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Feat/stack pinot noir

Merged Feat/stack pinot noir
feat/stack_pinot_noir into main
Merged Nicolas Richart requested to merge feat/stack_pinot_noir into main
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stacks/pinot-noir/spack.yaml
+ 92
− 60
@@ -3,11 +3,13 @@ spack:
- compiler_definitions.yaml
- packages_stack.yaml
- packages_accel.yaml
- packages_env.yaml
- modules_stack.yaml
- modules_env.yaml
- definitions_accel.yaml
- definitions_env.yaml
- config_stack.yaml
@@ -23,7 +25,7 @@ spack:
- intel-oneapi-mpi@2021.12.1
- blas_gcc:
- openblas@0.3.26
- openblas@0.3.27
- blas_oneapi:
- intel-oneapi-mkl@2024.1.0
@@ -39,8 +41,8 @@ spack:
# -------------------------------------------------------------------------
- core_codes:
- bzip2
- cmake
- emacs +tls
- cmake +ncurses
- emacs
- fastqc
- fio
- git
@@ -48,24 +50,27 @@ spack:
- gmp
- gnuplot
- gzip
- imagemagick +ghostscript
- intel-oneapi-advisor
- intel-oneapi-inspector
- intel-oneapi-vtune
- libarchive
- libgd
- libjpeg-turbo
- libpng
- libtiff
- libxml2
- likwid
- lmod
- mpfr
- neovim
- ninja
#- ninja
- papi
- parallel
- picard
- rclone
- rust
- sbt
- squashfs
- squashfs-mount
- sratoolkit
- subversion
- tar
@@ -80,43 +85,42 @@ spack:
# Serial codes
# -------------------------------------------------------------------------
- serial_codes:
- bwa
- fftw +openmp ~mpi
- fftw ~openmp ~mpi
- eigen
- fftw +openmp ~~mpi
- fftw ~~openmp ~~mpi
- gsl
- hdf5@1.14.1 ~mpi
- hisat2
- hdf5@1.14.3 ~~mpi
- htslib
- intel-oneapi-tbb
- jasper
- kallisto ^hdf5 ~mpi
- kallisto ^hdf5 ~~mpi
- kokkos
- kokkos-kernels
- mafft
- metis
- muscle
- netcdf-c~mpi ^hdf5~mpi
- netcdf-fortran ^netcdf-c ~mpi ^hdf5 ~mpi
- nfft ^fftw~mpi~openmp
- netcdf-c ~~mpi
- netcdf-fortran ^netcdf-c ~~mpi
- nfft ^fftw~~mpi~~openmp
- python
- scotch ~mpi
- scotch ~~mpi
- star
- subread
- unblur ^fftw~mpi~openmp
- unblur ^fftw~~mpi ~~openmp
- voropp
- gcc_serial_codes:
- cistem ^fftw~mpi
- ctffind ^fftw ~mpi
- ffmpeg +libx264
- bwa
- eigen
- ffmpeg
- glpk+gmp
- hwloc
- intel-oneapi-mkl
- libxc
- ncview ^hdf5 ~mpi ^netcdf-c ~mpi ~parallel-netcdf
- qperf
- ncview ^netcdf-c ~~mpi ~parallel-netcdf
- sox
- stacks
- xgboost
- oneapi_serial_codes:
- abaqus@2023
@@ -129,16 +133,18 @@ spack:
- cuda_serial_codes: []
- cuda_mpi_codes: []
# -------------------------------------------------------------------------
# Blas dependent codes
# -------------------------------------------------------------------------
- blas_codes:
- arpack-ng ~mpi
- arpack-ng ~~mpi
- superlu
- suite-sparse
- gcc_blas_codes:
- armadillo +hdf5 ^arpack-ng ~mpi ^hdf5 ~mpi
- armadillo +hdf5 ^arpack-ng ~~mpi ^hdf5 ~~mpi
- octave
# -------------------------------------------------------------------------
@@ -188,111 +194,120 @@ spack:
- snakemake
- python_blas_codes:
- boost ~mpi
#- gmsh ~mpi +hdf5 +cgns +eigen ~opencascade +openmp ~fltk ~med
- boost ~~mpi
#- gmsh ~~mpi +hdf5 +cgns +eigen ~opencascade +openmp ~fltk ~med
- iq-tree
- py-biopython
- py-keras-preprocessing
- py-macs2
- py-macs3
- py-matplotlib
- py-numpy
- py-opt-einsum
- py-pandas
- py-pybigwig
- py-xarray
- valgrind
- valgrind ~~mpi
- gcc_python_codes:
- blast-plus
- caffe +python
- cistem ^fftw~~mpi
- ctffind ^fftw ~~mpi
- gatk
- gdb +tui +source-highlight +xz
- hisat2
- imagemagick +ghostscript
- julia+openlibm
- libgd
- mesa
- mummer
- node-js
- openbabel +python ^boost ~mpi
- r
- rust
