Merge branch 'main' of gitlab.epfl.ch:SCITAS/software-stack/scitas-software-stacks

.gitlab-ci.yml

@@ -29,6 +29,11 @@ variables:
         slurm_options: ["-c 36"]
         stack: ["pinot-noir"]
         app_image: ["registry.c4science.ch/scitas-stack/rhel9-kuma"]
+      - environment: [kuma_h100]
+        slurm_options: ["-c 64 -p h100"]
+        stack: ["pinot-noir-gcc"]
+        app_image: ["registry.c4science.ch/scitas-stack/rhel9-kuma"]
+
       # - environment: [izar]
       #   slurm_options: ['-c 40 --gpus 2']
       #   apptainer_options: ['-nv']

dockerfiles/rhel9-kuma/Dockerfile

@@ -6,8 +6,18 @@ FROM registry.c4science.ch/scitas-stack/rhel9-base:9.0
 
 # zlib-devel needed to compiler gcc ?
 
+# repos for kuma
+ARG APPSTREAM_REPO=rhel-9-for-x86_64-appstream-rpms
+ARG SLURM_REPO=SCITAS_product-slurm_repo-slurm-2311
+ARG PMIX_REPO=SCITAS_product-scitas_repo-scitas-cluster
+ARG MLNX_REPO=SCITAS_product-mlnx_repo-mlnx-ofed-24_01-0_3_3_1-5_14_0-70_30_1-rhel90
+ARG CUDA_REPO=SCITAS_product-cuda_repo-cuda-535_154_05-x86_64-rhel9
+ARG GPFS_REPO=SCITAS_product-gpfs_repo-gpfs-519
+
+RUN sed /etc/yum.repos.d/ubi.repo -i -e 's/enabled = 1/enabled = 0/'
+
 # spack dependencies
-RUN yum install -y \
+RUN yum install -y --enablerepo=$APPSTREAM_REPO \
     gcc-g++ gcc-gfortran \
     patchelf findutils patch \
     xz bzip2 file gnupg2 hostname iproute unzip zlib-devel\
@@ -17,20 +27,13 @@ RUN yum install -y \
     jq \
     && yum -y clean all && rm -fr /var/cache 
 
-# repos for kuma
-ARG SLURM_REPO=SCITAS_product-slurm_repo-slurm-2311
-ARG PMIX_REPO=SCITAS_product-scitas_repo-scitas-cluster
-ARG MLNX_REPO=SCITAS_product-mlnx_repo-mlnx-ofed-24_01-0_3_3_1-5_14_0-70_30_1-rhel90
-ARG CUDA_REPO=SCITAS_product-cuda_repo-cuda-535_154_05-x86_64-rhel9
-ARG GPFS_REPO=SCITAS_product-gpfs_repo-gpfs-519
-
 # stack dependencies
 RUN yum install -y --enablerepo=$SLURM_REPO \
     slurm-devel slurm-libpmi \
     && yum -y clean all && rm -fr /var/cache 
 
 RUN yum install -y --enablerepo=$PMIX_REPO \
-    slurm-devel slurm-libpmi \
+    pmix \
     && yum -y clean all && rm -fr /var/cache
 
 RUN yum install -y --enablerepo=$MLNX_REPO \

stacks/pinot-noir-gcc/concretizer.yaml

+concretizer:
+  reuse: false
+  unify: false
+  duplicates:
+    strategy: minimal

