From 07ba3046161450ffbffd018f343c483e10f38898 Mon Sep 17 00:00:00 2001
From: Nicolas Richart <nicolas.richart@epfl.ch>
Date: Fri, 9 Aug 2024 11:47:23 +0200
Subject: [PATCH] Switching back pinot-noir-gcc13 to pinot-noir
---
.gitlab-ci.yml | 20 +-
stacks/pinot-noir-gcc13/concretizer.yaml | 12 -
stacks/pinot-noir-gcc13/config.json | 133 -----
stacks/pinot-noir-gcc13/config.yaml | 9 -
stacks/pinot-noir-gcc13/definitions_cuda.yaml | 11 -
.../pinot-noir-gcc13/definitions_empty.yaml | 1 -
.../definitions_helvetios.yaml | 1 -
stacks/pinot-noir-gcc13/definitions_izar.yaml | 1 -
stacks/pinot-noir-gcc13/definitions_jed.yaml | 7 -
.../definitions_kuma-h100.yaml | 1 -
.../definitions_kuma-l40s.yaml | 1 -
stacks/pinot-noir-gcc13/mirrors.yaml | 1 -
stacks/pinot-noir-gcc13/modules.yaml | 125 -----
stacks/pinot-noir-gcc13/modules_empty.yaml | 3 -
.../pinot-noir-gcc13/modules_helvetios.yaml | 1 -
stacks/pinot-noir-gcc13/modules_izar.yaml | 1 -
stacks/pinot-noir-gcc13/modules_jed.yaml | 1 -
.../pinot-noir-gcc13/modules_kuma-h100.yaml | 14 -
.../pinot-noir-gcc13/modules_kuma-l40s.yaml | 14 -
stacks/pinot-noir-gcc13/packages.yaml | 26 -
.../pinot-noir-gcc13/packages_helvetios.yaml | 8 -
stacks/pinot-noir-gcc13/packages_izar.yaml | 11 -
stacks/pinot-noir-gcc13/packages_jed.yaml | 85 ---
.../pinot-noir-gcc13/packages_kuma-h100.yaml | 114 ----
.../pinot-noir-gcc13/packages_kuma-l40s.yaml | 108 ----
stacks/pinot-noir-gcc13/packages_stack.yaml | 416 ---------------
stacks/pinot-noir-gcc13/spack.yaml | 503 ------------------
.../templates/modules/group_restricted.lua | 10 -
stacks/pinot-noir/config.json | 4 +-
stacks/pinot-noir/packages_kuma-h100.yaml | 21 +-
stacks/pinot-noir/packages_kuma-l40s.yaml | 20 +-
stacks/pinot-noir/packages_stack.yaml | 66 ++-
stacks/pinot-noir/spack.yaml | 16 +-
33 files changed, 100 insertions(+), 1665 deletions(-)
delete mode 100644 stacks/pinot-noir-gcc13/concretizer.yaml
delete mode 100644 stacks/pinot-noir-gcc13/config.json
delete mode 100644 stacks/pinot-noir-gcc13/config.yaml
delete mode 100644 stacks/pinot-noir-gcc13/definitions_cuda.yaml
delete mode 100644 stacks/pinot-noir-gcc13/definitions_empty.yaml
delete mode 120000 stacks/pinot-noir-gcc13/definitions_helvetios.yaml
delete mode 120000 stacks/pinot-noir-gcc13/definitions_izar.yaml
delete mode 100644 stacks/pinot-noir-gcc13/definitions_jed.yaml
delete mode 120000 stacks/pinot-noir-gcc13/definitions_kuma-h100.yaml
delete mode 120000 stacks/pinot-noir-gcc13/definitions_kuma-l40s.yaml
delete mode 100644 stacks/pinot-noir-gcc13/mirrors.yaml
delete mode 100644 stacks/pinot-noir-gcc13/modules.yaml
delete mode 100644 stacks/pinot-noir-gcc13/modules_empty.yaml
delete mode 120000 stacks/pinot-noir-gcc13/modules_helvetios.yaml
delete mode 120000 stacks/pinot-noir-gcc13/modules_izar.yaml
delete mode 120000 stacks/pinot-noir-gcc13/modules_jed.yaml
delete mode 100644 stacks/pinot-noir-gcc13/modules_kuma-h100.yaml
delete mode 100644 stacks/pinot-noir-gcc13/modules_kuma-l40s.yaml
delete mode 100644 stacks/pinot-noir-gcc13/packages.yaml
delete mode 100644 stacks/pinot-noir-gcc13/packages_helvetios.yaml
delete mode 100644 stacks/pinot-noir-gcc13/packages_izar.yaml
delete mode 100644 stacks/pinot-noir-gcc13/packages_jed.yaml
delete mode 100644 stacks/pinot-noir-gcc13/packages_kuma-h100.yaml
delete mode 100644 stacks/pinot-noir-gcc13/packages_kuma-l40s.yaml
delete mode 100644 stacks/pinot-noir-gcc13/packages_stack.yaml
delete mode 100644 stacks/pinot-noir-gcc13/spack.yaml
delete mode 100644 stacks/pinot-noir-gcc13/templates/modules/group_restricted.lua
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a5dea33..2041cd7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -23,28 +23,28 @@ variables:
.parallel_definition:
parallel:
matrix:
- # - environment: [jed]
- # slurm_options: ["-c 72 -p jed -q jed"]
- # stack: ["pinot-noir"]
- # app_image: ["registry.c4science.ch/scitas-stack/rhel9-kuma"]
# - environment: [helvetios]
# slurm_options: ["-c 36"]
# stack: ["pinot-noir"]
# app_image: ["registry.c4science.ch/scitas-stack/rhel9-kuma"]
+ # - environment: [izar]
+ # slurm_options: ['-c 40 --gpus 2']
+ # apptainer_options: ['-nv']
+ # stack: ["pinot-noir"]
+ # - environment: [jed]
+ # slurm_options: ["-c 72 -p jed -q jed"]
+ # stack: ["pinot-noir"]
+ # app_image: ["registry.c4science.ch/scitas-stack/rhel9-kuma"]
- environment: [kuma-h100]
slurm_options: ["-c 64"]
- stack: ["pinot-noir-gcc13"]
+ stack: ["pinot-noir"]
apptainer_options: ['--nv']
app_image: ["registry.c4science.ch/scitas-stack/rhel9-kuma"]
- environment: [kuma-l40s]
slurm_options: ["-c 64"]
- stack: ["pinot-noir-gcc13"]
+ stack: ["pinot-noir"]
apptainer_options: ['--nv']
app_image: ["registry.c4science.ch/scitas-stack/rhel9-kuma"]
