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Update pipeline configurations

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Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
This commit is contained in:
Massimiliano Culpo 2024-09-13 10:50:29 +02:00
parent 66d7085567
commit 8b14500fdc
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GPG Key ID: 3E52BB992233066C
12 changed files with 168 additions and 198 deletions
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2
share/spack/gitlab/cloud_pipelines/configs/config.yaml
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@ -4,5 +4,5 @@ config:
root: /home/software/spack
padded_length: 256
projections:
all: '{architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}'
all: "{architecture.platform}/{architecture.target}/{name}-{version}-{hash}"

4
share/spack/gitlab/cloud_pipelines/scripts/pcluster/setup-pcluster.sh
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@ -73,8 +73,8 @@ install_compilers() {
# in packages.yaml files and add a fallback `%gcc` version for each application.
if [ -f "/bootstrap-compilers/spack/etc/spack/compilers.yaml" ]; then
# Running inside a gitlab CI container
# Intel and gcc@12 compiler are pre-installed and their location is known in
cp /bootstrap-compilers/spack/etc/spack/compilers.yaml "${SPACK_ROOT}"/etc/spack/
# Intel and gcc@12 compiler are pre-installed and their location is known in
spack compiler list
else
spack compiler add --scope site
# We need to treat compilers as essentially external, i.e. their installation location

21
share/spack/gitlab/cloud_pipelines/stacks/aws-isc-aarch64/spack.yaml
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@ -57,34 +57,22 @@ spack:
- compiler_specs:
- gcc@11.2
# Licensing OK?
# - intel-oneapi-compilers@2022.1
# - nvhpc
- app_specs:
- bwa
# Depends on simde which requires newer compiler?
#- bowtie2
# Requires x86_64 specific ASM
#- cistem
- cromwell
- fastqc
- flux-sched
- flux-core
- flux-pmix
- gatk
- gromacs
- lammps
- wrf build_type=dm+sm
- mfem
- mpas-model ^parallelio+pnetcdf
- nextflow
- octave
- openfoam
- osu-micro-benchmarks
- parallel
# - paraview
- picard
- quantum-espresso
- raja
# Depends on bowtie2 -> simde which requires newer compiler?
@ -94,12 +82,9 @@ spack:
- salmon
- samtools
- seqtk
- snakemake
- star
# Requires gcc@9:
#- ufs-weather-model
# requires LLVM which fails without constraint
#- visit
- lib_specs:
- openmpi fabrics=ofi
@ -115,7 +100,6 @@ spack:
- target=aarch64
- target=neoverse_n1
specs:
- matrix:
@ -131,7 +115,10 @@ spack:
- matrix:
- - $compiler_specs
- - $compiler
- - $target
- matrix:
- [cromwell, fastqc, gatk, nextflow, parallel, picard, snakemake]
- [$target]
ci:
pipeline-gen:

45
share/spack/gitlab/cloud_pipelines/stacks/aws-isc/spack.yaml
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@ -2,6 +2,8 @@ spack:
view: false
packages:
all:
require:
- target=x86_64_v3
providers:
blas:
- openblas
@ -12,7 +14,8 @@ spack:
- mpich
variants: +mpi
tbb:
require: intel-tbb
require:
- intel-tbb
binutils:
variants: +ld +gold +headers +libiberty ~nls
version:
@ -43,8 +46,6 @@ spack:
- '1.18'
relion:
variants: ~mklfft
# texlive:
# version: [20210325]
trilinos:
variants: +amesos +amesos2 +anasazi +aztec +belos +boost +epetra +epetraext
+ifpack +ifpack2 +intrepid +intrepid2 +isorropia +kokkos +ml +minitensor +muelu
@ -57,56 +58,35 @@ spack:
- compiler_specs:
- gcc@11.2
# Licensing OK?
# - intel-oneapi-compilers@2022.1
# - nvhpc
- cuda_specs:
# Disabled for consistency with aarch64
#- relion +cuda cuda_arch=70
- raja +cuda cuda_arch=70
- mfem +cuda cuda_arch=70
- app_specs:
- bwa
# Disabled for consistency with aarch64
#- bowtie2
# Disabled for consistency with aarch64
#- cistem
- cromwell
- fastqc
- flux-sched
- flux-core
- flux-pmix
- gatk
- gromacs
- lammps
- wrf build_type=dm+sm
- mfem
- mpas-model ^parallelio+pnetcdf
- nextflow
- octave
- openfoam
- osu-micro-benchmarks
- parallel
# - paraview
- picard
- quantum-espresso
# Build broken for gcc@7.3.1 x86_64_v4 (error: '_mm512_loadu_epi32' was not declared in this scope)
#- raja
# Disabled for consistency with aarch64
#- rsem
# Errors on texlive
#- rstudio
- salmon
- samtools
- seqtk
- snakemake
- star
# Requires gcc@9:
#- ufs-weather-model
# Disabled for consistency with aarch64
#- visit
- lib_specs:
- openmpi fabrics=ofi
@ -118,31 +98,32 @@ spack:
- compiler:
- '%gcc@7.3.1'
- target:
- target=x86_64_v3
specs:
- matrix:
- - $cuda_specs
- - $compiler
- - $target
- matrix:
- - $app_specs
- - $compiler
- - $target
- matrix:
- - $lib_specs
- - $compiler
- - $target
- matrix:
- - $compiler_specs
- - $compiler
- - $target
- cromwell
- fastqc
- gatk
- parallel
- nextflow
- picard
- snakemake
ci:
pipeline-gen:

4
share/spack/gitlab/cloud_pipelines/stacks/aws-pcluster-neoverse_v1/packages.yaml
View File

@ -55,9 +55,11 @@ packages:
- "wrf%arm"
- "wrf%gcc"
all:
compiler: [gcc, arm, nvhpc, clang]
providers:
blas: [armpl-gcc, openblas]
c: [gcc, arm, nvhpc, llvm]
cxx: [gcc, arm, nvhpc, llvm]
fortran: [gcc, arm, nvhpc, llvm]
fftw-api: [armpl-gcc, fftw]
lapack: [armpl-gcc, openblas]
mpi: [openmpi, mpich]

27
share/spack/gitlab/cloud_pipelines/stacks/aws-pcluster-x86_64_v4/packages.yaml
View File

@ -23,8 +23,6 @@ packages:
- "+intel_provided_gcc target=x86_64_v4 ^intel-oneapi-mkl"
- "+intel_provided_gcc target=x86_64_v3 ^intel-oneapi-mkl"
when: "%oneapi"
intel-oneapi-compilers:
require: "intel-oneapi-compilers %gcc target=x86_64_v3"
intel-oneapi-mpi:
variants: +external-libfabric generic-names=True
lammps:
@ -124,14 +122,16 @@ packages:
when: "%oneapi"
all:
compiler: [oneapi, gcc]
permissions:
read: world
write: user
providers:
blas: [intel-oneapi-mkl]
c: [intel-oneapi-compilers, gcc]
cxx: [intel-oneapi-compilers, gcc]
daal: [intel-oneapi-dal]
fftw-api: [intel-oneapi-mkl]
fortran: [intel-oneapi-compilers, gcc]
ipp: [intel-oneapi-ipp]
lapack: [intel-oneapi-mkl]
mkl: [intel-oneapi-mkl]
@ -139,5 +139,22 @@ packages:
tbb: [intel-oneapi-tbb, intel-tbb]
scalapack: [intel-oneapi-mkl]
# compilers
gcc:
externals:
- spec: gcc@12.4.0 languages='c,c++,fortran'
prefix: /home/software/spack/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeh/linux-amzn2-x86_64_v3/gcc-7.3.1/gcc-12.4.0-pttzchh7o54nhmycj4wgzw5mic6rk2nb
extra_attributes:
compilers:
c: /home/software/spack/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeh/linux-amzn2-x86_64_v3/gcc-7.3.1/gcc-12.4.0-pttzchh7o54nhmycj4wgzw5mic6rk2nb/bin/gcc
cxx: /home/software/spack/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeh/linux-amzn2-x86_64_v3/gcc-7.3.1/gcc-12.4.0-pttzchh7o54nhmycj4wgzw5mic6rk2nb/bin/g++
fortran: /home/software/spack/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeh/linux-amzn2-x86_64_v3/gcc-7.3.1/gcc-12.4.0-pttzchh7o54nhmycj4wgzw5mic6rk2nb/bin/gfortran
intel-oneapi-compilers:
externals:
- spec: intel-oneapi-compilers@2024.1.0 target=x86_64_v3
prefix: /home/software/spack/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeh/linux-amzn2-x86_64_v3/gcc-12.4.0/intel-oneapi-compilers-2024.1.0-f5u3psfhbwscasajkn324igtupn3blop/compiler/2024.1
extra_attributes:
compilers:
c: /home/software/spack/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeh/linux-amzn2-x86_64_v3/gcc-12.4.0/intel-oneapi-compilers-2024.1.0-f5u3psfhbwscasajkn324igtupn3blop/compiler/2024.1/bin/icx
cxx: /home/software/spack/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeh/linux-amzn2-x86_64_v3/gcc-12.4.0/intel-oneapi-compilers-2024.1.0-f5u3psfhbwscasajkn324igtupn3blop/compiler/2024.1/bin/icpx
fortran: /home/software/spack/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeh/linux-amzn2-x86_64_v3/gcc-12.4.0/intel-oneapi-compilers-2024.1.0-f5u3psfhbwscasajkn324igtupn3blop/compiler/2024.1/bin/ifx

