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cornalin.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_E5v2:x86_E5v2_IntelIB:x86_E5v2_Mellanox_GPU:x86_E5v3_IntelIB: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_E5v2_IntelIB:x86_E5v3_IntelIB'
- 'x86_E5v4_Mellanox:x86_S6g1_Mellanox'
- 'x86_E5v2'
compiler: 'gcc@5.4.0'
mpi:
- 'openmpi@2.0.2 fabrics=pmi,psm schedulers=slurm +thread_multiple+sqlite3:mvapich2@2.2 fabrics=psm process_managers=slurm'
- 'openmpi@2.0.2 fabrics=pmi schedulers=slurm +thread_multiple+sqlite3:mvapich2@2.2 fabrics=mrail process_managers=slurm'
- 'openmpi@2.0.2 fabrics=pmi schedulers=slurm +thread_multiple+sqlite3:mvapich2@2.2 fabrics=sock process_managers=slurm'
lapack: 'openblas@0.2.19~openmp:openblas@0.2.19+openmp'
python: 'python@3.6.1:python@2.7.13'
# GNU is the matrix used to build software that runs on CPUs
# with a FOSS stack - bleeding edge version
gnu-bleeding-edge:
architecture:
- 'x86_E5v2_IntelIB:x86_E5v3_IntelIB'
- 'x86_E5v4_Mellanox:x86_S6g1_Mellanox'
- 'x86_E5v2'
compiler: 'gcc@7.1.0'
mpi:
- 'openmpi@2.1.0 fabrics=pmi,psm schedulers=slurm +thread_multiple+sqlite3:mvapich2@2.3a fabrics=psm process_managers=slurm'
- 'openmpi@2.1.0 fabrics=pmi schedulers=slurm +thread_multiple+sqlite3:mvapich2@2.3a fabrics=mrail process_managers=slurm'
- 'openmpi@2.1.0 fabrics=pmi schedulers=slurm +thread_multiple+sqlite3'
lapack: 'openblas@0.2.19~openmp:openblas@0.2.19+openmp'
python: 'python@3.6.1:python@2.7.13'
# GNU-GPU is the matrix used to build software that runs on GPUs
# with a FOSS stack
gnu-gpu:
architecture: 'x86_E5v2_Mellanox_GPU'
compiler: 'gcc@5.4.0'
mpi:
- 'openmpi@2.0.2 fabrics=pmi schedulers=slurm +thread_multiple+sqlite3:mvapich2@2.2 fabrics=mrail process_managers=slurm'
lapack: 'openblas@0.2.19~openmp'
python: 'python@3.6.1:python@2.7.13'
# Intel is the stack used to build software that runs on CPUs with
# a proprietary stack
intel:
architecture: 'x86_E5v2:x86_E5v2_IntelIB:x86_E5v3_IntelIB:x86_E5v4_Mellanox:x86_S6g1_Mellanox'
compiler: 'intel@17.0.2'
mpi: 'intel-mpi@2017.2.174'
lapack: 'intel-mkl@2017.2.174'
python: 'python@3.6.1:python@2.7.13'
packages:
# List of packages that are built with core compilers
core:
target_matrix:
- core
requires:
- architecture
- compiler
specs:
- adf@2017.111
- cmake@3.8.0
- m4@1.4.18
- autoconf@2.69
- automake@1.15
- libtool@2.4.6
- lmod@7.4.8
- likwid@4.3.0
- gnuplot@5.0.5~wx
- git@2.12.2
- tmux@2.4
- maple@2017
- matlab@R2016a
- mathematica@9.0.1
- ansys@17.1
- totalview@2017.2.11
- comsol@5.2a
- gaussian@g09-D.01
- scala@2.12.1
- smr@2017.06
- spark@2.1.0+hadoop
- sra-tools@2.8.2-5
- picard@2.9.2
- tar@1.29
- cfdplusplus@16.1
- fdtd@8.19.1416-1
- beast@2.4.8
- molden
# List of python packages that do not require
# BLAS / LAPACK
serial_python:
target_matrix:
- gnu-stable
- gnu-bleeding-edge
- gnu-gpu
