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Commit df5ddfda authored by Giovanni La Mura's avatar Giovanni La Mura
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Merge branch 'prepare_magma' into 'master' 

Prepare MAGMA

See merge request giacomo.mulas/np_tmcode!33
parents 535c5bc3 a278a6c2
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build/README.md
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− 1
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......@@ -111,4 +111,3 @@ where the arguments must be valid paths to binary transition matrix files saved
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
\ No newline at end of file
containers/docker/README.md
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− 1
View file @ df5ddfda
......@@ -26,4 +26,3 @@ where `<image name>` is either `np-tmcode` or `np-tmcode-run`. One may also add
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
\ No newline at end of file
containers/singularity/README.md
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− 1
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......@@ -33,4 +33,3 @@ where `<full path to image name>` is the name of the sif image, including full o
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
\ No newline at end of file
doc/src/README.md
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− 1
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......@@ -29,4 +29,3 @@ Alternatively, you can use `make` from the project `src` folder (named `np_tmcod
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
\ No newline at end of file
src/README.md
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− 1
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......@@ -51,4 +51,3 @@ In all cases, build commands executed through `make` will output the object file
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
\ No newline at end of file
src/cluster/cluster.cpp
+ 110
− 7
View file @ df5ddfda
......@@ -30,6 +30,12 @@
#include <mpi.h>
#endif
#endif
#ifdef USE_NVTX
#include <nvtx3/nvToolsExt.h>
#endif
#ifdef USE_MAGMA
#include <cuda_runtime.h>
#endif
#ifndef INCLUDE_TYPES_H_
#include "../include/types.h"
......@@ -86,9 +92,27 @@ void cluster(const string& config_file, const string& data_file, const string& o
string timing_name = output_path + "/c_timing_mpi"+ to_string(mpidata->rank) +".log";
FILE *timing_file = fopen(timing_name.c_str(), "w");
Logger *time_logger = new Logger(LOG_DEBG, timing_file);
Logger *logger = new Logger(LOG_INFO);
Logger *logger = new Logger(LOG_DEBG);
#ifdef USE_MAGMA
int device_count;
cudaGetDeviceCount(&device_count);
logger->log("DEBUG: Proc-" + to_string(mpidata->rank) + " found " + to_string(device_count) + " CUDA devices.\n", LOG_DEBG);
logger->log("INFO: Process " + to_string(mpidata->rank) + " initializes MAGMA.\n");
magma_int_t magma_result = magma_init();
if (magma_result != MAGMA_SUCCESS) {
logger->err("ERROR: Process " + to_string(mpidata->rank) + " failed to initilize MAGMA.\n");
logger->err("PROC-" + to_string(mpidata->rank) + ": MAGMA error code " + to_string(magma_result) + "\n");
fclose(timing_file);
delete time_logger;
delete logger;
return;
}
#endif
// the following only happens on MPI process 0
if (mpidata->rank == 0) {
#ifdef USE_NVTX
nvtxRangePush("Set up");
#endif
logger->log("INFO: making legacy configuration...", LOG_INFO);
ScattererConfiguration *sconf = NULL;
try {
......@@ -97,7 +121,10 @@ void cluster(const string& config_file, const string& data_file, const string& o
logger->err("\nERROR: failed to open scatterer configuration file.\n");
string message = "FILE: " + string(ex.what()) + "\n";
logger->err(message);
exit(1);
fclose(timing_file);
delete time_logger;
delete logger;
return;
}
sconf->write_formatted(output_path + "/c_OEDFB");
sconf->write_binary(output_path + "/c_TEDF");
......@@ -110,9 +137,15 @@ void cluster(const string& config_file, const string& data_file, const string& o
string message = "FILE: " + string(ex.what()) + "\n";
logger->err(message);
if (sconf) delete sconf;
exit(1);
fclose(timing_file);
delete time_logger;
delete logger;
return;
}
logger->log(" done.\n", LOG_INFO);
#ifdef USE_NVTX
nvtxRangePop();
#endif
int s_nsph = sconf->number_of_spheres;
int nsph = gconf->number_of_spheres;
if (s_nsph == nsph) {
......@@ -167,7 +200,9 @@ void cluster(const string& config_file, const string& data_file, const string& o
string tppoan_name = output_path + "/c_TPPOAN";
tppoan.open(tppoan_name.c_str(), ios::out | ios::binary);
if (tppoan.is_open()) {
#ifdef USE_LAPACK
#ifdef USE_MAGMA
logger->log("INFO: using MAGMA calls.\n", LOG_INFO);
#elif defined USE_LAPACK
logger->log("INFO: using LAPACK calls.\n", LOG_INFO);
#else
logger->log("INFO: using fall-back lucin() calls.\n", LOG_INFO);
......@@ -196,7 +231,13 @@ void cluster(const string& config_file, const string& data_file, const string& o
// do the first iteration on jxi488 separately, since it seems to be different from the others
int jxi488 = 1;
chrono::time_point<chrono::high_resolution_clock> start_iter_1 = chrono::high_resolution_clock::now();
#ifdef USE_NVTX
nvtxRangePush("First iteration");
#endif
int jer = cluster_jxi488_cycle(jxi488, sconf, gconf, p_scattering_angles, cid, output, output_path, tppoan);
#ifdef USE_NVTX
nvtxRangePop();
#endif
chrono::time_point<chrono::high_resolution_clock> end_iter_1 = chrono::high_resolution_clock::now();
elapsed = start_iter_1 - t_start;
string message = "INFO: Calculation setup took " + to_string(elapsed.count()) + "s.\n";
......@@ -206,6 +247,19 @@ void cluster(const string& config_file, const string& data_file, const string& o
message = "INFO: First iteration took " + to_string(elapsed.count()) + "s.\n";
logger->log(message);
time_logger->log(message);
if (jer != 0) {
// First loop failed. Halt the calculation.
