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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: 'gcc@4.8.5'
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: 'gcc@7.4.0'
mpi: 'mvapich2@2.3.1 fabrics=mrail process_managers=slurm'
lapack: 'openblas@0.3.6:openblas@0.3.6 threads=openmp'
python: 'python@3.7.3+optimizations+tkinter:python@2.7.16+tkinter'
gnu-openmpi:
architecture: 'x86_E5v4_Mellanox:x86_S6g1_Mellanox'
compiler: 'gcc@7.4.0'
mpi: 'openmpi@3.1.4+pmi fabrics=verbs schedulers=slurm +thread_multiple+sqlite3 ^hwloc+cairo'
lapack: 'openblas@0.3.6:openblas@0.3.6 threads=openmp'
python: 'python@3.7.3+optimizations+tkinter:python@2.7.16+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: 'gcc@8.3.0'
mpi: 'openmpi@3.1.4+pmi fabrics=verbs schedulers=slurm +thread_multiple+sqlite3 ^hwloc+cairo:mvapich2@2.3.1 fabrics=mrail process_managers=slurm'
lapack: 'openblas@0.3.6:openblas@0.3.6 threads=openmp'
python: 'python@3.7.3+optimizations+tkinter:python@2.7.16+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: 'intel@18.0.5'
mpi: 'intel-mpi@2018.4.274'
lapack: 'intel-mkl@2018.5.274'
python: 'python@3.7.3+optimizations+tkinter:python@2.7.16+tkinter'
packages:
# List of packages that are built with core compilers
# and are maintained upstream
core:
target_matrix:
- core
requires:
- architecture
- compiler
specs:
- autoconf@2.69
- automake@1.16.1
- cmake@3.14.4
- curl@7.63.0
- fastqc@0.11.8
- fio@2.19
- gcc@6.5.0
- git@2.21.0
- git-lfs@2.7.2 ^git@2.21.0
# - gnuplot@5.2.2 +X+pbm+wx ^pango+X
- i7z@epfl-scitas
- libtool@2.4.6
- lmod@8.1.5
- m4@1.4.18
- mercurial@4.4.1
- molden+gmolden+ambfor+surf
- parallel@20190222
- picard@2.19.0
- sbt@1.1.6
# TODO: need update: - scala@2.12.5
# TODO: need update: - spark@2.3.0+hadoop
- sra-toolkit@2.9.6
- tar@1.31
- tmux@2.8
- trimmomatic@0.38
# List of third-party tools or of packages that are maintained
# in our own repository
externals:
target_matrix:
- core
requires:
- architecture
- compiler
specs:
- adf@2017.111
- likwid@4.3.0
- maple@2017
- matlab@R2018a
- matlab@R2019b
- mathematica@11.1.1
- ansys@17.1
- ansys@19.2
- totalview@2017.2.11
- comsol@5.3
- comsol@5.4
- gaussian@g16-A.03
- gurobi@8.1.1
- smr@2017.06
- cfdplusplus@16.1
- cfdplusplus@19.1
- fdtd@8.20.1703
# TODO: check where to put these applications
# - beast@2.4.8
# - 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
- scons@3.0.4
# 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: ['python@3.7.3+optimizations+tkinter']
requires:
- architecture
- compiler
- python
specs:
- boost@1.70.0+python
# Python packages that requires LAPACK
python_lapack_openmp:
target_matrix:
- gnu-stable
- intel-stable
target_filter:
lapack: ['openblas@0.3.6 threads=openmp', 'intel-mkl@2018.2.199']
requires:
- architecture
- compiler
- python
- lapack
specs:
- py-numpy+blas+lapack@1.16.3
- py-scipy@1.2.1 ^py-numpy+blas+lapack@1.16.3
- py-matplotlib@2.2.3 ^py-numpy+blas+lapack@1.16.3
# FIXME: These are missing in develop. Check if they are still needed.
# - py-qutip+f90mc@3.1.0^py-scipy@0.17.0^py-numpy+blas+lapack@1.11.0^py-cython@0.23.5
# - py-ase+matplotlib+scipy@3.11.0^py-matplotlib@1.4.3^py-numpy+blas+lapack@1.11.0
- py-scikit-learn@0.20.2 ^py-scipy@1.2.1 ^py-numpy+blas+lapack@1.16.3
- py-theano@1.0.4~gpu ^py-scipy@1.2.1 ^py-numpy+blas+lapack@1.16.3
- py-pandas@0.24.1 ^py-numpy+blas+lapack@1.16.3
- py-xarray@0.11.0 ^py-pandas@0.24.1 ^py-numpy+blas+lapack@1.16.3
- py-deeptools@3.2.1 ^py-matplotlib@2.2.3 ^py-scipy@1.2.1 ^py-numpy+blas+lapack@1.16.3
# gnu-python_lapack_openmp:
# target_matrix:
# - gnu-stable
# target_filter:
# lapack: ['openblas@0.3.6 threads=openmp']
# requires:
# - architecture
# - compiler
# - python
# - lapack
# specs:
# # TODO: Pytorch apparently requires CMake
# # - py-pytorch~cuda ^py-numpy+blas+lapack@1.16.3
# # TODO: The code has 8 contributors and 80 followers on github, is it needed?
# # - py-htseq@0.10.0 ^py-matplotlib@2.2.3 ^py-numpy+blas+lapack@1.16.3
# gnu_python_2_only_lapack_openmp:
# target_matrix:
# - gnu-stable
# target_filter:
# python: ['python@2.7.16+tkinter']
# lapack: ['openblas@0.3.6 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
# ^py-numpy+blas+lapack@1.16.3
# Python 2 only packages
python_2_only:
target_matrix:
- gnu-stable
- intel-stable
target_filter:
python: ['python@2.7.16+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: ['openblas@0.3.6 threads=openmp', 'intel-mkl@2018.2.199']
python: ['python@2.7.16+tkinter']
requires:
- architecture
- compiler
- python
- lapack
specs:
# TODO: doesn't compile with Intel compilers
# - py-macs2 ^py-numpy +blas +lapack@1.16.3
- py-bioepic ^jellyfish ^py-scipy@1.2.1 ^py-numpy+blas+lapack@1.16.3
- sicer ^py-numpy+blas+lapack@1.16.3
# Python 3 only packages
gnu_python_3:
target_matrix:
- gnu-stable
target_filter:
python: ['python@3.7.3+optimizations+tkinter']
requires:
- architecture
- compiler
- python
specs:
- openbabel@2.4.1+python
intel_python_3:
target_matrix:
- intel-stable
target_filter:
python: ['python@3.7.3+optimizations+tkinter']
requires:
- architecture
- compiler
- python
specs:
- openbabel@2.4.1+python ^freetype@2.7.1
# 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
- 'fftw@3.3.8~mpi~openmp+fma simd=sse2,avx,avx2,avx512'
- 'fftw@3.3.8~mpi+openmp+fma simd=sse2,avx,avx2,avx512'
- nfft@3.4.1 ^fftw@3.3.8~mpi~openmp+fma simd=sse2,avx,avx2,avx512
- gsl
- hdf5+szip~mpi+hl+fortran+cxx
- metis@5.1.0+real64 ^guile~threads
- scotch@6.0.6+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
- bedtools2@2.27.1
- intel-tbb ^guile~threads
- eigen~fftw~suitesparse~metis~scotch~mpfr ^guile~threads
- qt@5.11.3 +opengl+webkit ^python@3.7.3+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
# - opencv@3.4.1 +qt+zlib+tiff+vtk+png+jpeg+imgproc+highgui build_type=Release ^qt@4.8.6 +gtk+opengl+webkit ^mesa
- htslib
- hisat2
- samtools
- subread
serial_gnu:
target_matrix:
- gnu-stable
requires:
- architecture
- compiler
specs:
- libgd
- glpk@4.65+gmp
# Serial code that uses LAPACK
lapack:
target_matrix:
- gnu-stable
