Update pipeline configurations

Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>

share/spack/gitlab/cloud_pipelines/configs/config.yaml

@@ -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}"
 

share/spack/gitlab/cloud_pipelines/scripts/pcluster/setup-pcluster.sh

@@ -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 
+        # 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/
+        spack compiler list
     else
         spack compiler add --scope site
         # We need to treat compilers as essentially external, i.e. their installation location

share/spack/gitlab/cloud_pipelines/stacks/aws-isc-aarch64/spack.yaml

@@ -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:

share/spack/gitlab/cloud_pipelines/stacks/aws-isc/spack.yaml

@@ -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:

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

@@ -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]

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

@@ -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

share/spack/gitlab/cloud_pipelines/stacks/build_systems/spack.yaml

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

share/spack/gitlab/cloud_pipelines/stacks/developer-tools-manylinux2014/spack.yaml

@@ -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:
+    # editors
-    - - $default_specs
+  - neovim~no_luajit
-    - - $arch
+  - py-pynvim
-
+  # FIXME (compiler as nodes): recover dependency on gcc as a library when +native
-  compilers:
+  - emacs+json~native+treesitter   # note, pulls in gcc
-  - compiler:
+    # - tree-sitter is a dep, should also have cli but no package
-      spec: gcc@=10.2.1
+  - nano   # just in case
-      paths:
+    # tags and scope search helpers
-        cc: /opt/rh/devtoolset-10/root/usr/bin/gcc
+  - universal-ctags   # only maintained ctags, works better with c++
-        cxx: /opt/rh/devtoolset-10/root/usr/bin/g++
+  - direnv
-        f77: /opt/rh/devtoolset-10/root/usr/bin/gfortran
+    # runtimes and compilers
-        fc: /opt/rh/devtoolset-10/root/usr/bin/gfortran
+  - python
-      flags: {}
+  - llvm+link_llvm_dylib~lld~lldb~polly+python build_type=MinSizeRel   # for clangd, clang-format
-      operating_system: centos7
+  - node-js   # for editor plugins etc., pyright language server
-      target: x86_64
+  - npm
-      modules: []
+  - cmake
-      environment: {}
+  - libtool
-      extra_rpaths: []
+  - 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:

share/spack/gitlab/cloud_pipelines/stacks/e4s-cray-rhel/spack.yaml

@@ -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]

share/spack/gitlab/cloud_pipelines/stacks/e4s-power/spack.yaml

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

share/spack/gitlab/cloud_pipelines/stacks/gpu-tests/spack.yaml

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

share/spack/gitlab/cloud_pipelines/stacks/radiuss/spack.yaml

@@ -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:
+  - ascent  # ^conduit@0.6.0
-    - [$radiuss]
+  - axom
-    - [$compilers]
+  - 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