tppoan.close();
fclose(timing_file);
fclose(output);
delete p_scattering_angles;
delete cid;
delete logger;
delete time_logger;
delete sconf;
delete gconf;
return;
}
// here go the calls that send data to be duplicated on other MPI processes from process 0 to others, using MPI broadcasts, but only if MPI is actually used
#ifdef MPI_VERSION
......@@ -219,6 +273,9 @@ void cluster(const string& config_file, const string& data_file, const string& o
// Create this variable and initialise it with a default here, so that it is defined anyway, with or without OpenMP support enabled
int ompnumthreads = 1;
#ifdef USE_NVTX
nvtxRangePush("Parallel loop");
#endif
#pragma omp parallel
{
// Create and initialise this variable here, so that if OpenMP is enabled it is local to the thread, and if OpenMP is not enabled it has a well-defiled value anyway
......@@ -247,7 +304,9 @@ void cluster(const string& config_file, const string& data_file, const string& o
fstream &tppoan_2 = *tppoanp_2;
// make sure all threads align here: I don't want the following loop to accidentally start for thread 0, possibly modifying some variables before they are copied by all other threads
#pragma omp barrier
if (myompthread==0) logger->log("Syncing OpenMP threads and starting the loop on wavelengths\n");
if (myompthread==0) {
logger->log("Syncing OpenMP threads and starting the loop on wavelengths\n");
}
// ok, now I can actually start the parallel calculations
#pragma omp for
for (jxi488 = cid_2->firstxi; jxi488 <= cid_2->lastxi; jxi488++) {
......@@ -268,6 +327,11 @@ void cluster(const string& config_file, const string& data_file, const string& o
logger->log(message);
}
} // closes pragma omp parallel
#ifdef USE_NVTX
nvtxRangePop();
nvtxRangePush("Output concatenation");
#endif
#ifdef _OPENMP
#pragma omp barrier
{
......@@ -340,6 +404,9 @@ void cluster(const string& config_file, const string& data_file, const string& o
}
}
}
#endif
#ifdef USE_NVTX
nvtxRangePop();
#endif
tppoanp->close();
delete tppoanp;
......@@ -510,6 +577,10 @@ void cluster(const string& config_file, const string& data_file, const string& o
delete gconf;
}
#endif
#ifdef USE_MAGMA
logger->log("INFO: Process " + to_string(mpidata->rank) + " finalizes MAGMA.\n");
magma_finalize();
#endif
fclose(timing_file);
delete time_logger;
......@@ -520,7 +591,7 @@ int cluster_jxi488_cycle(int jxi488, ScattererConfiguration *sconf, GeometryConf
{
int nxi = sconf->number_of_scales;
string message = "INFO: running scale iteration " + to_string(jxi488) + " of " + to_string(nxi) + ".\n";
Logger *logger = new Logger(LOG_INFO);
Logger *logger = new Logger(LOG_DEBG);
logger->log(message);
chrono::duration<double> elapsed;
chrono::time_point<chrono::high_resolution_clock> interval_start, interval_end;
......@@ -542,7 +613,10 @@ int cluster_jxi488_cycle(int jxi488, ScattererConfiguration *sconf, GeometryConf
int jwtm = gconf->jwtm;
np_int ndit = 2 * nsph * cid->c4->nlim;
int isq, ibf;
#ifdef USE_NVTX
nvtxRangePush("Prepare matrix calculation");
#endif
fprintf(output, "========== JXI =%3d ====================\n", jxi488);
double xi = sconf->get_scale(jxi488 - 1);
double exdc = sconf->exdc;
......@@ -599,23 +673,43 @@ int cluster_jxi488_cycle(int jxi488, ScattererConfiguration *sconf, GeometryConf
//break;
}
} // i132 loop
#ifdef USE_NVTX
nvtxRangePop();
#endif
interval_start = chrono::high_resolution_clock::now();
#ifdef USE_NVTX
nvtxRangePush("Calculate inverted matrix");
#endif
cms(cid->am, cid->c1, cid->c1ao, cid->c4, cid->c6);
#ifdef USE_NVTX
nvtxRangePop();
#endif
interval_end = chrono::high_resolution_clock::now();
elapsed = interval_end - interval_start;
message = "INFO: matrix calculation for scale " + to_string(jxi488) + " took " + to_string(elapsed.count()) + "s.\n";
logger->log(message);
interval_start = chrono::high_resolution_clock::now();
#ifdef USE_NVTX
nvtxRangePush("Invert the matrix");
#endif
invert_matrix(cid->am, ndit, jer, mxndm);
#ifdef USE_NVTX
nvtxRangePop();
#endif
interval_end = chrono::high_resolution_clock::now();
elapsed = interval_end - interval_start;
message = "INFO: matrix inversion for scale " + to_string(jxi488) + " took " + to_string(elapsed.count()) + "s.\n";
logger->log(message);
if (jer != 0) {
message = "ERROR: matrix inversion ended with error code " + to_string(jer) + ".\n";
logger->err(message);
return jer;
// break; // jxi488 loop: goes to memory clean
}
interval_start = chrono::high_resolution_clock::now();
#ifdef USE_NVTX
nvtxRangePush("Average calculation");
#endif
ztm(cid->am, cid->c1, cid->c1ao, cid->c4, cid->c6, cid->c9);
if (idfc >= 0) {
if (jxi488 == jwtm) {
......@@ -683,11 +777,17 @@ int cluster_jxi488_cycle(int jxi488, ScattererConfiguration *sconf, GeometryConf
tppoan.write(reinterpret_cast<char *>(&(cid->vk)), sizeof(double));
pcrsm0(cid->vk, exri, inpol, cid->c1, cid->c1ao, cid->c4);
apcra(cid->zpv, cid->c4->le, cid->c1ao->am0m, inpol, sqk, cid->gapm, cid->gappm);
#ifdef USE_NVTX
nvtxRangePop();
#endif
interval_end = chrono::high_resolution_clock::now();
elapsed = interval_end - interval_start;
message = "INFO: average calculation for scale " + to_string(jxi488) + " took " + to_string(elapsed.count()) + "s.\n";
logger->log(message);
interval_start = chrono::high_resolution_clock::now();
#ifdef USE_NVTX
nvtxRangePush("Angle loop");
#endif
double th = sa->th;
for (int jth486 = 1; jth486 <= sa->nth; jth486++) { // OpenMP portable?
double ph = sa->ph;
......@@ -1172,6 +1272,9 @@ int cluster_jxi488_cycle(int jxi488, ScattererConfiguration *sconf, GeometryConf
} // jph484 loop
th += sa->thstp;
} // jth486 loop
#ifdef USE_NVTX
nvtxRangePop();
#endif
interval_end = chrono::high_resolution_clock::now();
elapsed = interval_end - interval_start;
message = "INFO: angle loop for scale " + to_string(jxi488) + " took " + to_string(elapsed.count()) + "s.\n";
......
src/include/magma_calls.h 0 → 100644
+ 36
− 0
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/* Copyright 2004 INAF - Osservatorio Astronomico di Cagliari
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
*/
/*! \file magma_calls.h
*
* \brief C++ interface to MAGMA calls.
