Merge master with HDF5 output (9cef6470) · Commits · Giacomo Mulas / NP_TMcode

.gitlab-ci.yml

+55 −12

Original line number	Original line	Diff line number	Diff line
	@@ -154,7 +154,7 @@ building_stage:
	- cat /etc/os-release		- cat /etc/os-release
	- cd build		- cd build
	- echo "Configuring with default compilers (MAGMA disabled)..."		- echo "Configuring with default compilers (MAGMA disabled)..."
	- ./configure --without-magma --without-cublas --disable-offload --enable-refinement		- ./configure --without-magma --without-cublas --disable-offload --enable-refinement --enable-shared
	- make wipe		- make wipe
	- echo "Building the default configuration..."		- echo "Building the default configuration..."
	- make -j		- make -j
	@@ -174,7 +174,7 @@ sanity_stage:
	- building_stage		- building_stage
	artifacts:		artifacts:
	paths:		paths:
	- build/testing/valgrind.log		- build/testing/valgrind_*.log
	exclude:		exclude:
	- ".git*"		- ".git*"
	- ".git/*/"		- ".git/*/"
	@@ -185,11 +185,26 @@ sanity_stage:
	- hostname		- hostname
	- echo $CI_COMMIT_SHA		- echo $CI_COMMIT_SHA
	- echo $CI_COMMIT_BRANCH		- echo $CI_COMMIT_BRANCH
	- cd build/testing		- cd build/libnptm
	- echo "Running memory sanity check"		- export LD_LIBRARY_PATH="$LD_LIBRARY_PATH;$PWD"
			- cd ../testing
			- echo "Running memory sanity check for ParticleDescriptor"
	- chmod +x test_ParticleDescriptor		- chmod +x test_ParticleDescriptor
	- valgrind --leak-check=full --log-file=valgrind.log ./test_ParticleDescriptor		- valgrind --leak-check=full --log-file=valgrind_Particle.log ./test_ParticleDescriptor
	- grep "no leaks are possible" valgrind.log		- grep "0 errors from 0 contexts" valgrind_Particle.log
			- echo "Running memory sanity check for output classes"
			- chmod +x test_cluster_outputs
			- valgrind --leak-check=full --log-file=valgrind_cluster.log ./test_cluster_outputs
			- grep "0 errors from 0 contexts" valgrind_cluster.log
			- rm -rf c_OCLU_24
			- chmod +x test_inclusion_outputs
			- valgrind --leak-check=full --log-file=valgrind_inclusion.log ./test_inclusion_outputs
			- grep "0 errors from 0 contexts" valgrind_inclusion.log
			- rm -rf c_OINCLU
			- chmod +x test_sphere_outputs
			- valgrind --leak-check=full --log-file=valgrind_sphere.log ./test_sphere_outputs
			- grep "0 errors from 0 contexts" valgrind_sphere.log
			- rm -rf c_OSPH

