From 2c026c1370ed254685c9f323283f7cd8e06087f9 Mon Sep 17 00:00:00 2001
From: Nicolas Richart <nicolas.richart@epfl.ch>
Date: Tue, 9 Jul 2024 15:10:06 +0200
Subject: [PATCH] Adding missing files and more constraints to help
concretizing
---
.../pinot-noir-gcc/definitions_kuma_h100.yaml | 7 ++
stacks/pinot-noir-gcc/packages_kuma_h100.yaml | 6 +-
stacks/pinot-noir/definitions_kuma_h100.yaml | 7 ++
stacks/pinot-noir/packages_jed.yaml | 5 +
stacks/pinot-noir/packages_stack.yaml | 54 ++-------
stacks/pinot-noir/spack.yaml | 114 +++++++++---------
6 files changed, 90 insertions(+), 103 deletions(-)
create mode 100644 stacks/pinot-noir-gcc/definitions_kuma_h100.yaml
create mode 100644 stacks/pinot-noir/definitions_kuma_h100.yaml
diff --git a/stacks/pinot-noir-gcc/definitions_kuma_h100.yaml b/stacks/pinot-noir-gcc/definitions_kuma_h100.yaml
new file mode 100644
index 0000000..0f156fa
--- /dev/null
+++ b/stacks/pinot-noir-gcc/definitions_kuma_h100.yaml
@@ -0,0 +1,7 @@
+definitions:
+ - cuda_system_codes:
+ - cuda
+ - cudnn
+
+ - cuda_serial_codes:
+ - nccl
diff --git a/stacks/pinot-noir-gcc/packages_kuma_h100.yaml b/stacks/pinot-noir-gcc/packages_kuma_h100.yaml
index 425f8b3..07fab46 100644
--- a/stacks/pinot-noir-gcc/packages_kuma_h100.yaml
+++ b/stacks/pinot-noir-gcc/packages_kuma_h100.yaml
@@ -4,7 +4,7 @@ packages:
require:
- "~rocm"
- - spec: cuda_arch=90 target=icelake
+ - spec: cuda_arch=90 target=zen4
when: '+cuda'
- spec: '+cuda'
@@ -23,7 +23,7 @@ packages:
openmpi:
require:
- - spec: '+cuda cuda_arch=90 target=icelake'
+ - spec: '+cuda cuda_arch=90 target=zen4'
petsc:
require:
@@ -48,7 +48,7 @@ packages:
ucx:
require:
- - spec: '+xpmem +cma +rdmacm +rc +ud +dc +verbs +ib_hw_tm +gdrcopy +cuda cuda_arch=90 target=icelake ~rocm'
+ - spec: '+xpmem +cma +rdmacm +rc +ud +dc +verbs +ib_hw_tm +gdrcopy +cuda cuda_arch=90 ~rocm target=zen4'
# ---------------------------------------------------------------------------
# Externals
diff --git a/stacks/pinot-noir/definitions_kuma_h100.yaml b/stacks/pinot-noir/definitions_kuma_h100.yaml
new file mode 100644
index 0000000..0f156fa
--- /dev/null
+++ b/stacks/pinot-noir/definitions_kuma_h100.yaml
@@ -0,0 +1,7 @@
+definitions:
+ - cuda_system_codes:
+ - cuda
+ - cudnn
+
+ - cuda_serial_codes:
+ - nccl
diff --git a/stacks/pinot-noir/packages_jed.yaml b/stacks/pinot-noir/packages_jed.yaml
index 186b82d..822d1e2 100644
--- a/stacks/pinot-noir/packages_jed.yaml
+++ b/stacks/pinot-noir/packages_jed.yaml
@@ -23,6 +23,11 @@ packages:
- spec: '+cuda cuda_arch=90 +cuda_uvm +wrapper ~openmptarget'
when: '%gcc'
+ kokkos-kernels:
+ require:
+ - spec: '+cuda cuda_arch=90'
+ when: '%gcc'
+
openmpi:
require:
- spec: '+cuda cuda_arch=90 target=icelake'
