diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0d1c5c5a2a300f40a2b03f788259e89d2b7710c0..678603b7eaa484798c09aed6c0fc51d352b9a541 100644
--- a/.gitlab-ci.yml
+++ b/.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']
diff --git a/dockerfiles/rhel9-kuma/Dockerfile b/dockerfiles/rhel9-kuma/Dockerfile
index 5ce577fa1642e3c3f5d62e6bbb380df7135d42d8..2b6da7785b43457cd47e7bfe42d6ba42018cd013 100644
--- a/dockerfiles/rhel9-kuma/Dockerfile
+++ b/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 \
diff --git a/stacks/pinot-noir-gcc/concretizer.yaml b/stacks/pinot-noir-gcc/concretizer.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..698e4c7865156575e6807306e18573c647c921c2
--- /dev/null
+++ b/stacks/pinot-noir-gcc/concretizer.yaml
@@ -0,0 +1,5 @@
+concretizer:
+ reuse: false
+ unify: false
+ duplicates:
+ strategy: minimal
diff --git a/stacks/pinot-noir-gcc/config.json b/stacks/pinot-noir-gcc/config.json
new file mode 100644
index 0000000000000000000000000000000000000000..dd541dc7663a4a173cce978bdc14486addd959c9
--- /dev/null
+++ b/stacks/pinot-noir-gcc/config.json
@@ -0,0 +1,121 @@
+{
+ "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"
+ ]
+ }
+}
diff --git a/stacks/pinot-noir-gcc/config.yaml b/stacks/pinot-noir-gcc/config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..aff2737c506bb6ddb8fdbe7e8c81676ab70d5ec6
--- /dev/null
+++ b/stacks/pinot-noir-gcc/config.yaml
@@ -0,0 +1,9 @@
+config:
+# ccache: true
+ install_missing_compilers: false
+
+ install_tree:
+ padded_length: 242
+
+ build_stage:
+ - $tempdir/$user/spack-stage
diff --git a/stacks/pinot-noir-gcc/definitions_helvetios.yaml b/stacks/pinot-noir-gcc/definitions_helvetios.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..ca4ba7fe51ad3279cebc61ff97ee72782db03b81
--- /dev/null
+++ b/stacks/pinot-noir-gcc/definitions_helvetios.yaml
@@ -0,0 +1 @@
+definitions: []
diff --git a/stacks/pinot-noir-gcc/definitions_jed.yaml b/stacks/pinot-noir-gcc/definitions_jed.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..0f156fa830b9567b3e7839218a0a88c16076c6ca
--- /dev/null
+++ b/stacks/pinot-noir-gcc/definitions_jed.yaml
@@ -0,0 +1,7 @@
+definitions:
+ - cuda_system_codes:
+ - cuda
+ - cudnn
+
+ - cuda_serial_codes:
+ - nccl
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 0000000000000000000000000000000000000000..0f156fa830b9567b3e7839218a0a88c16076c6ca
--- /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/mirrors.yaml b/stacks/pinot-noir-gcc/mirrors.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..2c338aa265ca4ab7735374e44dd491d1f2c81115
--- /dev/null
+++ b/stacks/pinot-noir-gcc/mirrors.yaml
@@ -0,0 +1 @@
+mirrors: {}
diff --git a/stacks/pinot-noir-gcc/modules.yaml b/stacks/pinot-noir-gcc/modules.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..99f6f3e104d547f086fd83a4e77d1b4f3be316a0
--- /dev/null
+++ b/stacks/pinot-noir-gcc/modules.yaml
@@ -0,0 +1,141 @@
+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
diff --git a/stacks/pinot-noir-gcc/packages_helvetios.yaml b/stacks/pinot-noir-gcc/packages_helvetios.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..fe0d4ad01829f0895adce34a9071fe0eb4218e18
--- /dev/null
+++ b/stacks/pinot-noir-gcc/packages_helvetios.yaml
@@ -0,0 +1,8 @@
+packages:
+ all:
+ target: ["skylake_avx512"]
+ require: ['~cuda', '~rocm']
+
+ # py-torch:
+ # require:
+ # - spec: '~cuda ~cudnn ~nccl ~rocm'
diff --git a/stacks/pinot-noir-gcc/packages_izar.yaml b/stacks/pinot-noir-gcc/packages_izar.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..9ce65d95e200925fe7b5bd50d0f76c18b2f33097
--- /dev/null
+++ b/stacks/pinot-noir-gcc/packages_izar.yaml
@@ -0,0 +1,11 @@
+packages:
+ all:
+ target: ["cannonlake"]
+ require:
+ - spec: ^openmpi +cuda
+ when: '%gcc ^mpi'
+
+ - spec: cuda_arch=70
+ when: '+cuda'
+
+ - '+cuda'
diff --git a/stacks/pinot-noir-gcc/packages_jed.yaml b/stacks/pinot-noir-gcc/packages_jed.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..186b82d655ded03701bd8fff6750cd56779a51dd
--- /dev/null
+++ b/stacks/pinot-noir-gcc/packages_jed.yaml
@@ -0,0 +1,80 @@
+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
diff --git a/stacks/pinot-noir-gcc/packages_kuma_h100.yaml b/stacks/pinot-noir-gcc/packages_kuma_h100.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..07fab46b1d2c1b45b5ea688ff8eb341829e37bb6
--- /dev/null
+++ b/stacks/pinot-noir-gcc/packages_kuma_h100.yaml
@@ -0,0 +1,78 @@
+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
diff --git a/stacks/pinot-noir-gcc/packages_kuma_l40s.yaml b/stacks/pinot-noir-gcc/packages_kuma_l40s.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..ad6b8fb44336cd6730bb956c5d8489ff7f0acf0b
--- /dev/null
+++ b/stacks/pinot-noir-gcc/packages_kuma_l40s.yaml
@@ -0,0 +1,11 @@
+packages:
+ all:
+ target: ["zen4"]
+ require:
+ - spec: ^openmpi +cuda
+ when: '%gcc ^mpi'
+
+ - spec: cuda_arch=89
+ when: '+cuda'
+
+ - '+cuda'
diff --git a/stacks/pinot-noir-gcc/packages_stack.yaml b/stacks/pinot-noir-gcc/packages_stack.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..c9f989de74c7d3466e7429fce7f815828cd1da59
--- /dev/null
+++ b/stacks/pinot-noir-gcc/packages_stack.yaml
@@ -0,0 +1,276 @@
+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}
diff --git a/stacks/pinot-noir-gcc/spack.yaml b/stacks/pinot-noir-gcc/spack.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..b1195d1e7e381f38879378957817e46a211565ac
--- /dev/null
+++ b/stacks/pinot-noir-gcc/spack.yaml
@@ -0,0 +1,422 @@
+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/
diff --git a/stacks/pinot-noir-gcc/templates/modules/group_restricted.lua b/stacks/pinot-noir-gcc/templates/modules/group_restricted.lua
new file mode 100644
index 0000000000000000000000000000000000000000..1511796f6bb6dfc84b64c9ec5af200c7d4fe2c12
--- /dev/null
+++ b/stacks/pinot-noir-gcc/templates/modules/group_restricted.lua
@@ -0,0 +1,10 @@
+{% 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 %}
diff --git a/stacks/pinot-noir/concretizer.yaml b/stacks/pinot-noir/concretizer.yaml
index aa4e2548b74a093e7baa09e04a7d391f7288b605..698e4c7865156575e6807306e18573c647c921c2 100644
--- a/stacks/pinot-noir/concretizer.yaml
+++ b/stacks/pinot-noir/concretizer.yaml
@@ -1,5 +1,5 @@
concretizer:
reuse: false
- unify: when_possible
+ unify: false
duplicates:
strategy: minimal
diff --git a/stacks/pinot-noir/config.json b/stacks/pinot-noir/config.json
index 38a3b97973ff78da524aaae680922f1aa3ba2f76..fae5342bf5077ffaf0114ea4379a7a277a69faac 100644
--- a/stacks/pinot-noir/config.json
+++ b/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",
diff --git a/stacks/pinot-noir/definitions_kuma_h100.yaml b/stacks/pinot-noir/definitions_kuma_h100.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..0f156fa830b9567b3e7839218a0a88c16076c6ca
--- /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_helvetios.yaml b/stacks/pinot-noir/packages_helvetios.yaml
index f654aa42a02e2392b5c852e3febeb9518ec1ec78..fe0d4ad01829f0895adce34a9071fe0eb4218e18 100644
--- a/stacks/pinot-noir/packages_helvetios.yaml
+++ b/stacks/pinot-noir/packages_helvetios.yaml
@@ -1,5 +1,8 @@
packages:
all:
target: ["skylake_avx512"]
- require:
- - '~cuda'
+ require: ['~cuda', '~rocm']
+
+ # py-torch:
+ # require:
+ # - spec: '~cuda ~cudnn ~nccl ~rocm'
diff --git a/stacks/pinot-noir/packages_jed.yaml b/stacks/pinot-noir/packages_jed.yaml
index dcc04e3ecacc5be4b2e480c5b8056bd880dae8f8..822d1e2f6b56828d7269ba821ecb27be99c9d6d2 100644
--- a/stacks/pinot-noir/packages_jed.yaml
+++ b/stacks/pinot-noir/packages_jed.yaml
@@ -15,23 +15,32 @@ packages:
# ---------------------------------------------------------------------------
hypre:
require:
- - spec: '+cuda cuda_arch=90'
+ - spec: '+cuda cuda_arch=90 +unified-memory'
when: '%gcc'
kokkos:
require:
- - spec: '+cuda cuda_arch=90 +cuda_uvm'
+ - spec: '+cuda cuda_arch=90 +cuda_uvm +wrapper ~openmptarget'
+ when: '%gcc'
+
+ kokkos-kernels:
+ require:
+ - spec: '+cuda cuda_arch=90'
when: '%gcc'
openmpi:
require:
- - spec: 'fabrics=hcoll +cuda cuda_arch=90 target=icelake'
+ - 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'
@@ -46,17 +55,11 @@ packages:
ucx:
require:
- - spec: '+xpmem +cma +rdmacm +rc +ud +dc +verbs +ib_hw_tm +vfs +gdrcopy +cuda cuda_arch=90 target=icelake ~rocm'
+ - spec: '+xpmem +cma +rdmacm +rc +ud +dc +verbs +ib_hw_tm +gdrcopy +cuda cuda_arch=90 target=icelake ~rocm'
# ---------------------------------------------------------------------------
# Externals
# ---------------------------------------------------------------------------
- hcoll:
- buildable: False
- externals:
- - spec: 'hcoll@4.8.3227'
- prefix: /usr
-
pmix:
buildable: false
externals:
diff --git a/stacks/pinot-noir/packages_stack.yaml b/stacks/pinot-noir/packages_stack.yaml
index dbb2084f075cdc958a7a430f0fbd9e35e2ba5f99..d12a3aa85defa2721cc41fe5bb6811632456b7d7 100644
--- a/stacks/pinot-noir/packages_stack.yaml
+++ b/stacks/pinot-noir/packages_stack.yaml
@@ -1,45 +1,14 @@
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
- # when: '%gcc ^blas'
-
- # - 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'
@@ -85,16 +54,17 @@ packages:
hypre:
prefer:
- - spec: '@2.31.0'
- require:
- - spec: '+unified-memory ~magma'
- when: '+cuda'
+ - spec: '@2.31.0 ~magma'
intel-oneapi-mkl:
- prefer: ['+cluster']
+ prefer: ['~cluster']
kokkos:
- prefer: ['+openmp', '+openmptarget', '+numactl', '+memkind', '+threads', '+aggressive_vectorization']
+ prefer: ['+openmp', '+numactl', '+memkind', '+threads',
+ '+aggressive_vectorization']
+
+ kokkos-kernel:
+ prefer: ['+openmp', '+threads']
lammps:
require: ['build_type=Release', '+asphere', '+atc', '+body', '+class2',
@@ -124,7 +94,7 @@ packages:
prefer: ['+mpi']
openblas:
- prefer: ['threads=pthreads']
+ prefer: ['threads=pthreads symbol_suffix=none ~ilp64']
opencv:
prefer: ['+vtk', '+python3']
@@ -132,8 +102,6 @@ packages:
openmpi:
require:
- spec: '@5.0.3 fabrics=ofi,ucx,verbs schedulers=slurm ~rsh +romio romio-filesystem=gpfs +internal-pmix ~memchecker'
- - spec: ^ucx +cuda
- when: +cuda
petsc:
require:
@@ -146,10 +114,13 @@ packages:
when: '%gcc'
py-tensorflow:
- require: ['+mpi']
+ require: ['+mpi', '+mkl']
py-torch:
- require: ['+mpi', '~magma']
+ require: ['+mpi']
+
+ scotch:
+ prefer: ['~mpi']
suite-sparse:
require:
@@ -160,9 +131,10 @@ packages:
ucx:
require:
- - spec: +rdmacm +rc +dc +ud +cma +verbs
- - spec: +gdrcopy
- when: +cuda
+ - spec: '+rdmacm +rc +dc +ud +cma +verbs'
+
+ zlib-ng:
+ require: ['build_system=autotools']
# ----------------------------------------------------------------------------
# System dependencies
diff --git a/stacks/pinot-noir/spack.yaml b/stacks/pinot-noir/spack.yaml
index 1bafcf146002f28db65dd8101454e522fac2da11..d80e2cc8ab5f37da522e571dfb1818155c18598c 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/