*
*/
#ifndef INCLUDE_MAGMA_CALLS_H_
#define INCLUDE_MAGMA_CALLS_H_
/*! \brief Invert a complex matrix with double precision elements.
*
* Use LAPACKE64 to perform an in-place matrix inversion for a complex
* matrix with double precision elements.
*
* \param mat: Matrix of complex. The matrix to be inverted.
* \param n: `np_int` The number of rows and columns of the [n x n] matrix.
* \param jer: `int &` Reference to an integer return flag.
*/
void magma_zinvert(dcomplex **mat, np_int n, int &jer);
#endif
src/include/types.h
+ 22
− 5
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......@@ -25,24 +25,41 @@
typedef __complex__ double dcomplex;
#ifdef USE_LAPACK
#ifdef USE_MKL
#ifdef USE_ILP64
#ifndef MKL_INT
#define MKL_INT int64_t
#endif
#endif // MKL_INT
#else
#ifndef MKL_INT
#define MKL_INT int32_t
#endif // MKL_INT
#endif // USE_ILP64
#endif // USE_MKL
#ifdef USE_LAPACK
#ifdef USE_MKL
#include <mkl_lapacke.h>
#else
#include <lapacke.h>
#endif
#endif // USE_MKL
#endif // USE_LAPACK
#ifdef USE_MAGMA
#include <magma_v2.h>
#endif
#ifndef np_int
#ifdef lapack_int
#define np_int lapack_int
#else
#ifdef USE_ILP64
#define np_int int64_t
#endif
#endif
#else
#define np_int int32_t
#endif // USE_ILP64
#endif // lapack_int
#endif // np_int
/*! \brief Get the real part of a complex number.
*
......
src/libnptm/Makefile
+ 3
− 3
View file @ df5ddfda
......@@ -19,11 +19,11 @@ endif
include ../make.inc
CXX_NPTM_OBJS=$(OBJDIR)/Commons.o $(OBJDIR)/Configuration.o $(OBJDIR)/file_io.o $(OBJDIR)/Parsers.o $(OBJDIR)/sph_subs.o $(OBJDIR)/clu_subs.o $(OBJDIR)/tfrfme.o $(OBJDIR)/tra_subs.o $(OBJDIR)/TransitionMatrix.o $(OBJDIR)/lapack_calls.o $(OBJDIR)/algebraic.o $(OBJDIR)/types.o $(OBJDIR)/logging.o
CXX_NPTM_OBJS=$(OBJDIR)/Commons.o $(OBJDIR)/Configuration.o $(OBJDIR)/file_io.o $(OBJDIR)/Parsers.o $(OBJDIR)/sph_subs.o $(OBJDIR)/clu_subs.o $(OBJDIR)/tfrfme.o $(OBJDIR)/tra_subs.o $(OBJDIR)/TransitionMatrix.o $(OBJDIR)/lapack_calls.o $(OBJDIR)/magma_calls.o $(OBJDIR)/algebraic.o $(OBJDIR)/types.o $(OBJDIR)/logging.o
CXX_NPTM_DYNOBJS=$(DYNOBJDIR)/Commons.o $(DYNOBJDIR)/Configuration.o $(DYNOBJDIR)/file_io.o $(DYNOBJDIR)/Parsers.o $(DYNOBJDIR)/sph_subs.o $(DYNOBJDIR)/clu_subs.o $(DYNOBJDIR)/tfrfme.o $(DYNOBJDIR)/tra_subs.o $(DYNOBJDIR)/TransitionMatrix.o $(DYNOBJDIR)/lapack_calls.o $(DYNOBJDIR)/algebraic.o $(DYNOBJDIR)/types.o $(DYNOBJDIR)/logging.o
CXX_NPTM_DYNOBJS=$(DYNOBJDIR)/Commons.o $(DYNOBJDIR)/Configuration.o $(DYNOBJDIR)/file_io.o $(DYNOBJDIR)/Parsers.o $(DYNOBJDIR)/sph_subs.o $(DYNOBJDIR)/clu_subs.o $(DYNOBJDIR)/tfrfme.o $(DYNOBJDIR)/tra_subs.o $(DYNOBJDIR)/TransitionMatrix.o $(DYNOBJDIR)/lapack_calls.o $(DYNOBJDIR)/magma_calls.o $(DYNOBJDIR)/algebraic.o $(DYNOBJDIR)/types.o $(DYNOBJDIR)/logging.o
CXX_NPTM_DEBUG=$(OBJDIR)/Commons.g* $(OBJDIR)/Configuration.g* $(OBJDIR)/file_io.g* $(OBJDIR)/Parsers.g* $(OBJDIR)/sph_subs.g* $(OBJDIR)/clu_subs.g* $(OBJDIR)/tfrfme.g* $(OBJDIR)/tra_subs.g* $(OBJDIR)/TransitionMatrix.g* $(OBJDIR)/lapack_calls.g* $(OBJDIR)/algebraic.g* $(OBJDIR)/types.g* $(OBJDIR)/logging.g* $(DYNOBJDIR)/Commons.g* $(DYNOBJDIR)/Configuration.g* $(DYNOBJDIR)/file_io.g* $(DYNOBJDIR)/Parsers.g* $(DYNOBJDIR)/sph_subs.g* $(DYNOBJDIR)/clu_subs.g* $(DYNOBJDIR)/tfrfme.g* $(DYNOBJDIR)/tra_subs.g* $(DYNOBJDIR)/TransitionMatrix.g* $(DYNOBJDIR)/lapack_calls.g* $(DYNOBJDIR)/algebraic.g* $(DYNOBJDIR)/types.g* $(DYNOBJDIR)/logging.g*
CXX_NPTM_DEBUG=$(OBJDIR)/Commons.g* $(OBJDIR)/Configuration.g* $(OBJDIR)/file_io.g* $(OBJDIR)/Parsers.g* $(OBJDIR)/sph_subs.g* $(OBJDIR)/clu_subs.g* $(OBJDIR)/tfrfme.g* $(OBJDIR)/tra_subs.g* $(OBJDIR)/TransitionMatrix.g* $(OBJDIR)/lapack_calls.g* $(OBJDIR)/magma_calls.g* $(OBJDIR)/algebraic.g* $(OBJDIR)/types.g* $(OBJDIR)/logging.g* $(DYNOBJDIR)/Commons.g* $(DYNOBJDIR)/Configuration.g* $(DYNOBJDIR)/file_io.g* $(DYNOBJDIR)/Parsers.g* $(DYNOBJDIR)/sph_subs.g* $(DYNOBJDIR)/clu_subs.g* $(DYNOBJDIR)/tfrfme.g* $(DYNOBJDIR)/tra_subs.g* $(DYNOBJDIR)/TransitionMatrix.g* $(DYNOBJDIR)/lapack_calls.g* $(DYNOBJDIR)/magma_calls.g* $(DYNOBJDIR)/algebraic.g* $(DYNOBJDIR)/types.g* $(DYNOBJDIR)/logging.g*
all: $(BUILDDIR_NPTM)/libnptm.a $(BUILDDIR_NPTM)/libnptm.so
......