	running_stage:		running_stage:
	stage: run		stage: run
	@@ -215,10 +230,12 @@ running_stage:
	- hostname		- hostname
	- echo $CI_COMMIT_SHA		- echo $CI_COMMIT_SHA
	- echo $CI_COMMIT_BRANCH		- echo $CI_COMMIT_BRANCH
	- cd build/sphere		- cd build/libnptm
			- export LD_LIBRARY_PATH="$LD_LIBRARY_PATH;$PWD"
			- cd ../sphere
	- echo "Running np_sphere"		- echo "Running np_sphere"
	- chmod +x np_sphere		- chmod +x np_sphere
	- ./np_sphere		- OMP_NUM_THREADS=1 ./np_sphere
	- cd ../cluster		- cd ../cluster
	- echo "Running np_cluster"		- echo "Running np_cluster"
	- chmod +x np_cluster		- chmod +x np_cluster
	@@ -240,7 +257,7 @@ testing_stage:
	- running_stage		- running_stage
	artifacts:		artifacts:
	paths:		paths:
	- build/cluster/pycompare.html		- build/cluster/pycompare_*.html
	- build/inclusion/pycompare.html		- build/inclusion/pycompare.html
	- build/sphere/pycompare.html		- build/sphere/pycompare.html
	exclude:		exclude:
	@@ -253,7 +270,9 @@ testing_stage:
	- hostname		- hostname
	- echo $CI_COMMIT_SHA		- echo $CI_COMMIT_SHA
	- echo $CI_COMMIT_BRANCH		- echo $CI_COMMIT_BRANCH
	- cd build/sphere		- cd build/libnptm
			- export LD_LIBRARY_PATH="$LD_LIBRARY_PATH;$PWD"
			- cd ../sphere
	- export FFILE=../../test_data/sphere/OSPH		- export FFILE=../../test_data/sphere/OSPH
	- echo "Comparing output of SPHERE"		- echo "Comparing output of SPHERE"
	- python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OSPH --html		- python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OSPH --html
	@@ -266,13 +285,37 @@ testing_stage:
	- cd ../cluster		- cd ../cluster
	- echo "Comparing output of CLUSTER"		- echo "Comparing output of CLUSTER"
	- export FFILE=../../test_data/cluster/OCLU		- export FFILE=../../test_data/cluster/OCLU
	- python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OCLU --html		- python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OCLU --html=pycompare_dev.html
	- echo "Testing cluster with 24 spheres"		- echo "Testing cluster with 24 spheres"
	- OMP_NUM_THREADS=1 OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 mpirun -n 2 ./np_cluster ../../test_data/cluster/DEDFB_24 ../../test_data/cluster/DCLU_24 .		- OMP_NUM_THREADS=1 OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 mpirun -n 2 ./np_cluster ../../test_data/cluster/DEDFB_24 ../../test_data/cluster/DCLU_24 .
	- echo "Comparing output of CLUSTER with 24 spheres"		- echo "Comparing output of CLUSTER with 24 spheres"
	- export FFILE=../../test_data/cluster/OCLU_24		- export FFILE=../../test_data/cluster/OCLU_24
	- python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OCLU --html		- python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OCLU --html=pycompare_24.html
	- echo "Checking consistency among legacy and HDF5 configuration files"		- echo "Checking consistency among legacy and HDF5 configuration files"
	- ../testing/test_TEDF ../../test_data/cluster/DEDFB_24 c_TEDF c_TEDF.hd5		- ../testing/test_TEDF ../../test_data/cluster/DEDFB_24 c_TEDF c_TEDF.hd5
	- echo "Checking consistency among legacy and HDF5 TM files"		- echo "Checking consistency among legacy and HDF5 TM files"
	- ../testing/test_TTMS c_TTMS c_TTMS.hd5		- ../testing/test_TTMS c_TTMS c_TTMS.hd5
			- echo "Testing cluster with 48 spheres"
			- OMP_NUM_THREADS=5 ./np_cluster ../../test_data/cluster/DEDFB_48 ../../test_data/cluster/DCLU_48 .
			- echo "Comparing output of CLUSTER with 48 spheres"
			- export FFILE=../../test_data/cluster/OCLU_48
			- python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OCLU --html=pycompare_48.html
			- cd ../testing
			- echo "Checking consistency of HDF5 cluster output"
			- chmod u+x test_cluster_outputs
			- ./test_cluster_outputs
			- export FFILE=../../test_data/cluster/OCLU_24
			- python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OCLU_24
			- rm -rf c_OCLU_24
			- echo "Checking consistency of HDF5 incluson output"
			- chmod u+x test_inclusion_outputs
			- ./test_inclusion_outputs
			- export FFILE=../../test_data/inclusion/OINCLU
			- python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OINCLU
			- rm -rf c_OINCLU
			- chmod u+x test_sphere_outputs
			- ./test_sphere_outputs
			- export FFILE=../../test_data/sphere/OSPH
			- python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OSPH
			- rm -rf c_OSPH

			No newline at end of file

README.md

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -11,7 +11,7 @@ Distributing the code and its sources is possible under the terms of the GNU GPL
	- Saija et al. 2001, ApJ, 559, 993, DOI:10.1086/322350		- Saija et al. 2001, ApJ, 559, 993, DOI:10.1086/322350
	- Borghese, Denti, Saija 2007, Scattering from Model Nonspherical Particles (ISBN 978-3-540-37413-8), DOI:10.1007/978-3-540-37414-5		- Borghese, Denti, Saija 2007, Scattering from Model Nonspherical Particles (ISBN 978-3-540-37413-8), DOI:10.1007/978-3-540-37414-5

