Skip to content
Snippets Groups Projects
Commit a84fec69 authored by Nicolas Richart's avatar Nicolas Richart
Browse files

Creating minimal stack for kuma beta

parent 2c026c13
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
stacks/pinot-noir-gcc/config.json
+ 2
− 2
View file @ a84fec69
......@@ -23,8 +23,8 @@
}
},
"stack": {
"version": "v1",
"mount_point": "/stack",
"version": "beta-v1",
"mount_point": "/ssoft/spack",
"system_arch": "target=x86_64_v3",
"system_compiler": {
"gcc@11": {
......
stacks/pinot-noir-gcc/spack.yaml
+ 11
− 302
View file @ a84fec69
......@@ -40,17 +40,9 @@ spack:
- bzip2
- cmake
- emacs +tls
- fastqc
- fio
- git
- git-lfs
- gmp
- gnuplot
- gzip
- imagemagick +ghostscript
- intel-oneapi-advisor
- intel-oneapi-inspector
- intel-oneapi-vtune
- libarchive
- libjpeg-turbo
- libpng
......@@ -60,19 +52,12 @@ spack:
- mpfr
- neovim
- ninja
- parallel
- picard
- rclone
- rust
- sbt
- sratoolkit
- subversion
- tar
- tcl
- tk
- tmux
- trimmomatic
- valgrind
- xclip
- zlib-ng
......@@ -80,48 +65,7 @@ spack:
# Serial codes
# -------------------------------------------------------------------------
- serial_codes:
- bwa
- boost ~mpi
- fftw +openmp ~mpi
- fftw ~openmp ~mpi
- eigen
- gsl
- hdf5@1.14.1 ~mpi
- hisat2
- htslib
- intel-oneapi-tbb
- jasper
- kallisto ^hdf5 ~mpi
- kokkos
- mafft
- metis
- muscle
- netcdf-c~mpi ^hdf5~mpi
- netcdf-fortran ^netcdf-c ~mpi ^hdf5 ~mpi
- nfft ^fftw~mpi~openmp
- python
- scotch ~mpi
- star
- subread
- superlu
- unblur ^fftw~mpi~openmp
- voropp
- gcc_serial_codes:
- cistem ^fftw~mpi
- ctffind ^fftw ~mpi
- ffmpeg +libx264
- glpk+gmp
- hwloc
- intel-oneapi-mkl
- libxc
- ncview ^hdf5 ~mpi ^netcdf-c ~mpi ~parallel-netcdf
- sox
- stacks
- oneapi_serial_codes:
- abaqus@2023
- intel-oneapi-ipp
# -------------------------------------------------------------------------
# Empty to specialize in environments
......@@ -130,191 +74,6 @@ spack:
- cuda_serial_codes: []
# -------------------------------------------------------------------------
# Blas dependent codes
# -------------------------------------------------------------------------
- blas_codes:
- arpack-ng ~mpi
- superlu
- suite-sparse
- gcc_blas_codes:
- armadillo +hdf5 ^arpack-ng ~mpi ^hdf5 ~mpi
- octave
# -------------------------------------------------------------------------
# Python packages
# -------------------------------------------------------------------------
- python_codes:
- bedtools2
- bowtie2
- cairo
- mercurial
- prinseq-lite
- py-absl-py
- py-astunparse
- py-backports-entry-points-selectable
- py-certifi
- py-charset-normalizer
- py-cycler
- py-cython
- py-distlib
- py-filelock
- py-gast
- py-google-pasta
- py-idna
- py-kiwisolver
- py-mpmath
- py-packaging
- py-pillow
- py-pip
- py-platformdirs
- py-ply
- py-protobuf
- py-pybind11
- py-pyparsing
- py-python-dateutil
- py-pytz
- py-requests
- py-semver
- py-six
- py-sympy
- py-termcolor
- py-urllib3
- py-virtualenv
- py-wheel
- py-wrapt
- samtools
- scons
- snakemake
- python_blas_codes:
- boost
- gmsh ~mpi +hdf5 +cgns +eigen ~opencascade +openmp ~fltk ~med
- iq-tree
- py-biopython
- py-keras-preprocessing
- py-macs2
- py-matplotlib
- py-numpy
- py-opt-einsum
- py-pandas
- py-pybigwig
- py-xarray
- gcc_python_codes:
- blast-plus
- caffe +python
- gatk
- gdb +tui +source-highlight +xz
- julia+openlibm
- libgd
- mesa