src/libnptm/algebraic.cpp
+ 9
− 1
View file @ df5ddfda
......@@ -27,6 +27,12 @@
#endif
#endif
#ifdef USE_MAGMA
#ifndef INCLUDE_MAGMA_CALLS_H_
#include "../include/magma_calls.h"
#endif
#endif
#ifndef INCLUDE_ALGEBRAIC_H_
#include "../include/algebraic.h"
#endif
......@@ -39,7 +45,9 @@ using namespace std;
void invert_matrix(dcomplex **mat, np_int size, int &ier, np_int max_size) {
ier = 0;
#ifdef USE_LAPACK
#ifdef USE_MAGMA
magma_zinvert(mat, size, ier);
#elif defined USE_LAPACK
zinvert(mat, size, ier);
#else
lucin(mat, max_size, size, ier);
......
src/libnptm/lapack_calls.cpp
+ 3
− 2
View file @ df5ddfda
......@@ -21,19 +21,20 @@
#include "../include/types.h"
#endif
/*
#ifdef USE_LAPACK
#ifdef USE_MKL
#include <mkl_lapacke.h>
#else
#include <lapacke.h>
#endif
*/
#ifdef USE_LAPACK
#ifndef INCLUDE_LAPACK_CALLS_H_
#include "../include/lapack_calls.h"
#endif
#endif
#ifdef USE_LAPACK
void zinvert(dcomplex **mat, np_int n, int &jer) {
jer = 0;
dcomplex *arr = &(mat[0][0]);
......
src/libnptm/logging.cpp
+ 25
− 37
View file @ df5ddfda
......@@ -39,56 +39,44 @@ Logger::~Logger() {
}
void Logger::err(const std::string& message) {
//#pragma omp critical
{
fprintf(err_output, "%s", message.c_str());
fflush(err_output);
}
fprintf(err_output, "%s", message.c_str());
fflush(err_output);
}
void Logger::flush(int level) {
//#pragma omp critical
{
string summary = "\"" + *last_message + "\" issued " + to_string(repetitions);
if (repetitions == 1) summary += " time.\n";
else summary += " times.\n";
if (level == LOG_ERRO) err(summary);
else {
if (level >= log_threshold) {
fprintf(log_output, "%s", summary.c_str());
fflush(log_output);
}
string summary = "\"" + *last_message + "\" issued " + to_string(repetitions);
if (repetitions == 1) summary += " time.\n";
else summary += " times.\n";
if (level == LOG_ERRO) err(summary);
else {
if (level >= log_threshold) {
fprintf(log_output, "%s", summary.c_str());
fflush(log_output);
}
delete last_message;
last_message = new string("");
repetitions = 0;
}
delete last_message;
last_message = new string("");
repetitions = 0;
}
void Logger::log(const std::string& message, int level) {
//#pragma omp critical
{
if (level == LOG_ERRO) err(message);
else {
if (level >= log_threshold) {
fprintf(log_output, "%s", message.c_str());
fflush(log_output);
}
if (level == LOG_ERRO) err(message);
else {
if (level >= log_threshold) {
fprintf(log_output, "%s", message.c_str());
fflush(log_output);
}
}
}
void Logger::push(const std::string& message) {
//#pragma omp critical
{
if (repetitions > 0) {
if (message.compare(*last_message) != 0) {
flush(LOG_DEBG);
}
if (repetitions > 0) {
if (message.compare(*last_message) != 0) {
flush(LOG_DEBG);
}
log(message, LOG_DEBG);
delete last_message;
last_message = new string(message);
repetitions++;
}
log(message, LOG_DEBG);
delete last_message;
last_message = new string(message);
repetitions++;
}
src/libnptm/magma_calls.cpp 0 → 100644
+ 59
− 0
View file @ df5ddfda
/* Copyright 2004 INAF - Osservatorio Astronomico di Cagliari
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
*/
/*! \file magma_calls.cpp
*
* \brief Implementation of the interface with MAGMA libraries.
*/
#ifndef INCLUDE_TYPES_H_
#include "../include/types.h"
#endif
#ifdef USE_MAGMA
#ifndef INCLUDE_MAGMA_CALLS_H_
#include "../include/magma_calls.h"
#endif
void magma_zinvert(dcomplex **mat, np_int n, int &jer) {
// magma_int_t result = magma_init();
magma_int_t err = MAGMA_SUCCESS;
magma_queue_t queue = NULL;
magma_device_t dev = 0;
magma_queue_create(dev, &queue);
magmaDoubleComplex *dwork; // dwork - workspace
magma_int_t ldwork; // size of dwork
magma_int_t *piv , info; // piv - array of indices of inter -
magma_int_t m = (magma_int_t)n; // changed rows; a - mxm matrix
magma_int_t mm = m * m; // size of a, r, c
magmaDoubleComplex *a = (magmaDoubleComplex *)&(mat[0][0]); // a - mxm matrix on the host
magmaDoubleComplex *d_a; // d_a - mxm matrix a on the device
ldwork = m * magma_get_zgetri_nb(m); // optimal block size
// allocate matrices
err = magma_zmalloc(&d_a, mm); // device memory for a
err = magma_zmalloc(&dwork, ldwork); // dev. mem. for ldwork
piv = new magma_int_t[m]; // host mem.