- intel
requires:
- architecture
- compiler
- python
specs:
- py-cython@0.25.2
- py-pip@9.0.1
# - py-psycopg2@2.6.2 ^py-pip@9.0.1 # FIXME: missing in develop
- py-sympy@1.0
- py-ply@3.8
- py-virtualenv@15.1.0
- py-pytest@3.0.7
# Python packages that requires LAPACK
python_lapack_openmp:
target_matrix:
- gnu-stable
- gnu-bleeding-edge
- intel
target_filter:
lapack: ['openblas@0.2.19~openmp', 'intel-mkl@2017.2.174']
requires:
- architecture
- compiler
- python
- lapack
specs:
- py-numpy+blas+lapack@1.12.1
- py-scipy@0.19.0 ^py-numpy+blas+lapack@1.12.1
- py-matplotlib@2.0.0 ^py-numpy+blas+lapack@1.12.1
# FIXME: missing in develop
# - 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@0.18.1 ^py-scipy@0.19.0 ^py-numpy+blas+lapack@1.12.1
- py-theano@0.8.2~gpu ^py-scipy@0.19.0 ^py-numpy+blas+lapack@1.12.1
# Python 2 only packages
python_2_only:
target_matrix:
- gnu-stable
- gnu-bleeding-edge
- intel
target_filter:
python: ['python@2.7.13']
requires:
- architecture
- compiler
- python
specs:
- py-macs@1.4.2-1
# Python 2 only packages that require LAPACK
python_2_lapack:
target_matrix:
- gnu-stable
- gnu-bleeding-edge
- intel
target_filter:
lapack: ['openblas@0.2.19~openmp', 'intel-mkl@2017.2.174']
python: ['python@2.7.13']
requires:
- architecture
- compiler
- python
- lapack
specs:
- py-macs2@2.1.1.20160309 ^py-numpy+blas+lapack@1.12.1
# Code compiled with all the stacks that does not require
# MPI or LAPACK
serial:
target_matrix:
- gnu-stable
- gnu-bleeding-edge
- intel
requires:
- architecture
- compiler
specs:
- valgrind@3.12.0~boost~mpi
- gdb@7.12.1
- fftw@3.3.6-pl2~mpi
- fftw@3.3.6-pl2~mpi+openmp
- nfft@3.3.2 ^fftw@3.3.6-pl2~mpi
- glpk@4.61+gmp
- gsl@2.3
- hdf5@1.10.1+szip~mpi
- metis@5.1.0+real64
- scotch@6.0.4+esmumps~metis~mpi
- python@3.6.1
- python@2.7.13
- netcdf@4.4.1.1~mpi ^hdf5@1.10.1+szip~mpi
- netcdf-fortran@4.4.4 ^netcdf@4.4.1.1~mpi ^hdf5@1.10.1+szip~mpi
- gts@121130
- voropp@0.4.6
- tcl@8.6.6
- tk@8.6.6 ^tcl@8.6.6
- mercurial@4.1.2 ^python@2.7.13
- bedtools2@2.26.0
- tbb@2017.5
# Serial code that uses LAPACK
lapack:
target_matrix:
- gnu-stable
- gnu-bleeding-edge
- intel
requires:
- architecture
- compiler
- lapack
specs:
- arpack-ng@3.4.0~mpi
- suite-sparse@4.5.5 ^metis@5.1.0+real64
# MPI code that doesn't use LAPACK
mpi:
target_matrix:
- gnu-stable
- gnu-bleeding-edge
- intel
requires:
- architecture
- compiler
- mpi
specs:
- boost@1.63.0+icu+mpi+python ^python@2.7.13
- fftw@3.3.6-pl2+mpi~openmp
- fftw@3.3.6-pl2+mpi+openmp
- hdf5@1.10.1+szip+mpi~cxx
- scotch@6.0.4+esmumps+mpi~metis
- scorep@3.0
- parmetis@4.0.3 ^metis@5.1.0+real64
- netcdf@4.4.1.1+mpi ^hdf5@1.10.1+szip+mpi~cxx
- netcdf-fortran@4.4.4 ^netcdf@4.4.1.1+mpi ^hdf5@1.10.1+szip+mpi~cxx
- cgal@4.9.1 ^boost@1.63.0+icu+mpi+python ^python@2.7.13
- gerris@snapshot ^gsl@2.3 ^gts@121130
# Libraries that needs both MPI and LAPACK
mpi-lapack-libraries:
target_matrix:
- gnu-stable
- gnu-bleeding-edge
- intel
requires:
- architecture
- compiler
- mpi
- lapack
specs:
- arpack-ng@3.4.0+mpi
# Libraries that needs both MPI and LAPACK - GNU specific
mpi-lapack-libraries-gnu:
target_matrix:
- gnu-stable
- gnu-bleeding-edge
requires:
- architecture
- compiler
- mpi
- lapack
specs:
- netlib-scalapack@2.0.2
- elpa@2016.05.004 ^netlib-scalapack@2.0.2
- eigen@3.3.1~debug+fftw+metis+mpfr+scotch+suitesparse ^fftw@3.3.6-pl2+mpi~openmp
- mumps@5.1.1+mpi+parmetis+metis+scotch+ptscotch ^parmetis@4.0.3 ^metis@5.1.0+real64 ^scotch@6.0.4+esmumps+mpi~metis ^netlib-scalapack@2.0.2
mpi-lapack-libraries-intel:
target_matrix:
- intel
requires:
- architecture
- compiler
- mpi
- lapack
specs:
- elpa@2016.05.004
- eigen@3.3.1~debug+fftw+metis+mpfr+scotch+suitesparse ^fftw@3.3.6-pl2+mpi~openmp
- mumps@5.1.1+mpi+parmetis+metis+scotch+ptscotch ^parmetis@4.0.3 ^metis@5.1.0+real64 ^scotch@6.0.4+esmumps+mpi~metis
##########
# Applications / Frameworks
##########
# Serial applications built with the Intel stack
intel-serial-applications:
target_matrix:
- intel
requires:
- architecture
- compiler
specs:
- qt@4.8.6
- opencv@3.2.0+qt~vtk~eigen ^qt@4.8.6
- hisat2@2.1.0
- samtools@1.4
- subread@1.5.2
# FIXME: abaqus
# MPI applications built with the Intel stack
intel-mpi-applications:
target_matrix:
- intel
requires:
- architecture
- compiler
- mpi
specs:
- gromacs@2016.3+mpi ^fftw@3.3.6-pl2+mpi~openmp
- foam-extend+metis+scotch+parmetis+ptscotch~paraview ^parmetis@4.0.3 ^metis@5.1.0+real64 ^scotch@6.0.4+esmumps+mpi~metis ^python@2.7.13
- openfoam-com~paraview+metis+scotch~int64+source ^scotch@6.0.4+esmumps+mpi~metis ^cgal@4.9.1 ^boost@1.63.0+icu+mpi+python ^python@2.7.13
- neuron@7.5+mpi+python+shared ^python@2.7.13
# MPI applications built with the Intel stack that use LAPACK
intel-mpi-lapack-applications:
target_matrix:
- intel
requires:
- architecture
- compiler
- mpi
- lapack
specs:
- plumed@2.3.0+mpi+gsl ^gsl@2.3
- gromacs@2016.1+mpi+plumed ^fftw@3.3.6-pl2+mpi~openmp ^plumed@2.3.0+mpi+gsl ^gsl@2.3
- cp2k@4.1+mpi~plumed ^parmetis@4.0.3 ^metis@5.1.0+real64
- cp2k@4.1+mpi+plumed ^parmetis@4.0.3 ^metis@5.1.0+real64 ^plumed@2.3.0+mpi+gsl ^gsl@2.3
- cp2k@5.1+mpi~plumed ^parmetis@4.0.3 ^metis@5.1.0+real64
- cp2k@5.1+mpi+plumed ^parmetis@4.0.3 ^metis@5.1.0+real64 ^plumed@2.3.0+mpi+gsl ^gsl@2.3
- espresso@6.1.0+mpi+scalapack+hdf5 ^fftw@3.3.6-pl2+mpi~openmp ^hdf5@1.10.1+szip+mpi~cxx
- espresso@6.1.0+mpi+scalapack ^fftw@3.3.6-pl2+mpi~openmp
- namd fftw=mkl interface=python @2.12 ^ charm backend=mpi @6.7.1 ^ python@2.7.13 ^ tcl@8.6.6
- amber@16+mpi ^netcdf-fortran@4.4.4 ^netcdf@4.4.1.1+mpi ^hdf5@1.10.1+szip+mpi~cxx ^py-scipy@0.19.0 ^py-matplotlib@2.0.0 ^py-numpy+blas+lapack@1.12.1 ^python@2.7.13
- yambo@4.1.3 ^netcdf-fortran@4.4.4 ^netcdf@4.4.1.1~mpi ^hdf5@1.10.1+szip~mpi
