Update script development branch to auto-configurable master (1bf81234) · Commits · Giacomo Mulas / NP_TMcode

.gitignore

+12 −3

Original line number	Original line	Diff line number	Diff line
	build/include		build/aclocal.m4
			build/autom4te.cache
			build/config.*
	build/cluster/*		build/cluster/*
			build/error.log
			build/libtool
			build/Makefile
	build/sphere/*		build/sphere/*
	build/testing/*		build/testing/*
	build/trapping/*		build/trapping/*
	build/libnptm/*		build/libnptm/*
			containers/singularity/*.sif
	doc/build/*		doc/build/*
	src//objects/		src/libnptm/.libs
	src//dynobjects/		src/libnptm/*.lo
			src/*/.deps
			src/*/.dirstamp
			src//.o
			No newline at end of file

.gitlab-ci.yml

+86 −28

Original line number	Original line	Diff line number	Diff line
	@@ -29,11 +29,7 @@ compatibility_stage:
	allow_failure: true		allow_failure: true
	artifacts:		artifacts:
	paths:		paths:
	- build/cluster/*		- build_*
	- build/sphere/*
	- build/testing/*
	- build/trapping/*
	- build/libnptm/*
	exclude:		exclude:
	- ".git*"		- ".git*"
	- ".git/*/"		- ".git/*/"
	@@ -46,25 +42,80 @@ compatibility_stage:
	- echo $CI_COMMIT_BRANCH		- echo $CI_COMMIT_BRANCH
	- echo "Getting system info ..."		- echo "Getting system info ..."
	- cat /etc/os-release		- cat /etc/os-release
	- cd src
	- echo "Running make with gnu compilers version 11..."		- echo "Running make with gnu compilers version 11..."
	- make clean && BUILDDIR=$PWD/../build_gnu11 CXX=g++-11 FC=gfortran-11 make -j		- mkdir build_gnu11
			- cd build_gnu11
			- cp -r ../build/* .
			- CXX=g++-11 F77=gfortran-11 ./configure
			- make clean
			- make -j
	- echo "Running make with gnu compilers version 12..."		- echo "Running make with gnu compilers version 12..."
	- make clean && BUILDDIR=$PWD/../build_gnu12 CXX=g++-12 FC=gfortran-12 make -j		- cd ..
	- echo "Running make with flang version 16 and clang version 13..."		- rm -rf build_gnu11
	- make clean && BUILDDIR=$PWD/../build_clang13-flang16 CXX="clang++-13 -stdlib=libstdc++ -I/usr/include/c++/12 -I/usr/include/x86_64-linux-gnu/c++/12" FC=flang-new-16 FCFLAGS=-O3 LDFLAGS="-L/usr/lib/llvm-16/lib -L/usr/lib/gcc/x86_64-linux-gnu/12" make -j		- mkdir build_gnu12
	- echo "Running make with flang version 16 and clang version 14..."		- cd build_gnu12
	- make clean && BUILDDIR=$PWD/../build_clang14-flang16 CXX="clang++-14 -stdlib=libstdc++ -I/usr/include/c++/12 -I/usr/include/x86_64-linux-gnu/c++/12" FC=flang-new-16 FCFLAGS=-O3 LDFLAGS="-L/usr/lib/llvm-16/lib -L/usr/lib/gcc/x86_64-linux-gnu/12" make -j		- cp -r ../build/* .
	- echo "Running make with flang version 16 and clang version 15..."		- CXX=g++-12 F77=gfortran-12 ./configure
	- make clean && BUILDDIR=$PWD/../build_clang15-flang16 CXX="clang++-15 -stdlib=libstdc++ -I/usr/include/c++/12 -I/usr/include/x86_64-linux-gnu/c++/12" FC=flang-new-16 FCFLAGS=-O3 LDFLAGS="-L/usr/lib/llvm-16/lib -L/usr/lib/gcc/x86_64-linux-gnu/12" make -j		- make clean
			- make -j
			- echo "Running make with gnu compilers version 13..."
			- cd ..
			- rm -rf build_gnu12
