Librairies installées¶
CUDA¶
PETSc¶
VTK¶
HDF5¶
CGNS¶
Autres librairies¶
MMG (remeshing tool)¶
Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries:- the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation and generation of a triangulation from a set of points or from given boundary edges
- the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation and isovalue discretization
- the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh and implicit domain meshing
- see https://www.mmgtools.org/
- Pour l’utiliser via les modules :
module load module compilers/gcc/10.2 compilers/intel/compilers_2020u2 mpi/hpempi-1.6/mpt/2.22 lib/vtk/7.1.1 lib/scotch/6.0.3 lib/mmg/5.5.2- Usage (voir https://www.mmgtools.org/mmg-remesher-try-mmg/mmg-remesher-tutorials) :
[homer@vision ~]$ mmgs_O3 -h -- MMGS, Release 5.5.2 (Nov. 17, 2020) Copyright (c) Bdx INP/CNRS/Inria/UPMC, 2004- Nov 3 2021 14:40:36 Usage: mmgs_O3 [-v [n]] [opts..] filein [fileout] ** Generic options -h Print this message -v [n] Tune level of verbosity, [-1..10] -m [n] Set maximal memory size to n Mbytes -d Turn on debug mode -val Print the default parameters values -default Save a local parameters file for default parameters values ** File specifications -in file input triangulation -out file output triangulation -sol file load solution or metric file -met file load metric file ** Mode specifications (mesh adaptation by default) -ls val create mesh of isovalue val (0 if no argument provided) ** Parameters -A enable anisotropy (without metric file). -ar val angle detection -nr no angle detection -hausd val control Hausdorff distance -hgrad val control gradation -hmax val maximal mesh size -hmin val minimal mesh size -hsiz val constant mesh size -keep-ref preserve initial domain references in level-set mode. -rn [n] Turn on or off the renumbering using SCOTCH [0/1] -noinsert no point insertion/deletion -nomove no point relocation -noswap no edge or face flipping -nreg normal regul. -nsd val save the subdomain number val (0==all subdomain) -optim mesh optimization ** Parameters for advanced users -nosizreq disable setting of required edge sizes over required vertices. -hgradreq val control gradation from required entities toward others ELAPSED TIME 0.003s
Mesh partitionning metis/scotch¶
- Le répertoire d’installation de la librairie METIS :
/softs/lib/metis/5.1.0/
Pour l’utiliser via les modules :
module load lib/metis/5.1.0
- Le répertoire d’installation de la librairie SCOTCH (et PTSCOTCH) :
/softs/lib/scotch/6.0.3/mpt
Pour l’utiliser via les modules :
module load/scotch/6.0.3
Ces librairies ont été compilées avec l’environnement Intel 2020.
Boost¶
- A c++ framework
- see https://www.boost.org/doc/libs/1_75_0/libs/libraries.htm
- Module Usage
[homer@vision codes]$ module av lib/boost/
--------------------------------------- /zfs/softs/modulefiles ---------------------------------------
lib/boost/1.70_gcc4.8 lib/boost/1.70_gcc4.8_anac3.7 lib/boost/1.70_gcc10 lib/boost/1.70_intel20
[homer@vision codes]$ module help lib/boost/1.70_gcc4.8_anac3.7
-------------------------------------------------------------------
Module Specific Help for /zfs/softs/modulefiles/lib/boost/1.70_gcc4.8_anac3.7:
modules - loads the boost library environment
This adds /softs/lib/boost/1.70/gnu4.8_anac3.7/* to several of the
environment variables.
Version Gnu Compiler 4.8 / python 3.7 interface
. the boost mpi is linked to MPT (HPE MPI)
Version 1.70
Eigen¶
- A c++ library (header only)
- see https://eigen.tuxfamily.org/dox/index.html
- Compile information
Enabled backends: Boost.Multiprecision, MPFR C++, fftw, Default order: Column-major Maximal matrix/vector size: 320 AVX: ON AVX512: ON C++11: OFF SYCL: OFF CUDA: ON (using nvcc) CXX: /usr/bin/c++ CXX_VERSION: c++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) CXX_FLAGS: -march=native -mavx2 -std=c++03 -pedantic -Wall -Wextra -Wundef -Wcast-align -Wchar-subscripts -Wnon-virtual-dtor -Wunused-local-typedefs -Wpointer-arith -Wwrite-strings -Wformat-security -Wlogical-op -Wdouble-promotion -Wno-psabi -Wno-variadic-macros -Wno-long-long -fno-check-new -fno-common -fstrict-aliasing -ansi -mavx -mavx512f -fabi-version=6 -DEIGEN_ENABLE_AVX512
- Module Usage
[homer@vision codes]$ module show lib/eigen/
-------------------------------------------------------------------
/zfs/softs/modulefiles/lib/eigen/3.3.8:
module-whatis {loads the Eigen3 environment}
setenv EIGEN3_INCLUDE_DIR /zfs/softs/lib/eigen/3.3.8/include/eigen3
prepend-path INCLUDE_PATH /zfs/softs/lib/eigen/3.3.8/include
-------------------------------------------------------------------
[homer@vision codes]$ module help lib/eigen/
-------------------------------------------------------------------
Module Specific Help for /zfs/softs/modulefiles/lib/eigen/3.3.8:
modules - loads the Eigen3 environment,
This adds /zfs/softs/lib/eigen/3.3.8/* to several of the
environment variables.