	NOTE: The building process requires a working installation of a C++ and a FORTRAN compiler. Many solutions are available, but the recommended option is the GNU Compiler Collection `gcc` with the addition of `g++` and `gfortran`. The parallel code implementation further requires the use of parallel compilers complying with the MPI standard (OpenMPI, MPICH).		NOTE: The building process requires a working installation of a C++ and a FORTRAN compiler. Many solutions are available, but the recommended option is the GNU Compiler Collection `gcc` with the addition of `g++` and `gfortran`. Single-workstation multi-threaded parallelism is supported through _OpenMP_, while the multi-node code implementation further requires the use of parallel compilers complying with the _MPI_ standard (_OpenMPI_, _MPICH_).

	# Acknowledgments		# Acknowledgments

build/Makefile

+22 −4

Original line number	Original line	Diff line number	Diff line
	@@ -14,21 +14,29 @@ else
	NPTM_LIB=libnptm/libnptm.a		NPTM_LIB=libnptm/libnptm.a
	CXXFLAGSLIB=-static		CXXFLAGSLIB=-static
	endif # LIBMODE		endif # LIBMODE
	NP_LIBNPTM_SRCS=../src/libnptm/algebraic.cpp ../src/libnptm/clu_subs.cpp ../src/libnptm/Commons.cpp ../src/libnptm/Configuration.cpp ../src/libnptm/cublas_calls.cpp ../src/libnptm/file_io.cpp ../src/libnptm/inclu_subs.cpp ../src/libnptm/logging.cpp ../src/libnptm/lapack_calls.cpp ../src/libnptm/magma_calls.cpp ../src/libnptm/Parsers.cpp ../src/libnptm/sph_subs.cpp ../src/libnptm/tfrfme.cpp ../src/libnptm/tra_subs.cpp ../src/libnptm/TransitionMatrix.cpp ../src/libnptm/utils.cpp		NP_DOC_SRCS=../doc/src/config.dox
	NP_LIBNPTM_OBJS=../src/libnptm/algebraic.o ../src/libnptm/clu_subs.o ../src/libnptm/Commons.o ../src/libnptm/Configuration.o ../src/libnptm/cublas_calls.o ../src/libnptm/file_io.o ../src/libnptm/inclu_subs.o ../src/libnptm/logging.o ../src/libnptm/lapack_calls.o ../src/libnptm/magma_calls.o ../src/libnptm/Parsers.o ../src/libnptm/sph_subs.o ../src/libnptm/tfrfme.o ../src/libnptm/tra_subs.o ../src/libnptm/TransitionMatrix.o ../src/libnptm/utils.o		NP_LIBNPTM_SRCS=../src/libnptm/algebraic.cpp ../src/libnptm/clu_subs.cpp ../src/libnptm/Commons.cpp ../src/libnptm/Configuration.cpp ../src/libnptm/cublas_calls.cpp ../src/libnptm/file_io.cpp ../src/libnptm/inclu_subs.cpp ../src/libnptm/logging.cpp ../src/libnptm/lapack_calls.cpp ../src/libnptm/magma_calls.cpp ../src/libnptm/outputs.cpp ../src/libnptm/Parsers.cpp ../src/libnptm/sph_subs.cpp ../src/libnptm/tfrfme.cpp ../src/libnptm/tra_subs.cpp ../src/libnptm/TransitionMatrix.cpp ../src/libnptm/utils.cpp