diff --git a/stacks/pinot-noir/packages_stack.yaml b/stacks/pinot-noir/packages_stack.yaml
index d75c10a..d12a3aa 100644
--- a/stacks/pinot-noir/packages_stack.yaml
+++ b/stacks/pinot-noir/packages_stack.yaml
@@ -9,48 +9,6 @@ packages:
- spec: "^libiconv"
when: "^iconv"
- # - spec: ^intel-oneapi-mpi
- # when: '%oneapi ^mpi'
-
- # - spec: ^openmpi
- # when: '%gcc ^mpi'
-
- # - spec: ^openmpi
- # when: '%aocc ^mpi'
-
- # - spec: ^nvhpc+mpi
- # when: '%nvhpc ^mpi'
-
- - spec: ^openblas %gcc
- when: '%gcc ^blas'
-
- - spec: ^eigen %gcc
- when: '%gcc ^eigen'
-
- - spec: ^kokkos %gcc
- when: '%gcc ^kokkos'
-
- # - spec: ^openblas
- # when: '%gcc ^lapack'
-
- # - spec: ^intel-oneapi-mkl
- # when: '%oneapi ^blas'
-
- # - spec: ^intel-oneapi-mkl
- # when: '%oneapi ^lapack'
-
- # - spec: ^nvhpc+blas
- # when: '%nvhpc ^blas'
-
- # - spec: ^nvhpc+lapack
- # when: '%nvhpc ^lapack'
-
- # - spec: ^openblas
- # when: '%gcc ^py-numpy'
-
- # - spec: ^intel-oneapi-mkl
- # when: '%oneapi ^py-numpy'
-
- spec: '+ipo'
when: '%gcc'
@@ -99,12 +57,15 @@ packages:
- spec: '@2.31.0 ~magma'
intel-oneapi-mkl:
- prefer: ['+cluster']
+ prefer: ['~cluster']
kokkos:
- prefer: ['+openmp', '+openmptarget', '+numactl', '+memkind', '+threads',
+ prefer: ['+openmp', '+numactl', '+memkind', '+threads',
'+aggressive_vectorization']
+ kokkos-kernel:
+ prefer: ['+openmp', '+threads']
+
lammps:
require: ['build_type=Release', '+asphere', '+atc', '+body', '+class2',
'+colloid', '+compress', '+coreshell', '+dipole', '+diffraction', '+extra-dump',
@@ -158,6 +119,9 @@ packages:
py-torch:
require: ['+mpi']
+ scotch:
+ prefer: ['~mpi']
+
suite-sparse:
require:
- spec: '+graphblas'
@@ -167,7 +131,7 @@ packages:
ucx:
require:
- - spec: +rdmacm +rc +dc +ud +cma +verbs
+ - spec: '+rdmacm +rc +dc +ud +cma +verbs'
zlib-ng:
require: ['build_system=autotools']
diff --git a/stacks/pinot-noir/spack.yaml b/stacks/pinot-noir/spack.yaml
index 1bafcf1..d80e2cc 100644
--- a/stacks/pinot-noir/spack.yaml
+++ b/stacks/pinot-noir/spack.yaml
@@ -72,7 +72,6 @@ spack:
- tk
- tmux
- trimmomatic
- - valgrind
- xclip
- zlib-ng
@@ -81,7 +80,6 @@ spack:
# -------------------------------------------------------------------------
- serial_codes:
- bwa
- - boost ~mpi
- fftw +openmp ~mpi
- fftw ~openmp ~mpi
- eigen
@@ -93,17 +91,17 @@ spack:
- jasper
- kallisto ^hdf5 ~mpi
- kokkos
+ - kokkos-kernels
- mafft
- metis
- muscle
- netcdf-c~mpi ^hdf5~mpi
- netcdf-fortran ^netcdf-c ~mpi ^hdf5 ~mpi
- - nfft
+ - nfft ^fftw~mpi~openmp
- python
- - scotch
+ - scotch ~mpi
- star
- subread
- - superlu
- unblur ^fftw~mpi~openmp
- voropp
@@ -189,8 +187,8 @@ spack:
- snakemake
- python_blas_codes:
- - boost
- - gmsh ~mpi +hdf5 +cgns +eigen ~opencascade +openmp ~fltk ~med