- cpmd@v4.1~openmp ^fftw@3.3.6-pl2+mpi~openmp
- petsc@3.7.6+boost+double+hdf5+metis+mpi+mumps~superlu-dist~hypre ^hdf5@1.10.1+szip+mpi~cxx ^mumps@5.1.1+mpi+parmetis+metis+scotch+ptscotch ^parmetis@4.0.3 ^metis@5.1.0+real64 ^scotch@6.0.4+esmumps+mpi~metis ^boost@1.63.0+icu+mpi+python ^python@2.7.13
# TODO: - nwchem@6.6 ^python@2.7.13
# TODO: - caffe@1.0+python+opencv ^hdf5@1.10.1+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@1.10.1+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@1.10.1+szip+mpi~cxx ^mumps@5.1.1+mpi+parmetis+metis+scotch+ptscotch ^parmetis@4.0.3 ^metis@5.1.0+real64 ^scotch@6.0.4+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
- lammps@20170901+lib+rigid+user-nc-dump+meam+voronoi+user-atc+manybody ^netcdf@4.4.1.1+mpi ^hdf5@1.10.1+szip+mpi~cxx ^voropp@0.4.6+pic
- molpro+mpi
# Serial applications built with the Intel stack that use LAPACK
intel-lapack-applications:
target_matrix:
- intel
requires:
- architecture
- compiler
- lapack
specs:
- r@3.3.2+external-lapack
# Serial applications built with the GNU stable stack
gnu-serial-applications:
target_matrix:
- gnu-stable
requires:
- architecture
- compiler
specs:
- qt@4.8.6
- opencv@3.2.0+qt~vtk~eigen ^qt@4.8.6
- hisat2@2.1.0
- samtools@1.4
- subread@1.5.2
- bowtie@1.2+tbb ^tbb@2017.5
- bowtie2@2.3.1 ^tbb@2017.5
- tophat@2.1.1 ^bowtie2@2.3.1 ^tbb@2017.5
# MPI applications built with the GNU stable stack
gnu-mpi-applications:
target_matrix:
- gnu-stable
target_filter:
mpi:
- 'mvapich2@2.2 fabrics=psm process_managers=slurm'
- 'mvapich2@2.2 fabrics=mrail process_managers=slurm'
- 'mvapich2@2.2 fabrics=sock process_managers=slurm'
requires:
- architecture
- compiler
- mpi
specs:
- gromacs@2016.3+mpi ^fftw@3.3.6-pl2+mpi~openmp
- namd fftw=3 interface=python @2.12 ^ charm backend=mpi @6.7.1 ^ fftw@3.3.6-pl2 ^ python@2.7.13 ^ tcl@8.6.6
- foam-extend+metis+scotch+parmetis+ptscotch~paraview ^parmetis@4.0.3
^metis@5.1.0+real64 ^scotch@6.0.4+esmumps+mpi~metis ^python@2.7.13
- openfoam-com~paraview~int64+metis+scotch+source ^scotch@6.0.4+esmumps+mpi~metis ^cgal@4.9.1 ^boost@1.63.0+icu+mpi+python ^python@2.7.13
- neuron@7.5+mpi+python+shared ^python@2.7.13
# MPI applications built with the GNU stable stack that use LAPACK
gnu-mpi-lapack-applications:
target_matrix:
- gnu-stable
target_filter:
lapack: ['openblas@0.2.19~openmp']
mpi:
- 'mvapich2@2.2 fabrics=psm process_managers=slurm'
- 'mvapich2@2.2 fabrics=mrail process_managers=slurm'
- 'mvapich2@2.2 fabrics=sock process_managers=slurm'
requires:
- architecture
- compiler
- mpi
- lapack
specs:
- plumed@2.3.0+mpi+gsl ^gsl@2.3
- gromacs@2016.1+mpi+plumed ^fftw@3.3.6-pl2+mpi~openmp ^plumed@2.3.0+mpi+gsl ^gsl@2.3
- cp2k@4.1+mpi~plumed ^netlib-scalapack@2.0.2 ^parmetis@4.0.3 ^metis@5.1.0+real64
- cp2k@4.1+mpi+plumed ^netlib-scalapack@2.0.2 ^parmetis@4.0.3 ^metis@5.1.0+real64 ^plumed@2.3.0+mpi+gsl ^gsl@2.3