magma_zsetmatrix(m, m, a, m, d_a , m, queue); // copy a -> d_a
magma_zgetrf_gpu(m, m, d_a, m, piv, &info);
magma_zgetri_gpu(m, d_a, m, piv, dwork, ldwork, &info);
magma_zgetmatrix( m, m, d_a , m, a, m, queue); // copy d_a -> a
delete[] piv; // free host memory
magma_free(d_a); // free device memory
magma_queue_destroy(queue); // destroy queue
// result = magma_finalize();
jer = (int)err;
}
#endif
src/make.inc
+ 129
− 56
View file @ df5ddfda
# FC defines the fortran compiler to use. If undefined, GNU Make tries to use `f77`
ifndef FC
override FC=gfortran
override FC=gfortran
endif
# FCFLAGS defines the compilation options for the fortran compiler
ifndef FCFLAGS
override FCFLAGS=-std=legacy -O3
override FCFLAGS=-std=legacy -O3
endif
# AR defines the command to create static library files
ifndef AR
override AR=ar
override AR=ar
endif
# ARFLAGS defines the flags for AR to create static library files
ifndef ARFLAGS
override ARFLAGS=-rs
override ARFLAGS=-rs
endif
# PICFLAGS defines the additional flags for the c++ compiler to create objects suitable for shared library creation
ifndef PICFLAGS
override PICFLAGS=-fPIC
override PICFLAGS=-fPIC
endif
# LDFLAGS defines the default linker flags
ifndef LDFLAGS
override LDFLAGS=
override LDFLAGS=
endif
# CXX defines the default C++ compiler to use. If undefined, GNU Make tries to use g++
ifndef CXX
ifdef USE_MPI
override CXX=mpicxx
else
override CXX=g++
endif
ifdef USE_MPI
override CXX=mpicxx
else
override CXX=g++
endif
endif
ifdef USE_MPI
override MPI_CXXFLAGS+=-DUSE_MPI
override MPI_CXXFLAGS+=-DUSE_MPI
endif
# HDF5_INCLUDE defines the default path to the HDF5 include files to use
ifndef HDF5_INCLUDE
override HDF5_INCLUDE=/usr/include/hdf5/serial
override HDF5_INCLUDE=/usr/include/hdf5/serial
endif
# define (outside) USE_LAPACK for lapacke support, LAPACK_ILP64 for ilp64 interface, MKL_ILP64 the same if using MKL implementation
ifdef USE_LAPACK
ifndef LAPACK_ILP64
override LAPACK_ILP64=1
endif
# define (outside) USE_ILP64 for long long int support in lapack/mkl/magma interfaces
ifdef USE_ILP64
ifndef LAPACK_ILP64
override LAPACK_ILP64=1
endif #LAPACK_ILP64
endif
# define (outside) USE_MKL to use the MKL implementation of lapacke
ifdef USE_MKL
ifndef MKL_ILP64
override MKL_ILP64=1
endif
ifndef LAPACK_INCLUDE
ifdef USE_MKL
# define (outside) USE_ILP64 for long long int support in lapack/mkl/magma interfaces
ifdef USE_ILP64
ifndef MKL_ILP64
override MKL_ILP64=1
endif #MKL_ILP64
endif #USE_ILP64
ifndef LAPACK_INCLUDE
# this is for the MKL implementation
override LAPACK_INCLUDE=$(MKLROOT)/include
endif
ifndef LAPACK_LDFLAGS
override LAPACK_INCLUDE=$(MKLROOT)/include
endif #LAPACK_INCLUDE
ifndef LAPACK_LDFLAGS
# this is for the MKL implementation
override LAPACK_LDFLAGS=-L$(MKLROOT)/lib -Wl,--no-as-needed -lmkl_intel_ilp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl
endif
# the next else refers to USE_MKL
# define (outside) USE_ILP64 for long long int support in lapack/mkl/magma interfaces
ifdef USE_ILP64
override LAPACK_LDFLAGS=-L$(MKLROOT)/lib -Wl,--no-as-needed -lmkl_intel_ilp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl
else
ifndef LAPACK_INCLUDE
override LAPACK_LDFLAGS=-L$(MKLROOT)/lib -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl
endif #USE_ILP64
endif #LAPACK_LDFLAGS
# the next else refers to USE_MKL
else #this is for when USE_MKL is _not_ defined
ifndef LAPACK_INCLUDE
# this is for standard "vanilla" lapacke64
override LAPACK_INCLUDE=/usr/include
endif
ifndef LAPACK_LDFLAGS
override LAPACK_INCLUDE=/usr/include
endif # LAPACK_INCLUDE
ifndef LAPACK_LDFLAGS
ifdef USE_ILP64
# this is for standard "vanilla" lapacke64
override LAPACK_LDFLAGS=-llapacke64
endif
override LAPACK_LDFLAGS=-llapacke64
else
override LAPACK_LDFLAGS=-llapacke
endif #USE_ILP64
endif #LAPACK_LDFLAGS
# the next endif is for USE_MKL
endif
endif
#the next endif is for USE_LAPACK
endif
# define (outside) USE_MAGMA for magma support
ifdef USE_MAGMA
ifndef MAGMA_LDFLAGS
ifdef MAGMA_LIB
override MAGMA_LDFLAGS= -L$(MAGMA_LIB)
endif
ifdef CUDA_HOME
override MAGMA_LDFLAGS+= -L$(CUDA_HOME)/lib64
endif
override MAGMA_LDFLAGS+= -lmagma -lcudart
#the next endif is for MAGMA_LDFLAGS
endif
#the next endif is for USE_MAGMA
endif
# define (outside) USE_NVTX for NVIDIA profiling
ifdef USE_NVTX
ifndef NVTX_CXXFLAGS
override NVTX_CXXFLAGS= -DUSE_NVTX
ifdef CUDA_HOME
override NVTX_CXXFLAGS+= -I$(CUDA_HOME)/include
# closes CUDA_HOME
endif
# closes NVTX_CXXFLAGS
endif
# closes USE_NVTX
endif
# CXXFLAGS defines the default compilation options for the C++ compiler
ifndef CXXFLAGS
override CXXFLAGS=-O3 -ggdb -pg -coverage -I$(HDF5_INCLUDE) $(MPI_CXXFLAGS)
ifdef USE_OPENMP
override CXXFLAGS+= -fopenmp
endif
ifdef USE_LAPACK
override CXXFLAGS+= -DUSE_LAPACK -DLAPACK_ILP64
ifdef USE_MKL
override CXXFLAGS+= -DMKL_ILP64 -DUSE_MKL -I$(MKLROOT)/include
endif