stacks/pinot-noir-gcc/config.json

+{
+    "spack": {
+        "version": "v0.22.0",
+        "repos": {
+            "scitas-externals": {
+                "url": "https://gitlab.epfl.ch/SCITAS/software-stack/spack-repo-externals.git",
+                "branch": "releases/2024.0.0"
+            },
+            "scitas-packages": {
+                "url": "https://gitlab.epfl.ch/SCITAS/software-stack/scitas-spack-packages.git",
+                "branch": "releases/2024.0.0"
+            }
+        },
+        "mirrors": {
+            "local": {
+                "url": "spack-mirror",
+                "type": "relative"
+            },
+            "restricted": {
+                "url": "spack-mirror-restriced",
+                "type": "relative"
+            }
+        }
+    },
+    "stack": {
+        "version": "v1",
+        "mount_point": "/stack",
+        "system_arch": "target=x86_64_v3",
+        "system_compiler": {
+            "gcc@11": {
+                "compiler": "gcc",
+                "spec": "gcc@11.2.1",
+                "version": "11.2.1"
+            }
+        },
+        "targets": {
+            "helvetios": "skylake_avx512",
+            "izar": "cascadelake",
+            "jed": "icelake",
+            "kuma_l40s": "zen4",
+            "kuma_h100": "zen4"
+        },
+        "compilers": {
+            "gcc": {
+                "compiler": "gcc",
+                "spec": "gcc@12.3.0 %gcc@11.2.1",
+                "version": "12.3.0"
+            }
+        },
+        "system_packages": [
+            "autoconf",
+            "autoconf-archive",
+            "automake",
+            "autotools",
+            "berkley-db",
+            "bzip2",
+            "ca-certificates-mozilla",
+            "check",
+            "cmake",
+            "cuda",
+            "curl",
+            "diffutils",
+            "expat",
+            "findutils",
+            "flex",
+            "font-util",
+            "freetype",
+            "gawk",
+            "gdbm",
+            "gettext",
+            "git",
+            "glibc",
+            "gmake",
+            "gmp",
+            "gnuplot",
+            "hcoll",
+            "help2man",
+            "libaec",
+            "libedit",
+            "libevent",
+            "libfuse",
+            "libidn2",
+            "libpciaccess",
+            "libsigsegv",
+            "libssh2",
+            "libtiff",
+            "libtool",
+            "libunistring",
+            "libuuid",
+            "libxml2",
+            "lz4",
+            "m4",
+            "macro-utils",
+            "meson",
+            "mpc",
+            "mpfr",
+            "ncurses",
+            "ninja",
+            "openssl",
+            "pcre",
+            "pcre2",
+            "perl",
+            "pigz",
+            "pkgconf",
+            "pmix",
+            "rdma-core",
+            "readline",
+            "slurm",
+            "sqlite",
+            "tar",
+            "texinfo",
+            "utf8proc",
+            "util-linux-uuid",
+            "xpmem",
+            "xxd-standalon",
+            "xz",
+            "zlib-ng",
+            "zstd"
+        ]
+    }
+}

stacks/pinot-noir-gcc/config.yaml

+config:
+#  ccache: true
+  install_missing_compilers: false
+
+  install_tree:
+    padded_length: 242
+
+  build_stage:
+    - $tempdir/$user/spack-stage

stacks/pinot-noir-gcc/definitions_helvetios.yaml

+definitions: []

stacks/pinot-noir-gcc/definitions_jed.yaml

+definitions:
+  - cuda_system_codes:
+      - cuda
+      - cudnn
+
+  - cuda_serial_codes:
+      - nccl

stacks/pinot-noir-gcc/definitions_kuma_h100.yaml

+definitions:
+  - cuda_system_codes:
+      - cuda
+      - cudnn
+
+  - cuda_serial_codes:
+      - nccl

