --- a/unittest/formats/test_dump_local_compressed.cpp +++ b/unittest/formats/test_dump_local_compressed.cpp @@ -69,6 +69,135 @@ TEST_F(DumpLocalCompressTest, compressed_run0) delete_file(converted_file_0); } +TEST_F(DumpLocalCompressTest, compressed_no_buffer_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "no_buffer_run*.melt.local"; + auto base_name_0 = "no_buffer_run0.melt.local"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "index c_comp[1]"; + + if(compression_style == "local/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "buffer no", "buffer no checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "buffer no", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + +TEST_F(DumpLocalCompressTest, compressed_with_time_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "with_time_run*.melt.local"; + auto base_name_0 = "with_time_run0.melt.local"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "index c_comp[1]"; + + if(compression_style == "local/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "time yes", "time yes checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "time yes", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + +TEST_F(DumpLocalCompressTest, compressed_with_units_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "with_units_run*.melt.local"; + auto base_name_0 = "with_units_run0.melt.local"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "index c_comp[1]"; + + if(compression_style == "local/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "units yes", "units yes checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "units yes", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + +TEST_F(DumpLocalCompressTest, compressed_triclinic_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + enable_triclinic(); + + auto base_name = "triclinic_run*.melt.local"; + auto base_name_0 = "triclinic_run0.melt.local"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "index c_comp[1]"; + + if(compression_style == "local/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "", "checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + TEST_F(DumpLocalCompressTest, compressed_multi_file_run1) { if (!COMPRESS_BINARY) GTEST_SKIP(); @@ -209,7 +338,7 @@ TEST_F(DumpLocalCompressTest, compressed_modify_bad_param) command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.local"), fields)); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 compression_level 12"); ); } @@ -224,7 +353,7 @@ TEST_F(DumpLocalCompressTest, compressed_modify_multi_bad_param) command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.local"), fields)); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); ); }