ifdef USE_OPENMP
override CXXFLAGS+= -fopenmp
endif
endif
override CXXFLAGS=-O3 -ggdb -pg -coverage -I$(HDF5_INCLUDE) $(MPI_CXXFLAGS) $(NVTX_CXXFLAGS)
ifdef USE_OPENMP
override CXXFLAGS+= -fopenmp
# closes USE_OPENMP
endif
ifdef USE_ILP64
override CXXFLAGS+= -DUSE_ILP64
endif
ifdef USE_LAPACK
override CXXFLAGS+= -DUSE_LAPACK
ifdef USE_ILP64
override CXXFLAGS+= -DLAPACK_ILP64
endif
# closes USE_LAPACK
endif
ifdef USE_MKL
override CXXFLAGS+= -DUSE_MKL -I$(MKLROOT)/include
ifdef USE_ILP64
override CXXFLAGS+= -DMKL_ILP64
endif
# closes USE_MKL
endif
ifdef USE_OPENMP
override CXXFLAGS+= -fopenmp
# closes USE_OPENMP
endif
ifdef USE_MAGMA
override CXXFLAGS+= -DUSE_MAGMA
ifdef CUDA_HOME
override CXXFLAGS+= -I$(CUDA_HOME)/include
endif
ifdef MAGMA_INCLUDE
override CXXFLAGS+= -I$(MAGMA_INCLUDE)
endif
ifdef USE_ILP64
override CXXFLAGS+= -DMAGMA_ILP64
endif
# closes USE_MAGMA
endif
#closes CXXFLAGS
endif
# HDF5_LIB defines the default path to the HDF5 libraries to use
# CXXLDFLAGS defines the default linker flags to use for C++ codes
ifndef CXXLDFLAGS
ifndef HDF5_LIB
override HDF5_LIB=/usr/lib/x86_64-linux-gnu/hdf5/serial
endif
override CXXLDFLAGS=-L/usr/lib64 -L$(HDF5_LIB) -lhdf5 $(STATICFLAG)
ifdef USE_LAPACK
override CXXLDFLAGS+= $(LAPACK_LDFLAGS)
endif
override CXXLDFLAGS+= $(LDFLAGS)
ifndef HDF5_LIB
override HDF5_LIB=/usr/lib/x86_64-linux-gnu/hdf5/serial
endif
override CXXLDFLAGS=-L/usr/lib64 -L$(HDF5_LIB) -lhdf5 $(STATICFLAG)
ifdef USE_LAPACK
override CXXLDFLAGS+= $(LAPACK_LDFLAGS)
endif
ifdef USE_MAGMA
override CXXLDFLAGS+= $(MAGMA_LDFLAGS)
endif
override CXXLDFLAGS+= $(LDFLAGS)
endif
#SOFLAGS defines the additional flags for the c++ compiler to create a shared object file
ifndef SOFLAGS
override SOFLAGS=-shared
override SOFLAGS=-shared
endif
%.o : %.f
......
src/scripts/README.md
+ 8
− 1
View file @ df5ddfda
......@@ -27,6 +27,14 @@ or just:
will print a help screen, giving a brief explanation of all the possible options.
## Estimating the execution time from a terminal log
Performance estimates can be obtained from the code logging system, assuming the uses chose to save the terminal output to some log file. To obtain the time spent by the code in performing a specific operation, the syntax is:
> $PATH_TO_SCRIPT/pytiming.py --logname=LOG_FILE [--filter=FILTER --threads=NUM_THREADS]
where `LOG_FILE` must be the name of a file containing the output that would normally go to terminal, `FILTER` must be the starting character sequence of the log line identifying the operation that should be taken into account, and `NUM_THREADS` is the number of processes that were used to perform the whole calculation loop. In case no filter is given, the script provides an estimate of the total amount of time spent in doing the calculation. This estimate, however, is known not to be reliable, because it ignores thread concurrency effects. A more accurate estimate of the total time spent in executing the code is always saved in a file named `c_timing.log`.
# License
Copyright 2004 INAF - Osservatorio Astronomico di Cagliari
......@@ -42,4 +50,3 @@ will print a help screen, giving a brief explanation of all the possible options
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
\ No newline at end of file
src/scripts/pycompare.py
+ 108
− 51
View file @ df5ddfda
......@@ -19,6 +19,7 @@
# The script execution requires python3.
import re
import os
from math import log10
from sys import argv
......@@ -99,51 +100,98 @@ def compare_files(config):
fortran_file = open(config['fortran_file_name'], 'r')
c_file = open(config['c_file_name'], 'r')
l_file = None
f_lines = fortran_file.readlines()
c_lines = c_file.readlines()
fortran_file.close()
c_file.close()
if (len(f_lines) == len(c_lines)):
f_lines = []
c_lines = []
line_count = 0
if (not config['linewise']):
f_lines = fortran_file.readlines()
c_lines = c_file.readlines()
line_count = len(f_lines)
num_len = 1
if (line_count > 0):
num_len = max(4, int(log10(line_count)) + 1)
if (config['log_html']):
l_file = open(config['html_output'], 'w')
l_file.write("<!DOCTYPE html>\n")
l_file.write("<html xmnls=\"http://www.w3.org/1999/xhtml\">\n")
l_file.write(" <header>\n")
l_file.write(
" <h1>Comparison between {0:s} and {1:s}</h1>\n".format(
config['fortran_file_name'], config['c_file_name']
)
fortran_file.close()
c_file.close()
else: # line-wise comparison mode
f_lines = [fortran_file.readline()]
c_lines = [c_file.readline()]
print("INFO: using line-wise mode")
print("INFO: counting result lines...")
while (f_lines[0] != ''):
if (c_lines[0] != ''):
line_count += 1
else:
print("ERROR: C++ file is shorter than FORTRAN file.")
fortran_file.close()
c_file.close()
mismatch_count['errors'] = line_count
return mismatch_count
f_lines[0] = fortran_file.readline()
c_lines[0] = c_file.readline()
if (c_lines[0] != ''):
print("ERROR: C++ file is longer than FORTRAN file.")