			NP_LIBNPTM_OBJS=../src/libnptm/algebraic.o ../src/libnptm/clu_subs.o ../src/libnptm/Commons.o ../src/libnptm/Configuration.o ../src/libnptm/cublas_calls.o ../src/libnptm/file_io.o ../src/libnptm/inclu_subs.o ../src/libnptm/logging.o ../src/libnptm/lapack_calls.o ../src/libnptm/magma_calls.o ../src/libnptm/outputs.o ../src/libnptm/Parsers.o ../src/libnptm/sph_subs.o ../src/libnptm/tfrfme.o ../src/libnptm/tra_subs.o ../src/libnptm/TransitionMatrix.o ../src/libnptm/utils.o
			NP_CLUSTER_SRCS=../src/cluster/np_cluster.cpp ../src/cluster/cluster.cpp
	NP_CLUSTER_OBJS=../src/cluster/np_cluster.o ../src/cluster/cluster.o		NP_CLUSTER_OBJS=../src/cluster/np_cluster.o ../src/cluster/cluster.o
	NP_CLUSTER_BINS=cluster/np_cluster		NP_CLUSTER_BINS=cluster/np_cluster
			NP_INCLUSION_SRCS=../src/inclusion/np_inclusion.cpp ../src/inclusion/inclusion.cpp
	NP_INCLUSION_OBJS=../src/inclusion/np_inclusion.o ../src/inclusion/inclusion.o		NP_INCLUSION_OBJS=../src/inclusion/np_inclusion.o ../src/inclusion/inclusion.o
	NP_INCLUSION_BINS=inclusion/np_inclusion		NP_INCLUSION_BINS=inclusion/np_inclusion
			NP_SPHERE_SRCS=../src/sphere/np_sphere.cpp ../src/sphere/sphere.cpp
	NP_SPHERE_OBJS=../src/sphere/np_sphere.o ../src/sphere/sphere.o		NP_SPHERE_OBJS=../src/sphere/np_sphere.o ../src/sphere/sphere.o
	NP_SPHERE_BINS=sphere/np_sphere		NP_SPHERE_BINS=sphere/np_sphere
			NP_TRAPPING_SRCS=../src/trapping/np_trapping.cpp ../src/trapping/cfrfme.cpp ../src/trapping/clffft.cpp
	NP_TRAPPING_OBJS=../src/trapping/np_trapping.o ../src/trapping/cfrfme.o ../src/trapping/clffft.o		NP_TRAPPING_OBJS=../src/trapping/np_trapping.o ../src/trapping/cfrfme.o ../src/trapping/clffft.o
	NP_TRAPPING_BINS=trapping/np_trapping		NP_TRAPPING_BINS=trapping/np_trapping
	NP_TESTING_OBJS=../src/testing/test_ParticleDescriptor.o ../src/testing/test_TEDF.o ../src/testing/test_TTMS.o		NP_TESTING_OBJS=../src/testing/test_cluster_outputs.o ../src/testing/test_inclusion_outputs.o ../src/testing/test_sphere_outputs.o ../src/testing/test_ParticleDescriptor.o ../src/testing/test_TEDF.o ../src/testing/test_TTMS.o
	NP_TESTING_BINS=testing/test_ParticleDescriptor testing/test_TEDF testing/test_TTMS		NP_TESTING_BINS=testing/test_cluster_outputs testing/test_inclusion_outputs testing/test_sphere_outputs testing/test_ParticleDescriptor testing/test_TEDF testing/test_TTMS

	all: $(NPTM_LIB) $(FORTRAN_BINS) $(NP_CLUSTER_BINS) $(NP_INCLUSION_BINS) $(NP_SPHERE_BINS) $(NP_TRAPPING_BINS) $(NP_TESTING_BINS)		all: $(NPTM_LIB) $(FORTRAN_BINS) $(NP_CLUSTER_BINS) $(NP_INCLUSION_BINS) $(NP_SPHERE_BINS) $(NP_TRAPPING_BINS) $(NP_TESTING_BINS)

			docs: $(NP_LIBNPTM_SRCS) $(NP_CLUSTER_SRCS) $(NP_DOC_SRCS) $(NP_INCLUSION_SRCS) $(NP_SPHERE_SRCS) $(NP_TRAPPING_SRCS)
			cd ../doc/src; doxygen config.dox

	libnptm/libnptm.a: $(NP_LIBNPTM_OBJS)		libnptm/libnptm.a: $(NP_LIBNPTM_OBJS)
	$(AR) $(ARFLAGS) $@ $(NP_LIBNPTM_OBJS)		$(AR) $(ARFLAGS) $@ $(NP_LIBNPTM_OBJS)

	@@ -75,6 +83,15 @@ trapping/np_trapping: $(NPTM_LIB) $(NP_TRAPPING_OBJS)
	testing/test_ParticleDescriptor: $(NPTM_LIB) ../src/testing/test_ParticleDescriptor.o		testing/test_ParticleDescriptor: $(NPTM_LIB) ../src/testing/test_ParticleDescriptor.o
	$(CXX) $(CXXFLAGS) ../src/testing/test_ParticleDescriptor.o -o $@ $(CXXLDFLAGS)		$(CXX) $(CXXFLAGS) ../src/testing/test_ParticleDescriptor.o -o $@ $(CXXLDFLAGS)

			testing/test_cluster_outputs: $(NPTM_LIB) ../src/testing/test_cluster_outputs.o
			$(CXX) $(CXXFLAGS) ../src/testing/test_cluster_outputs.o -o $@ $(CXXLDFLAGS)

			testing/test_inclusion_outputs: $(NPTM_LIB) ../src/testing/test_inclusion_outputs.o
			$(CXX) $(CXXFLAGS) ../src/testing/test_inclusion_outputs.o -o $@ $(CXXLDFLAGS)

			testing/test_sphere_outputs: $(NPTM_LIB) ../src/testing/test_sphere_outputs.o
			$(CXX) $(CXXFLAGS) ../src/testing/test_sphere_outputs.o -o $@ $(CXXLDFLAGS)

	testing/test_TEDF: $(NPTM_LIB) ../src/testing/test_TEDF.o		testing/test_TEDF: $(NPTM_LIB) ../src/testing/test_TEDF.o
	$(CXX) $(CXXFLAGS) ../src/testing/test_TEDF.o -o $@ $(CXXLDFLAGS)		$(CXX) $(CXXFLAGS) ../src/testing/test_TEDF.o -o $@ $(CXXLDFLAGS)

	@@ -146,3 +163,4 @@ clean:
	wipe:		wipe:
	rm -rf $(FORTRAN_OBJS) $(NP_LIBNPTM_OBJS) $(NP_CLUSTER_OBJS) $(NP_INCLUSION_OBJS) $(NP_SPHERE_OBJS) $(NP_TRAPPING_OBJS) $(NP_TESTING_OBJS)		rm -rf $(FORTRAN_OBJS) $(NP_LIBNPTM_OBJS) $(NP_CLUSTER_OBJS) $(NP_INCLUSION_OBJS) $(NP_SPHERE_OBJS) $(NP_TRAPPING_OBJS) $(NP_TESTING_OBJS)
	rm -rf $(FORTRAN_BINS) libnptm/libnptm.a libnptm/libnptm.so $(NP_CLUSTER_BINS) $(NP_INCLUSION_BINS) $(NP_SPHERE_BINS) $(NP_TRAPPING_BINS) $(NP_TESTING_BINS)		rm -rf $(FORTRAN_BINS) libnptm/libnptm.a libnptm/libnptm.so $(NP_CLUSTER_BINS) $(NP_INCLUSION_BINS) $(NP_SPHERE_BINS) $(NP_TRAPPING_BINS) $(NP_TESTING_BINS)
			rm -rf ../doc/build

src/cluster/cluster.cpp

+873 −426

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src/cluster/np_cluster.cpp

+24 −17

Original line number	Original line	Diff line number	Diff line
	@@ -35,6 +35,12 @@
	#include <cstdio>		#include <cstdio>
	#include <string>		#include <string>

			#ifdef USE_MPI
			#ifndef MPI_VERSION
			#include <mpi.h>
			#endif
			#endif

	#ifndef INCLUDE_TYPES_H_		#ifndef INCLUDE_TYPES_H_
	#include "../include/types.h"		#include "../include/types.h"
	#endif		#endif
	@@ -64,8 +70,9 @@ extern void cluster(const string& config_file, const string& data_file, const st
	* \return result: `int` An exit code passed to the OS (0 for succesful execution).		* \return result: `int` An exit code passed to the OS (0 for succesful execution).
	*/		*/
	int main(int argc, char **argv) {		int main(int argc, char **argv) {
			int ierr = 0;
	#ifdef MPI_VERSION		#ifdef MPI_VERSION
	int ierr = MPI_Init(&argc, &argv);		ierr = MPI_Init(&argc, &argv);
	// create and initialise class with essential MPI data		// create and initialise class with essential MPI data
	mixMPI *mpidata = new mixMPI(MPI_COMM_WORLD);		mixMPI *mpidata = new mixMPI(MPI_COMM_WORLD);
	#else		#else
	@@ -85,5 +92,5 @@ int main(int argc, char **argv) {
	MPI_Finalize();		MPI_Finalize();
	#endif		#endif
	delete mpidata;		delete mpidata;
	return 0;		return ierr;
	}		}