- intel-stable
requires:
- architecture
- compiler
- lapack
specs:
- arpack-ng~mpi
- suite-sparse ^metis@5.1.0+real64
# MPI code that doesn't use LAPACK
mpi:
target_matrix:
- gnu-stable
- intel-stable
requires:
- architecture
- compiler
- mpi
specs:
- osu-micro-benchmarks~cuda
- boost@1.67.0+icu+mpi+python ^python@2.7.16+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
- scotch@6.0.6+esmumps+mpi~metis
# FIXME: recipe is broken as it depends on cube unconditionally
# - scorep~shmem~pdt
- parmetis ^metis@5.1.0+real64
- netcdf+mpi ^hdf5+szip+mpi+hl+fortran+cxx
- netcdf-fortran ^netcdf+mpi ^hdf5+szip+mpi+hl+fortran+cxx
- cgal@4.13 ^boost@1.67.0+icu+mpi+python ^python@2.7.16+tkinter
# TODO: this package needs to be ported to the list of external repositories
# - gerris@snapshot ^gsl@2.3 ^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
- elpa@2017.11.001 ^netlib-scalapack
- mumps+mpi+parmetis+metis+scotch+ptscotch ^parmetis ^metis@5.1.0+real64 ^scotch@6.0.6+esmumps+mpi~metis ^netlib-scalapack
mpi-lapack-libraries-intel:
target_matrix:
- intel-stable
requires:
- architecture
- compiler
- mpi
- lapack
specs:
- hpl~openmp
- elpa@2017.11.001
- mumps+mpi+parmetis+metis+scotch+ptscotch ^parmetis ^metis@5.1.0+real64 ^scotch@6.0.6+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:
- gromacs@2019.4+mpi
^fftw@3.3.8+mpi~openmp+fma simd=sse2,avx,avx2,avx512
- foam-extend+metis+scotch+parmetis+ptscotch~paraview
^parmetis@4.0.3 ^metis@5.1.0+real64
^scotch@6.0.6+esmumps+mpi~metis
^python@2.7.16+tkinter
# FIXME: broken build with intel 18.0.5
# - openfoam-com~paraview~int64+metis+scotch+source
# ^scotch@6.0.6+esmumps+mpi~metis
# ^cgal ^boost@1.67.0+icu+mpi+python
# ^fftw~mpi~openmp+fma simd=sse2,avx,avx2,avx512 ^python@2.7.16+tkinter
- neuron+mpi+python+shared ^python@2.7.16+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:
- crystal17@1.0.2
- vasp@5.4.4
# - namd fftw=mkl interface=python @2.12 ^charm backend=mpi ^python@2.7.16+tkinter
# - amber@16+mpi ^netcdf-fortran ^netcdf@4.4.1.1+mpi ^hdf5+szip+mpi~cxx ^py-scipy@0.19.0 ^py-matplotlib@2.2.3 ^py-numpy+blas+lapack@1.12.1 ^python@2.7.13
# - nwchem@6.8 ^netlib-scalapack@2.0.2 ^python@2.7.16+tkinter
# # TODO: - caffe@1.0+python+opencv ^hdf5+szip+mpi~cxx ^opencv@3.2.0+qt~vtk~eigen ^qt@4.8.6 ^py-numpy+blas+lapack@1.12.1 ^boost@1.63.0+icu+mpi+python ^python@2.7.13
# # TODO: - gmsh@3.0.1+mpi+hdf5+fltk+compression ^hdf5+szip+mpi~cxx
# - fenics@2017.1.0+petsc+hdf5~trilinos+suite-sparse+mpi ^petsc@3.7.6+boost+double+hdf5+metis+mpi+mumps~superlu-dist~hypre ^hdf5+szip+mpi~cxx ^mumps@5.1.1+mpi+parmetis+metis+scotch+ptscotch ^parmetis@4.0.3 ^metis@5.1.0+real64 ^scotch@6.0.6+esmumps+mpi~metis ^boost@1.61.0+icu_support+mpi+python ^python@2.7.13 ^eigen@3.3.1~debug+fftw+metis+mpfr+scotch+suitesparse ^fftw@3.3.6-pl2+mpi~openmp
# # FIXME: - simpson@master ^gsl@2.1 ^nfft@3.3.2 ^fftw@3.3.4 ^tk@8.6.3 ^tcl@8.6.5
# 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 ^freetype@2.7.1 ^harfbuzz@2.2.0
# Serial applications built with the GNU stable stack
gnu-serial-applications:
target_matrix:
- gnu-stable
requires:
- architecture
- compiler
specs:
- bcl2fastq2 ^boost+icu~mpi+python ^python@2.7.16+tkinter