29
share/spack/gitlab/cloud_pipelines/stacks/build_systems/spack.yaml
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@ -2,24 +2,21 @@ spack:
view: false
packages:
all:
require: target=x86_64_v3
definitions:
- default_specs:
- 'uncrustify build_system=autotools'
- 'uncrustify build_system=cmake'
- lz4 # MakefilePackage
- mpich~fortran # AutotoolsPackage
- py-setuptools # PythonPackage
- openjpeg # CMakePackage
- r-rcpp # RPackage
- ruby-rake # RubyPackage
- arch:
- '%gcc'
require:
- target=x86_64_v3
c:
require:
- gcc
specs:
- matrix:
- - $default_specs
- - $arch
- 'uncrustify build_system=autotools'
- 'uncrustify build_system=cmake'
- lz4 # MakefilePackage
- mpich~fortran # AutotoolsPackage
- py-setuptools # PythonPackage
- openjpeg # CMakePackage
- r-rcpp # RPackage
- ruby-rake # RubyPackage
cdash:
build-group: Build Systems

158
share/spack/gitlab/cloud_pipelines/stacks/developer-tools-manylinux2014/spack.yaml
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@ -1,95 +1,87 @@
spack:
view: false
packages:
all:
require: target=x86_64_v3
require:
- target=x86_64_v3
prefer:
- '%gcc'
gcc:
externals:
- spec: gcc@=10.2.1 languages=c,c++,fortran
prefix: /opt/rh/devtoolset-10/root/usr
extra_attributes:
compilers:
c: /opt/rh/devtoolset-10/root/usr/bin/gcc
cxx: /opt/rh/devtoolset-10/root/usr/bin/g++
fortran: /opt/rh/devtoolset-10/root/usr/bin/gfortran
concretizer:
unify: true
reuse: false
definitions:
- default_specs:
# editors
- neovim~no_luajit
- py-pynvim
- emacs+json+native+treesitter # note, pulls in gcc
# - tree-sitter is a dep, should also have cli but no package
- nano # just in case
# tags and scope search helpers
- universal-ctags # only maintained ctags, works better with c++
- direnv
# runtimes and compilers
- python
- llvm+link_llvm_dylib~lld~lldb~polly+python build_type=MinSizeRel # for clangd, clang-format
- node-js # for editor plugins etc., pyright language server
- npm
- cmake
- libtool
- go # to build fzf, gh, hub
- rust+dev # fd, ripgrep, hyperfine, exa, rust-analyzer
- binutils+ld+gold+plugins # support linking with built gcc
# styling and lints
- astyle
- cppcheck
- uncrustify
- py-fprettify
- py-fortran-language-server
- py-python-lsp-server
# cli dev tools
- ripgrep
- gh
- fd
# - bfs # liburing: /usr/include/linux/ipv6.h:19:8: error: redefinition of 'struct in6_pktinfo'
- fzf
- tree
- jq
- py-yq
- hub
- ncdu
- eza
- lsd
- hyperfine
- htop
- tmux
- ccache
# ensure we can use a jobserver build and do this fast
- gmake
- ninja # should be @kitware, can't be because of meson requirement
- openssl certs=system # must be this, system external does not work
- libtree
- patchelf
- sed
- which
- elfutils
- fontconfig
- font-util
- gdb
- flex
- graphviz
- doxygen
- meson
- arch:
- '%gcc target=x86_64_v3'
specs:
- matrix:
- - $default_specs
- - $arch
compilers:
- compiler:
spec: gcc@=10.2.1
paths:
cc: /opt/rh/devtoolset-10/root/usr/bin/gcc
cxx: /opt/rh/devtoolset-10/root/usr/bin/g++
f77: /opt/rh/devtoolset-10/root/usr/bin/gfortran
fc: /opt/rh/devtoolset-10/root/usr/bin/gfortran
flags: {}
operating_system: centos7
target: x86_64
modules: []
environment: {}
extra_rpaths: []
# editors
- neovim~no_luajit
- py-pynvim
# FIXME (compiler as nodes): recover dependency on gcc as a library when +native
- emacs+json~native+treesitter # note, pulls in gcc
# - tree-sitter is a dep, should also have cli but no package
- nano # just in case
# tags and scope search helpers
- universal-ctags # only maintained ctags, works better with c++
- direnv
# runtimes and compilers
- python
- llvm+link_llvm_dylib~lld~lldb~polly+python build_type=MinSizeRel # for clangd, clang-format
- node-js # for editor plugins etc., pyright language server
- npm
- cmake
- libtool
- go # to build fzf, gh, hub
- rust+dev # fd, ripgrep, hyperfine, exa, rust-analyzer
- binutils+ld+gold+plugins # support linking with built gcc
# styling and lints
- astyle
- cppcheck
- uncrustify
- py-fprettify
- py-fortran-language-server
- py-python-lsp-server
# cli dev tools
- ripgrep
- gh
- fd
# - bfs # liburing: /usr/include/linux/ipv6.h:19:8: error: redefinition of 'struct in6_pktinfo'
- fzf
- tree
- jq
- py-yq
- hub
- ncdu
- eza
- lsd
- hyperfine
- htop
- tmux
- ccache
# ensure we can use a jobserver build and do this fast
- gmake
- ninja # should be @kitware, can't be because of meson requirement
- openssl certs=system # must be this, system external does not work
- libtree
- patchelf
- sed
- which
- elfutils
- fontconfig
- font-util
- gdb
- flex
- graphviz
- doxygen
- meson
ci:
pipeline-gen:

4
share/spack/gitlab/cloud_pipelines/stacks/e4s-cray-rhel/spack.yaml
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@ -12,9 +12,11 @@ spack:
all:
prefer:
- "%cce"
compiler: [cce]
providers:
blas: [cray-libsci]
c: [cce]
cxx: [cce]
fortran: [cce]
lapack: [cray-libsci]
mpi: [cray-mpich]
tbb: [intel-tbb]

5
share/spack/gitlab/cloud_pipelines/stacks/e4s-power/spack.yaml
View File

@ -7,8 +7,9 @@ spack:
packages:
all:
require: "%gcc@9.4.0 target=ppc64le"
compiler: [gcc@9.4.0]
prefer:
- "%gcc@9.4.0"
- target=ppc64le
providers:
blas: [openblas]
mpi: [mpich]

1
share/spack/gitlab/cloud_pipelines/stacks/gpu-tests/spack.yaml
View File

@ -3,7 +3,6 @@ spack:
packages:
all:
compiler: [gcc@11.1.0]
providers:
blas: [openblas]
mpi: [mpich]

66
share/spack/gitlab/cloud_pipelines/stacks/radiuss/spack.yaml
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@ -2,48 +2,40 @@ spack:
view: false
packages:
all:
require: target=x86_64_v3
require:
- target=x86_64_v3
- '%gcc@7.5.0'
providers:
mpi: [mvapich2]
definitions:
#- compilers: ['%gcc@8.3.1', '%clang@10.0.0']
- compilers: ['%gcc@7.5.0']
# Note skipping spot since no spack package for it
- radiuss:
- ascent # ^conduit@0.6.0
- axom
- blt
- caliper
- care # ~benchmarks ~examples ~tests
- chai # ~examples
- conduit # ^hdf5+shared
- flux-core
#- flux-sched
- hypre
- lbann
- lvarray ~tests # per Spack issue #23192 # ~examples
- mfem
- py-hatchet
- py-maestrowf
- py-merlin
- py-shroud
- raja # ~examples # ~tests
- raja-perf
- samrai
- scr
- sundials
- umpire # ~openmp
#- visit # ^mesa-glu@9.0.0
- xbraid
- zfp
specs:
- matrix:
- [$radiuss]
- [$compilers]
- ascent # ^conduit@0.6.0
- axom
- blt
- caliper
- care # ~benchmarks ~examples ~tests
- chai # ~examples
- conduit # ^hdf5+shared
- flux-core
# - flux-sched
- hypre
- lbann
- lvarray ~tests # per Spack issue #23192 # ~examples
- mfem
- py-hatchet
- py-maestrowf
- py-merlin
- py-shroud
- raja # ~examples # ~tests
- raja-perf
- samrai
- scr
- sundials
- umpire # ~openmp
# - visit # ^mesa-glu@9.0.0
- xbraid
- zfp
cdash:
build-group: RADIUSS