Install

Two methods are available for this software install, form sources or a container images. The softwares are already available for LEGOS colleagues on summit2.

From sources

WARNING: the instalation from source can be very long due to library conflict, unlinked library path, etc. and may require adaptation to your own system. So if you are not confortable with source building on UNIX, please go directly to container images installation.

The sources are available on the IN2P3 GitLab and you will need to download the three following directories:

To better control on your install, we recommande to install all the dependencies on a specific directory local

ncpu=6 #the number of available CPUs to speedup the compilation
INSTALL_PATH=$PWD #where poc-solvers, tools and pocvip directory are
LOCAL_INSTALL_PATH=$PWD/local

mkdir $LOCAL_INSTALL_PATH
for dir in lib include bin ubin
do 
mkdir $LOCAL_INSTALL_PATH/$dir
done

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$LOCAL_INSTALL_PATH/lib
export CMAKE_LIBRARY_PATH=$LD_LIBRARY_PATH
export CMAKE_INCLUDE_PATH=$LOCAL_INSTALL_PATH/include

The poc-solvers will need several dependencies to be installed in local (comment the one you already have):

#Download the poc-solver librairies
wget http://www.netlib.org/blas/blas.tgz
wget http://www.netlib.org/lapack/lapack-3.5.0.tgz
wget http://www.netlib.org/scalapack/scalapack-2.0.2.tgz
wget http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.3.tar.gz
wget https://download.open-mpi.org/release/hwloc/v2.5/hwloc-2.5.0.tar.bz2

# Unfold the librairies sources
tar -xf blas.tgz
tar -xf lapack-3.5.0.tgz
tar -xf scalapack-2.0.2.tgz
tar -xf SuiteSparse-4.4.3.tar.gz
tar -xf hwloc-2.5.0.tar.bz2

### COMPILATION
# BLAS
cd BLAS-3.12.0
make
cp -v *.a $LOCAL_INSTALL_PATH/lib/libblas.a
cd ..

# LAPACK
cd lapack-3.5.0
sed -re "s|= (-O)|= -g \1|;s|-O2|-O3|;\
s|^( *BLASLIB *= *).*|\1$LOCAL_INSTALL_PATH/lib/libblas.a|" make.inc.example >make.inc
make
make lapackelib
cp -v liblapack.a $LOCAL_INSTALL_PATH/lib
cd ..

# SCALAPACK
cd scalapack-2.0.2
sed -re "s|= (-O)|= -g \1|" SLmake.inc.example >SLmake.inc
make
cp -v libscalapack.a $LOCAL_INSTALL_PATH/lib
cd ..

# SuiteSparse
cd SuiteSparse/SuiteSparse_config
sed -re "s|^( *INSTALL_[^ ]+ *= *).*/([^/]+$)|\1$LOCAL_INSTALL_PATH/\2|;\
s|^( *(LAPACK\|BLAS) *= *)|\1-L$LOCAL_INSTALL_PATH/lib |;\
/^\s*#/! s| -O| -g -O|#;" \
SuiteSparse_config_linux.mk >SuiteSparse_config.mk
cd ..
make -j$ncpu library
make install
cd ..

# HWLOC
cd hwloc-2.5.0
./configure --prefix=$LOCAL_INSTALL_PATH
make -j$ncpu
make install
cd ..

Now install poc-solvers :

cd poc-solvers
mkdir cmade-mpi
cd  cmade-mpi
cmake ../src -DLOCAL_INSTALL=$LOCAL_INSTALL_PATH/ -DHIPS=NO -DMUMPS=NO -DPASTIX_5=NO -DPASTIX_6=NO -DPETSC=NO -DUMFPACK=NO -DARPACK=NO -DPARPACK=NO
make -j$ncpu install
cd ../..