stacks/pinot-noir-gcc/mirrors.yaml

+mirrors: {}

stacks/pinot-noir-gcc/modules.yaml

+modules:
+  default:
+    enable: [lmod]
+    lmod:
+      hash_length: 0
+      core_compilers:
+        - gcc@11.4.1
+      hierarchy:
+        - mpi
+      all:
+        environment:
+          set:
+            ${PACKAGE}_ROOT: ${PREFIX}
+        suffixes:
+          '+mpi': mpi
+          '+openmp': openmp
+          'threads=openmp': openmp
+          '^fftw+openmp': openmp
+          'hdf5=parallel': h5
+          '+cuda': cuda
+          '+double-gpu': double-gpu
+          '+plumed': plumed
+          '+unwind': unwind
+          '+debug': dbg
+          '+ilp64': int64
+          '+int64': int64
+          'version_suffix=jl': julia
+
+      blacklist_implicits: true
+
+      blacklist:
+        - lmod
+
+      gcc:
+        environment:
+          set:
+            CC: ${PREFIX}/bin/gcc
+            CXX: ${PREFIX}/bin/g++
+            F77: ${PREFIX}/bin/gfortran
+            FC: ${PREFIX}/bin/gfortran
+            F90: ${PREFIX}/bin/gfortran
+      cuda@12.4.0:
+        environment:
+          append_path:
+            JULIA_LOAD_PATH: ":/ssoft/spack/external/julia/syrah.v1/cuda"
+
+      openmpi:
+        environment:
+          set:
+            SLURM_MPI_TYPE: pmi2
+            OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
+          append_path:
+            JULIA_LOAD_PATH: ":/ssoft/spack/external/julia/syrah.v1/mpi"
+      openblas threads=pthreads:
+        environment:
+          set:
+            OPENBLAS_NUM_THREADS: '1'
+      hdf5~mpi+cxx:
+        environment:
+          set:
+            HDF5_CC: h5cc
+            HDF5_CXX: h5c++
+            HDF5_FC: h5fc
+      hdf5+mpi~cxx:
+        environment:
+          set:
+            HDF5_CC: h5pcc
+            HDF5_FC: h5pfc
+      intel-oneapi-mpi:
+        environment:
+          set:
+            I_MPI_PMI_LIBRARY: /usr/lib64/libpmi2.so
+            I_MPI_EXTRA_FILESYSTEM: '0'
+            SLURM_MPI_TYPE: pmi2
+      julia:
+        autoload: direct
+      metis:
+        suffixes:
+          ~real64: sp
+      molpro:
+        template: modules/group_restricted.lua
+      plumed:
+        environment:
+          set:
+            PLUMED_KERNEL: ${PREFIX}/lib/libplumedKernel.so
+          unset:
+          - PLUMED_ROOT
+      py-horovod:
+        autoload: direct
+      py-keras:
+        autoload: direct
+      py-tensorflow:
+        autoload: direct
+      py-theano:
+        autoload: direct
+      py-torch:
+        autoload: direct
+      py-torchvision:
+        autoload: direct
+      quantum-espresso:
+        suffixes:
+          hdf5=parallel: hdf5
+      scala:
+        autoload: direct
+      scons:
+        suffixes:
+          '^python@:2.99': py2
+          '^python@3:': py3
+
+      abaqus:
+        template: modules/group_restricted.lua
+      adf:
+        template: modules/group_restricted.lua
+      ams:
+        template: modules/group_restricted.lua
+      comsol:
+        environment:
+          prepend_path:
+            MATLABPATH: ${PREFIX}/mli
+      crystal17:
+        template: modules/group_restricted.lua
+      fdtd:
+        environment:
+          prepend_path:
+            PATH: ${PREFIX}/mpich2/nemesis/bin
+            LD_LIBRARY_PATH: ${PREFIX}/mpich2/nemesis/lib
+          set:
+            SLURM_MPI_TYPE: pmi2
+      gaussian:
+        template: modules/group_restricted.lua
+      spark:
+        autoload: direct
+        environment:
+          prepend_path:
+            PATH: /ssoft/spack/scripts/all/spark
+      ucx:
+        environment:
+          unset:
+            - UCX_ROOT
+      vasp:
+        template: modules/group_restricted.lua

stacks/pinot-noir-gcc/packages_helvetios.yaml

+packages:
+  all:
+    target: ["skylake_avx512"]
+    require: ['~cuda', '~rocm']
+
+  # py-torch:
+  #   require:
+  #   - spec: '~cuda ~cudnn ~nccl ~rocm'

stacks/pinot-noir-gcc/packages_izar.yaml

+packages:
+  all:
+    target: ["cannonlake"]
+    require:
+      - spec: ^openmpi +cuda
+        when: '%gcc ^mpi'
+
+      - spec: cuda_arch=70
+        when: '+cuda'
+
+      - '+cuda'

stacks/pinot-noir-gcc/packages_jed.yaml

+packages:
+  all:
+    target: ["icelake"]
+    require:
+      - "~rocm"
+
+      - spec: cuda_arch=90 target=icelake
+        when: '+cuda'
+      # - spec: '~cuda'
+      #   when: '%oneapi'
+
+      - spec: '+cuda'
+        when: '%gcc'
+
+  # ---------------------------------------------------------------------------
+  hypre:
+    require:
+    - spec: '+cuda cuda_arch=90 +unified-memory'
+      when: '%gcc'
+
+  kokkos:
+    require:
+    - spec: '+cuda cuda_arch=90 +cuda_uvm +wrapper ~openmptarget'
+      when: '%gcc'
+
+  openmpi:
+    require:
+      - spec: '+cuda cuda_arch=90 target=icelake'
+
+  petsc:
+    require:
+    - spec: '+cuda cuda_arch=90'
+      when: '%gcc'
+
+  py-tensorflow:
+    require:
+    - spec: '+cuda cuda_arch=90 +nccl'
+
+  py-torch:
+    require:
+    - spec: '+cuda cuda_arch=90 +nccl +cudnn'
+
+  quantum-espresso:
+    require:
+    - spec: '~cuda'
+
+  suite-sparse:
+    require:
+    - spec: '+cuda'
+
+  ucx:
+    require:
+      - spec: '+xpmem +cma +rdmacm +rc +ud +dc +verbs +ib_hw_tm +gdrcopy +cuda cuda_arch=90 target=icelake ~rocm'
+
+  # ---------------------------------------------------------------------------
+  # Externals
+  # ---------------------------------------------------------------------------
+  pmix:
+    buildable: false
+    externals:
+    - spec: 'pmix@5.0.2'
+      prefix: /usr
+
+  rdma-core:
+    buildable: false
+    externals:
+    - spec: 'rdma-core@47.1'
+      prefix: /usr
+
+  slurm:
+    buildable: false
+    externals:
+    - spec: 'slurm@24-05-0-2'
+      prefix: /usr
+
+  xpmem:
+    buildable: false
+    externals:
+    - spec: 'xpmem@2.7.3'
+      prefix: /usr