- # - environment: [izar]
- # slurm_options: ['-c 40 --gpus 2']
- # apptainer_options: ['-nv']
- # stack: ["pinot-noir"]
tags:
- ${environment}
- stack
diff --git a/stacks/pinot-noir-gcc13/concretizer.yaml b/stacks/pinot-noir-gcc13/concretizer.yaml
deleted file mode 100644
index 3ed6dcf..0000000
--- a/stacks/pinot-noir-gcc13/concretizer.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-concretizer:
- reuse: false
- # roots: true
- # include:
- # - "%gcc@12.3.0"
- # exclude:
- # - 'python'
- # from:
- # - type: local
- unify: false
- duplicates:
- strategy: minimal
diff --git a/stacks/pinot-noir-gcc13/config.json b/stacks/pinot-noir-gcc13/config.json
deleted file mode 100644
index 5a5c053..0000000
--- a/stacks/pinot-noir-gcc13/config.json
+++ /dev/null
@@ -1,133 +0,0 @@
-{
- "spack": {
- "version": "releases/v0.22",
- "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": "/ssoft/spack",
- "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": {
- "oneapi": {
- "compiler": "oneapi",
- "spec": "intel-oneapi-compilers@2024.1.0 %gcc@11.2.1",
- "version": "2024.1.0",
- "constraint": "env['environment'] in ['jed', 'helvetios']"
- },
- "gcc": {
- "compiler": "gcc",
- "spec": "gcc@13.2.0 %gcc@11.2.1",
- "version": "13.2.0"
- }
- },
- "system_packages": [
- "autoconf",
- "autoconf-archive",
- "automake",
- "autotools",
- "berkley-db",
- "bzip2",
- "ca-certificates-mozilla",
- "check",
- "cmake",
- "curl",
- "diffutils",
- "expat",
- "findutils",
- "flex",
- "font-util",
- "fontconfig",
- "freetype",
- "gawk",
- "gdbm",
- "gettext",
- "git",
- "gmake",
- "gmp",
- "gnuplot",
- "gperf",
- "hcoll",
- "help2man",
- "libaec",
- "libedit",
- "libevent",
- "libffi",
- "libfuse",
- "libidn2",
- "libpciaccess",
- "libpng",
- "libsigsegv",
- "libssh2",
- "libtiff",
- "libtool",
- "libunistring",
- "libuuid",
- "libx11",
- "libxcrypt",
- "libxct",
- "libxft",
- "libxml2",
- "lz4",
- "m4",
- "macro-utils",
- "mpc",
- "mpfr",
- "ncurses",
- "openssl",
- "pcre",
- "pcre2",
- "perl",
- "pigz",
- "pkgconf",
- "pmix",
- "rdma-core",
- "readline",
- "slurm",
- "sqlite",
- "tar",
- "tcl",
- "texinfo",
- "tk",
- "utf8proc",
- "util-linux-uuid",
- "xpmem",
- "xxd-standalon",
- "xz",
- "zlib-ng",
- "zstd"
- ]
- }
-}
diff --git a/stacks/pinot-noir-gcc13/config.yaml b/stacks/pinot-noir-gcc13/config.yaml
deleted file mode 100644
index bac71f0..0000000
--- a/stacks/pinot-noir-gcc13/config.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-config:
-# ccache: true
- install_missing_compilers: false
-
- install_tree:
- padded_length: False
-
- build_stage:
- - $tempdir/$user/spack-stage
diff --git a/stacks/pinot-noir-gcc13/definitions_cuda.yaml b/stacks/pinot-noir-gcc13/definitions_cuda.yaml
deleted file mode 100644
index 99f5093..0000000
--- a/stacks/pinot-noir-gcc13/definitions_cuda.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-definitions:
- - cuda_system_codes: []
-
- - cuda_serial_codes:
- - cuda
- - cudnn
- - nccl
-
- - cuda_mpi_codes:
- - nvshmem
- - nccl-tests
diff --git a/stacks/pinot-noir-gcc13/definitions_empty.yaml b/stacks/pinot-noir-gcc13/definitions_empty.yaml
deleted file mode 100644
index ca4ba7f..0000000
--- a/stacks/pinot-noir-gcc13/definitions_empty.yaml
+++ /dev/null
@@ -1 +0,0 @@
-definitions: []
diff --git a/stacks/pinot-noir-gcc13/definitions_helvetios.yaml b/stacks/pinot-noir-gcc13/definitions_helvetios.yaml
deleted file mode 120000
index 3552a78..0000000
--- a/stacks/pinot-noir-gcc13/definitions_helvetios.yaml
+++ /dev/null
@@ -1 +0,0 @@
-definitions_empty.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir-gcc13/definitions_izar.yaml b/stacks/pinot-noir-gcc13/definitions_izar.yaml
deleted file mode 120000
index 2c65e6a..0000000
--- a/stacks/pinot-noir-gcc13/definitions_izar.yaml
+++ /dev/null
@@ -1 +0,0 @@
-definitions_cuda.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir-gcc13/definitions_jed.yaml b/stacks/pinot-noir-gcc13/definitions_jed.yaml
deleted file mode 100644
index 0f156fa..0000000
--- a/stacks/pinot-noir-gcc13/definitions_jed.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-definitions:
- - cuda_system_codes:
- - cuda
- - cudnn
-
- - cuda_serial_codes:
- - nccl
diff --git a/stacks/pinot-noir-gcc13/definitions_kuma-h100.yaml b/stacks/pinot-noir-gcc13/definitions_kuma-h100.yaml
deleted file mode 120000
index 2c65e6a..0000000
--- a/stacks/pinot-noir-gcc13/definitions_kuma-h100.yaml
+++ /dev/null
@@ -1 +0,0 @@
-definitions_cuda.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir-gcc13/definitions_kuma-l40s.yaml b/stacks/pinot-noir-gcc13/definitions_kuma-l40s.yaml
deleted file mode 120000
index 2c65e6a..0000000
--- a/stacks/pinot-noir-gcc13/definitions_kuma-l40s.yaml