- nwchem@6.6 ^netlib-scalapack@2.0.2 ^python@2.7.13
- abinit@8.2.2~hdf5~openmp+mpi+scalapack ^fftw@3.3.6-pl2+mpi~openmp ^netlib-scalapack@2.0.2
- espresso@6.1.0+mpi+scalapack ^fftw@3.3.6-pl2+mpi~openmp ^netlib-scalapack@2.0.2
- espresso@6.1.0+mpi+scalapack+hdf5 ^fftw@3.3.6-pl2+mpi~openmp ^netlib-scalapack@2.0.2 ^hdf5@1.10.1+szip+mpi~cxx
- cpmd@v4.1~openmp ^fftw@3.3.6-pl2+mpi~openmp
# TODO: - petsc@3.7.6+boost+double+hdf5+metis+mpi+mumps~superlu-dist~hypre ^hdf5@1.10.1+szip+mpi~cxx ^mumps@5.1.1+mpi+parmetis+metis+scotch+ptscotch ^parmetis@4.0.3 ^metis@5.1.0+real64 ^scotch@6.0.4+esmumps+mpi~metis ^netlib-scalapack@2.0.2 ^boost@1.63.0+icu+mpi+python ^python@2.7.13
# TODO: - caffe@1.0+python+opencv ^hdf5@1.10.1+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
- amber@16+mpi ^netcdf-fortran@4.4.4 ^netcdf@4.4.1.1+mpi ^hdf5@1.10.1+szip+mpi~cxx ^py-scipy@0.19.0 ^py-matplotlib@2.0.0 ^py-numpy+blas+lapack@1.12.1 ^python@2.7.13
- yambo@4.1.3 ^netcdf-fortran@4.4.4 ^netcdf@4.4.1.1~mpi ^hdf5@1.10.1+szip~mpi
# TODO: - gmsh@3.0.1+mpi+hdf5+fltk+compression ^hdf5@1.10.1+szip+mpi~cxx
# TODO: - paraview@5.3.0+mpi+osmesa+qt+python ^py-matplotlib@2.0.0 ^py-numpy+blas+lapack@1.12.1 ^python@2.7.13 ^qt@4.8.6
# 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@1.10.1+szip+mpi~cxx ^mumps@5.1.1+mpi+parmetis+metis+scotch+ptscotch ^parmetis@4.0.3 ^metis@5.1.0+real64 ^scotch@6.0.4+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
- lammps@20170901+lib+rigid+user-nc-dump+meam+voronoi+user-atc+manybody ^netcdf@4.4.1.1+mpi ^hdf5@1.10.1+szip+mpi~cxx ^voropp@0.4.6+pic
##########
# GPU Nodes
##########
gnu-gpu-serial:
target_matrix:
- gnu-gpu
requires:
- architecture
- compiler
specs:
- fftw@3.3.6-pl2~mpi
- fftw@3.3.6-pl2~mpi+openmp
- cuda@8.0.61
- cudnn@6.0 ^cuda@8.0.61
# FIXME: tensorflow+cuda is missing
gnu-gpu-python-lapack:
target_matrix:
- gnu-gpu
requires:
- architecture
- compiler
- python
- lapack
specs:
- py-theano@0.8.2+gpu ^py-scipy@0.19.0 ^py-numpy+blas+lapack@1.12.1 ^cuda@8.0.61
gnu-gpu-mpi-libraries:
target_matrix:
- gnu-gpu
requires:
- architecture
- compiler
- mpi
specs:
- boost@1.63.0+icu+mpi+python ^python@2.7.13
gnu-gpu-lapack-libraries:
target_matrix:
- gnu-gpu
requires:
- architecture
- compiler
- lapack
specs:
- magma+fortran
gnu-gpu-mpi-applications:
target_matrix:
- gnu-gpu
requires:
- architecture
- compiler
- mpi
specs:
- relion@2.0.3+cuda+double+double-gpu+gui ^fftw@3.3.6-pl2+mpi~openmp ^cuda@8.0.61
gnu-gpu-mpi-lapack-applications:
target_matrix:
- gnu-gpu
requires:
- architecture
- compiler
- lapack
- mpi
specs:
- amber@16+mpi+cuda ^py-scipy@0.19.0 ^py-matplotlib@2.0.0 ^py-numpy+blas+lapack@1.12.1 ^python@2.7.13 ^cuda@8.0.61
# TODO: - caffe@1.0+python+opencv+cuda ^hdf5@1.10.1+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 ^cuda@8.0.61