stacks/pinot-noir-gcc/packages_kuma_h100.yaml

+packages:
+  all:
+    target: ["zen4"]
+    require:
+      - "~rocm"
+
+      - spec: cuda_arch=90 target=zen4
+        when: '+cuda'
+
+      - spec: '+cuda'
+        when: '%gcc'
+
+  # ---------------------------------------------------------------------------
+  hypre:
+    require:
+    - spec: '+cuda cuda_arch=90 +unified-memory'
+      when: '%gcc'
+
+  kokkos:
+    require:
+    - spec: '+cuda cuda_arch=90 +cuda_uvm +wrapper ~openmptarget'
+      when: '%gcc'
+
+  openmpi:
+    require:
+      - spec: '+cuda cuda_arch=90 target=zen4'
+
+  petsc:
+    require:
+    - spec: '+cuda cuda_arch=90'
+      when: '%gcc'
+
+  py-tensorflow:
+    require:
+    - spec: '+cuda cuda_arch=90 +nccl'
+
+  py-torch:
+    require:
+    - spec: '+cuda cuda_arch=90 +nccl +cudnn'
+
+  quantum-espresso:
+    require:
+    - spec: '~cuda'
+
+  suite-sparse:
+    require:
+    - spec: '+cuda'
+
+  ucx:
+    require:
+      - spec: '+xpmem +cma +rdmacm +rc +ud +dc +verbs +ib_hw_tm +gdrcopy +cuda cuda_arch=90 ~rocm target=zen4'
+
+  # ---------------------------------------------------------------------------
+  # Externals
+  # ---------------------------------------------------------------------------
+  pmix:
+    buildable: false
+    externals:
+    - spec: 'pmix@5.0.2'
+      prefix: /usr
+
+  rdma-core:
+    buildable: false
+    externals:
+    - spec: 'rdma-core@47.1'
+      prefix: /usr
+
+  slurm:
+    buildable: false
+    externals:
+    - spec: 'slurm@24-05-0-2'
+      prefix: /usr
+
+  xpmem:
+    buildable: false
+    externals:
+    - spec: 'xpmem@2.7.3'
+      prefix: /usr

stacks/pinot-noir-gcc/packages_kuma_l40s.yaml

+packages:
+  all:
+    target: ["zen4"]
+    require:
+      - spec: ^openmpi +cuda
+        when: '%gcc ^mpi'
+
+      - spec: cuda_arch=89
+        when: '+cuda'
+
+      - '+cuda'

