From ba4d5eb14d82777ec93c4e283f4e26ff0fd200a6 Mon Sep 17 00:00:00 2001
From: Nicolas Richart <nicolas.richart@epfl.ch>
Date: Sun, 23 Jun 2024 23:56:33 +0200
Subject: [PATCH] Adding most of the mpi codes
---
stacks/pinot-noir/packages_stack.yaml | 20 ++++-
stacks/pinot-noir/spack.yaml | 123 +++++++++++++++++++++++++-
2 files changed, 137 insertions(+), 6 deletions(-)
diff --git a/stacks/pinot-noir/packages_stack.yaml b/stacks/pinot-noir/packages_stack.yaml
index c8df86f..076ef54 100644
--- a/stacks/pinot-noir/packages_stack.yaml
+++ b/stacks/pinot-noir/packages_stack.yaml
@@ -44,6 +44,13 @@ 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'
+
cuda:
require:
- spec: '@12.4.0'
@@ -54,9 +61,15 @@ packages:
require:
- spec: '@5.4.10'
+ fftw:
+ prefer:
+ - spec: '+mpi +openmp'
+
hdf5:
- require:
+ prefer:
+ - spec: '+mpi'
- spec: '@1.14.3'
+ require:
- spec: '+hl +threadsafe +szip +cxx +fortran'
- spec: '+ipo'
when: '%gcc'
@@ -84,6 +97,9 @@ packages:
metis:
require: ['+real64']
+ netcdf-c:
+ prefer: ['+mpi']
+
openblas:
prefer: ['threads=pthreads']
@@ -95,7 +111,7 @@ packages:
petsc:
require:
- - spec: '+hypre +mumps +saws +scalapack'
+ - spec: '+hypre +mumps +saws +scalapack +mpi'
python:
require:
diff --git a/stacks/pinot-noir/spack.yaml b/stacks/pinot-noir/spack.yaml
index 3fec7b0..13371cc 100644
--- a/stacks/pinot-noir/spack.yaml
+++ b/stacks/pinot-noir/spack.yaml
@@ -79,17 +79,22 @@ spack:
# -------------------------------------------------------------------------
- serial_codes:
- bwa
+ - boost ~mpi
- fftw +openmp ~mpi
- fftw ~openmp ~mpi
+ - eigen
- gsl
- #- hdf5 ~mpi
+ - hdf5@1.14.1 ~mpi
- hisat2
- htslib
- intel-oneapi-tbb
- jasper
+ - kallisto ^hdf5 ~mpi
- mafft
- metis
- muscle
+ - netcdf-c~mpi ^hdf5~mpi
+ - netcdf-fortran ^netcdf-c ~mpi ^hdf5 ~mpi
- nfft
- python
- scotch
@@ -99,30 +104,105 @@ spack:
- 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
+ - rust
+ - sox
- stacks
-
+ - unblur ^fftw~mpi
+
+ - oneapi_serial_codes:
+ - abaqus@2023
+ - intel-oneapi-ipp
+
# -------------------------------------------------------------------------
# Empty to specialize in environments
# -------------------------------------------------------------------------
- cuda_system_codes: []
+ - 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
+
# -------------------------------------------------------------------------
# Parallel codes
# -------------------------------------------------------------------------
- mpi_codes:
- - osu-micro-benchmarks +graphing
+ - fftw +mpi +openmp
- hdf5@1.14.3 +mpi
+ - openfoam-org +metis ^scotch+mpi
+ - osu-micro-benchmarks +graphing
+ - parmetis
+ - phylobayesmpi
+ - scotch +mpi
+ - netcdf-c
+ - netcdf-fortran
- parmetis
+ - gcc_mpi_codes:
+ - wrf ~pnetcdf build_type=dm+sm
+
- blas_mpi_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
+
+ - gcc_blas_mpi_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:
- - petsc@3.21.1 +mpi
+ - boost +mpi
+ - cgal
+ - iq-tree@1.6.12+mpi
+ - neuron +mpi +python
+ - petsc@3.21.1
+ - plumed
+ - py-petsc4py
+ - slepc
+
+ - gcc_blas_mpi_python_codes:
+ - adios2
+ - eman2 +mpi
+ - 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
+ - py-horovod
+ - py-keras
+ - py-tensorflow +mpi
+ - py-topaz
+ - py-torch +mpi ~magma
+ - py-torchvision
+ - relion ~mklfft
+ - vtk
+ - paraview +shared +python3 +hdf5 ~osmesa +opengl2
+ - py-h5py
+ - cp2k +mpi +plumed +openmp smm=blas
# -------------------------------------------------------------------------
# Generic definitions
@@ -168,6 +248,29 @@ spack:
- [$gcc_serial_codes]
- [$%compiler_gcc]
+ - matrix:
+ - [$oneapi_serial_codes]
+ - [$%compiler_oneapi]
+
+ - matrix:
+ - [$cuda_serial_codes]
+ - [$%compiler_gcc]
+
+ - matrix:
+ - [blas_codes]
+ - [$^blas_gcc]
+ - [$%compiler_gcc]
+
+ - matrix:
+ - [blas_codes]
+ - [$^blas_oneapi]
+ - [$%compiler_oneapi]
+
+ - matrix:
+ - [gcc_blas_codes]
+ - [$^blas_gcc]
+ - [$%compiler_gcc]
+
- matrix:
- [$mpi_codes]
- [$^mpi_oneapi]
@@ -178,6 +281,11 @@ spack:
- [$^mpi_gcc]
- [$%compiler_gcc]
+ - matrix:
+ - [$gcc_mpi_codes]
+ - [$^mpi_gcc]
+ - [$%compiler_gcc]
+
- matrix:
- [$blas_mpi_codes]
- [$^blas_oneapi]
@@ -204,6 +312,13 @@ spack:
- [$^python_gcc]
- [$%compiler_gcc]
+ - matrix:
+ - [$gcc_blas_mpi_python_codes]
+ - [$^blas_gcc]
+ - [$^mpi_gcc]
+ - [$^python_gcc]
+ - [$%compiler_gcc]
+
view: false
# default:
# root: /stack/packages/
--
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