# FIXME: installation failing with gcc@7.4.0
# - bowtie+tbb ^intel-tbb
- bowtie2 ^intel-tbb
- gdb~python
- ncview ^netcdf~mpi ^hdf5+szip~mpi+hl+fortran+cxx
- polymake@3.5 ^boost+icu~mpi+python ^python@2.7.16+tkinter
# FIXME: see https://github.com/spack/spack/issues/8025
# - tophat ^bowtie2@2.3.4.1 ^intel-tbb@2018.2
# Serial applications built with the GNU stable stack and LAPACK
gnu-lapack-applications:
target_matrix:
- gnu-stable
target_filter:
lapack: ['openblas@0.3.6 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:
- gromacs@2019.4+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
# ^python@2.7.16+tkinter
- foam-extend+metis+scotch+parmetis+ptscotch~paraview
^parmetis ^metis@5.1.0+real64
^scotch@6.0.6+esmumps+mpi~metis
^python@2.7.16+tkinter
- openfoam-com~paraview~int64+metis+scotch+source
^scotch@6.0.6+esmumps+mpi~metis
^cgal ^boost@1.67.0+icu+mpi+python
^fftw~mpi~openmp+fma simd=sse2,avx,avx2,avx512
^python@2.7.16+tkinter
- neuron+mpi+python+shared ^python@2.7.16+tkinter
# MPI applications built with the GNU stable stack that use LAPACK
gnu-mpi-lapack-applications:
target_matrix:
- gnu-stable
target_filter:
lapack:
- 'openblas@0.3.6'
requires:
- architecture
- compiler
- mpi
- lapack
specs:
- abinit@8.8.2~hdf5~openmp+mpi+scalapack ^fftw@3.3.8+mpi~openmp+fma simd=sse2,avx,avx2,avx512 ^netlib-scalapack@2.0.2
- 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
- molpro@2015.1+mpi
- molpro@2019.2+mpi
- nwchem@6.8 ^netlib-scalapack@2.0.2 ^python@2.7.16+tkinter
- vasp@5.4.4 ^fftw~mpi~openmp+fma simd=sse2,avx,avx2,avx512
# TODO: - caffe@1.0+python+opencv ^hdf5+szip+mpi~cxx ^opencv@3.2.0+qt~vtk~eigen ^qt@4.8.6 ^py-numpy+blas+lapack@1.12.1 ^boost@1.63.0+icu+mpi+python ^python@2.7.13
# TODO: port amber from cornalin
# - amber@16+mpi ^netcdf-fortran ^netcdf@4.4.1.1+mpi ^hdf5+szip+mpi~cxx ^py-scipy@0.19.0 ^py-matplotlib@2.2.3 ^py-numpy+blas+lapack@1.12.1 ^python@2.7.13
# TODO: - gmsh@3.0.1+mpi+hdf5+fltk+compression ^hdf5+szip+mpi~cxx
# - paraview@5.5.2+mpi+osmesa~qt+python+hdf5
# ^py-matplotlib@2.2.3
# ^py-numpy+blas+lapack@1.16.3
# ^python@3.7.3+optimizations+tkinter
# ^hdf5+szip+mpi+hl+fortran+cxx
# TODO: - fenics@2017.1.0+petsc+hdf5~trilinos+suite-sparse+mpi ^petsc@3.7.6+boost+double+hdf5+metis+mpi+mumps~superlu-dist~hypre ^hdf5+szip+mpi~cxx ^mumps@5.1.1+mpi+parmetis+metis+scotch+ptscotch ^parmetis@4.0.3 ^metis@5.1.0+real64 ^scotch@6.0.6+esmumps+mpi~metis ^netlib-scalapack@2.0.2 ^boost@1.61.0+icu_support+mpi+python ^python@2.7.13 ^eigen@3.3.1~debug+fftw+metis+mpfr+scotch+suitesparse ^fftw@3.3.6-pl2+mpi~openmp
# FIXME: - simpson@master ^gsl@2.1 ^nfft@3.3.2 ^fftw@3.3.4 ^tk@8.6.3 ^tcl@8.6.5
mpi-lapack-applications:
target_matrix:
- gnu-stable
- intel-stable
target_filter:
lapack:
- 'openblas@0.3.6'
- 'intel-mkl@2018.5.274'
requires:
- architecture
- compiler
- mpi
- lapack
specs:
- plumed+mpi+gsl
- gromacs@2016.5+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 ^metis@5.1.0+real64 ^scotch@6.0.6+esmumps+mpi~metis
^python@2.7.16+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
^fftw@3.3.8+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:
- 'openblas@0.3.6'
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:
- 'openblas@0.3.6'
specs:
- hpl~openmp