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humagne.yaml
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humagne.yaml
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axis:
- architecture
- compiler
- mpi
- lapack
- python
combinations:
# Core is the matrix that is used to build software with system compilers
core:
architecture: 'x86_E5v4_Mellanox:x86_S6g1_Mellanox'
compiler: '[email protected]'
mpi: None
lapack: None
python: None
# GNU is the matrix used to build software that runs on CPUs
# with a FOSS stack - stable version
gnu-stable:
architecture: 'x86_E5v4_Mellanox:x86_S6g1_Mellanox'
compiler: '[email protected]'
mpi: '[email protected] fabrics=mrail process_managers=slurm'
lapack: '[email protected]:[email protected] threads=openmp'
python: '[email protected]+optimizations+tkinter:[email protected]+tkinter'
gnu-openmpi:
architecture: 'x86_E5v4_Mellanox:x86_S6g1_Mellanox'
compiler: '[email protected]'
mpi: '[email protected]+pmi fabrics=verbs schedulers=slurm +thread_multiple+sqlite3 ^hwloc+cairo'
lapack: '[email protected]:[email protected] threads=openmp'
python: '[email protected]+optimizations+tkinter:[email protected]+tkinter'
# GNU is the matrix used to build software that runs on CPUs
# with a FOSS stack - bleeding edge version
gnu-bleeding-edge:
architecture: 'x86_E5v4_Mellanox:x86_S6g1_Mellanox'
compiler: '[email protected]'
mpi: '[email protected]+pmi fabrics=verbs schedulers=slurm +thread_multiple+sqlite3 ^hwloc+cairo:[email protected] fabrics=mrail process_managers=slurm'
lapack: '[email protected]:[email protected] threads=openmp'
python: '[email protected]+optimizations+tkinter:[email protected]+tkinter'
# Intel is the stack used to build software that runs on CPUs with
# a proprietary stack
intel-stable:
architecture: 'x86_E5v4_Mellanox:x86_S6g1_Mellanox'
compiler: '[email protected]'
mpi: '[email protected]'
lapack: '[email protected]'
python: '[email protected]+optimizations+tkinter:[email protected]+tkinter'
packages:
# List of packages that are built with core compilers
# and are maintained upstream
core:
target_matrix:
- core
requires:
- architecture
- compiler
specs:
# - [email protected] +X+pbm+wx ^pango+X
- i7z@epfl-scitas
- molden+gmolden+ambfor+surf
- parallel@20190222
# TODO: need update: - [email protected]
# TODO: need update: - [email protected]+hadoop
# List of third-party tools or of packages that are maintained
# in our own repository
externals:
target_matrix:
- core
requires:
- architecture
- compiler
specs:
- maple@2017
- matlab@R2018a
- matlab@R2019b
# TODO: check where to put these applications
# - molden
# List of python packages that do not require
# BLAS / LAPACK
serial_python:
target_matrix:
- gnu-stable
- intel-stable
requires:
- architecture
- compiler
- python
specs:
- py-cython
- py-pip
- py-sympy
- py-ply
- py-virtualenv
# List of python packages that do not require
# BLAS / LAPACK installed with the bleeding edge stacks
bleeding_serial_python:
target_matrix:
- gnu-bleeding-edge
requires:
- architecture
- compiler
- python
specs:
- py-cython
- py-pip
- py-sympy
- py-ply
- py-virtualenv
# List of python 3 packages that do not require
# BLAS / LAPACK installed with the bleeding edge stacks
bleeding_serial_python3_only:
target_matrix:
- gnu-bleeding-edge
target_filter:
python: ['[email protected]+optimizations+tkinter']
requires:
- architecture
- compiler
- python
specs:
- [email protected]+python
# Python packages that requires LAPACK
python_lapack_openmp:
target_matrix:
- gnu-stable
- intel-stable
target_filter:
lapack: ['[email protected] threads=openmp', '[email protected]']
requires:
- architecture
- compiler
- python
- lapack
specs:
# FIXME: These are missing in develop. Check if they are still needed.
# gnu-python_lapack_openmp:
# target_matrix:
# - gnu-stable
# target_filter:
# lapack: ['[email protected] threads=openmp']
# requires:
# - architecture
# - compiler
# - python
# - lapack
# specs:
# # TODO: Pytorch apparently requires CMake
# # - py-pytorch~cuda ^[email protected]
# # TODO: The code has 8 contributors and 80 followers on github, is it needed?
# gnu_python_2_only_lapack_openmp:
# target_matrix:
# - gnu-stable
# target_filter:
# python: ['[email protected]+tkinter']
# lapack: ['[email protected] threads=openmp']
# requires:
# - architecture
# - compiler
# - python
# - lapack
# specs:
# TODO: issues concretizing meson
# - gdl~wx~x11~hdf4+hdf5+embed_python+python+proj+graphicsmagick+openmp
# ^eigen~fftw~suitesparse~metis~scotch~mpfr
# ^fftw~mpi~openmp+fma simd=sse2,avx,avx2,avx512
# ^netcdf~mpi
# ^hdf5+szip~mpi+hl+fortran+cxx
# Python 2 only packages
python_2_only:
target_matrix:
- gnu-stable
- intel-stable
target_filter:
python: ['[email protected]+tkinter']
requires:
- architecture
- compiler
- python
specs:
- py-macs
- jellyfish
# Python 2 only packages that require LAPACK
python_2_lapack:
target_matrix:
- gnu-stable
- intel-stable
target_filter:
lapack: ['[email protected] threads=openmp', '[email protected]']
python: ['[email protected]+tkinter']
requires:
- architecture
- compiler
- python
- lapack
specs:
# TODO: doesn't compile with Intel compilers
# - py-macs2 ^py-numpy +blas [email protected]
- py-bioepic ^jellyfish ^[email protected] ^[email protected]
- sicer ^[email protected]
# Python 3 only packages
gnu_python_3:
target_matrix:
- gnu-stable
target_filter:
python: ['[email protected]+optimizations+tkinter']
requires:
- architecture
- compiler
- python
specs:
- [email protected]+python
intel_python_3:
target_matrix:
- intel-stable
target_filter:
python: ['[email protected]+optimizations+tkinter']
requires:
- architecture
- compiler
- python
specs:
- [email protected]+python ^[email protected]
# Code compiled with all the stacks that does not require
# MPI or LAPACK
serial:
target_matrix:
- gnu-stable
- intel-stable
requires:
- architecture
- compiler
specs:
- valgrind~boost~mpi
- '[email protected]~mpi~openmp+fma simd=sse2,avx,avx2,avx512'
- '[email protected]~mpi+openmp+fma simd=sse2,avx,avx2,avx512'
- [email protected] ^[email protected]~mpi~openmp+fma simd=sse2,avx,avx2,avx512
- gsl
- hdf5+szip~mpi+hl+fortran+cxx
- [email protected]+real64 ^guile~threads
- [email protected]+esmumps~metis~mpi
- netcdf~mpi ^hdf5+szip~mpi+hl+fortran+cxx
- netcdf-fortran ^netcdf~mpi ^hdf5+szip~mpi+hl+fortran+cxx
- voropp
- tcl
- tk ^tcl
- intel-tbb ^guile~threads
- eigen~fftw~suitesparse~metis~scotch~mpfr ^guile~threads
- [email protected] +opengl+webkit ^[email protected]+optimizations+tkinter ^guile~threads
- star
# FIXME: gdl (intel internal compiler error on plplot) SL-577, see gnu-serial
- chip-seq
# FIXME: Concretization errors on gl vdep
# - [email protected] +qt+zlib+tiff+vtk+png+jpeg+imgproc+highgui build_type=Release ^[email protected] +gtk+opengl+webkit ^mesa
- htslib
- hisat2
- samtools
- subread