fortran_file.close()
c_file.close()
mismatch_count['errors'] = line_count
return mismatch_count
fortran_file.close()
c_file.close()
print("INFO: the output files have %d lines"%line_count)
fortran_file = open(config['fortran_file_name'], 'r')
c_file = open(config['c_file_name'], 'r')
num_read_lines = 0
# LOG FILE INITIALIZATION #
if (config['log_html']):
l_file = open(config['html_output'], 'w')
l_file.write("<!DOCTYPE html>\n")
l_file.write("<html xmnls=\"http://www.w3.org/1999/xhtml\">\n")
l_file.write(" <header>\n")
l_file.write(
" <h1>Comparison between {0:s} and {1:s}</h1>\n".format(
config['fortran_file_name'], config['c_file_name']
)
l_file.write(" </header>\n")
l_file.write(" <body>\n")
l_file.write(" <div>Numeric noise is marked <span style=\"font-weight: bold; color: rgb(0,185,0)\">"
+ "GREEN</span>, warnings are marked <span style=\"font-weight: bold; color: rgb(0,0,255)\">"
+ "BLUE</span> and errors are marked <span style=\"font-weight: bold; color: rgb(255,0,0)\">"
+ "RED</span>.</div>\n")
for li in range(line_count):
line_result = compare_lines(f_lines[li], c_lines[li], config, li + 1, num_len, l_file)
mismatch_count['errors'] += line_result[0]
mismatch_count['warnings'] += line_result[1]
mismatch_count['noisy'] += line_result[2]
if (mismatch_count['errors'] > 0 and not config['check_all']):
print("INFO: mismatch found at line %d"%(li + 1))
break
if l_file is not None:
l_file.write(" </body>\n")
l_file.write("</html>\n")
l_file.close()
else:
mismatch_count['errors'] = len(c_lines)
print("ERROR: {0:s} and {1:s} have different numbers of lines!".format(
config['fortran_file_name'], config['c_file_name']
))
if (config['log_html']):
print("Different file sizes. No log produced.")
config['log_html'] = False
)
l_file.write(" </header>\n")
l_file.write(" <body>\n")
l_file.write(" <div>Numeric noise is marked <span style=\"font-weight: bold; color: rgb(0,185,0)\">"
+ "GREEN</span>, warnings are marked <span style=\"font-weight: bold; color: rgb(0,0,255)\">"
+ "BLUE</span> and errors are marked <span style=\"font-weight: bold; color: rgb(255,0,0)\">"
+ "RED</span>.</div>\n")
# END LOG FILE INITIALIZATION #
line_loop = True
num_len = 1
if (line_count > 0):
num_len = max(4, int(log10(line_count)) + 1)
print("INFO: checking file contents...")
while (line_loop):
if (not config['linewise']):
line_loop = False
else:
f_lines = [fortran_file.readline()]
c_lines = [c_file.readline()]
num_read_lines += 1
# Start here the comparison loop
if (len(f_lines) == len(c_lines)):
for li in range(len(f_lines)):
line_result = compare_lines(f_lines[li], c_lines[li], config, li + 1, num_len, l_file)
mismatch_count['errors'] += line_result[0]
mismatch_count['warnings'] += line_result[1]
mismatch_count['noisy'] += line_result[2]
if (mismatch_count['errors'] > 0 and not config['check_all']):
print("INFO: mismatch found at line %d"%(li + 1))
break
else:
mismatch_count['errors'] = len(c_lines)
print("ERROR: {0:s} and {1:s} have different numbers of lines!".format(
config['fortran_file_name'], config['c_file_name']
))
if (config['log_html']):
print("Different file sizes. No log produced.")
config['log_html'] = False
if (num_read_lines >= line_count):
line_loop = False
#End line loop
if l_file is not None:
l_file.write(" </body>\n")
l_file.write("</html>\n")
l_file.close()
return mismatch_count
## \brief Perform the comparison of two file lines.
......@@ -381,6 +429,7 @@ def parse_arguments():
'fortran_file_name': '',
'c_file_name': '',
'full_log': False,
'linewise': False,
'log_html': False,
'html_output': 'pycompare.html',
'warning_threshold': 0.005,
......@@ -403,6 +452,8 @@ def parse_arguments():
config['warning_threshold'] = float(split_arg[1])
elif (arg.startswith("--help")):
config['help_mode'] = True
elif (arg.startswith("--linewise")):
config['linewise'] = True
elif (arg.startswith("--quick")):
config['check_all'] = False
else:
......@@ -424,8 +475,9 @@ def print_help():
print("--full Print all lines to log file (default prints only mismatches).")
print("--help Print this help and exit.")
print("--html[=OPT_OUTPUT_NAME] Enable logging to HTML file (default logs to \"pycompare.html\").")
print("--linewise Load only one line at a time. Useful to compare big files (false by default).")
print("--quick Stop on first mismatch (default is to perform a full check).")
print("--warn Set a fractional threshold for numeric warning (default=0.005).")
print("--warn Set a fractional threshold for numeric warning (default = 0.005).")
print(" ")
## \brief Add summary information to the HTML log file
......@@ -440,20 +492,25 @@ def print_help():
# \param noisy: `int` The number of noisy values detected by the comparison.
def reformat_log(config, errors, warnings, noisy):
log_file = open(config['html_output'], 'r')
log_lines = log_file.readlines()
log_file.close()
log_file = open(config['html_output'], 'w')
for i in range(7): log_file.write(log_lines[i] + "\n")
new_file = open("PYCOMPARE_TEMPORARY_LOG.html", 'w')
for hi in range(7):
log_line = log_file.readline()
new_file.write(log_line)
str_errors = "error" if errors == 1 else "errors"
str_warnings = "warning" if warnings == 1 else "warnings"
str_noisy = "noisy value" if noisy == 1 else "noisy values"
summary = " <div>Comparison yielded %d %s"%(errors, str_errors)
summary = summary + ", %d %s"%(warnings, str_warnings)
summary = summary + " and %d %s.</div>\n"%(noisy, str_noisy)
log_file.write(summary)
for i in range(7, len(log_lines)): log_file.write(log_lines[i] + "\n")
new_file.write(summary)
log_line = log_file.readline()
while (log_line != ''):
new_file.write(log_line)
log_line = log_file.readline()
log_file.close()
new_file.close()
os.remove(config['html_output'])
os.rename("PYCOMPARE_TEMPORARY_LOG.html", config['html_output'])
# ### PROGRAM EXECUTION ###
## \cond
......