stacks/pinot-noir-gcc/packages_stack.yaml

+packages:
+  all:
+    providers:
+      mpi: [openmpi, intel-oneapi-mpi]
+      iconv: [libiconv]
+      jpeg: [libjpeg]
+      zlib-api: [zlib-ng]
+    require:
+      - 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'
+
+  # ----------------------------------------------------------------------------
+  # Requirements
+  # ----------------------------------------------------------------------------
+  adios2:
+    require: ['+kokkos']
+
+  boost:
+    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:
+    - spec: '@12.4.0'
+    - spec: '+allow-unsupported-compilers'
+      when: '%oneapi'
+
+  fenics-dolfinx:
+    require: ['+slepc']
+
+  fftw:
+    prefer: ['+mpi', '+openmp']
+
+  gnuplot:
+    require:
+    - spec: '@5.4.10'
+
+  hdf5:
+    prefer:
+    - spec: '+mpi'
+    - spec: '@1.14.3'
+    require:
+    - spec: '+hl +threadsafe +szip +cxx +fortran'
+    - spec: '+ipo'
+      when: '%gcc'
+
+  hypre:
+    prefer:
+    - spec: '@2.31.0 ~magma'
+
+  intel-oneapi-mkl:
+    prefer: ['~cluster']
+
+  kokkos:
+    prefer: ['+openmp', '+openmptarget', '+numactl', '+memkind', '+threads',
+    '+aggressive_vectorization']
+
+  lammps:
+    require: ['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', '+kokkos']
+
+  libfabric:
+    require:
+    - spec: 'fabrics=mlx,mrail,psm3,verbs,udp,tcp,sockets,shm'
+
+  llvm:
+    prefer: ['~clang']
+
+  libxcb:
+    require: ['+use_spack_interpreter']
+
+  mesa:
+    require: ['~llvm', '+opengl', '+opengles', '+osmesa']
+
+  metis:
+    require: ['+real64']
+
+  netcdf-c:
+    prefer: ['+mpi']
+
+  openblas:
+    prefer: ['threads=pthreads symbol_suffix=none ~ilp64']
+
+  opencv:
+    prefer: ['+vtk', '+python3']
+
+  openmpi:
+    require:
+    - spec: '@5.0.3 fabrics=ofi,ucx,verbs schedulers=slurm ~rsh +romio romio-filesystem=gpfs +internal-pmix ~memchecker'
+
+  petsc:
+    require:
+    - spec: '+hypre +mumps +saws +scalapack +mpi +suite-sparse +kokkos'
+
+  python:
+    require:
+    - spec: '+ssl +tkinter'
+    - spec: '+optimizations'
+      when: '%gcc'
+
+  py-tensorflow:
+    require: ['+mpi', '+mkl']
+
+  py-torch:
+    require: ['+mpi']
+
+  suite-sparse:
+    require:
+    - spec: '+graphblas'
+
+  tk:
+    require: ['+xft', '+xss']
+
+  ucx:
+    require:
+    - spec: +rdmacm +rc +dc +ud +cma +verbs
+
+  zlib-ng:
+    require: ['build_system=autotools']
+
+  # ----------------------------------------------------------------------------
+  # System dependencies
+  # ----------------------------------------------------------------------------
+  egl:
+    buildable: false
+    externals:
+    - spec: 'egl@21.3.4'
+      prefix: /usr
+
+  pmix:
+    buildable: false
+    externals:
+    - spec: 'pmix@5.0.1'
+      prefix: /usr
+
+  rdma-core:
+    buildable: false
+    externals:
+    - spec: 'rdma-core@47.1'
+      prefix: /usr
+
+  slurm:
+    buildable: false
+    externals:
+    - spec: 'slurm@23-11-7-1'
+      prefix: /usr
+
+
+  # ----------------------------------------------------------------------------
+  # Externals
+  # ----------------------------------------------------------------------------
