diff --git a/stacks/pinot-noir-gcc/config.json b/stacks/pinot-noir-gcc/config.json
index dd541dc7663a4a173cce978bdc14486addd959c9..5527a93ec5c62dfb5d2560989833bdc9baaabade 100644
--- a/stacks/pinot-noir-gcc/config.json
+++ b/stacks/pinot-noir-gcc/config.json
@@ -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": {
diff --git a/stacks/pinot-noir-gcc/spack.yaml b/stacks/pinot-noir-gcc/spack.yaml
index b1195d1e7e381f38879378957817e46a211565ac..bc226accf7353bfef40695b18e5928f212eac34f 100644
--- a/stacks/pinot-noir-gcc/spack.yaml
+++ b/stacks/pinot-noir-gcc/spack.yaml
@@ -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