+++ /dev/null
@@ -1 +0,0 @@
-definitions_cuda.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir-gcc13/mirrors.yaml b/stacks/pinot-noir-gcc13/mirrors.yaml
deleted file mode 100644
index 2c338aa..0000000
--- a/stacks/pinot-noir-gcc13/mirrors.yaml
+++ /dev/null
@@ -1 +0,0 @@
-mirrors: {}
diff --git a/stacks/pinot-noir-gcc13/modules.yaml b/stacks/pinot-noir-gcc13/modules.yaml
deleted file mode 100644
index 38fcc67..0000000
--- a/stacks/pinot-noir-gcc13/modules.yaml
+++ /dev/null
@@ -1,125 +0,0 @@
-modules:
- default:
- enable: [lmod]
- lmod:
- hash_length: 0
- core_compilers:
- - gcc@11.2.1
- hierarchy:
- - mpi
- all:
- environment:
- set:
- "{name}_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
- autoload: run
-
- hide_implicits: true
-
- exclude:
- - 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: pmix
- 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
- metis:
- suffixes:
- ~real64: sp
- molpro:
- template: modules/group_restricted.lua
- plumed:
- environment:
- set:
- PLUMED_KERNEL: "{prefix}/lib/libplumedKernel.so"
- unset:
- - PLUMED_ROOT
- quantum-espresso:
- suffixes:
- hdf5=parallel: hdf5
- 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:
- 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-gcc13/modules_empty.yaml b/stacks/pinot-noir-gcc13/modules_empty.yaml
deleted file mode 100644
index 21d0544..0000000
--- a/stacks/pinot-noir-gcc13/modules_empty.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-modules:
- default:
- lmod: {}
diff --git a/stacks/pinot-noir-gcc13/modules_helvetios.yaml b/stacks/pinot-noir-gcc13/modules_helvetios.yaml
deleted file mode 120000
index 5be0f31..0000000
--- a/stacks/pinot-noir-gcc13/modules_helvetios.yaml
+++ /dev/null
@@ -1 +0,0 @@
-modules_empty.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir-gcc13/modules_izar.yaml b/stacks/pinot-noir-gcc13/modules_izar.yaml
deleted file mode 120000
index 5be0f31..0000000
--- a/stacks/pinot-noir-gcc13/modules_izar.yaml
+++ /dev/null
@@ -1 +0,0 @@
-modules_empty.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir-gcc13/modules_jed.yaml b/stacks/pinot-noir-gcc13/modules_jed.yaml
deleted file mode 120000
index 5be0f31..0000000
--- a/stacks/pinot-noir-gcc13/modules_jed.yaml
+++ /dev/null
@@ -1 +0,0 @@
-modules_empty.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir-gcc13/modules_kuma-h100.yaml b/stacks/pinot-noir-gcc13/modules_kuma-h100.yaml
deleted file mode 100644
index 4599ea4..0000000
--- a/stacks/pinot-noir-gcc13/modules_kuma-h100.yaml
+++ /dev/null
@@ -1,14 +0,0 @@
-modules:
- default:
- lmod:
- openmpi:
- environment:
- set:
- OMPI_MCA_pml: 'ucx'
- OMPI_MCA_osc: 'ucx'
- UCX_NET_DEVICES: 'mlx5_2:1,mlx5_3:1'
- nccl:
- environment:
- set:
- NCCL_IB_HCA: 'mlx5_2:1,mlx5_3:1'
- NCCL_SOCKET_IFNAME: 'bond0'
diff --git a/stacks/pinot-noir-gcc13/modules_kuma-l40s.yaml b/stacks/pinot-noir-gcc13/modules_kuma-l40s.yaml
deleted file mode 100644
index 1f147c1..0000000
--- a/stacks/pinot-noir-gcc13/modules_kuma-l40s.yaml
+++ /dev/null
@@ -1,14 +0,0 @@
-modules:
- default:
- lmod:
- openmpi:
- environment:
- set:
- OMPI_MCA_pml: 'ucx'
- OMPI_MCA_osc: 'ucx'
- UCX_NET_DEVICES: 'mlx5_0:1,mlx5_1:1'
- nccl:
- environment:
- set:
- NCCL_IB_HCA: 'mlx5_0:1,mlx5_1:1'
- NCCL_SOCKET_IFNAME: 'bond0'
diff --git a/stacks/pinot-noir-gcc13/packages.yaml b/stacks/pinot-noir-gcc13/packages.yaml
deleted file mode 100644
index 4b636f1..0000000
--- a/stacks/pinot-noir-gcc13/packages.yaml
+++ /dev/null
@@ -1,26 +0,0 @@
-packages:
- all:
- compiler:
- - gcc
- - aocc
- - nvhpc
-
- providers:
- mpi: [openmpi, intel-oneapi-mpi]
- jpeg: [libjpeg]
- zlib-api: [zlib-ng]
- pkgconfig: [pkgconf]
- szip: [libaec]
- unwind: [libunwind]
- uuid: [libuuid]
- zlib-api: [zlib-ng+compat]
-
- require:
- - spec: '^libuuid'
- when: '^uuid'
-
- glibc:
- prefer: ['%gcc@11.2.1']
-
- zlib-ng:
- require: ['build_system=autotools']
diff --git a/stacks/pinot-noir-gcc13/packages_helvetios.yaml b/stacks/pinot-noir-gcc13/packages_helvetios.yaml
deleted file mode 100644
index fe0d4ad..0000000
--- a/stacks/pinot-noir-gcc13/packages_helvetios.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-packages:
- all:
- target: ["skylake_avx512"]
- require: ['~cuda', '~rocm']
-
- # py-torch:
- # require:
- # - spec: '~cuda ~cudnn ~nccl ~rocm'
diff --git a/stacks/pinot-noir-gcc13/packages_izar.yaml b/stacks/pinot-noir-gcc13/packages_izar.yaml
deleted file mode 100644
index 9ce65d9..0000000
--- a/stacks/pinot-noir-gcc13/packages_izar.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-packages:
- all:
- target: ["cannonlake"]
- require:
- - spec: ^openmpi +cuda
- when: '%gcc ^mpi'
-
- - spec: cuda_arch=70
- when: '+cuda'
-
- - '+cuda'