+  abaqus:
+    buildable: false
+    permissions: {read: group, group: abaqus-soft}
+    externals:
+    - {spec: abaqus@2019, prefix: /ssoft/spack/external/abaqus/2019}
+    - {spec: abaqus@2023, prefix: /ssoft/spack/external/abaqus/2023}
+  ansys:
+    buildable: false
+    externals:
+    - {spec: ansys@2020R2, prefix: /ssoft/spack/external/ansys/2020R2/v202}
+    - {spec: ansys@2022R1, prefix: /ssoft/spack/external/ansys/2022R1/v221}
+    - {spec: ansys@2022R2, prefix: /ssoft/spack/external/ansys/2022R2/v222}
+    - {spec: ansys@2024R1, prefix: /ssoft/spack/external/ansys/2024R1/v241}
+  cfdplusplus:
+    buildable: false
+    externals:
+    - {spec: cfdplusplus@16.1, prefix: /ssoft/spack/external/CFD++/2016.05}
+    - {spec: cfdplusplus@19.1, prefix: /ssoft/spack/external/CFD++/19.1}
+  comsol:
+    buildable: false
+    permissions: {read: group, group: comsol-soft}
+    externals:
+    - {spec: comsol@5.6, prefix: /ssoft/spack/external/comsol/5.6/comsol56/multiphysics/}
+    - {spec: comsol@6.0, prefix: /ssoft/spack/external/comsol/6.0}
+    - {spec: comsol@6.2, prefix: /ssoft/spack/external/comsol/6.2}
+  fdtd:
+    buildable: false
+    permissions: {read: group, group: fdtd-soft}
+    externals:
+    - {spec: fdtd@2020-R2-2387, prefix: /ssoft/spack/external/fdtd/8.24.2387}
+    - {spec: fdtd@2020-R2.4-2502, prefix: /ssoft/spack/external/fdtd/2020-R2.4-2502}
+    - {spec: fdtd@2021-R2.2-2806, prefix: /ssoft/spack/external/fdtd/2021-R2.2-2806}
+    - {spec: fdtd@2022-R1.1-2963, prefix: /ssoft/spack/external/fdtd/2022-R1.1-2963}
+  gaussian:
+    buildable: false
+    externals:
+    - {spec: gaussian@g16-A.03, prefix: /ssoft/spack/external/gaussian/g16-A.03/avx2}
+    - {spec: gaussian@g16-C.01, prefix: /ssoft/spack/external/gaussian/g16-C.01/avx2}
+  gurobi:
+    buildable: false
+    externals:
+    - {spec: gurobi@8.1.1, prefix: /ssoft/spack/external/gurobi/8.1.1}
+    - {spec: gurobi@9.5.2, prefix: /ssoft/spack/external/gurobi/9.5.2}
+    - {spec: gurobi@10.0.1, prefix: /ssoft/spack/external/gurobi/10.0.1}
+  maple:
+    buildable: false
+    externals:
+    - {spec: maple@2017, prefix: /ssoft/spack/external/Maple/2017}
+  mathematica:
+    buildable: false
+    externals:
+    - {spec: mathematica@11.1.1, prefix: /ssoft/spack/external/Mathematica/11.1.1}
+    - {spec: mathematica@13.0, prefix: /ssoft/spack/external/Mathematica/13.0}
+  matlab:
+    buildable: false
+    externals:
+    - {spec: matlab@R2018a, prefix: /ssoft/spack/external/MATLAB/R2018a}
+    - {spec: matlab@R2019b, prefix: /ssoft/spack/external/MATLAB/R2019b}
+    - {spec: matlab@R2024a, prefix: /ssoft/spack/external/MATLAB/R2024a}
+  molpro:
+    buildable: false
+    externals:
+    - {spec: molpro@2022.3.0, prefix: /ssoft/spack/external/molpro/2022.3.0/mpi}
+  smr:
+    buildable: false
+    externals:
+    - {spec: smr@2017.0, prefix: /ssoft/spack/external/SMR/2017.06}
+  totalview:
+    externals:
+    - {spec: totalview@2017.2.11, prefix: /ssoft/spack/external/toolworks/totalview.2017.2.11}
+    - {spec: totalview@2020.3.11, prefix: /ssoft/spack/external/toolworks/totalview.2020.3.11}