Enabled backends: Boost.Multiprecision, MPFR C++, fftw, CUDA
Version 3.3.8
-------------------------------------------------------------------
Armadillo¶
- A c++ library for linear algebra and scientific computing, aiming towards a good balance between speed and ease of use.
It's useful for algorithm development directly in C++,and/or quick conversion of research code into production environments.
It has high-level syntax and functionality which is deliberately similar to Matlab. - See http://arma.sourceforge.net/docs.html
- Module Usage
[homer@vision codes]$ module show lib/armadillo
-------------------------------------------------------------------
/zfs/softs/modulefiles/lib/armadillo/10.3.0:
module-whatis {loads the Armadillo environment}
setenv ARMA_INCLUDE_DIR /zfs/softs/lib/armadillo/10.3.0/include
prepend-path INCLUDE_PATH /zfs/softs/lib/armadillo/10.3.0/include
prepend-path LD_LIBRARY_PATH /zfs/softs/lib/armadillo/10.3.0/lib64
setenv ARMA_DIR /zfs/softs/lib/armadillo/10.3.0/share/Armadillo/CMake/
-------------------------------------------------------------------
[homer@vision codes]$ module help lib/armadillo
-------------------------------------------------------------------
Module Specific Help for /zfs/softs/modulefiles/lib/armadillo/10.3.0:
modules - loads the Armadillo c++ lib environment,
This adds /zfs/softs/lib/armadillo/10.3.0/* to several of the
environment variables.
compilation ex :
g++ prog.cpp -o prog -std=c++11 -O2 -larmadillo
Enabled backends: OpenBLAS, MKL
Version 10.3.0
-------------------------------------------------------------------
mpi4py¶
fftw¶
gperftools¶
(originally Google Performance Tools)
OVERVIEW¶
gperftools is a collection of a high-performance multi-threaded
malloc() implementation, plus some pretty nifty performance analysis
tools.
gperftools is distributed under the terms of the BSD License. Join our
mailing list at gperftools@googlegroups.com for updates:
https://groups.google.com/forum/#!forum/gperftools
gperftools was original home for pprof program. But do note that
original pprof (which is still included with gperftools) is now
deprecated in favor of Go version at https://github.com/google/pprof
see https://github.com/gperftools/gperftools
- Installed in
/softs/tools/gperftools/
Kokkos¶
Overview¶
Kokkos Core implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms. For that purpose it provides abstractions for both parallel execution of code and data management. Kokkos is designed to target complex node architectures with N-level memory hierarchies and multiple types of execution resources. It currently can use CUDA, HPX, OpenMP and Pthreads as backend programming models with several other backends in development.
Reference¶
Usage¶
- Compiled from github repository
- OpenMP only version (3.4)
[gueguenm@vision gperftools]$ module help lib/kokkos/3.4.0/openmp ------------------------------------------------------------------- Module Specific Help for /zfs/softs/modulefiles/lib/kokkos/3.4.0/openmp: loads the Kokkos parallel environment optimized OPENMP/libnuma version, compiled with gcc10 see https://github.com/kokkos/kokkos usage : module load compilers/gcc/10.2 lib/kokkos/3.4.0/openmp
- Cuda/OpenMP version (3.4)
[gueguenm@vision gperftools]$ module help lib/kokkos/3.4.0/cuda_omp ------------------------------------------------------------------- Module Specific Help for /zfs/softs/modulefiles/lib/kokkos/3.4.0/cuda_omp: loads the Kokkos parallel environment optimized CUDA/OPENMP version, compiled with gcc10 see https://github.com/kokkos/kokkos usage : module load cuda/11.1 compilers/gcc/10.2 lib/kokkos/3.4.0/cuda