diff --git a/stacks/pinot-noir-gcc13/packages_jed.yaml b/stacks/pinot-noir-gcc13/packages_jed.yaml
deleted file mode 100644
index 822d1e2..0000000
--- a/stacks/pinot-noir-gcc13/packages_jed.yaml
+++ /dev/null
@@ -1,85 +0,0 @@
-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'
-
- kokkos-kernels:
- require:
- - spec: '+cuda cuda_arch=90'
- 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-gcc13/packages_kuma-h100.yaml b/stacks/pinot-noir-gcc13/packages_kuma-h100.yaml
deleted file mode 100644
index 516d817..0000000
--- a/stacks/pinot-noir-gcc13/packages_kuma-h100.yaml
+++ /dev/null
@@ -1,114 +0,0 @@
-packages:
- all:
- target: ["zen4"]
- prefer: ['target=zen4']
- require:
- - "~rocm"
-
- - spec: cuda_arch=90
- when: '+cuda'
-
- - spec: '+cuda'
- when: '%gcc'
-
- # ---------------------------------------------------------------------------
- cp2k:
- require: ['+cuda', 'cuda_arch=90']
-
- cuda:
- prefer:
- - spec: "^gcc-runtime@13.2.0"
- when: "%gcc"
- - spec: "%gcc@13.2.0 target=zen4"
- when: "%gcc"
- require:
- - '@12.4.1'
-
- hypre:
- require:
- - spec: '+cuda cuda_arch=90 +unified-memory'
- when: '%gcc'
-
- kokkos:
- require:
- - spec: '+cuda +cuda_lambda cuda_arch=90 +wrapper ~openmptarget'
- when: '%gcc'
-
- kokkos-kernels:
- require: ['+cuda', '+cublas', '+cusolver', '+cusparse', 'cuda_arch=90']
-
- libxc:
- require: ['+cuda', 'cuda_arch=90']
-
- nvshmem:
- require:
- - spec: '+cuda cuda_arch=90 +ibgda +nccl +ucx +mpi'
-
- openmpi:
- require: ['+cuda', 'cuda_arch=90']
-
- papi:
- require: ['+nvml', '+infiniband', '+cuda']
-
- paraview:
- require: ['~cuda']
-
- 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'
-
- python:
- require:
- - spec: 'target=zen4'
- when: '%gcc@13.2.0'
-
- quantum-espresso:
- require:
- - spec: '+nvtx'
-
- suite-sparse:
- require:
- - spec: '+cuda'
- when: '@7.3.1'
- - spec: '~cuda'
- when: '@7.2.1'
-
- ucx:
- require:
- - spec: '+xpmem +cma +rdmacm +rc +ud +dc +verbs +ib_hw_tm +gdrcopy +cuda cuda_arch=90 ~rocm'
-
- # ---------------------------------------------------------------------------
- # Externals
- # ---------------------------------------------------------------------------
- pmix:
- buildable: false
- externals:
- - spec: 'pmix@5.0.2'
- prefix: /usr
-
- rdma-core:
- buildable: false
- externals:
- - spec: 'rdma-core@51.1'
- 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-gcc13/packages_kuma-l40s.yaml b/stacks/pinot-noir-gcc13/packages_kuma-l40s.yaml
deleted file mode 100644
index 323b8b2..0000000
--- a/stacks/pinot-noir-gcc13/packages_kuma-l40s.yaml
+++ /dev/null
@@ -1,108 +0,0 @@
-packages:
- all:
- target: ["zen4"]
- prefer: ["target=zen4"]
- require:
- - "~rocm"
-
- - spec: cuda_arch=89
- when: '+cuda'
-
- - spec: '+cuda'
- when: '%gcc'
-
- # ---------------------------------------------------------------------------
- cuda:
- prefer:
- - spec: "^gcc-runtime@13.2.0"
- when: "%gcc"
- - spec: "%gcc@13.2.0 target=zen4"
- when: "%gcc"
- require:
- - '@12.4.1'
-
- hypre:
- require:
- - spec: '+cuda cuda_arch=89 +unified-memory'
- when: '%gcc'
-
- kokkos:
- require:
- - spec: '+cuda +cuda_lambda cuda_arch=89 +wrapper ~openmptarget'
- when: '%gcc'
-
- kokkos-kernels:
- require: ['+cuda', '+cublas', '+cusolver', '+cusparse', 'cuda_arch=89']
-
- nvshmem:
- require:
- - spec: '+cuda cuda_arch=89 +ibgda +nccl +ucx +mpi'
-
- openmpi:
- require: ['+cuda', 'cuda_arch=89']
-
- papi:
- require: ['+nvml', '+infiniband', '+cuda']
-
- paraview:
- require: ['~cuda']
-
- petsc:
- require:
- - spec: '+cuda cuda_arch=89'
- when: '%gcc'
-
- py-tensorflow:
- require:
- - spec: '+cuda cuda_arch=89 +nccl'
-
- py-torch:
- require:
- - spec: '+cuda cuda_arch=89 +nccl +cudnn'
-
- python:
- require:
- - spec: 'target=zen4'
- when: '%gcc@13.2.0'
-
- quantum-espresso:
- require:
- - spec: '+nvtx'
-
- suite-sparse:
- require:
- - spec: '+cuda'
- when: '@7.3.1'
- - spec: '~cuda'
- when: '@7.2.1'
-
- ucx:
- require:
- - spec: '+xpmem +cma +rdmacm +rc +ud +dc +verbs +ib_hw_tm +gdrcopy +cuda cuda_arch=89 ~rocm'
-
- # ---------------------------------------------------------------------------
- # Externals
- # ---------------------------------------------------------------------------
- pmix:
- buildable: false
- externals:
- - spec: 'pmix@5.0.2'
- prefix: /usr
-
- rdma-core:
- buildable: false
- externals:
- - spec: 'rdma-core@51.1'
- 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-gcc13/packages_stack.yaml b/stacks/pinot-noir-gcc13/packages_stack.yaml
deleted file mode 100644
index 5ca72c6..0000000
--- a/stacks/pinot-noir-gcc13/packages_stack.yaml
+++ /dev/null
@@ -1,416 +0,0 @@
-packages:
- all:
- require:
- - spec: '+ipo'
- when: '%gcc'
- - spec: '^netlib-scalapack'
- when: '%gcc ^scalapack'
-