+ - boost ~mpi
+ #- gmsh ~mpi +hdf5 +cgns +eigen ~opencascade +openmp ~fltk ~med
- iq-tree
- py-biopython
- py-keras-preprocessing
@@ -201,6 +199,7 @@ spack:
- py-pandas
- py-pybigwig
- py-xarray
+ - valgrind
- gcc_python_codes:
- blast-plus
@@ -212,7 +211,7 @@ spack:
- mesa
- mummer
- node-js
- - openbabel +python
+ - openbabel +python ^boost ~mpi
- r
- spades
- xgboost
@@ -327,18 +326,10 @@ spack:
- matrix:
- [$compilers_specs]
- - matrix:
- - [$blas_oneapi]
- - [$%compiler_oneapi]
-
- matrix:
- [$blas_gcc]
- [$%compiler_gcc]
- - matrix:
- - [$mpi_oneapi]
- - [$%compiler_oneapi]
-
- matrix:
- [$mpi_gcc]
- [$%compiler_gcc]
@@ -353,16 +344,12 @@ spack:
- matrix:
- [$serial_codes]
- - [$%compilers]
+ - [$%compiler_gcc]
- matrix:
- [$gcc_serial_codes]
- [$%compiler_gcc]
- - matrix:
- - [$oneapi_serial_codes]
- - [$%compiler_oneapi]
-
- matrix:
- [$cuda_serial_codes]
- [$%compiler_gcc]
@@ -372,11 +359,6 @@ spack:
- [$^blas_gcc]
- [$%compiler_gcc]
- - matrix:
- - [$blas_codes]
- - [$^blas_oneapi]
- - [$%compiler_oneapi]
-
- matrix:
- [$gcc_blas_codes]
- [$^blas_gcc]
@@ -392,34 +374,18 @@ spack:
- [$^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]
- - matrix:
- - [$mpi_codes]
- - [$^mpi_oneapi]
- - [$%compiler_oneapi]
-
- matrix:
- [$mpi_codes]
- [$^mpi_gcc]
@@ -430,25 +396,12 @@ spack:
- [$^mpi_gcc]
- [$%compiler_gcc]
- - matrix:
- - [$mpi_blas_codes]
- - [$^blas_oneapi]
- - [$^mpi_oneapi]
- - [$%compiler_oneapi]
-
- matrix:
- [$mpi_blas_codes]
- [$^blas_gcc]
- [$^mpi_gcc]
- [$%compiler_gcc]
- - matrix:
- - [$mpi_blas_python_codes]
- - [$^blas_oneapi]
- - [$^mpi_oneapi]
- - [$^python_oneapi]
- - [$%compiler_oneapi]
-
- matrix:
- [$mpi_blas_python_codes]
- [$^blas_gcc]
@@ -463,6 +416,57 @@ spack:
- [$^python_gcc]
- [$%compiler_gcc]
+ # --------------------------------------------------------------------------
+ - matrix:
+ - [$serial_codes]
+ - [$%compiler_oneapi]
+
+ - matrix:
+ - [$blas_oneapi]
+ - [$%compiler_oneapi]
+
+ - matrix:
+ - [$mpi_oneapi]
+ - [$%compiler_oneapi]
+
+ - matrix:
+ - [$oneapi_serial_codes]
+ - [$%compiler_oneapi]
+
+ - matrix:
+ - [$blas_codes]
+ - [$^blas_oneapi]
+ - [$%compiler_oneapi]
+
+ - matrix:
+ - [$python_codes]
+ - [$^python_oneapi]
+ - [$%compiler_oneapi]
+
+ - matrix:
+ - [$python_blas_codes]
+ - [$^python_oneapi]
+ - [$^blas_oneapi]
+ - [$%compiler_oneapi]
+
+ - matrix:
+ - [$mpi_codes]
+ - [$^mpi_oneapi]
+ - [$%compiler_oneapi]
+
+ - matrix:
+ - [$mpi_blas_codes]
+ - [$^blas_oneapi]
+ - [$^mpi_oneapi]
+ - [$%compiler_oneapi]
+
+ - matrix:
+ - [$mpi_blas_python_codes]
+ - [$^blas_oneapi]
+ - [$^mpi_oneapi]
+ - [$^python_oneapi]
+ - [$%compiler_oneapi]
+
view: false
# default:
# root: /stack/packages/
--
GitLab