			- mkdir build_gnu13
			- cd build_gnu13
			- cp -r ../build/* .
			- CXX=g++-13 F77=gfortran-13 ./configure
			- make clean
			- make -j
			- echo "Running make with gnu compilers version 14..."
			- cd ..
			- rm -rf build_gnu13
			- mkdir build_gnu14
			- cd build_gnu14
			- cp -r ../build/* .
			- CXX=g++-14 F77=gfortran-14 ./configure
			- make clean
			- make -j
	- echo "Running make with flang version 16 and clang version 16..."		- echo "Running make with flang version 16 and clang version 16..."
	- make clean && BUILDDIR=$PWD/../build_clang16-flang16 CXX="clang++-16 -stdlib=libstdc++ -I/usr/include/c++/12 -I/usr/include/x86_64-linux-gnu/c++/12" FC=flang-new-16 FCFLAGS=-O3 LDFLAGS="-L/usr/lib/llvm-16/lib -L/usr/lib/gcc/x86_64-linux-gnu/12" make -j		- cd ..
			- rm -rf build_gnu14
			- mkdir build_clang16
			- cd build_clang16
			- cp -r ../build/* .
			- CXX=clang++-16 F77=flang-new-16 ./configure --with-fflags="-O3" --with-include="-I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13" --with-ldflags="-L/usr/lib/llvm-16/lib -L/usr/lib/gcc/x86_64-linux-gnu/13" --disable-openmp
			- make clean
			- make -j
			- echo "Running make with flang version 17 and clang version 17..."
			- cd ..
			- rm -rf build_clang16
			- mkdir build_clang17
			- cd build_clang17
			- cp -r ../build/* .
			- CXX=clang++-17 F77=flang-new-17 ./configure --with-fflags="-O3" --with-include="-I/usr/include/c++/13 -I/usr/include/x86_64-linux-gnu/c++/13" --with-ldflags="-L/usr/lib/llvm-17/lib -L/usr/lib/gcc/x86_64-linux-gnu/13" --disable-openmp
			- make clean
			- make -j
	- echo "Running make with Intel ifort and Intel icpx..."		- echo "Running make with Intel ifort and Intel icpx..."
	- make clean && LD_LIBRARY_PATH=/opt/intel/oneapi/compiler/2024.1/lib PATH=/opt/intel/oneapi/compiler/2024.1/bin:$PATH BUILDDIR=$PWD/../build_ifort-icpx CXX=icpx FC=ifort FCFLAGS="-O3 -diag-disable=10448" make -j		- cd ..
			- rm -rf build_clang17
			- mkdir build_ifort_icpx
			- cd build_ifort_icpx
			- cp -r ../build/* .
			- export LD_LIBRARY_PATH=/opt/intel/oneapi/compiler/2024.2/lib
			- export PATH=/opt/intel/oneapi/compiler/2024.2/bin:$PATH
			- CXX=icpx F77=ifort ./configure --with-fflags="-O3 -diag-disable=10448" --disable-openmp
			- make clean
			- make -j
	- echo "Running make with Intel ifx and Intel icpx..."		- echo "Running make with Intel ifx and Intel icpx..."
	- make clean && LD_LIBRARY_PATH=/opt/intel/oneapi/compiler/2024.1/lib PATH=/opt/intel/oneapi/compiler/2024.1/bin:$PATH BUILDDIR=$PWD/../build_ifx-icpx CXX=icpx FC=ifx FCFLAGS=-O3 make -j		- cd ..
	- echo "Running make with default MPI compilers"		- rm -rf build_ifort_icpx
	- make clean && BUILDDIR=$PWD/../build_mpi CXX=mpicxx FC=mpif90 USE_MPI=1 make -j		- mkdir build_ifx_icpx
			- cd build_ifx_icpx
			- cp -r ../build/* .
			- export LD_LIBRARY_PATH=/opt/intel/oneapi/compiler/2024.2/lib
			- export PATH=/opt/intel/oneapi/compiler/2024.2/bin:$PATH
			- CXX=icpx F77=ifx ./configure --with-fflags="-O3" --disable-openmp
			- make clean
			- make -j