- # ----------------------------------------------------------------------------
- # Requirements
- # ----------------------------------------------------------------------------
- adios2:
- require: ['+kokkos', '+mgard']
-
- apr:
- # https://issues.apache.org/jira/browse/SVN-4813
- require: ['@1.6.2']
-
- arpack-ng:
- prefer: ['+mpi']
-
- 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']
-
- cairo:
- # ~X avoids a dependency to python (only prefer due to gtkplus)
- prefer: ['~X', '+svg']
- require: ['+fc', '+ft', '+pdf', '+gobject']
-
- cmake:
- prefer: ['~ncurses']
-
- costa:
- require: ['~apps']
-
- cp2k:
- require: ['~ipo']
-
- cuda:
- require:
- - spec: '+allow-unsupported-compilers'
- when: '%oneapi'
-
- curl:
- require:
- - '+nghttp2'
- - '+libidn2'
- - '+libssh2'
- - one_of: ['tls=openssl', 'tls=mbedtls']
-
- emacs:
- prefer: ['+tls', '+X', 'toolkit=athena']
-
- expat:
- prefer: ['libbsd']
-
- fenics-dolfinx:
- require: ['@0.8.0', '+slepc']
-
- ffmpeg:
- require: ['+libx264']
-
- fftw:
- prefer: ['+mpi', '+openmp']
-
- gettext:
- require: ['+libxml2', '+xz']
-
- gnuplot:
- require: ['@5.4.10', '+cairo']
-
- hdf5:
- prefer:
- - 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']
-
- julia:
- require: ['@1.10.4']
-
- kokkos:
- require: ['+numactl', '+memkind', '+serial',
- '+openmp', '~openmptarget',
- '~threads', '~sycl',
- '+aggressive_vectorization', '@4.3.01']
-
- kokkos-kernels:
- require: ['@4.3.01', '+openmp', '~threads', '~ipo']
-
- kokkos-nvcc-wrapper:
- prefer: ['@4.3.01']
-
- lammps:
- require: ['@20230802.3',
- 'build_type=Release', '+asphere', '+atc', '+body', '+class2',
- '+colloid', '+compress', '+coreshell', '+dipole', '+diffraction',
- '+extra-dump', '+granular', '+h5md', '+kspace', '+latboltz',
- '+lib', '+manybody', '+mc', '+misc', '+molecule',
- '+mpi', '+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'
-
- libffi:
- require: ['@3.4.6']
-
- libssh2:
- prefer: ['crypto=openssl']
-
- libtiff:
- require: ['build_system=cmake', '+pic', '+shared', '+jpeg']
-
- libtool:
- require: ['@2.4.6']
-
- libxc:
- require: ['build_system=cmake', '+shared']
-
- libxcb:
- require: ['+use_spack_interpreter']
-
- libxml2:
- # python depends on libxml2 this avoid cyclic dependency
- require: ['~python']
-
- likwid:
- require: ['@5.3.0']
-
- llvm:
- # avoid compiler in lmod module
- prefer: ['~clang']
- require:
- - spec: '~cuda'
- when: '@15:'
-
- m4:
- require: ['+sigsegv']
-
- magma:
- # https://groups.google.com/a/icl.utk.edu/g/magma-user/c/l2XWTKmuBH0
- require: ['~ipo']
-
- mbedtls:
- prefer: ['@3.3.0']
-
- mesa:
- require: ['~llvm', '+opengl', '+opengles', '+osmesa']
-
- meson:
- prefer: ['@1.2.1']
-
- metis:
- require: ['+real64']
-
- mgard:
- require: ['~cuda']
-
- mpfr:
- require: ['@4.0.2']
-
- mumps:
- require: ['+openmp', '+metis', '+parmetis']
-
- netcdf-c:
- prefer: ['+mpi']
-
- openblas:
- require: ['build_system=makefile']
- prefer: ['threads=pthreads symbol_suffix=none ~ilp64']
-
- opencv:
- prefer: ['+vtk', '+python3']
-
- openmpi:
- require: ['@5.0.3',
- 'fabrics=ofi,ucx,verbs',
- 'schedulers=slurm',
- '+romio', 'romio-filesystem=gpfs',
- '+internal-pmix', '~rsh',
- '~memchecker']
-
- openssl:
- prefer: ['+shared', 'certs=system', '~docs']
-
- pango:
- prefer: [~X]
-
- papi:
- require: ['+powercap', '+rapl']
-
- petsc:
- require: ['+hypre', '+mumps', '+saws', '+scalapack', '+mpi', '+suite-sparse', '+kokkos', '+openmp']
-
- python:
- require:
- - spec: '+ssl +tkinter +crypt +bz2 +pyexpat +libxml2 +ctypes +uuid ~sqlite3'
- - spec: '+optimizations'
- when: '%gcc'
- prefer:
- - spec: '%gcc@13.2.0'
- when: '%gcc'
-
- py-cython:
- require:
- - one_of: ['@0.29.36', '@3.0.8']
- prefer: ['@3.0.8']
-
- py-fenics-dolfinx:
- require: ['@0.8.0']
-
- py-horovod:
- require: ['frameworks=pytorch,keras,tensorflow', 'controllers=mpi', 'tensor_ops=nccl']
-
- py-mpmath:
- require: ['@1.2.1']
-
- py-numpy:
- prefer: ['@1.26.4']
-
- py-pandas:
- prefer: ['@2.2.1']
-
- py-pysam:
- prefer: ['@0.22.1']
-
- # https://github.com/tensorflow/tensorflow/issues/63360#issuecomment-2142735122
- # MKL support seams not maintained
- py-tensorflow:
- require: ['+mpi', '~mkl']
-
- py-torch:
- require: ['@2.3.1', '+mpi', '~valgrind']
-
- py-scipy:
- require: ['@1.13.0']
-
- py-setuptools:
- require: ['@63.4.3']
-
- qt:
- require: ['@5.15.2']
-
- quantum-espresso:
- require:
- - spec: '++mpi +gipaw +scalapack hdf5=parallel'
- - spec: '~openmp'
- when: '%gcc'
-
- rust:
- require: ['+dev']
-
- scotch:
- prefer: ['~mpi']
-
- sirius:
- prefer: ['+fortran', '~elpa', '+wannier90']
-
- slepc:
- require:
- - spec: '^arpack-ng +mpi'
-
- spades:
- require: ['~ipo']
-
- suite-sparse:
- require:
- - '+graphblas'