serial_gnu:
target_matrix:
- gnu-stable
requires:
- architecture
- compiler
specs:
- libgd
- [email protected]+gmp
# Serial code that uses LAPACK
lapack:
target_matrix:
- gnu-stable
- intel-stable
requires:
- architecture
- compiler
- lapack
specs:
- arpack-ng~mpi
- suite-sparse ^[email protected]+real64
# MPI code that doesn't use LAPACK
mpi:
target_matrix:
- gnu-stable
- intel-stable
requires:
- architecture
- compiler
- mpi
specs:
- osu-micro-benchmarks~cuda
- [email protected]+icu+mpi+python ^[email protected]+tkinter
- fftw+mpi~openmp+fma simd=sse2,avx,avx2,avx512
- fftw+mpi+openmp+fma simd=sse2,avx,avx2,avx512
- hdf5+szip+mpi+hl+fortran+cxx
- [email protected]+esmumps+mpi~metis
# FIXME: recipe is broken as it depends on cube unconditionally
# - scorep~shmem~pdt
- parmetis ^[email protected]+real64
- netcdf+mpi ^hdf5+szip+mpi+hl+fortran+cxx
- netcdf-fortran ^netcdf+mpi ^hdf5+szip+mpi+hl+fortran+cxx
# TODO: this package needs to be ported to the list of external repositories
# - gerris@snapshot ^[email protected] ^gts@121130
# Libraries that needs both MPI and LAPACK
mpi-lapack-libraries:
target_matrix:
- gnu-stable
- intel-stable
requires:
- architecture
- compiler
- mpi
- lapack
specs:
- arpack-ng+mpi
# Libraries that needs both MPI and LAPACK - GNU specific
mpi-lapack-libraries-gnu:
target_matrix:
- gnu-stable
requires:
- architecture
- compiler
- mpi
- lapack
specs:
- hpl~openmp
- netlib-scalapack
- [email protected] ^netlib-scalapack
- mumps+mpi+parmetis+metis+scotch+ptscotch ^parmetis ^[email protected]+real64 ^[email protected]+esmumps+mpi~metis ^netlib-scalapack
mpi-lapack-libraries-intel:
target_matrix:
- intel-stable
requires:
- architecture
- compiler
- mpi
- lapack
specs:
- hpl~openmp
- mumps+mpi+parmetis+metis+scotch+ptscotch ^parmetis ^[email protected]+real64 ^[email protected]+esmumps+mpi~metis
##########
# Applications / Frameworks
##########
# Serial applications built with the Intel stack
intel-serial-applications:
target_matrix:
- intel-stable
requires:
- architecture
- compiler
specs:
- abaqus
# MPI applications built with the Intel stack
intel-mpi-applications:
target_matrix:
- intel-stable
requires:
- architecture
- compiler
- mpi
specs:
- [email protected]+mpi
^[email protected]+mpi~openmp+fma simd=sse2,avx,avx2,avx512
- foam-extend+metis+scotch+parmetis+ptscotch~paraview
^[email protected] ^[email protected]+real64
^[email protected]+esmumps+mpi~metis
^[email protected]+tkinter
# FIXME: broken build with intel 18.0.5
# - openfoam-com~paraview~int64+metis+scotch+source
# ^[email protected]+esmumps+mpi~metis
# ^cgal ^[email protected]+icu+mpi+python
# ^fftw~mpi~openmp+fma simd=sse2,avx,avx2,avx512 ^[email protected]+tkinter
- neuron+mpi+python+shared ^[email protected]+tkinter
# MPI applications built with the Intel stack that use LAPACK
intel-mpi-lapack-applications:
target_matrix:
- intel-stable
requires:
- architecture
- compiler
- mpi
- lapack
specs:
# - namd fftw=mkl interface=python @2.12 ^charm backend=mpi ^[email protected]+tkinter
# - amber@16+mpi ^netcdf-fortran ^[email protected]+mpi ^hdf5+szip+mpi~cxx ^[email protected] ^[email protected] ^[email protected] ^[email protected]
# # TODO: - [email protected]+python+opencv ^hdf5+szip+mpi~cxx ^[email protected]+qt~vtk~eigen ^[email protected] ^[email protected] ^[email protected]+icu+mpi+python ^[email protected]
# # TODO: - [email protected]+mpi+hdf5+fltk+compression ^hdf5+szip+mpi~cxx
# - [email protected]+petsc+hdf5~trilinos+suite-sparse+mpi ^[email protected]+boost+double+hdf5+metis+mpi+mumps~superlu-dist~hypre ^hdf5+szip+mpi~cxx ^[email protected]+mpi+parmetis+metis+scotch+ptscotch ^[email protected] ^[email protected]+real64 ^[email protected]+esmumps+mpi~metis ^[email protected]+icu_support+mpi+python ^[email protected] ^[email protected]~debug+fftw+metis+mpfr+scotch+suitesparse ^[email protected]+mpi~openmp
# # FIXME: - simpson@master ^[email protected] ^[email protected] ^[email protected] ^[email protected] ^[email protected]
# Serial applications built with the Intel stack that use LAPACK
intel-lapack-applications:
target_matrix:
- intel-stable
requires:
- architecture
- compiler
- lapack
specs:
- r+external-lapack ^[email protected] ^[email protected]
# Serial applications built with the GNU stable stack
gnu-serial-applications:
target_matrix:
- gnu-stable
requires:
- architecture
- compiler
specs:
- bcl2fastq2 ^boost+icu~mpi+python ^[email protected]+tkinter
# FIXME: installation failing with [email protected]
# - bowtie+tbb ^intel-tbb
- bowtie2 ^intel-tbb
- gdb~python
- ncview ^netcdf~mpi ^hdf5+szip~mpi+hl+fortran+cxx
- [email protected] ^boost+icu~mpi+python ^[email protected]+tkinter
# FIXME: see https://github.com/spack/spack/issues/8025
# - tophat ^[email protected] ^[email protected]
# Serial applications built with the GNU stable stack and LAPACK
gnu-lapack-applications:
target_matrix:
- gnu-stable
target_filter:
lapack: ['[email protected] threads=openmp']
requires:
- architecture
- compiler
- lapack
specs:
- r+external-lapack
# MPI applications built with the GNU stable stack
gnu-mpi-applications:
target_matrix:
- gnu-stable
requires:
- architecture
- compiler
- mpi
specs:
- [email protected]+mpi ^fftw+mpi~openmp+fma simd=sse2,avx,avx2,avx512
# - namd fftw=3 interface=python
# ^charm backend=mpi
# ^fftw+mpi~openmp+fma simd=sse2,avx,avx2,avx512
# ^[email protected]+tkinter
- foam-extend+metis+scotch+parmetis+ptscotch~paraview
^parmetis ^[email protected]+real64
^[email protected]+esmumps+mpi~metis
^[email protected]+tkinter
- openfoam-com~paraview~int64+metis+scotch+source
^[email protected]+esmumps+mpi~metis
^cgal ^[email protected]+icu+mpi+python
^fftw~mpi~openmp+fma simd=sse2,avx,avx2,avx512
^[email protected]+tkinter
- neuron+mpi+python+shared ^[email protected]+tkinter
# MPI applications built with the GNU stable stack that use LAPACK
gnu-mpi-lapack-applications:
target_matrix:
- gnu-stable
target_filter:
lapack:
requires:
- architecture
- compiler
- mpi
- lapack
specs:
- [email protected]~hdf5~openmp+mpi+scalapack ^[email protected]+mpi~openmp+fma simd=sse2,avx,avx2,avx512 ^[email protected]
- cp2k+mpi~plumed
^fftw+mpi~openmp+fma simd=sse2,avx,avx2,avx512
- cp2k+mpi+plumed
^fftw+mpi~openmp+fma simd=sse2,avx,avx2,avx512
^plumed+mpi+gsl
