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Commit 90b8f736 authored by Nicolas Richart's avatar Nicolas Richart
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Adding the python packages

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Pipeline #198105 failed
Stage: .pre
Stage: environment
Stage: compilers
Stage: concretize
Stage: install
Stage: deploy
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stacks/pinot-noir/packages_jed.yaml
+ 11
− 1
View file @ 90b8f736
......@@ -2,6 +2,8 @@ packages:
all:
target: ["icelake"]
require:
- "~rocm"
- spec: cuda_arch=90 target=icelake
when: '+cuda'
......@@ -26,9 +28,17 @@ packages:
- spec: '+cuda cuda_arch=90'
when: '%gcc'
# py-torch:
# require:
# - spec: '+cuda cuda_arch=90 +nccl'
quantum-espresso:
require:
- spec: '~cuda'
ucx:
require:
- spec: '+xpmem +cma +rdmacm +rc +ud +dc +verbs +ib_hw_tm +vfs +gdrcopy +cuda cuda_arch=90 target=icelake'
- spec: '+xpmem +cma +rdmacm +rc +ud +dc +verbs +ib_hw_tm +vfs +gdrcopy +cuda cuda_arch=90 target=icelake ~rocm'
# ---------------------------------------------------------------------------
# Externals
......
stacks/pinot-noir/packages_stack.yaml
+ 14
− 10
View file @ 90b8f736
......@@ -45,11 +45,13 @@ packages:
# Requirements
# ----------------------------------------------------------------------------
boost:
prefer:
- spec: 'cxxstd=14 +icu ~mpi +python +numpy +atomic +chrono +container +date_time
+filesystem +graph +iostreams ~json +locale +log +math ~pic +program_options
+random +regex +serialization +shared +signals ~singlethreaded ~stacktrace +system
~taggedlayout +test +thread +timer ~type_erasure ~versionedlayout +wave +exception'
prefer: ['~mpi']
require: ['cxxstd=14', '+icu', '+python', '+numpy', '+atomic', '+chrono',
'+container', '+date_time', '+filesystem', '+graph', '+iostreams', '~json',
'+locale', '+log', '+math', '~pic', '+program_options', '+random', '+regex',
'+serialization', '+shared', '+signals', '~singlethreaded', '~stacktrace',
'+system', '~taggedlayout', '+test', '+thread', '+timer', '~type_erasure',
'~versionedlayout', '+wave', '+exception']
cuda:
require:
......@@ -62,8 +64,7 @@ packages:
- spec: '@5.4.10'
fftw:
prefer:
- spec: '+mpi +openmp'
prefer: ['+mpi', '+openmp']
hdf5:
prefer:
......@@ -91,6 +92,9 @@ packages:
llvm:
prefer: ['~clang']
libxcb:
require: ['+use_spack_interpreter']
mesa:
require: ['~llvm', '+opengl', '+opengles', '+osmesa']
......@@ -105,7 +109,7 @@ packages:
openmpi:
require:
- spec: '@5.0.3 fabrics=ofi,ucx,verbs schedulers=slurm ~rsh +romio romio-filesystem=gpfs +internal-pmix'
- spec: '@5.0.3 fabrics=ofi,ucx,verbs schedulers=slurm ~rsh +romio romio-filesystem=gpfs +internal-pmix ~memchecker'
- spec: ^ucx +cuda
when: +cuda
......@@ -115,8 +119,8 @@ packages:
python:
require:
- spec: +ssl
- spec: +optimizations
- spec: '+ssl +tkinter'
- spec: '+optimizations'
when: '%gcc'
tk:
......
stacks/pinot-noir/spack.yaml
+ 142
− 22
View file @ 90b8f736
......@@ -59,6 +59,7 @@ spack:
- lmod
- mpfr
- neovim
- ninja
- parallel
- picard
- rclone
......@@ -101,6 +102,7 @@ spack:
- star
- subread
- superlu
- unblur ^fftw~mpi~openmp
- voropp
- gcc_serial_codes:
......@@ -115,7 +117,6 @@ spack:
- rust
- sox
- stacks
- unblur ^fftw~mpi
- oneapi_serial_codes:
- abaqus@2023
......@@ -140,6 +141,92 @@ spack:
- 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-h5py
- 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-deeptools
- py-scikit-learn
- py-scipy
- py-statsmodels
- py-theano +cuda cuda_arch=70
- py-cryolobm
- py-pymol
# -------------------------------------------------------------------------
# Parallel codes
# -------------------------------------------------------------------------
......@@ -150,6 +237,7 @@ spack:
- osu-micro-benchmarks +graphing
- parmetis
- phylobayesmpi
- py-mpi4py
- scotch +mpi
- netcdf-c
- netcdf-fortran
......@@ -158,23 +246,22 @@ spack:
- gcc_mpi_codes:
- wrf ~pnetcdf build_type=dm+sm
- blas_mpi_codes:
- 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
- py-mpi4py
#- quantum-espresso +mpi +scalapack +gipaw
#- quantum-espresso +mpi +scalapack +gipaw hdf5=parallel
- gcc_blas_mpi_codes:
- 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
- blas_mpi_python_codes:
- mpi_blas_python_codes:
- boost +mpi
- cgal
- iq-tree@1.6.12+mpi
......@@ -184,25 +271,25 @@ spack:
- py-petsc4py
- slepc
- gcc_blas_mpi_python_codes:
- adios2
- gcc_mpi_blas_python_codes:
#- eman2 +mpi
- adios2
- cp2k +mpi +plumed +openmp smm=blas
- fenics +parmetis +hdf5 +scotch +suite-sparse ~vtk ~trilinos
- gromacs +mpi +plumed
- lammps build_type=Release +asphere +atc +body +class2 +colloid +compress +coreshell +dipole +diffraction +extra-dump +granular +h5md +kspace +latboltz +latte +lib +manybody +mc +misc +molecule +mpi +mpiio +netcdf +peri ~poems +python +qeq +replica +rigid +shock +ml-snap +srd +voronoi +plumed
- opencv +vtk +python3
- openfoam +metis
- paraview +shared +python +hdf5 ~osmesa +opengl2 +egl
- py-h5py
- py-horovod
- py-keras
- py-tensorflow +mpi
- py-topaz
- py-torch +mpi ~magma
- py-torch@2.3.0 +mpi ~magma
- py-torchvision
- relion ~mklfft
- topaz
- vtk
- paraview +shared +python3 +hdf5 ~osmesa +opengl2
- py-h5py
- cp2k +mpi +plumed +openmp smm=blas
# -------------------------------------------------------------------------
# External packages
......@@ -279,17 +366,50 @@ spack:
- [$%compiler_gcc]
- matrix:
- [blas_codes]
- [$blas_codes]
- [$^blas_gcc]
- [$%compiler_gcc]
- matrix:
- [blas_codes]
- [$blas_codes]
- [$^blas_oneapi]
- [$%compiler_oneapi]
- matrix:
- [gcc_blas_codes]
- [$gcc_blas_codes]
- [$^blas_gcc]
- [$%compiler_gcc]
- matrix:
- [$python_codes]
- [$^python_gcc]
- [$%compiler_gcc]
- matrix:
- [$gcc_python_codes]
- [$^python_gcc]
- [$%compiler_gcc]
- matrix:
- [$python_codes]
- [$^python_oneapi]
- [$%compiler_oneapi]
- matrix:
- [$python_blas_codes]
- [$^python_gcc]
- [$^blas_gcc]
- [$%compiler_gcc]
- matrix:
- [$python_blas_codes]
- [$^python_oneapi]
- [$^blas_oneapi]
- [$%compiler_oneapi]
- matrix:
- [$gcc_python_blas_codes]
- [$^python_gcc]
- [$^blas_gcc]
- [$%compiler_gcc]
......@@ -309,33 +429,33 @@ spack:
- [$%compiler_gcc]
- matrix:
- [$blas_mpi_codes]
- [$mpi_blas_codes]
- [$^blas_oneapi]
- [$^mpi_oneapi]
- [$%compiler_oneapi]
- matrix:
- [$blas_mpi_codes]
- [$mpi_blas_codes]
- [$^blas_gcc]
- [$^mpi_gcc]
- [$%compiler_gcc]
- matrix:
- [$blas_mpi_python_codes]
- [$mpi_blas_python_codes]
- [$^blas_oneapi]
- [$^mpi_oneapi]
- [$^python_oneapi]
- [$%compiler_oneapi]
- matrix:
- [$blas_mpi_python_codes]
- [$mpi_blas_python_codes]
- [$^blas_gcc]
- [$^mpi_gcc]
- [$^python_gcc]
- [$%compiler_gcc]
- matrix:
- [$gcc_blas_mpi_python_codes]
- [$gcc_mpi_blas_python_codes]
- [$^blas_gcc]
- [$^mpi_gcc]
- [$^python_gcc]
......
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