- - one_of: ['@7.3.1', '@7.2.1']
- prefer: ['@7.3.1']
-
- tk:
- require: ['+xft', '+xss']
-
- ucx:
- require:
- - spec: '+rdmacm +rc +dc +ud +cma +verbs'
-
- vtk:
- require:
- - spec: '~python ++mpi +xdmf +ffmpeg'
-
- xmlto:
- require: ['@0.0.29']
-
- # ----------------------------------------------------------------------------
- # System dependencies
- # ----------------------------------------------------------------------------
- egl:
- buildable: false
- externals:
- - spec: 'egl@21.3.4'
- prefix: /usr
-
- ninja:
- buildable: false
- externals:
- - spec: 'ninja@1.10.2'
- prefix: /usr
-
- opengl:
- buildable: false
- externals:
- - spec: 'opengl@4.6'
- 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-gcc13/spack.yaml b/stacks/pinot-noir-gcc13/spack.yaml
deleted file mode 100644
index cef8b49..0000000
--- a/stacks/pinot-noir-gcc13/spack.yaml
+++ /dev/null
@@ -1,503 +0,0 @@
-spack:
- include:
- - compiler_definitions.yaml
-
- - packages_stack.yaml
- - packages_env.yaml
-
- - modules_stack.yaml
- - modules_env.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@0.3.27
-
- - 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 +ncurses
- - emacs
- - fastqc
- - fio
- - git
- - git-lfs
- - gmp
- - gnuplot
- - gzip
- - intel-oneapi-advisor
- - intel-oneapi-inspector
- - intel-oneapi-vtune
- - libarchive
- - libgd
- - libjpeg-turbo
- - libpng
- - libtiff
- - libxml2
- - likwid
- - lmod
- - mpfr
- - neovim
- #- ninja
- - papi
- - parallel
- - picard
- - rclone
- - sbt
- - squashfs
- - squashfs-mount
- - sratoolkit
- - subversion
- - tar
- - tcl
- - tk
- - tmux
- - trimmomatic
- - xclip
- - zlib-ng
-
- # -------------------------------------------------------------------------
- # Serial codes
- # -------------------------------------------------------------------------
- - serial_codes:
- - fftw +openmp ~~mpi
- - fftw ~~openmp ~~mpi
- - gsl
- - hdf5@1.14.3 ~~mpi
- - htslib
- - intel-oneapi-tbb
- - jasper
- - kallisto ^hdf5 ~~mpi
- - kokkos
- - kokkos-kernels
- - mafft
- - metis
- - muscle
- - netcdf-c ~~mpi
- - netcdf-fortran ^netcdf-c ~~mpi
- - nfft ^fftw~~mpi~~openmp
- - python
- - scotch ~~mpi
- - star
- - subread
- - unblur ^fftw~~mpi ~~openmp
- - voropp
-
- - gcc_serial_codes:
- - bwa
- - eigen
- - ffmpeg
- - glpk+gmp
- - hwloc
- - intel-oneapi-mkl
- - libxc
- - qperf
- - ncview ^netcdf-c ~~mpi ~parallel-netcdf
- - sox
- - stacks
- - xgboost
-
- - oneapi_serial_codes:
- - abaqus@2023
- - intel-oneapi-ipp
-
- # -------------------------------------------------------------------------
- # Empty to specialize in environments
- # -------------------------------------------------------------------------
- - cuda_system_codes: []
-
- - cuda_serial_codes: []
-
- - cuda_mpi_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 ~~mpi
- #- gmsh ~~mpi +hdf5 +cgns +eigen ~opencascade +openmp ~fltk ~med
- - iq-tree
- - py-biopython
- - py-keras-preprocessing
- - py-macs3
- - py-matplotlib
- - py-numpy
- - py-opt-einsum
- - py-pandas
- - py-pybigwig
- - py-xarray
- - valgrind ~~mpi
-
- - gcc_python_codes:
- - blast-plus
- - cistem ^fftw~~mpi
- - ctffind ^fftw ~~mpi
- - gatk
- - hisat2
- - imagemagick +ghostscript
- - julia+openlibm
- - mesa
- - mummer
- - node-js
- - rust
- - spades
-
- - gcc_python_blas_codes:
- - caffe +python ^hdf5~mpi
- - gdb +tui +source-highlight +xz
- - openbabel ++python ^boost ~~mpi
- - polymake ^cddlib@0.94h
- - py-cryolobm
- - py-deeptools
- - py-h5py ~~mpi
- - py-pymol ^hdf5~mpi
- - py-scikit-learn
- - py-scipy
- #- py-statsmodels
- - py-theano
- - r
-
- # -------------------------------------------------------------------------
- # Parallel codes
- # -------------------------------------------------------------------------
- - mpi_codes:
- - fftw ++mpi +openmp
- - hdf5@1.14.3 ++mpi
- - openfoam-org +metis
- - osu-micro-benchmarks +graphing
- - parmetis
- - phylobayesmpi
- - scotch ++mpi
- - netcdf-c
- - netcdf-fortran
- - parmetis
- - scorep
-
- - mpi_python_codes:
- - py-mpi4py
-
- - 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:
- - armadillo +hdf5 ^arpack-ng ++mpi ^hdf5 ++mpi
- - gmsh ++mpi +eigen +openmp +hdf5 ~fltk ~opencascade ~med ^mmg ~vtk
- - cpmd ~openmp
- - elmerfem +mumps +openmp +hypre
- - netlib-scalapack
- - trilinos
- - vtk
- - yambo ++mpi io=iotk,etsf-io
-
- - mpi_blas_python_codes:
- - boost ++mpi
- - cgal
- - iq-tree@1.6.12++mpi
- - neuron ++mpi +python
- - petsc
- - plumed
- - py-petsc4py
- - slepc
- - sirius
-
- - 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@5.12.0 +shared +python +hdf5 +opengl2
- - py-fenics-dolfinx
- - py-h5py ++mpi
- # - py-horovod cannot resolve dependencies with pytorch
- - py-keras
- - py-tensorflow
- - py-torch
- - py-torchvision
- - relion ~mklfft
- - topaz
-
- # -------------------------------------------------------------------------
- # 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:
- - [$serial_codes]
- - [$%compiler_gcc]
-
- - 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]
- - [$%compiler_gcc]
-
- - matrix:
- - [$mpi_python_codes]
- - [$^python_gcc]
- - [$^mpi_gcc]
- - [$%compiler_gcc]
-
- - matrix:
- - [$gcc_mpi_codes]
- - [$^mpi_gcc]
- - [$%compiler_gcc]
-
- - matrix:
- - [$cuda_mpi_codes]
- - [$^mpi_gcc]
- - [$%compiler_gcc]
-
- - matrix:
- - [$mpi_blas_codes]
- - [$^blas_gcc]
- - [$^mpi_gcc]
- - [$%compiler_gcc]
-
- - matrix:
- - [$mpi_blas_python_codes]
- - [$^python_gcc]
- - [$^blas_gcc]
- - [$^mpi_gcc]
- - [$%compiler_gcc]
-
- - matrix:
- - [$gcc_mpi_blas_python_codes]
- - [$^python_gcc]
- - [$^blas_gcc]
- - [$^mpi_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:
- - [$mpi_python_codes]
- - [$^python_oneapi]
- - [$^mpi_oneapi]
- - [$%compiler_oneapi]
-
- - matrix:
- - [$mpi_blas_codes]
- - [$^blas_oneapi]
- - [$^mpi_oneapi]
- - [$%compiler_oneapi]
-
- - matrix:
- - [$mpi_blas_python_codes]
- - [$^python_oneapi]
- - [$^blas_oneapi]
- - [$^mpi_oneapi]
- - [$%compiler_oneapi]
-
- view: false
-# default:
-# root: /stack/packages/
diff --git a/stacks/pinot-noir-gcc13/templates/modules/group_restricted.lua b/stacks/pinot-noir-gcc13/templates/modules/group_restricted.lua
deleted file mode 100644
index 1511796..0000000
--- a/stacks/pinot-noir-gcc13/templates/modules/group_restricted.lua
+++ /dev/null
@@ -1,10 +0,0 @@
-{% 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/config.json b/stacks/pinot-noir/config.json
index 12fdda3..5a5c053 100644
--- a/stacks/pinot-noir/config.json
+++ b/stacks/pinot-noir/config.json
@@ -49,8 +49,8 @@
},
"gcc": {
"compiler": "gcc",
- "spec": "gcc@12.3.0 %gcc@11.2.1",
- "version": "12.3.0"
+ "spec": "gcc@13.2.0 %gcc@11.2.1",
+ "version": "13.2.0"
}
},
"system_packages": [
diff --git a/stacks/pinot-noir/packages_kuma-h100.yaml b/stacks/pinot-noir/packages_kuma-h100.yaml
index a1da6ae..516d817 100644
--- a/stacks/pinot-noir/packages_kuma-h100.yaml
+++ b/stacks/pinot-noir/packages_kuma-h100.yaml
@@ -12,14 +12,17 @@ packages:
when: '%gcc'
# ---------------------------------------------------------------------------
+ cp2k:
+ require: ['+cuda', 'cuda_arch=90']
+
cuda:
prefer:
- - spec: "^gcc-runtime@12.3.0"
+ - spec: "^gcc-runtime@13.2.0"
when: "%gcc"
- - spec: "%gcc@12.3.0 target=zen4"
+ - spec: "%gcc@13.2.0 target=zen4"
when: "%gcc"
require:
- - '@12.4.0'
+ - '@12.4.1'
hypre:
require:
@@ -28,19 +31,21 @@ packages:
kokkos:
require:
- - spec: '+cuda +cuda_lambda cuda_arch=90 +cuda_uvm +wrapper ~openmptarget'
+ - spec: '+cuda +cuda_lambda cuda_arch=90 +wrapper ~openmptarget'
when: '%gcc'
kokkos-kernels:
require: ['+cuda', '+cublas', '+cusolver', '+cusparse', 'cuda_arch=90']
+ libxc:
+ require: ['+cuda', 'cuda_arch=90']
+
nvshmem:
require:
- spec: '+cuda cuda_arch=90 +ibgda +nccl +ucx +mpi'
openmpi:
- require:
- - spec: '+cuda cuda_arch=90'
+ require: ['+cuda', 'cuda_arch=90']
papi:
require: ['+nvml', '+infiniband', '+cuda']
@@ -64,11 +69,11 @@ packages:
python:
require:
- spec: 'target=zen4'
- when: '%gcc@12.3.0'
+ when: '%gcc@13.2.0'
quantum-espresso:
require:
- - spec: '~cuda'
+ - spec: '+nvtx'
suite-sparse:
require:
diff --git a/stacks/pinot-noir/packages_kuma-l40s.yaml b/stacks/pinot-noir/packages_kuma-l40s.yaml
index a3d8533..323b8b2 100644
--- a/stacks/pinot-noir/packages_kuma-l40s.yaml
+++ b/stacks/pinot-noir/packages_kuma-l40s.yaml
@@ -1,7 +1,7 @@
packages:
all:
target: ["zen4"]
- prefer: ["zen4"]
+ prefer: ["target=zen4"]
require:
- "~rocm"
@@ -14,12 +14,12 @@ packages:
# ---------------------------------------------------------------------------
cuda:
prefer:
- - spec: "^gcc-runtime@12.3.0"
+ - spec: "^gcc-runtime@13.2.0"
when: "%gcc"
- - spec: "%gcc@12.3.0 target=zen4"
+ - spec: "%gcc@13.2.0 target=zen4"
when: "%gcc"
require:
- - '@12.4.0'
+ - '@12.4.1'
hypre:
require:
@@ -28,7 +28,7 @@ packages:
kokkos:
require:
- - spec: '+cuda +cuda_lambda cuda_arch=89 +cuda_uvm +wrapper ~openmptarget'
+ - spec: '+cuda +cuda_lambda cuda_arch=89 +wrapper ~openmptarget'
when: '%gcc'
kokkos-kernels:
@@ -39,8 +39,7 @@ packages:
- spec: '+cuda cuda_arch=89 +ibgda +nccl +ucx +mpi'
openmpi:
- require:
- - spec: '+cuda cuda_arch=89'
+ require: ['+cuda', 'cuda_arch=89']
papi:
require: ['+nvml', '+infiniband', '+cuda']
@@ -64,15 +63,18 @@ packages:
python:
require:
- spec: 'target=zen4'
- when: '%gcc@12.3.0'
+ when: '%gcc@13.2.0'
quantum-espresso:
require:
- - spec: '~cuda'
+ - spec: '+nvtx'
suite-sparse:
require:
- spec: '+cuda'
+ when: '@7.3.1'
+ - spec: '~cuda'
+ when: '@7.2.1'
ucx:
require:
diff --git a/stacks/pinot-noir/packages_stack.yaml b/stacks/pinot-noir/packages_stack.yaml
index 7ae1a64..5ca72c6 100644
--- a/stacks/pinot-noir/packages_stack.yaml
+++ b/stacks/pinot-noir/packages_stack.yaml
@@ -30,7 +30,17 @@ packages:
cairo:
# ~X avoids a dependency to python (only prefer due to gtkplus)
- prefer: ['~X']
+ prefer: ['~X', '+svg']
+ require: ['+fc', '+ft', '+pdf', '+gobject']
+
+ cmake:
+ prefer: ['~ncurses']
+
+ costa:
+ require: ['~apps']
+
+ cp2k:
+ require: ['~ipo']
cuda:
require:
@@ -84,8 +94,10 @@ packages:
require: ['@1.10.4']
kokkos:
- require: ['+openmp', '+numactl', '+memkind', '~threads',
- '+aggressive_vectorization', '@4.3.01']
+ require: ['+numactl', '+memkind', '+serial',
+ '+openmp', '~openmptarget',
+ '~threads', '~sycl',
+ '+aggressive_vectorization', '@4.3.01']
kokkos-kernels:
require: ['@4.3.01', '+openmp', '~threads', '~ipo']
@@ -119,6 +131,9 @@ packages:
libtool:
require: ['@2.4.6']
+ libxc:
+ require: ['build_system=cmake', '+shared']
+
libxcb:
require: ['+use_spack_interpreter']
@@ -161,6 +176,9 @@ packages:
mpfr:
require: ['@4.0.2']
+ mumps:
+ require: ['+openmp', '+metis', '+parmetis']
+
netcdf-c:
prefer: ['+mpi']
@@ -172,8 +190,12 @@ packages:
prefer: ['+vtk', '+python3']
openmpi:
- require:
- - spec: '@5.0.3 fabrics=ofi,ucx,verbs schedulers=slurm ~rsh +romio romio-filesystem=gpfs +internal-pmix'
+ require: ['@5.0.3',
+ 'fabrics=ofi,ucx,verbs',
+ 'schedulers=slurm',
+ '+romio', 'romio-filesystem=gpfs',
+ '+internal-pmix', '~rsh',
+ '~memchecker']
openssl:
prefer: ['+shared', 'certs=system', '~docs']
@@ -185,8 +207,7 @@ packages:
require: ['+powercap', '+rapl']
petsc:
- require:
- - spec: '+hypre +mumps +saws +scalapack +mpi +suite-sparse +kokkos'
+ require: ['+hypre', '+mumps', '+saws', '+scalapack', '+mpi', '+suite-sparse', '+kokkos', '+openmp']
python:
require:
@@ -194,7 +215,7 @@ packages:
- spec: '+optimizations'
when: '%gcc'
prefer:
- - spec: '%gcc@12.3.0'
+ - spec: '%gcc@13.2.0'
when: '%gcc'
py-cython:
@@ -205,17 +226,28 @@ packages:
py-fenics-dolfinx:
require: ['@0.8.0']
+ py-horovod:
+ require: ['frameworks=pytorch,keras,tensorflow', 'controllers=mpi', 'tensor_ops=nccl']
+
+ py-mpmath:
+ require: ['@1.2.1']
+
py-numpy:
prefer: ['@1.26.4']
py-pandas:
prefer: ['@2.2.1']
+ py-pysam:
+ prefer: ['@0.22.1']
+
+ # https://github.com/tensorflow/tensorflow/issues/63360#issuecomment-2142735122
+ # MKL support seams not maintained
py-tensorflow:
- require: ['+mpi', '+mkl']
+ require: ['+mpi', '~mkl']
py-torch:
- require: ['+mpi']
+ require: ['@2.3.1', '+mpi', '~valgrind']
py-scipy:
require: ['@1.13.0']
@@ -223,6 +255,15 @@ packages:
py-setuptools:
require: ['@63.4.3']
+ qt:
+ require: ['@5.15.2']
+
+ quantum-espresso:
+ require:
+ - spec: '++mpi +gipaw +scalapack hdf5=parallel'
+ - spec: '~openmp'
+ when: '%gcc'
+
rust:
require: ['+dev']
@@ -230,12 +271,15 @@ packages:
prefer: ['~mpi']
sirius:
- prefer: ['+fortran', '+elpa', '+wannier90']
+ prefer: ['+fortran', '~elpa', '+wannier90']
slepc:
require:
- spec: '^arpack-ng +mpi'
+ spades:
+ require: ['~ipo']
+
suite-sparse:
require:
- '+graphblas'
diff --git a/stacks/pinot-noir/spack.yaml b/stacks/pinot-noir/spack.yaml
index 01584c3..cef8b49 100644
--- a/stacks/pinot-noir/spack.yaml
+++ b/stacks/pinot-noir/spack.yaml
@@ -39,7 +39,7 @@ spack:
# -------------------------------------------------------------------------
- core_codes:
- bzip2
- - cmake
+ - cmake +ncurses
- emacs
- fastqc
- fio
@@ -52,6 +52,7 @@ spack:
- intel-oneapi-inspector
- intel-oneapi-vtune
- libarchive
+ - libgd
- libjpeg-turbo
- libpng
- libtiff
@@ -66,6 +67,8 @@ spack:
- picard
- rclone
- sbt
+ - squashfs
+ - squashfs-mount
- sratoolkit
- subversion
- tar
@@ -115,6 +118,7 @@ spack:
- ncview ^netcdf-c ~~mpi ~parallel-netcdf
- sox
- stacks
+ - xgboost
- oneapi_serial_codes:
- abaqus@2023
@@ -210,13 +214,11 @@ spack:
- hisat2
- imagemagick +ghostscript
- julia+openlibm
- - libgd
- mesa
- mummer
- node-js
- rust
- spades
- - xgboost
- gcc_python_blas_codes:
- caffe +python ^hdf5~mpi
@@ -261,7 +263,7 @@ spack:
- mumps@5.6.2
- superlu-dist@8.2.1
#- quantum-espresso ++mpi +scalapack +gipaw
- - quantum-espresso
+ #- quantum-espresso ++mpi +scalapack +gipaw hdf5=parallel
- gcc_mpi_blas_codes:
- armadillo +hdf5 ^arpack-ng ++mpi ^hdf5 ++mpi
@@ -278,7 +280,7 @@ spack:
- cgal
- iq-tree@1.6.12++mpi
- neuron ++mpi +python
- - petsc@3.21.1
+ - petsc
- plumed
- py-petsc4py
- slepc
@@ -294,10 +296,10 @@ spack:
- lammps
- opencv
- openfoam +metis
- - paraview +shared +python +hdf5 +opengl2
+ - paraview@5.12.0 +shared +python +hdf5 +opengl2
- py-fenics-dolfinx
- py-h5py ++mpi
- - py-horovod
+ # - py-horovod cannot resolve dependencies with pytorch
- py-keras
- py-tensorflow
- py-torch
--
GitLab