- spades
- xgboost
- gcc_python_blas_codes:
- caffe +python ^hdf5~mpi
- gdb +tui +source-highlight +xz
- openbabel ++python ^boost ~~mpi
- polymake ^cddlib@0.94h
- py-cryolobm
- py-deeptools
- py-h5py ~mpi ^hdf5 ~mpi
- py-pymol
- py-h5py ~~mpi
- py-pymol ^hdf5~mpi
- py-scikit-learn
- py-scipy
- py-statsmodels
#- py-statsmodels
- py-theano
- r
# -------------------------------------------------------------------------
# Parallel codes
# -------------------------------------------------------------------------
- mpi_codes:
- fftw +mpi +openmp
- hdf5@1.14.3 +mpi
- fftw ++mpi +openmp
- hdf5@1.14.3 ++mpi
- openfoam-org +metis
- osu-micro-benchmarks +graphing
- parmetis
- phylobayesmpi
- py-mpi4py
- scotch +mpi
- scotch ++mpi
- netcdf-c
- netcdf-fortran
- parmetis
- scorep
- mpi_python_codes:
- py-mpi4py
- gcc_mpi_codes:
- wrf ~pnetcdf build_type=dm+sm
- mpi_blas_codes:
- arpack-ng +mpi
- arpack-ng ++mpi
- hypre@2.31.0
- mumps@5.6.2
- superlu-dist@8.2.1
#- quantum-espresso +mpi +scalapack +gipaw
#- quantum-espresso +mpi +scalapack +gipaw hdf5=parallel
#- quantum-espresso ++mpi +scalapack +gipaw
- quantum-espresso
- gcc_mpi_blas_codes:
- gmsh +mpi +eigen +openmp +hdf5 ~fltk ~opencascade ~med ^mmg ~vtk
- armadillo +hdf5 ^arpack-ng ++mpi ^hdf5 ++mpi
- gmsh ++mpi +eigen +openmp +hdf5 ~fltk ~opencascade ~med ^mmg ~vtk
- cpmd ~openmp
- elmerfem +mumps +openmp +hypre
- netlib-scalapack
- yambo +mpi io=iotk,etsf-io
- trilinos
- vtk
- yambo ++mpi io=iotk,etsf-io
- mpi_blas_python_codes:
- boost +mpi
- boost ++mpi
- cgal
- iq-tree@1.6.12+mpi
- neuron +mpi +python
- petsc@3.21.1
- iq-tree@1.6.12++mpi
- neuron ++mpi +python
- petsc
- plumed
- py-petsc4py
- slepc
- sirius
- gcc_mpi_blas_python_codes:
# - eman2 +mpi
# - eman2 ++mpi
- adios2
- cp2k +mpi +plumed +openmp smm=blas
- cp2k ++mpi +plumed +openmp smm=blas
# - fenics +parmetis +hdf5 +scotch +suite-sparse ~vtk ~trilinos
- fenics-dolfinx
- gromacs +mpi +plumed
- gromacs ++mpi +plumed
- lammps
- opencv
- openfoam +metis
- paraview +shared +python +hdf5 ~osmesa +opengl2 +egl
- paraview@5.12.0 +shared +python +hdf5 +opengl2
- py-fenics-dolfinx
- py-h5py +mpi
- py-horovod
- py-h5py ++mpi
# - py-horovod cannot resolve dependencies with pytorch
- py-keras
- py-tensorflow
- py-torch
- py-torchvision
- relion ~mklfft
- topaz
- vtk
# -------------------------------------------------------------------------
# External packages
@@ -392,11 +407,22 @@ spack:
- [$^mpi_gcc]
- [$%compiler_gcc]
- matrix:
- [$mpi_python_codes]
- [$^python_gcc]
- [$^mpi_gcc]
- [$%compiler_gcc]
- matrix:
- [$gcc_mpi_codes]
- [$^mpi_gcc]
- [$%compiler_gcc]
- matrix:
- [$cuda_mpi_codes]
- [$^mpi_gcc]
- [$%compiler_gcc]
- matrix:
- [$mpi_blas_codes]
- [$^blas_gcc]
@@ -405,16 +431,16 @@ spack:
- matrix:
- [$mpi_blas_python_codes]
- [$^python_gcc]
- [$^blas_gcc]
- [$^mpi_gcc]
- [$^python_gcc]
- [$%compiler_gcc]
- matrix:
- [$gcc_mpi_blas_python_codes]
- [$^python_gcc]
- [$^blas_gcc]
- [$^mpi_gcc]
- [$^python_gcc]
- [$%compiler_gcc]
# --------------------------------------------------------------------------
@@ -455,6 +481,12 @@ spack:
- [$^mpi_oneapi]
- [$%compiler_oneapi]
- matrix:
- [$mpi_python_codes]
- [$^python_oneapi]
- [$^mpi_oneapi]
- [$%compiler_oneapi]
- matrix:
- [$mpi_blas_codes]
- [$^blas_oneapi]
@@ -463,9 +495,9 @@ spack:
- matrix:
- [$mpi_blas_python_codes]
- [$^python_oneapi]
- [$^blas_oneapi]
- [$^mpi_oneapi]
- [$^python_oneapi]
- [$%compiler_oneapi]
view: false