The tools will need several dependencies to be installed in local (comment the one you already have):

#Download the tools librairies
wget https://sqlite.org/2024/sqlite-autoconf-3460100.tar.gz
wget http://download.osgeo.org/proj/proj-6.3.1.tar.gz
wget http://ftpmirror.gnu.org/gsl/gsl-1.16.tar.gz
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.6/src/hdf5-1.10.6.tar.bz2
wget https://downloads.unidata.ucar.edu/netcdf-c/4.9.2/netcdf-c-4.9.2.tar.gz
wget https://confluence.ecmwf.int/download/attachments/45757960/eccodes-2.27.1-Source.tar.gz
wget https://github.com/OSGeo/gdal/releases/download/v3.7.3/gdal-3.7.3.tar.gz
wget http://download.osgeo.org/geotiff/libgeotiff/libgeotiff-1.6.0.tar.gz
wget https://github.com/LASzip/LASzip/releases/download/v2.2.0/laszip-src-2.2.0.tar.gz
wget http://download.osgeo.org/liblas/libLAS-1.8.1.tar.bz2


# Unfold the librairies sources
tar -xf sqlite-autoconf-3460100.tar.gz
tar -xf proj-6.3.1.tar.gz
tar -xf gsl-1.16.tar.gz
tar -xf hdf5-1.10.6/src/hdf5-1.10.6.tar.bz2
tar -xf netcdf-c-4.9.2.tar.gz
tar -xf eccodes-2.27.1-Source.tar.gz
tar -xf gdal-3.7.3.tar.gz
tar -xf libgeotiff-1.6.0.tar.gz
tar -xf laszip-src-2.2.0.tar.gz
tar -xf libLAS-1.8.1.tar.bz2

### COMPILATION
# SQLITE3
cd sqlite-autoconf-3460100
./configure --prefix=$LOCAL_INSTALL_PATH
make -j$ncpu
make install
cd ..

#PROJ (need sqlite3)
cd proj-6.3.1
./configure --prefix=$LOCAL_INSTALL_PATH
make -j$ncpu
make install
cd ..

#GSL
cd gsl-1.16
./configure --prefix=$LOCAL_INSTALL_PATH
make -j$ncpu
make install
cd ..

#ECCODES
cd eccodes-2.27.1-Source
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=$LOCAL_INSTALL_PATH \
    -DENABLE_{PYTHON,FORTRAN,NETCDF,JPG,AEC}=OFF
make -j$ncpu
make install
cp -v lib/libgrib_api.so $LOCAL_INSTALL_PATH/lib/
cp -v ../src/grib_api.h $LOCAL_INSTALL_PATH/include/
cd ../../

# GDAL (need proj)
cd gdal-3.7.3 #### WARNING Highly buggy version !!
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=$LOCAL_INSTALL_PATH
make -j$ncpu
make install
cd ..
# ln -s $CONDA_PREFIX/lib/libgdal.so $LOCAL_INSTALL_PATH/lib/libgdal.so

#libGEOTIFF
cd libgeotiff-1.6.0
./configure --prefix=$LOCAL_INSTALL_PATH
make -j$ncpu
make install
cd ..
# ln -s $CONDA_PREFIX/lib/libgeotiff.so $LOCAL_INSTALL_PATH/lib/libgeotiff.so

#LASzip
cd laszip-src-2.2.0
./configure --prefix=$LOCAL_INSTALL_PATH
make -j$ncpu
make install
cd ..

# libLAS (need libgeotiff)
cd libLAS-1.8.1
mkdir build
cd build
cmake .. -DGEOTIFF_INCLUDE_DIR=$LOCAL_INSTALL_PATH/include -DCMAKE_INSTALL_PREFIX=$LOCAL_INSTALL_PATH
make -j$ncpu
make install
cd ..