- mummer
- node-js
- openbabel +python
- r
- spades
- xgboost
- gcc_python_blas_codes:
- polymake ^cddlib@0.94h
- py-cryolobm
- py-deeptools
- py-h5py ~mpi ^hdf5 ~mpi
- py-pymol
- py-scikit-learn
- py-scipy
- py-statsmodels
- py-theano
# -------------------------------------------------------------------------
# Parallel codes
# -------------------------------------------------------------------------
- mpi_codes:
- fftw +mpi +openmp
- hdf5@1.14.3 +mpi
- openfoam-org +metis
- osu-micro-benchmarks +graphing
- parmetis
- phylobayesmpi
- py-mpi4py
- scotch +mpi
- netcdf-c
- netcdf-fortran
- parmetis
- gcc_mpi_codes:
- wrf ~pnetcdf build_type=dm+sm
- mpi_blas_codes:
- 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
- gcc_mpi_blas_codes:
- gmsh +mpi +eigen +openmp +hdf5 ~fltk ~opencascade ~med ^mmg ~vtk
- cpmd ~openmp
- elmerfem +mumps +openmp +hypre
- netlib-scalapack
- yambo +mpi io=iotk,etsf-io
- mpi_blas_python_codes:
- boost +mpi
- cgal
- iq-tree@1.6.12+mpi
- neuron +mpi +python
- petsc@3.21.1
- plumed
- py-petsc4py
- slepc
- gcc_mpi_blas_python_codes:
# - eman2 +mpi
- adios2
- cp2k +mpi +plumed +openmp smm=blas
# - fenics +parmetis +hdf5 +scotch +suite-sparse ~vtk ~trilinos
- fenics-dolfinx
- gromacs +mpi +plumed
- lammps
- opencv
- openfoam +metis
- paraview +shared +python +hdf5 ~osmesa +opengl2 +egl
- py-fenics-dolfinx
- py-h5py +mpi
- py-horovod
- py-keras
- py-tensorflow
- py-torch
- py-torchvision
- relion ~mklfft
- topaz
- vtk
# -------------------------------------------------------------------------
# External packages
# -------------------------------------------------------------------------
- external_packages: []
- when: env['environment_type'] != 'cloud'
external_packages:
- ansys
- cfdplusplus
- comsol
- fdtd
- gurobi
- gaussian
- matlab
- maple
- mathematica
- molpro
- smr
- when: env['environment_type'] != 'cloud'
blas_mpi_codes:
- vasp +hdf5 +scalapack +shmem +wannier90
# -------------------------------------------------------------------------
# Generic definitions
......@@ -327,10 +86,18 @@ spack:
- matrix:
- [$compilers_specs]
- matrix:
- [$blas_oneapi]
- [$%compiler_oneapi]
- matrix:
- [$blas_gcc]
- [$%compiler_gcc]
- matrix:
- [$mpi_oneapi]
- [$%compiler_oneapi]
- matrix:
- [$mpi_gcc]
- [$%compiler_gcc]
......@@ -352,69 +119,11 @@ spack:
- [$%compiler_gcc]
- matrix:
- [$cuda_serial_codes]
- [$%compiler_gcc]
- matrix:
- [$blas_codes]
- [$^blas_gcc]
- [$%compiler_gcc]
- matrix:
- [$gcc_blas_codes]
- [$^blas_gcc]
- [$%compiler_gcc]
- matrix:
- [$python_codes]
- [$^python_gcc]
- [$%compiler_gcc]
- matrix:
- [$gcc_python_codes]
- [$^python_gcc]
- [$%compiler_gcc]
- matrix:
- [$python_blas_codes]
- [$^python_gcc]
- [$^blas_gcc]
- [$%compiler_gcc]
- matrix:
- [$gcc_python_blas_codes]
- [$^python_gcc]
- [$^blas_gcc]
- [$%compiler_gcc]
- matrix:
- [$mpi_codes]
- [$^mpi_gcc]
- [$%compiler_gcc]
- matrix:
- [$gcc_mpi_codes]
- [$^mpi_gcc]
- [$%compiler_gcc]
- [$oneapi_serial_codes]
- [$%compiler_oneapi]
- matrix:
- [$mpi_blas_codes]
- [$^blas_gcc]
- [$^mpi_gcc]
- [$%compiler_gcc]
- matrix:
- [$mpi_blas_python_codes]
- [$^blas_gcc]
- [$^mpi_gcc]
- [$^python_gcc]
- [$%compiler_gcc]
- matrix:
- [$gcc_mpi_blas_python_codes]
- [$^blas_gcc]
- [$^mpi_gcc]
- [$^python_gcc]
- [$cuda_serial_codes]
- [$%compiler_gcc]
view: false
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment