From 90b8f736f8dc8c7d545083f7ca5c2cb7341b36e2 Mon Sep 17 00:00:00 2001
From: Nicolas Richart <nicolas.richart@epfl.ch>
Date: Wed, 26 Jun 2024 09:53:29 +0200
Subject: [PATCH] Adding the python packages
---
stacks/pinot-noir/packages_jed.yaml | 12 +-
stacks/pinot-noir/packages_stack.yaml | 24 ++--
stacks/pinot-noir/spack.yaml | 164 ++++++++++++++++++++++----
3 files changed, 167 insertions(+), 33 deletions(-)
diff --git a/stacks/pinot-noir/packages_jed.yaml b/stacks/pinot-noir/packages_jed.yaml
index d43e828..d70bcd7 100644
--- a/stacks/pinot-noir/packages_jed.yaml
+++ b/stacks/pinot-noir/packages_jed.yaml
@@ -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
diff --git a/stacks/pinot-noir/packages_stack.yaml b/stacks/pinot-noir/packages_stack.yaml
index 076ef54..c125cf4 100644
--- a/stacks/pinot-noir/packages_stack.yaml
+++ b/stacks/pinot-noir/packages_stack.yaml
@@ -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:
diff --git a/stacks/pinot-noir/spack.yaml b/stacks/pinot-noir/spack.yaml
index 4256067..5341663 100644
--- a/stacks/pinot-noir/spack.yaml
+++ b/stacks/pinot-noir/spack.yaml
@@ -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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