	building_stage:		building_stage:
	stage: build		stage: build
	@@ -90,10 +141,17 @@ building_stage:
	- echo $CI_COMMIT_BRANCH		- echo $CI_COMMIT_BRANCH
	- echo "Getting system info ..."		- echo "Getting system info ..."
	- cat /etc/os-release		- cat /etc/os-release
	- cd src		- cd build
	- echo "Running make with default compilers..."		- echo "Configuring with default compilers (MAGMA disabled)..."
	- make clean && make -j		- ./configure --without-magma
	- make docs -j && make -C ../doc/build/latex -j		- make clean
			- echo "Building the default configuration..."
			- make -j
			- echo "Building the documentation..."
			- cd ../doc/src
			- doxygen config.dox
			- cd ../build/latex
			- make

	running_stage:		running_stage:
	stage: run		stage: run
	@@ -125,7 +183,7 @@ running_stage:
	- cd ../cluster		- cd ../cluster
	- echo "Running np_cluster"		- echo "Running np_cluster"
	- chmod +x np_cluster		- chmod +x np_cluster
	- ./np_cluster		- OMP_NUM_THREADS=1 ./np_cluster

	testing_stage:		testing_stage:
	stage: test		stage: test
	@@ -154,18 +212,18 @@ testing_stage:
	- cd build/sphere		- cd build/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 --ffile=$FFILE --cfile=c_OSPH --html		- python3 ../../src/scripts/pycompare.py --no-progress --ffile=$FFILE --cfile=c_OSPH --html
	- echo "Checking consistency among legacy and HDF5 configuration files"		- echo "Checking consistency among legacy and HDF5 configuration files"
	- ../testing/test_TEDF ../../test_data/sphere/DEDFB c_TEDF c_TEDF.hd5		- ../testing/test_TEDF ../../test_data/sphere/DEDFB c_TEDF c_TEDF.hd5
	- 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 --ffile=$FFILE --cfile=c_OCLU --html		- python3 ../../src/scripts/pycompare.py --no-progress --ffile=$FFILE --cfile=c_OCLU --html
	- echo "Testing cluster with 24 spheres"		- echo "Testing cluster with 24 spheres"
	- ./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 --ffile=$FFILE --cfile=c_OCLU --html		- python3 ../../src/scripts/pycompare.py --no-progress --ffile=$FFILE --cfile=c_OCLU --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"

README.md

+6 −1

Original line number	Original line	Diff line number	Diff line
	@@ -6,7 +6,12 @@ The aim of the project, funded by PNRR-CNS, is to refactor the original, very ol

	The current implementation offers a set of elementary tests to check that the original FORTRAN code can be compiled and executed on a limited set of pre-defined input data. The functionality of this initial stage can be verified by cloning the gitLab repository on a local machine and building the binaries from the `src` folder.		The current implementation offers a set of elementary tests to check that the original FORTRAN code can be compiled and executed on a limited set of pre-defined input data. The functionality of this initial stage can be verified by cloning the gitLab repository on a local machine and building the binaries from the `src` folder.

	NOTE: The building process requires a working installation of the GNU Compiler Collection (`gcc`), of the GNU FORTRAN compiler (`gfortran`) and of the GNU `make` builder.		Distributing the code and its sources is possible under the terms of the GNU GPLv3 license (see License below). Use of this code and of any derived implementation should credit the original authors. Scientific publications should do so by citing the following references:

			- 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

			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).

	# License		# License

build/Makefile.am

0 → 100644

+15 −0

Original line number	Original line	Diff line number	Diff line
			LDADD=libnptm/libnptm.la -L/usr/lib64 ${USER_LDFLAGS} ${HDF5_LDFLAGS} ${LAPACKLDFLAGS} ${MAGMALDFLAGS}
			lib_LTLIBRARIES=libnptm/libnptm.la
			libnptm_libnptm_la_SOURCES=../src/libnptm/algebraic.cpp ../src/libnptm/clu_subs.cpp ../src/libnptm/Commons.cpp ../src/libnptm/Configuration.cpp ../src/libnptm/file_io.cpp ../src/libnptm/lapack_calls.cpp ../src/libnptm/logging.cpp ../src/libnptm/magma_calls.cpp ../src/libnptm/Parsers.cpp ../src/libnptm/sph_subs.cpp ../src/libnptm/tfrfme.cpp ../src/libnptm/TransitionMatrix.cpp ../src/libnptm/tra_subs.cpp ../src/libnptm/types.cpp
			bin_PROGRAMS=cluster/edfb_clu cluster/clu cluster/np_cluster sphere/edfb_sph sphere/sph sphere/np_sphere trapping/frfme trapping/lffft trapping/np_trapping testing/test_TEDF testing/test_TTMS
			cluster_edfb_clu_SOURCES=../src/cluster/edfb_clu.f
			cluster_clu_SOURCES=../src/cluster/clu.f
			cluster_np_cluster_SOURCES=../src/cluster/np_cluster.cpp ../src/cluster/cluster.cpp
			sphere_edfb_sph_SOURCES=../src/sphere/edfb_sph.f
			sphere_sph_SOURCES=../src/sphere/sph.f
			sphere_np_sphere_SOURCES=../src/sphere/np_sphere.cpp ../src/sphere/sphere.cpp
			trapping_frfme_SOURCES=../src/trapping/frfme.f
			trapping_lffft_SOURCES=../src/trapping/lffft.f
			trapping_np_trapping_SOURCES=../src/trapping/np_trapping.cpp ../src/trapping/cfrfme.cpp ../src/trapping/clffft.cpp
			testing_test_TEDF_SOURCES=../src/testing/test_TEDF.cpp
			testing_test_TTMS_SOURCES=../src/testing/test_TTMS.cpp

build/Makefile.in

0 → 100644

+1327 −0

File added.

Preview size limit exceeded, changes collapsed.