- [email protected]+mpi
- [email protected]+mpi
- [email protected] ^fftw~mpi~openmp+fma simd=sse2,avx,avx2,avx512
# TODO: - [email protected]+python+opencv ^hdf5+szip+mpi~cxx ^[email protected]+qt~vtk~eigen ^[email protected] ^[email protected] ^[email protected]+icu+mpi+python ^[email protected]
# TODO: port amber from cornalin
# - amber@16+mpi ^netcdf-fortran ^[email protected]+mpi ^hdf5+szip+mpi~cxx ^[email protected] ^[email protected] ^[email protected] ^[email protected]
# TODO: - [email protected]+mpi+hdf5+fltk+compression ^hdf5+szip+mpi~cxx
# - [email protected]+mpi+osmesa~qt+python+hdf5
# ^[email protected]+optimizations+tkinter
# ^hdf5+szip+mpi+hl+fortran+cxx
# TODO: - [email protected]+petsc+hdf5~trilinos+suite-sparse+mpi ^[email protected]+boost+double+hdf5+metis+mpi+mumps~superlu-dist~hypre ^hdf5+szip+mpi~cxx ^[email protected]+mpi+parmetis+metis+scotch+ptscotch ^[email protected] ^[email protected]+real64 ^[email protected]+esmumps+mpi~metis ^[email protected] ^[email protected]+icu_support+mpi+python ^[email protected] ^[email protected]~debug+fftw+metis+mpfr+scotch+suitesparse ^[email protected]+mpi~openmp
# FIXME: - simpson@master ^[email protected] ^[email protected] ^[email protected] ^[email protected] ^[email protected]
mpi-lapack-applications:
target_matrix:
- gnu-stable
- intel-stable
target_filter:
lapack:
requires:
- architecture
- compiler
- mpi
- lapack
specs:
- plumed+mpi+gsl
- [email protected]+mpi+plumed
^fftw+mpi~openmp+fma simd=sse2,avx,avx2,avx512
^plumed+mpi+gsl
- quantum-espresso+mpi+scalapack hdf5=parallel
^fftw+mpi~openmp+fma simd=sse2,avx,avx2,avx512
^hdf5+szip+mpi+hl+fortran+cxx
- quantum-espresso+mpi+scalapack
^fftw+mpi~openmp+fma simd=sse2,avx,avx2,avx512
- yambo+mpi io=iotk,etsf-io
^fftw+mpi~openmp+fma simd=sse2,avx,avx2,avx512
^netcdf-fortran ^netcdf+mpi ^hdf5+szip+mpi+hl+fortran+cxx
- cpmd~openmp
^fftw+mpi~openmp+fma simd=sse2,avx,avx2,avx512
- petsc~int64+double+hdf5+metis+mpi+mumps+superlu-dist+hypre+suite-sparse
^hdf5+szip+mpi+hl+fortran+cxx
^mumps+mpi+parmetis+metis+scotch+ptscotch
^parmetis ^[email protected]+real64 ^[email protected]+esmumps+mpi~metis
^[email protected]+tkinter
- lammps build_type=Release
+asphere +body +class2 +colloid +compress +coreshell
+dipole +granular +kspace +latte +lib +manybody +mc
+meam +misc +molecule +mpi +mpiio +peri ~poems +python
+qeq +reax +replica +rigid +shock +snap +srd +user-atc
+user-h5md +user-lb +user-misc +user-netcdf ~voronoi
^[email protected]+mpi~openmp+fma simd=sse2,avx,avx2,avx512
^netcdf+mpi ^hdf5+szip+mpi+hl+fortran+cxx
gnu-openmpi-benchmark:
target_matrix:
- gnu-openmpi
requires:
- architecture
- compiler
- mpi
specs:
- osu-micro-benchmarks~cuda
gnu-openmpi-lapack-benchmark:
target_matrix:
- gnu-openmpi
requires:
- architecture
- compiler
- mpi
- lapack
target_filter:
lapack:
specs:
- hpl~openmp
gnu-bleeding-edge-benchmark:
target_matrix:
- gnu-bleeding-edge
requires:
- architecture
- compiler
- mpi
specs:
- osu-micro-benchmarks~cuda
gnu-bleeding-edge-lapack-benchmark:
target_matrix:
- gnu-bleeding-edge
requires:
- architecture
- compiler
- mpi
- lapack
target_filter:
lapack:
specs:
- hpl~openmp