Merge auto-configurable master into parallel angles

build/include

build/aclocal.m4

build/autom4te.cache

build/config.*

build/cluster/*

build/error.log

build/libtool

build/Makefile

build/sphere/*

build/testing/*

build/trapping/*

build/libnptm/*

containers/singularity/*.sif

doc/build/*

src/*/objects/*

src/*/dynobjects/*

src/libnptm/.libs

src/libnptm/*.lo

src/*/.deps

src/*/.dirstamp

src/*/*.o

 No newline at end of file

   allow_failure: true

   artifacts:

      paths:

         - build/cluster/*

         - build/sphere/*

         - build/testing/*

         - build/trapping/*

         - build/libnptm/*

         - build_*

      exclude:

         - ".git*"

         - ".git/**/*"

      - echo $CI_COMMIT_BRANCH

      - echo "Getting system info ..."

      - cat /etc/os-release

      - cd src

      - 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..."

      - make clean && BUILDDIR=$PWD/../build_gnu12 CXX=g++-12 FC=gfortran-12 make -j

      - echo "Running make with flang version 16 and clang version 13..."

      - 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

      - echo "Running make with flang version 16 and clang version 14..."

      - 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

      - echo "Running make with flang version 16 and clang version 15..."

      - 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

      - cd ..

      - rm -rf build_gnu11

      - mkdir build_gnu12

      - cd build_gnu12

      - cp -r ../build/* .

      - CXX=g++-12 F77=gfortran-12 ./configure

      - 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..."

      - 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..."

      - 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..."

      - 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

      - echo "Running make with default MPI compilers"

      - make clean && BUILDDIR=$PWD/../build_mpi CXX=mpicxx FC=mpif90 USE_MPI=1 make -j

      - cd ..

      - rm -rf build_ifort_icpx

      - 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:

   stage: build

      - echo $CI_COMMIT_BRANCH

      - echo "Getting system info ..."

      - cat /etc/os-release

      - cd src

      - echo "Running make with default compilers..."

      - make clean && make -j

      - make docs -j && make -C ../doc/build/latex -j

      - cd build

      - echo "Configuring with default compilers (MAGMA disabled)..."

      - ./configure --without-magma

      - 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:

   stage: run

      - cd ../cluster

      - echo "Running np_cluster"

      - chmod +x np_cluster

      - ./np_cluster

      - OMP_NUM_THREADS=1 ./np_cluster

testing_stage:

   stage: test

      - cd build/sphere

      - export FFILE=../../test_data/sphere/OSPH

      - 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"

      - ../testing/test_TEDF ../../test_data/sphere/DEDFB c_TEDF c_TEDF.hd5

      - cd ../cluster

      - echo "Comparing output of CLUSTER"

      - 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"

      - ./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"

      - 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"

      - ../testing/test_TEDF ../../test_data/cluster/DEDFB_24 c_TEDF c_TEDF.hd5

      - echo "Checking consistency among legacy and HDF5 TM files"

                                Apache License

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                        http://www.apache.org/licenses/

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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:

# License

- 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*).

   Copyright 2004 INAF - Osservatorio Astronomico di Cagliari

# License

   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

   Copyright (C) 2024   INAF - Osservatorio Astronomico di Cagliari

       http://www.apache.org/licenses/LICENSE-2.0

   This program is free software: you can redistribute it and/or modify

   it under the terms of the GNU General Public License as published by

   the Free Software Foundation, either version 3 of the License, or

   (at your option) any later version.

   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.

   This program is distributed in the hope that it will be useful,

   but WITHOUT ANY WARRANTY; without even the implied warranty of

   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

   GNU General Public License for more details.

   A copy of the GNU General Public License is distributed along with

   this program in the COPYING file. If not, see: <https://www.gnu.org/licenses/>.