stacks/pinot-noir-gcc/spack.yaml

+spack:
+  include:
+      - compiler_definitions.yaml
+
+      - packages_stack.yaml
+      - packages_env.yaml
+
+      - modules_stack.yaml
+
+      - definitions_env.yaml
+
+      - config_stack.yaml
+
+  definitions:
+    # -------------------------------------------------------------------------
+    # PE definition
+    # -------------------------------------------------------------------------
+    - mpi_gcc:
+        - openmpi@5.0.3
+
+    - mpi_oneapi:
+        - intel-oneapi-mpi@2021.12.1
+
+    - blas_gcc:
+        - openblas@0.3.26
+
+    - blas_oneapi:
+        - intel-oneapi-mkl@2024.1.0
+
+    - python_gcc:
+        - python@3.11.7
+
+    - python_oneapi:
+        - python@3.11.7
+
+    # -------------------------------------------------------------------------
+    # Core packages
+    # -------------------------------------------------------------------------
+    - core_codes:
+        - bzip2
+        - cmake
+        - emacs +tls
+        - fastqc
+        - fio
+        - git
+        - git-lfs
+        - gmp
+        - gnuplot
+        - gzip
+        - imagemagick +ghostscript
+        - intel-oneapi-advisor
+        - intel-oneapi-inspector
+        - intel-oneapi-vtune
+        - libarchive
+        - libjpeg-turbo
+        - libpng
+        - libtiff
+        - libxml2
+        - lmod
+        - mpfr
+        - neovim
+        - ninja
+        - parallel
+        - picard
+        - rclone
+        - rust
+        - sbt
+        - sratoolkit
+        - subversion
+        - tar
+        - tcl
+        - tk
+        - tmux
+        - trimmomatic
+        - valgrind
+        - xclip
+        - zlib-ng
+
+    # -------------------------------------------------------------------------
+    # Serial codes
+    # -------------------------------------------------------------------------
+    - serial_codes:
+        - bwa
+        - boost ~mpi
+        - fftw +openmp ~mpi
+        - fftw ~openmp ~mpi
+        - eigen
+        - gsl
+        - hdf5@1.14.1 ~mpi
+        - hisat2
+        - htslib
+        - intel-oneapi-tbb
+        - jasper
+        - kallisto ^hdf5 ~mpi
+        - kokkos
+        - mafft
+        - metis
+        - muscle
+        - netcdf-c~mpi ^hdf5~mpi
+        - netcdf-fortran ^netcdf-c ~mpi ^hdf5 ~mpi
+        - nfft ^fftw~mpi~openmp
+        - python
+        - scotch ~mpi
+        - star
+        - subread
+        - superlu
+        - unblur ^fftw~mpi~openmp
+        - 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
+        - sox
+        - stacks
+
+    - 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
+
+    # -------------------------------------------------------------------------
+    # 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-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-cryolobm
+        - py-deeptools
+        - py-h5py ~mpi ^hdf5 ~mpi
+        - py-pymol
+        - py-scikit-learn
+        - py-scipy
+        - py-statsmodels
+        - py-theano
+
+    # -------------------------------------------------------------------------
+    # Parallel codes
+    # -------------------------------------------------------------------------
+    - mpi_codes:
+        - fftw +mpi +openmp
+        - hdf5@1.14.3 +mpi
+        - openfoam-org +metis
+        - osu-micro-benchmarks +graphing
+        - parmetis
+        - phylobayesmpi
+        - py-mpi4py
+        - scotch +mpi
+        - netcdf-c
+        - netcdf-fortran
+        - parmetis
+
+    - gcc_mpi_codes:
+        - wrf ~pnetcdf build_type=dm+sm
+
+    - 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
+
+    - 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
+
+    - mpi_blas_python_codes:
+        - boost +mpi
+        - cgal
+        - iq-tree@1.6.12+mpi
+        - neuron +mpi +python
+        - petsc@3.21.1
+        - plumed
+        - py-petsc4py
+        - slepc
+
+    - gcc_mpi_blas_python_codes:
+        # - eman2 +mpi
+        - adios2
+        - cp2k +mpi +plumed +openmp smm=blas
+        # - fenics +parmetis +hdf5 +scotch +suite-sparse ~vtk ~trilinos
+        - fenics-dolfinx
+        - gromacs +mpi +plumed
+        - lammps
+        - opencv
+        - openfoam +metis
+        - paraview +shared +python +hdf5 ~osmesa +opengl2 +egl
+        - py-fenics-dolfinx
+        - py-h5py +mpi
+        - py-horovod
+        - py-keras
+        - py-tensorflow
+        - py-torch
+        - py-torchvision
+        - relion ~mklfft
+        - topaz
+        - vtk
+
+    # -------------------------------------------------------------------------
+    # External packages
+    # -------------------------------------------------------------------------
+    - external_packages: []
+    - when: env['environment_type'] != 'cloud'
+      external_packages:
+        - ansys
+        - cfdplusplus
+        - comsol
+        - fdtd
+        - gurobi
+        - gaussian
+        - matlab
+        - maple
+        - mathematica
+        - molpro
+        - smr
+
+    - when: env['environment_type'] != 'cloud'
+      blas_mpi_codes:
+        - vasp +hdf5 +scalapack +shmem +wannier90
+
+    # -------------------------------------------------------------------------
+    # Generic definitions
+    # -------------------------------------------------------------------------
+    - mpis:
+        - $mpi_oneapi
+        - $mpi_gcc
+
+  specs:
+    - matrix:
+        - [$compilers_specs]
+
+    - matrix:
+        - [$blas_gcc]
+        - [$%compiler_gcc]
+
+    - matrix:
+        - [$mpi_gcc]
+        - [$%compiler_gcc]
+
+    - matrix:
+        - [$core_codes]
+        - [$%system_compiler]
+
+    - matrix:
+        - [$cuda_system_codes]
+        - [$%system_compiler]
+
+    - matrix:
+        - [$serial_codes]
+        - [$%compilers]
+
+    - matrix:
+        - [$gcc_serial_codes]
+        - [$%compiler_gcc]
+
+    - matrix:
+        - [$cuda_serial_codes]
+        - [$%compiler_gcc]
+
+    - matrix:
+        - [$blas_codes]
+        - [$^blas_gcc]
+        - [$%compiler_gcc]
+
+    - matrix:
+        - [$gcc_blas_codes]
+        - [$^blas_gcc]
+        - [$%compiler_gcc]
+
+    - matrix:
+        - [$python_codes]
+        - [$^python_gcc]
+        - [$%compiler_gcc]
+
+    - matrix:
+        - [$gcc_python_codes]
+        - [$^python_gcc]
+        - [$%compiler_gcc]
+
+    - matrix:
+        - [$python_blas_codes]
+        - [$^python_gcc]
+        - [$^blas_gcc]
+        - [$%compiler_gcc]
+
+    - matrix:
+        - [$gcc_python_blas_codes]
+        - [$^python_gcc]
+        - [$^blas_gcc]
+        - [$%compiler_gcc]
+
+    - matrix:
+        - [$mpi_codes]
+        - [$^mpi_gcc]
+        - [$%compiler_gcc]
+
+    - matrix:
+        - [$gcc_mpi_codes]
+        - [$^mpi_gcc]
+        - [$%compiler_gcc]
+
+    - matrix:
+        - [$mpi_blas_codes]
+        - [$^blas_gcc]
+        - [$^mpi_gcc]
+        - [$%compiler_gcc]
+
+    - matrix:
+        - [$mpi_blas_python_codes]
+        - [$^blas_gcc]
+        - [$^mpi_gcc]
+        - [$^python_gcc]
+        - [$%compiler_gcc]
+
+    - matrix:
+        - [$gcc_mpi_blas_python_codes]
+        - [$^blas_gcc]
+        - [$^mpi_gcc]
+        - [$^python_gcc]
+        - [$%compiler_gcc]
+
+  view: false
+#    default:
+#      root: /stack/packages/