src/scripts/pytiming.py 0 → 100755
+ 123
− 0
View file @ df5ddfda
#!/bin/python3
## @package pycompare
# \brief Script to calculate the execution time of logged operations
#
# Comparing the numeric output can be rendered hard by the amount of information
# contained in a typical output file and the necessity to determine whether a
# difference is actually significant or just caused by numeric noise hitting
# negligible values. The task of `pycompare.py` is to compare two output files, in
# the assumption that they were written by the FORTRAN and the C++ versions of
# the code and to flag all the possible inconsistencies according to various
# severity levels (namely: NOISE, WARNING, and ERROR).
#
# After execution, the script returns an exit code, which is set to 0, if no
# error-level inconsistencies were found, or 1 otherwise. This can be used by
# subsequent system calls to set up a testing suite checking whether the code
# is able to reproduce legacy results.
#
# The script execution requires python3.
import re
from sys import argv
## \cond
time_reg = re.compile(r'[0-9]+\.[0-9]+s')
## \endcond
## \brief Main execution code
#
# `main()` is the function that handles the creation of the script configuration
# and the execution of the calculation. It returns 0 on successful completion.
#
# \returns exit_code: `int` 0 on successful completion.
def main():
config = parse_arguments()
exit_code = 0
if config['help_mode'] or len(argv) == 1:
config['help_mode'] = True
print_help()
else:
if config['log_name'] is None:
exit_code = 1
else:
operation_time = get_time_from_log(config)
print("Calculation took %fs."%operation_time)
return exit_code
## \brief Parse a log file and extract the time.
#
# \param config: `dict` A dictionary containing the script configuration.
#
# \returns operation_time: `float` The time of the requested operation in seconds.
def get_time_from_log(config):
op_time = 0.0
log_file = open(config['log_name'], 'r')
file_lines = log_file.readlines()
log_file.close()
for li in range(len(file_lines)):
str_line = file_lines[li]
if (config['filter'] == "" or str_line.startswith(config['filter'])):
time_iters = time_reg.finditer(str_line)
time_groups = []
for ti in time_iters:
time_groups.append(ti.group())
if len(time_groups) == 1:
op_time += float(time_groups[0][:-1])
if config['threads'] > 1:
op_time /= config['threads']
return op_time
## \brief Parse the command line arguments.
#
# The script behaviour can be modified through a set of mandatory and optional
# arguments. The only mandatory argument is the name of the log file to be
# parsed. Additional optional arguments are an operation filter, which should
# be the starting sequence of the log strings to pe included in the timing
# calculation and the number of threads used during code execution.
#
# \returns config: `dict` A dictionary containing the script configuration.
def parse_arguments():
config = {
'log_name': None,
'help_mode': False,
'filter': "",
'threads': 1,
}
for arg in argv[1:]:
split_arg = arg.split("=")
if (arg.startswith("--logname")):
config['log_name'] = split_arg[1]
elif (arg.startswith("--filter")):
config['filter'] = split_arg[1]
elif (arg.startswith("--threads")):
config['threads'] = int(split_arg[1])
elif (arg.startswith("--help")):
config['help_mode'] = True
else:
raise Exception("Unrecognized argument \'{0:s}\'".format(arg))
return config
## \brief Print a command-line help summary.
def print_help():
print(" ")
print("*** PYTIMING ***")
print(" ")
print("Get the amount of time spent in calculation.")
print(" ")
print("Usage: \"./pytiming.py OPTIONS\" ")
print(" ")
print("Valid options are: ")
print("--logname=TIMING_LOG File containing log of timing (mandatory).")
print("--filter=FILTER Start of the log lines to be accounted for (optional).")
print("--help Print this help and exit.")
print("--threads=NUM_THREADS Number of threads or processes used in calculation (optional).")
print(" ")
# ### PROGRAM EXECUTION ###
## \cond
res = main()
## \endcond
exit(res)
test_data/README.md
+ 0
− 1
View file @ df5ddfda
......@@ -75,4 +75,3 @@ were the different lines have the following roles:
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
\ No newline at end of file
test_data/cluster/case_48_long/DCLU 0 → 100644
+ 53
− 0
View file @ df5ddfda
48 10 10 5760 1 149 300 0 0
0.0000000e+00 1.0000000e-08 0.0000000e+00
0.0000000e+00 -1.0000000e-08 0.0000000e+00
8.5355339e-09 5.0000000e-09 0.0000000e+00
8.5355339e-09 -5.0000000e-09 0.0000000e+00
-8.5355339e-09 5.0000000e-09 0.0000000e+00
-8.5355339e-09 -5.0000000e-09 0.0000000e+00
0.0000000e+00 1.0000000e-08 1.0000000e-08
0.0000000e+00 -1.0000000e-08 1.0000000e-08
8.5355339e-09 5.0000000e-09 1.0000000e-08
8.5355339e-09 -5.0000000e-09 1.0000000e-08
-8.5355339e-09 5.0000000e-09 1.0000000e-08
-8.5355339e-09 -5.0000000e-09 1.0000000e-08
0.0000000e+00 1.0000000e-08 2.0000000e-08
0.0000000e+00 -1.0000000e-08 2.0000000e-08
8.5355339e-09 5.0000000e-09 2.0000000e-08
8.5355339e-09 -5.0000000e-09 2.0000000e-08
-8.5355339e-09 5.0000000e-09 2.0000000e-08
-8.5355339e-09 -5.0000000e-09 2.0000000e-08
0.0000000e+00 1.0000000e-08 3.0000000e-08
0.0000000e+00 -1.0000000e-08 3.0000000e-08
8.5355339e-09 5.0000000e-09 3.0000000e-08
8.5355339e-09 -5.0000000e-09 3.0000000e-08
-8.5355339e-09 5.0000000e-09 3.0000000e-08
-8.5355339e-09 -5.0000000e-09 3.0000000e-08
-6.4278761e-09 7.6604444e-09 4.0000000e-08
6.4278761e-09 -7.6604444e-09 4.0000000e-08
3.3246603e-09 9.3167577e-09 4.0000000e-08
9.7525364e-09 1.6563132e-09 4.0000000e-08
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8.6602540e-09 -5.0000000e-09 5.0000000e-08
-6.2360066e-11 9.8919892e-09 5.0000000e-08
8.5978940e-09 4.8919892e-09 5.0000000e-08
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6.2360066e-11 -9.8919892e-09 5.0000000e-08
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5.0000000e-09 -8.6602540e-09 6.0000000e-08
4.8919892e-09 8.5978940e-09 6.0000000e-08
9.8919892e-09 -6.2360066e-11 6.0000000e-08
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2.5881905e-09 -9.6592583e-09 7.0000000e-08
6.9505974e-09 7.0387879e-09 7.0000000e-08
9.5387879e-09 -2.6204704e-09 7.0000000e-08
-9.5387879e-09 2.6204704e-09 7.0000000e-08
-6.9505974e-09 -7.0387879e-09 7.0000000e-08
0.00D01 0.00D00 0.00D01 180.00D00 0.00D01 0.00D01
0.00D01 0.00D00 0.00D01 0.00D00 0.00D01 0.00D01
1
0
test_data/cluster/case_48_long/DEDFB 0 → 100644
+ 370
− 0
View file @ df5ddfda
48 0
1.000D00 3.0000000D08 1.000000D00 0 181 0 3
4.2000000e-07
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6.0000000e-07
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 5.00d-9
1.000000D00
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0
\ No newline at end of file
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