Now install poc-solvers :

cd tools
autoreconf -si
# WARNING about pkg-config error during the configuration
# if not found, try autoreconf -si -I/usr/share/aclocal
# otherwise add pkg.m4 into $LOCAL_INSTALL_PATH/share/aclocal/ then run
# autoreconf -si -I$LOCAL_INSTALL_PATH/share/aclocal


#FOR MPI CALCULATION (cluster only)
export CXX='mpicxx -std=gnu++11'
rm -r parallel
mkdir parallel
cd parallel
../configure --with-parallel --prefix=$LOCAL_INSTALL_PATH POCSOLVERBUILDDIR=$INSTALL_PATH/poc-solvers/cmade-mpi 

### for all the command (11Go)
make -j$ncpu -k

# ### for custom install
# make -j$ncpu tools-config 
# for name in vertical-eigenmodes comodo-detidor showarg concatenator
# do
# make -j$ncpu $name
# # rm $LOCAL_INSTALL_PATH/bin/$name
# # ln -s $PWD/src/$name $LOCAL_INSTALL_PATH/bin/$name
# done

#verifier que le fichier ./src/tools-config exist

#installation:
exe_path=$PWD/src
cp -v src/*.a $LOCAL_INSTALL_PATH/lib/
cp -s $exe_path/* $LOCAL_INSTALL_PATH/ubin/
rm $LOCAL_INSTALL_PATH/ubin/*.*
cd ../../


#Cleaning to save some storage
rm src/*.*

The POCViP will need several dependencies to be installed in local (comment the one you already have):

Now install POCViP :

cd pocvip

autoreconf -si
# WARNING about pkg-config error during the configuration
# if not found, try autoreconf -si -I/usr/share/aclocal
# otherwise add pkg.m4 into $LOCAL_INSTALL_PATH/share/aclocal/ then run
# autoreconf -si -I$LOCAL_INSTALL_PATH/share/aclocal

rm -r fast
mkdir fast
cd fast

#FOR STANDARD CALCULATION (PC)
../configure TOOLSCONFIG=$INSTALL_PATH/ubin/tools-config

make -j $ncpu

#installation:
cp -s $PWD/pocvip $LOCAL_INSTALL_PATH/ubin/

From containers images

Docker and Apptainer/Singularity images are available upon request to Simon Barbot. A proper upload will be made available in the future.

Running containers require specific steps and privileges, so make sure you contacted the user service maintaining your computer/cluster, get the privilege to run containers and get the documentation of your cluster eventually.

WARNING: A container is mounting the working directory (where you run the job) so you cannot access to the files that are in upper directories. Make sure to run a command pointing at files that are in this current directory or below.

Install and command use with a Docker image

Apptainer/Singularity image does not need to be added to your system before using it (but may need to be in a dedicated directory for clusters). Copy the image into your system:

#Unpack and load image into your system
VERSION=5803
tar -xvf sirocco-tools.$VERSION.docker.tar.gz
docker image load -i sirocco-tools.$VERSION.docker.tar
rm sirocco-tools.$VERSION.docker.tar

#List the available images
docker images

Then, to use the command from SIROCCO tools (anywhere):

docker run -e LOCAL_UID=$(id -u) -e LOCAL_GID=$(id -g) <image_name:$VERSION> <command> <args>

It will ask to run the from the image <image_name:version>, mounting your directory from where you run this job.

Install and command use with a Apptainer/Singularity image

Apptainer/Singularity image does not need to be added to your system before using it (but may need to be in a dedicated directory for clusters). Copy the image into your system:

containerDIR=/your/conteneurs/directory/
VERSION=5803
mv sirocco-tools.$VERSION.sif $containerDIR/

Then, to use the command from SIROCCO tools (anywhere):

singularity run -i --containall --env LOCAL_UID=$(id -u) --env LOCAL_GID=$(id -g) --bind $(pwd):/mnt $containerDIR/sirocco-tools.$VERSION.sif <command> <args>

It will ask to run the from the container, mounting your directory from where you run this job.

On summit2 (LEGOS cluster)

The last version of the software is available for direct use on this cluster with the following commands (you can add them to your .bash_profile):

module use /ecola/share/modulefiles/
module load sirocco-gnu/latest