stacks/pinot-noir-gcc/templates/modules/group_restricted.lua

+{% extends "modules/modulefile.lua" %}
+{% block footer %}
+-- Access is granted only to specific groups, most likely because the software is licensed
+if not isDir("{{ spec.prefix }}") then
+    LmodError (
+        "You don't have the necessary rights to run \"{{ spec.name }}\".\n\n",
+        "\tPlease write an e-mail to 1234@epfl.ch if you need further information on how to get access to it.\n"
+    )
+end
+{% endblock %}

stacks/pinot-noir/concretizer.yaml

 concretizer:
   reuse: false
-  unify: when_possible
+  unify: false
   duplicates:
     strategy: minimal

stacks/pinot-noir/config.json

@@ -29,8 +29,8 @@
         "system_compiler": {
             "gcc@11": {
                 "compiler": "gcc",
-                "spec": "gcc@11.4.1",
-                "version": "11.4.1"
+                "spec": "gcc@11.2.1",
+                "version": "11.2.1"
             }
         },
         "targets": {
@@ -43,12 +43,12 @@
         "compilers": {
             "oneapi": {
                 "compiler": "oneapi",
-                "spec": "intel-oneapi-compilers@2024.1.0 %gcc@11.4.1",
+                "spec": "intel-oneapi-compilers@2024.1.0 %gcc@11.2.1",
                 "version": "2024.1.0"
             },
             "gcc": {
                 "compiler": "gcc",
-                "spec": "gcc@12.3.0 %gcc@11.4.1",
+                "spec": "gcc@12.3.0 %gcc@11.2.1",
                 "version": "12.3.0"
             }
         },
@@ -73,6 +73,7 @@
             "gawk",
             "gdbm",
             "gettext",
+            "git",
             "glibc",
             "gmake",
             "gmp",
@@ -80,13 +81,16 @@
             "hcoll",
             "help2man",
             "libaec",
+            "libedit",
             "libevent",
             "libfuse",
+            "libidn2",
             "libpciaccess",
             "libsigsegv",
             "libssh2",
             "libtiff",
             "libtool",
+            "libunistring",
             "libuuid",
             "libxml2",
             "lz4",
@@ -111,6 +115,7 @@
             "tar",
             "texinfo",
             "utf8proc",
+            "util-linux-uuid",
             "xpmem",
             "xxd-standalon",
             "xz",