diff --git a/.gitignore b/.gitignore
index 6e366f16c2dd577f85088670d4996c625e011333..1b99dcefc0df35933a79953ba3d329951f08e66c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,7 @@
.DS_Store
.idea
*.log
+spack_*.json
tmp/
.spack-env
compiler_definitions.yaml
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 59a70e6aa26bf092175e8a0c3542c0a3674785bb..659e863530229aff48c514d400a02ab3a64cb635 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: [kuma_h100]
+ # - 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-gcc"]
+ stack: ["pinot-noir"]
apptainer_options: ['--nv']
app_image: ["registry.c4science.ch/scitas-stack/rhel9-kuma"]
- - environment: [kuma_l40s]
+ - environment: [kuma-l40s]
slurm_options: ["-c 64"]
- stack: ["pinot-noir-gcc"]
+ 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:
- ${environment}
- stack
@@ -71,21 +71,19 @@ variables:
FAKEHOME: "/scratch/$(id -un)"
COMMAND_OPTIONS_SBATCH: ${slurm_options}
STACK_VERSION: $(jq -Mrc .stack.version ${CI_PROJECT_DIR}/stacks/${stack}/config.json)
- image_name: "${stack}-${environment}-${SQUASHFS_ID}"
+ image_name: ${stack}-${environment}-${SQUASHFS_ID}-${CI_PIPELINE_ID}
squashfs_image: $(ls -t1 ${CI_DATA_LT}/squashfs-cache/${image_name}*.sqfs 2> /dev/null | head -1)
APPTAINER_EXEC_OPTIONS: >-
${apptainer_options}
--cleanenv
-H $(mktemp -d -p ${FAKEHOME}/):/home/$(id -un)
+ --env PYTHONUNBUFFERED=1
--bind ${CI_DATA_LT}/buildcache:${MOUNT_POINT}/buildcache
--bind ${CI_DATA_LT}/spack-mirror:${MOUNT_POINT}/spack-mirror
--bind ${CI_DATA_ST}/squashfs-cache/:/squashfs-cache
--bind ${CI_DATA_ST}/overlayfs:/overlayfs
--fusemount "host:${CI_PROJECT_DIR}/ci/squashfuse_ll.sh ${CI_DATA_ST} ${image_name} ${squashfs_image} /overlayfs/lower-${image_name}"
--fusemount "container:${CI_PROJECT_DIR}/ci/fuse-overlayfs.sh ${image_name} ${MOUNT_POINT}/${stack}/${environment}/${STACK_VERSION}"
- # after_script:
- # - if [ $CI_JOB_STATUS != "success" ]; then exit 0; fi
- # - ${CI_PROJECT_DIR}/ci/update_squashfs.sh
.spack_cache:
cache:
@@ -116,7 +114,7 @@ spack:setup:
stage: environment
extends:
- .parallel_job
- - .spack_cache
+ #- .spack_cache
script:
- ci/setup_spack.sh
- ${CI_PROJECT_DIR}/ci/update_squashfs.sh
@@ -127,11 +125,11 @@ spack:install_compilers:
stage: compilers
extends:
- .parallel_job
- - .spack_cache
+ #- .spack_cache
script:
- ci/install_compilers.sh
- source ci/stack_env.sh
- - ${STACK_LOCATION}/spack/bin/spack -e ${environment} config blame compilers
+ - ${STACK_LOCATION}/spack/bin/spack --color always -e ${environment} config blame compilers
- ${CI_PROJECT_DIR}/ci/update_squashfs.sh
artifacts:
reports:
@@ -144,16 +142,19 @@ spack:concretize:
stage: concretize
extends:
- .parallel_job
- - .spack_cache
+ #- .spack_cache
script:
- source ci/stack_env.sh
- ${STACK_LOCATION}/spack/bin/spack -e ${environment}
config blame | tee config-${environment}-${stack}.log
- - ${STACK_LOCATION}/spack/bin/spack -e ${environment}
+ - ${STACK_LOCATION}/spack/bin/spack --color always -e ${environment}
concretize | tee concretize-${environment}-${stack}.log
+ - ${STACK_LOCATION}/spack/bin/spack --color always -e ${environment}
+ mirror create -D -d ${MOUNT_POINT}/spack-mirror -a || /usr//bin/true
+
- cp ${SPACK_SYSTEM_CONFIG_PATH}/spack.lock spack-${environment}-${stack}.lock
- ${CI_PROJECT_DIR}/ci/update_squashfs.sh
artifacts:
@@ -169,12 +170,15 @@ spack:install:
stage: install
extends:
- .parallel_job
- - .spack_cache
+ #- .spack_cache
script:
- source ci/stack_env.sh
- echo "{}" > spack-install-${environment}.xml
- - ${STACK_LOCATION}/spack/bin/spack -e ${environment} install
+ # Cleaning patches in case one has a different hash
+ - ${STACK_LOCATION}/spack/bin/spack --color always -e ${environment} clean -m
+
+ - ${STACK_LOCATION}/spack/bin/spack --color always -e ${environment} install
--log-file spack-install-${environment}.xml
--log-format junit
--only-concrete
@@ -206,15 +210,12 @@ spack:mksquashfs:
stage: deploy
extends:
- .parallel_job
- - .spack_cache
+ #- .spack_cache
script:
- source ci/stack_env.sh
+ - mksquashfs ${STACK_LOCATION} ${stack}-${environment}-${SQUASHFS_ID}.sqfs
- - echo "${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/generic/stack/${stack}/stack-${stack}-${environment}-${CI_COMMIT_REF_SLUG}.sqfs"
- - "mksquashfs ${STACK_LOCATION} stack-${stack}-${environment}-${CI_COMMIT_REF_SLUG}.sqfs"
- - 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file stack-${stack}-${environment}-${CI_COMMIT_REF_SLUG}.sqfs "${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/generic/stack/${stack}/stack-${stack}-${environment}-${CI_COMMIT_REF_SLUG}.sqfs"'
needs:
- job: spack:install
- timeout: 10h
- rules:
- - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+ #ressource_group: mksquashfs
+ timeout: 1h
diff --git a/ci/apptainer_by_hand.sh b/ci/apptainer_by_hand.sh
index ba95ef61b8d7e50ade9b205f9c4fe81aaf438cfc..21a7d68ddc0d10d242507d904faa90e4ef0b6d87 100755
--- a/ci/apptainer_by_hand.sh
+++ b/ci/apptainer_by_hand.sh
@@ -6,7 +6,7 @@ srun_options="-N1 -n1 -c 64 -p h100"
apptainer_options="--nv"
export stack=pinot-noir
-export environment=kuma_h100
+export environment=kuma-h100
export SQUASHFS_ID=local
export CI_PIPELINE_ID=1337
@@ -20,8 +20,10 @@ export STACK_VERSION=$(jq -Mrc .stack.version ${CI_PROJECT_DIR}/stacks/${stack}/
APPTAINER_IMAGE=~/rhel9-kuma.sif
image_name=${stack}-${environment}-${SQUASHFS_ID}-${CI_PIPELINE_ID}
+
+./ci/prepare_squashfs.sh
+
squashfs_image=$(ls -t1 ${CI_DATA_LT}/squashfs-cache/${image_name}*.sqfs 2> /dev/null | head -1)
-#./ci/prepare_squashfs.sh
srun ${srun_options} --pty apptainer run \
${apptainer_options}\
@@ -32,11 +34,12 @@ srun ${srun_options} --pty apptainer run \
--bind ${CI_DATA_LT}/spack-mirror:${MOUNT_POINT}/spack-mirror \
--bind ${CI_DATA_LT}/squashfs-cache/:/squashfs-cache \
--bind ${CI_DATA_ST}/overlayfs:/overlayfs \
+ --env PYTHONUNBUFFERED=1 \
--env stack=${stack} \
--env environment=${environment} \
--env GPG_PRIVATE_KEY=${GPG_PRIVATE_KEY} \
--env CI_PROJECT_DIR=${CI_PROJECT_DIR} \
- --env CI_JOB_ID=${CI_JOB_ID} \
+ --env CI_PIPELINE_ID=${CI_PIPELINE_ID} \
--env SQUASHFS_ID=${SQUASHFS_ID} \
--fusemount "host:${CI_PROJECT_DIR}/ci/squashfuse_ll.sh ${CI_DATA_ST} ${image_name} ${squashfs_image} /overlayfs/lower-${image_name}" \
--fusemount "container:${CI_PROJECT_DIR}/ci/fuse-overlayfs.sh ${image_name} ${MOUNT_POINT}/${stack}/${environment}/${STACK_VERSION}" \
diff --git a/ci/debug/spack_lock_info.sh b/ci/debug/spack_lock_info.sh
new file mode 100755
index 0000000000000000000000000000000000000000..da1df3267a26465b677bddb52fd27924e8e77b5d
--- /dev/null
+++ b/ci/debug/spack_lock_info.sh
@@ -0,0 +1,133 @@
+#!/usr/bin/env sh
+
+get_all_dep(){
+ file=$2
+ deps=$(jq --arg h "$1" -Mrc '.concrete_specs | to_entries | map(select(.key | match($h))) | .[] | .value.dependencies[] | "\(.hash)"' $file)
+ for i in $deps
+ do
+ jq --arg h "$i" -c '.concrete_specs
+ | to_entries
+ | map(select(.key | match($h)))
+ | .[]
+ | {
+ name: .value.name,
+ key: .key,
+ version: .value.version,
+ compiler: (.value.compiler | "\(.version)"),
+ target: (.value.arch.target | if type == "object" then .name else . end),
+ dep: .value.dependencies[]
+ | {
+ name: .name,
+ key: .hash,
+ type: .parameters.deptypes,
+ virtuals: .parameters.virtuals
+ }
+ }' $file
+ done
+}
+
+get_hash_dep(){
+ jq --arg h "$1" -c '.concrete_specs
+ | to_entries
+ | map(select(.key | match($h)))
+ | .[]
+ | {
+ name: .value.name,
+ key: .key,
+ version: .value.version,
+ compiler: (.value.compiler | "\(.version)"),
+ target: (.value.arch.target | if type == "object" then .name else . end),
+ dep: .value.dependencies[]
+ | {
+ name: .name,
+ key: .hash,
+ type: .parameters.deptypes,
+ virtuals: .parameters.virtuals
+ }
+ }' $2
+}
+
+get_name_dep(){
+ jq --arg n "$1" -c '.concrete_specs
+ | to_entries
+ | map(select(.value.name == $n))
+ | .[]
+ | {
+ name: .value.name,
+ key: .key,
+ version: .value.version,
+ compiler: (.value.compiler | "\(.version)"),
+ target: (.value.arch.target | if type == "object" then .name else . end),
+ dep: .value.dependencies[]
+ | {
+ name: .name,
+ key: .hash,
+ type: .parameters.deptypes,
+ virtuals: .parameters.virtuals
+ }
+ }' $2
+}
+
+
+usage() {
+ echo "-h [hash]"
+ echo "-n [name]"
+ echo "-f [file]"
+}
+
+OPTSTRING=":h:n:f:a"
+
+all=0
+hash=""
+name=""
+file=""
+while getopts ${OPTSTRING} opt; do
+ case ${opt} in
+ f)
+ file=${OPTARG}
+ ;;
+ h)
+ hash=${OPTARG}
+ ;;
+ n)
+ name=${OPTARG}
+ ;;
+ a)
+ all=1
+ ;;
+ :)
+ echo "Option -${OPTARG} requires an argument."
+ usage
+ exit 1
+ ;;
+ ?)
+ echo "Invalid option: -${OPTARG}."
+ usage
+ exit 1
+ ;;
+ esac
+done
+
+if [ "x$file" == "x" ]
+then
+ echo "No file specified"
+ usage
+ exit 1
+fi
+
+echo "name ($name), hash ($hash), file($file), all($all)"
+
+if [ "x$hash" != "x" ]
+then
+ if [ $all -eq 1 ]
+ then
+ get_all_dep $hash $file
+ else
+ get_hash_dep $hash $file
+ fi
+fi
+
+if [ "x$name" != "x" ]
+then
+ get_name_dep $name $file
+fi
diff --git a/ci/install_compilers.sh b/ci/install_compilers.sh
index 46e19e096f15c677de8d1eb1fd33a8165f82bd86..fbfeef455ccdf0d086f757426481a20f2c670f72 100755
--- a/ci/install_compilers.sh
+++ b/ci/install_compilers.sh
@@ -73,13 +73,6 @@ for c in "core_compilers" "compilers"; do
fi
done
-export target=$(jq -Mrc '
-.stack.targets
- | to_entries
- | .[]
- | select(.key == env.environment)
- | .value' ${STACK_CONFIG})
-
compilers_specs=$(jq -Mr '
.stack
| .system_arch as $arch
@@ -131,10 +124,21 @@ jq -Mrc '
| .system_arch as $arch
| .compilers
| to_entries
+ | map(select(.value.constraint == null))
| map(" - compiler_\(.key): [\(.value.compiler)@\(.value.version) target=\(env.target)]")
| .[]
' ${STACK_CONFIG} >> ${SPACK_SYSTEM_CONFIG_PATH}/compiler_definitions.yaml
+jq -Mrc '
+.stack
+ | .system_arch as $arch
+ | .compilers
+ | to_entries
+ | map(select(.value.constraint != null))
+ | map(" - compiler_\(.key): []\n - when: \(.value.constraint)\n compiler_\(.key): [\(.value.compiler)@\(.value.version) target=\(env.target)]")
+ | .[]
+' ${STACK_CONFIG} >> ${SPACK_SYSTEM_CONFIG_PATH}/compiler_definitions.yaml
+
cat ${SPACK_SYSTEM_CONFIG_PATH}/compiler_definitions.yaml
#yq -y -s ".[0].spack.definitions = .[1].definitions + .[0].spack.definitions | .[0]" ${SPACK_SYSTEM_CONFIG_PATH}/spack.yaml ${SPACK_SYSTEM_CONFIG_PATH}/compiler_definitions.yaml > ${SPACK_SYSTEM_CONFIG_PATH}/spack.yaml.new
diff --git a/ci/prepare_squashfs.sh b/ci/prepare_squashfs.sh
index ed5f5b33c97c7551cb7fc5301b8dc76a86947e51..b51e4b97beb3d65ee44336dab56f963e4ec9f50b 100755
--- a/ci/prepare_squashfs.sh
+++ b/ci/prepare_squashfs.sh
@@ -21,20 +21,29 @@ set +o errexit
sqfs_image=$(ls -t1 ${CI_DATA_LT}/squashfs-cache/${image_name}.sqfs 2> /dev/null | head -1)
if [ $? -ne 0 ]
then
- echo "No MR ($squash_id) squashfs found"
- # Check if MR default branch as squashfs
- sqfs_base_image=$(ls -t1 ${CI_DATA_LT}/squashfs-cache/${stack}-${environment}-${squash_base}*.sqfs 2> /dev/null | head -1)
+ echo "No MR ($squash_id-${CI_PIPELINE_ID}) squashfs found"
+
+ # look for base in the branch
+ sqfs_base_image=$(ls -t1 ${CI_DATA_LT}/squashfs-cache/${stack}-${environment}-${squash_id}.sqfs 2> /dev/null | head -1)
if [ $? -ne 0 ]
then
- echo "No default branch ($squash_base) squashfs found"
- echo "Creating an empty one"
- empty=$(mktemp -d)
- sqfs_base_image="${CI_DATA_LT}/squashfs-cache/${stack}-${environment}-${squash_base}-initial.sqfs"
- mksquashfs ${empty} ${sqfs_base_image}
+ echo "No MR ($squash_id) squashfs found"
+
+ # look for base in default branch
+ sqfs_base_image=$(ls -t1 ${CI_DATA_LT}/squashfs-cache/${stack}-${environment}-${squash_base}*.sqfs 2> /dev/null | head -1)
+ if [ $? -ne 0 ]
+ then
+ echo "No default branch ($squash_base) squashfs found"
+ echo "Creating an empty one"
+ empty=$(mktemp -d)
+ sqfs_base_image="${CI_DATA_LT}/squashfs-cache/${stack}-${environment}-${squash_base}-initial.sqfs"
+ mksquashfs ${empty} ${sqfs_base_image}
+ else
+ echo "Found ${sqfs_base_image}"
+ fi
else
echo "Found ${sqfs_base_image}"
fi
-
set -o errexit
# Link MR sqaushfs to the one of default branch
diff --git a/ci/setup_spack.sh b/ci/setup_spack.sh
index 8ce478151f1201b22841cc1dd0c642274793f026..5881e70b45f524f72e69573af0a072f5da35665d 100755
--- a/ci/setup_spack.sh
+++ b/ci/setup_spack.sh
@@ -26,30 +26,48 @@ then
spack/bin/spack env create ${environment}
fi
-for file in mirrors packages concretizer config spack definitions modules
-do
- if [ -e "${STACK_CONFIG_PATH}/${file}.yaml" ]; then
- echo "Copying ${STACK_CONFIG_PATH}/${file}.yaml to ${SPACK_SYSTEM_CONFIG_PATH}"
- cp "${STACK_CONFIG_PATH}/${file}.yaml" \
- ${SPACK_SYSTEM_CONFIG_PATH}
- cp "${STACK_CONFIG_PATH}/${file}.yaml" spack/etc/spack
- fi
-
- if [ -e "${STACK_CONFIG_PATH}/${file}_stack.yaml" ]; then
- echo "Copying ${STACK_CONFIG_PATH}/${file}_stack.yaml to ${SPACK_SYSTEM_CONFIG_PATH}"
- cp "${STACK_CONFIG_PATH}/${file}_stack.yaml" \
- ${SPACK_SYSTEM_CONFIG_PATH}
- fi
- if [ -e "${STACK_CONFIG_PATH}/${file}_${environment}.yaml" ]; then
- echo "Copying ${STACK_CONFIG_PATH}/${file}_${environment}.yaml to ${SPACK_SYSTEM_CONFIG_PATH}/${file}_env.yaml"
- cp "${STACK_CONFIG_PATH}/${file}_${environment}.yaml" \
- ${SPACK_SYSTEM_CONFIG_PATH}/${file}_env.yaml
- fi
-done
+echo "Copying cp ${STACK_CONFIG_PATH}/spack.yaml to ${SPACK_SYSTEM_CONFIG_PATH}/"
+cp ${STACK_CONFIG_PATH}/spack.yaml ${SPACK_SYSTEM_CONFIG_PATH}
cp -r "${STACK_CONFIG_PATH}/templates" ${SPACK_SYSTEM_CONFIG_PATH}
+declare -A file_mapping
+file_mapping["_common"]=""
+file_mapping["_stack"]="_stack"
+file_mapping["_acc_${acc_type}"]="_accel"
+file_mapping["_${environment}"]="_env"
+
+declare -A placeholders
+placeholders["{target}"]="${target}"
+placeholders["{gcc_version}"]=$(jq -Mrc '.stack.compilers.gcc.version' ${STACK_CONFIG})
+if [ "${accelerator}" != "none" ]
+then
+ placeholders["{${acc_type}_arch}"]="${acc_arch}"
+fi
+
+echo blip
+
+for file in mirrors packages concretizer config definitions modules
+do
+ for suffix in ${!file_mapping[@]}
+ do
+ src=${STACK_CONFIG_PATH}/${file}${suffix}.yaml
+ dst=${SPACK_SYSTEM_CONFIG_PATH}/${file}"${file_mapping[$suffix]}".yaml
+ if [ -e "${STACK_CONFIG_PATH}/${file}${suffix}.yaml" ]
+ then
+ echo "Copying $src to $dst"
+ cp "$src" "$dst"
+
+ for ph in ${!placeholders[@]}
+ do
+ rep=${placeholders[$ph]}
+ sed -i -e "s/$ph/$rep/g" "$dst"
+ done
+ fi
+ done
+done
+
cat <<EOF > ${SPACK_SYSTEM_CONFIG_PATH}/config_stack.yaml
config:
@@ -78,7 +96,6 @@ mirrors:
${mirrors}
EOF
-cp "${SPACK_SYSTEM_CONFIG_PATH}/mirrors.yaml" spack/etc/spack
echo "Setting up packages"
@@ -91,16 +108,19 @@ echo "packages:" > ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
export system_compiler=$(jq -Mrc '
.stack
- | .system_arch as $arch
| .system_compiler
| to_entries
| .[].value
- | "\(.compiler)@\(.version) \($arch)"
+ | "\(.compiler)@\(.version)"
+' ${STACK_CONFIG})
+
+export system_arch=$(jq -Mrc '
+.stack.system_arch
' ${STACK_CONFIG})
jq -Mrc '
.stack.system_packages
- | map(" \(.):\n require:\n - spec: \"%\(env.system_compiler)\"")
+ | map(" \(.):\n require:\n - \"%\(env.system_compiler)\"\n - \"\(env.system_arch)\"")
| .[]
' ${STACK_CONFIG} >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
@@ -111,8 +131,6 @@ then
rm packages.yaml.old
fi
-cp "${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml" spack/etc/spack
-
echo "Setting up extra repos"
EXTERNAL_REPOS=$(jq -r '.spack.repos | keys[]' ${STACK_CONFIG})
@@ -140,7 +158,14 @@ do
fi
done
-cp "${SPACK_SYSTEM_CONFIG_PATH}/repos.yaml" spack/etc/spack
+for file in mirrors packages concretizer config modules repos
+do
+ if [ -e "${SPACK_SYSTEM_CONFIG_PATH}/${file}.yaml" ]
+ then
+ cp "${SPACK_SYSTEM_CONFIG_PATH}/${file}.yaml" spack/etc/spack
+ fi
+done
+
echo "Setting up buildcache"
diff --git a/ci/stack_env.sh b/ci/stack_env.sh
index 66bae86e7222f400c6ab761523938e966f2a4ea2..fb6d028c5cb0273523cdb867b80b93a7731933cb 100644
--- a/ci/stack_env.sh
+++ b/ci/stack_env.sh
@@ -14,6 +14,18 @@ export SPACK_SYSTEM_CONFIG_PATH=${STACK_LOCATION}/spack/var/spack/environments/$
#export SPACK_USER_CONFIG_PATH=$(mktemp -p /tmp -d slurm_user_config_XXXXXXX)
export environment_type="local_cluster"
+export SPACK_VERSION=$(jq -r .spack.version ${STACK_CONFIG})
+
+env_json=$(jq '.stack.environments | to_entries | .[] | select(.key == env.environment) | .value' ${STACK_CONFIG})
+
+export target=$(echo $env_json | jq -Mrc '.target')
+export accelerator=$(echo $env_json | jq -Mrc '.accelerator // "none"')
+
+if [ "$accelerator" != "none" ]
+then
+ export acc_type=$(echo $env_json | jq -Mrc '.accelerator.type')
+ export acc_arch=$(echo $env_json | jq -Mrc '.accelerator.arch')
+fi
echo "STACK_CONFIG_PATH: ${STACK_CONFIG_PATH}"
echo "STACK_CONFIG: ${STACK_CONFIG}"
diff --git a/ci/update_squashfs.sh b/ci/update_squashfs.sh
index 66e962e1205abacb0a779232368687368f591073..7c63d4dfe7b3f2d6951e7c1405df3335ea979d24 100755
--- a/ci/update_squashfs.sh
+++ b/ci/update_squashfs.sh
@@ -8,6 +8,6 @@ source ${CI_PROJECT_DIR}/ci/stack_env.sh
cd /squashfs-cache
-mksquashfs ${STACK_LOCATION} ${stack}-${environment}-${squash_id}-$(date +'%Y%m%d_%H%M').sqfs
+mksquashfs ${STACK_LOCATION} ${stack}-${environment}-${squash_id}-${CI_PIPELINE_ID}-$(date +'%Y%m%d_%H%M').sqfs
#ln -sf ${stack}-${environment}-${squash_id}-$(date +'%Y%m%d_%H%M').sqfs ${stack}-${environment}-${squash_id}.sqfs
diff --git a/stacks/pinot-noir-gcc/concretizer.yaml b/stacks/pinot-noir-gcc/concretizer_common.yaml
similarity index 100%
rename from stacks/pinot-noir-gcc/concretizer.yaml
rename to stacks/pinot-noir-gcc/concretizer_common.yaml
diff --git a/stacks/pinot-noir-gcc/config.json b/stacks/pinot-noir-gcc/config.json
index 530523f1986eaa170a83399cacdfa20fa1732a74..1066541f266774bb8cb8b21558aafae0d8c438df 100644
--- a/stacks/pinot-noir-gcc/config.json
+++ b/stacks/pinot-noir-gcc/config.json
@@ -37,8 +37,8 @@
"helvetios": "skylake_avx512",
"izar": "cascadelake",
"jed": "icelake",
- "kuma_l40s": "zen4",
- "kuma_h100": "zen4"
+ "kuma-l40s": "zen4",
+ "kuma-h100": "zen4"
},
"compilers": {
"gcc": {
diff --git a/stacks/pinot-noir-gcc/config.yaml b/stacks/pinot-noir-gcc/config_common.yaml
similarity index 100%
rename from stacks/pinot-noir-gcc/config.yaml
rename to stacks/pinot-noir-gcc/config_common.yaml
diff --git a/stacks/pinot-noir-gcc/definitions_cuda.yaml b/stacks/pinot-noir-gcc/definitions_acc_cuda.yaml
similarity index 100%
rename from stacks/pinot-noir-gcc/definitions_cuda.yaml
rename to stacks/pinot-noir-gcc/definitions_acc_cuda.yaml
diff --git a/stacks/pinot-noir-gcc/definitions_empty.yaml b/stacks/pinot-noir-gcc/definitions_acc_none.yaml
similarity index 100%
rename from stacks/pinot-noir-gcc/definitions_empty.yaml
rename to stacks/pinot-noir-gcc/definitions_acc_none.yaml
diff --git a/stacks/pinot-noir-gcc/definitions_izar.yaml b/stacks/pinot-noir-gcc/definitions_izar.yaml
deleted file mode 120000
index 2c65e6a4923cf87b9addc7a71f26c0e6acb0f36f..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir-gcc/definitions_izar.yaml
+++ /dev/null
@@ -1 +0,0 @@
-definitions_cuda.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir-gcc/definitions_kuma_h100.yaml b/stacks/pinot-noir-gcc/definitions_kuma_h100.yaml
deleted file mode 120000
index 2c65e6a4923cf87b9addc7a71f26c0e6acb0f36f..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir-gcc/definitions_kuma_h100.yaml
+++ /dev/null
@@ -1 +0,0 @@
-definitions_cuda.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir-gcc/definitions_kuma_l40s.yaml b/stacks/pinot-noir-gcc/definitions_kuma_l40s.yaml
deleted file mode 120000
index 2c65e6a4923cf87b9addc7a71f26c0e6acb0f36f..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir-gcc/definitions_kuma_l40s.yaml
+++ /dev/null
@@ -1 +0,0 @@
-definitions_cuda.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir-gcc/mirrors.yaml b/stacks/pinot-noir-gcc/mirrors.yaml
deleted file mode 100644
index 2c338aa265ca4ab7735374e44dd491d1f2c81115..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir-gcc/mirrors.yaml
+++ /dev/null
@@ -1 +0,0 @@
-mirrors: {}
diff --git a/stacks/pinot-noir-gcc/modules_empty.yaml b/stacks/pinot-noir-gcc/modules_acc_none.yaml
similarity index 100%
rename from stacks/pinot-noir-gcc/modules_empty.yaml
rename to stacks/pinot-noir-gcc/modules_acc_none.yaml
diff --git a/stacks/pinot-noir-gcc/modules.yaml b/stacks/pinot-noir-gcc/modules_common.yaml
similarity index 100%
rename from stacks/pinot-noir-gcc/modules.yaml
rename to stacks/pinot-noir-gcc/modules_common.yaml
diff --git a/stacks/pinot-noir-gcc/modules_kuma_h100.yaml b/stacks/pinot-noir-gcc/modules_kuma-h100.yaml
similarity index 100%
rename from stacks/pinot-noir-gcc/modules_kuma_h100.yaml
rename to stacks/pinot-noir-gcc/modules_kuma-h100.yaml
diff --git a/stacks/pinot-noir-gcc/modules_kuma_l40s.yaml b/stacks/pinot-noir-gcc/modules_kuma-l40s.yaml
similarity index 100%
rename from stacks/pinot-noir-gcc/modules_kuma_l40s.yaml
rename to stacks/pinot-noir-gcc/modules_kuma-l40s.yaml
diff --git a/stacks/pinot-noir-gcc/packages.yaml b/stacks/pinot-noir-gcc/packages_common.yaml
similarity index 100%
rename from stacks/pinot-noir-gcc/packages.yaml
rename to stacks/pinot-noir-gcc/packages_common.yaml
diff --git a/stacks/pinot-noir-gcc/packages_kuma_h100.yaml b/stacks/pinot-noir-gcc/packages_kuma-h100.yaml
similarity index 100%
rename from stacks/pinot-noir-gcc/packages_kuma_h100.yaml
rename to stacks/pinot-noir-gcc/packages_kuma-h100.yaml
diff --git a/stacks/pinot-noir-gcc/packages_kuma_l40s.yaml b/stacks/pinot-noir-gcc/packages_kuma-l40s.yaml
similarity index 100%
rename from stacks/pinot-noir-gcc/packages_kuma_l40s.yaml
rename to stacks/pinot-noir-gcc/packages_kuma-l40s.yaml
diff --git a/stacks/pinot-noir/concretizer.yaml b/stacks/pinot-noir/concretizer.yaml
deleted file mode 100644
index 698e4c7865156575e6807306e18573c647c921c2..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir/concretizer.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-concretizer:
- reuse: false
- unify: false
- duplicates:
- strategy: minimal
diff --git a/stacks/pinot-noir/concretizer_common.yaml b/stacks/pinot-noir/concretizer_common.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..220ee695ee554146894ea39fb6a6ffd10d288de1
--- /dev/null
+++ b/stacks/pinot-noir/concretizer_common.yaml
@@ -0,0 +1,10 @@
+concretizer:
+ reuse:
+ roots: true
+ include:
+ - "%gcc@12.3.0"
+ from:
+ - type: local
+ unify: false
+ duplicates:
+ strategy: minimal
diff --git a/stacks/pinot-noir/config.json b/stacks/pinot-noir/config.json
index f566368b0be457dde11b8e463541c5e18f73a1b4..174e76651437e2fb2a016aa9243c3e0237c4fe5a 100644
--- a/stacks/pinot-noir/config.json
+++ b/stacks/pinot-noir/config.json
@@ -1,6 +1,6 @@
{
"spack": {
- "version": "v0.22.0",
+ "version": "releases/v0.22",
"repos": {
"scitas-externals": {
"url": "https://gitlab.epfl.ch/SCITAS/software-stack/spack-repo-externals.git",
@@ -33,23 +33,47 @@
"version": "11.2.1"
}
},
- "targets": {
- "helvetios": "skylake_avx512",
- "izar": "cascadelake",
- "jed": "icelake",
- "kuma_l40s": "zen4",
- "kuma_h100": "zen4"
+ "environments": {
+ "helvetios": {
+ "target": "skylake_avx512",
+ "accelerator": "none"
+ },
+ "izar": {
+ "target": "cascadelake",
+ "accelerator": {
+ "type": "cuda",
+ "arch": "75"
+ }
+ },
+ "jed": {
+ "target": "icelake"
+ },
+ "kuma-l40s": {
+ "target": "zen4",
+ "accelerator": {
+ "type": "cuda",
+ "arch": "89"
+ }
+ },
+ "kuma-h100": {
+ "target": "zen4",
+ "accelerator": {
+ "type": "cuda",
+ "arch": "90"
+ }
+ }
},
"compilers": {
"oneapi": {
"compiler": "oneapi",
"spec": "intel-oneapi-compilers@2024.1.0 %gcc@11.2.1",
- "version": "2024.1.0"
+ "version": "2024.1.0",
+ "constraint": "env['environment'] in ['jed', 'helvetios']"
},
"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": [
@@ -62,45 +86,49 @@
"ca-certificates-mozilla",
"check",
"cmake",
- "cuda",
"curl",
"diffutils",
"expat",
"findutils",
"flex",
"font-util",
+ "fontconfig",
"freetype",
"gawk",
"gdbm",
"gettext",
"git",
- "glibc",
"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",
- "meson",
"mpc",
"mpfr",
"ncurses",
- "ninja",
"openssl",
"pcre",
"pcre2",
@@ -113,7 +141,9 @@
"slurm",
"sqlite",
"tar",
+ "tcl",
"texinfo",
+ "tk",
"utf8proc",
"util-linux-uuid",
"xpmem",
diff --git a/stacks/pinot-noir/config.yaml b/stacks/pinot-noir/config_common.yaml
similarity index 100%
rename from stacks/pinot-noir/config.yaml
rename to stacks/pinot-noir/config_common.yaml
diff --git a/stacks/pinot-noir/definitions_cuda.yaml b/stacks/pinot-noir/definitions_acc_cuda.yaml
similarity index 58%
rename from stacks/pinot-noir/definitions_cuda.yaml
rename to stacks/pinot-noir/definitions_acc_cuda.yaml
index 4710276c2be849f7ba905a7c66ce192ee3a206eb..99f50932cbb96ebe4318e34748304fa099769aec 100644
--- a/stacks/pinot-noir/definitions_cuda.yaml
+++ b/stacks/pinot-noir/definitions_acc_cuda.yaml
@@ -1,8 +1,11 @@
definitions:
- - cuda_system_codes:
- - cuda
- - cudnn
+ - cuda_system_codes: []
- cuda_serial_codes:
+ - cuda
+ - cudnn
- nccl
+
+ - cuda_mpi_codes:
- nvshmem
+ - nccl-tests
diff --git a/stacks/pinot-noir-gcc/definitions_helvetios.yaml b/stacks/pinot-noir/definitions_acc_none.yaml
similarity index 100%
rename from stacks/pinot-noir-gcc/definitions_helvetios.yaml
rename to stacks/pinot-noir/definitions_acc_none.yaml
diff --git a/stacks/pinot-noir/definitions_izar.yaml b/stacks/pinot-noir/definitions_izar.yaml
index 2c65e6a4923cf87b9addc7a71f26c0e6acb0f36f..3552a78f67656b1b6647cced51cbfb18b5882f10 120000
--- a/stacks/pinot-noir/definitions_izar.yaml
+++ b/stacks/pinot-noir/definitions_izar.yaml
@@ -1 +1 @@
-definitions_cuda.yaml
\ No newline at end of file
+definitions_empty.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir/definitions_jed.yaml b/stacks/pinot-noir/definitions_jed.yaml
deleted file mode 100644
index 0f156fa830b9567b3e7839218a0a88c16076c6ca..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir/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/definitions_jed.yaml b/stacks/pinot-noir/definitions_jed.yaml
new file mode 120000
index 0000000000000000000000000000000000000000..3552a78f67656b1b6647cced51cbfb18b5882f10
--- /dev/null
+++ b/stacks/pinot-noir/definitions_jed.yaml
@@ -0,0 +1 @@
+definitions_empty.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir/definitions_kuma-h100.yaml b/stacks/pinot-noir/definitions_kuma-h100.yaml
new file mode 120000
index 0000000000000000000000000000000000000000..3552a78f67656b1b6647cced51cbfb18b5882f10
--- /dev/null
+++ b/stacks/pinot-noir/definitions_kuma-h100.yaml
@@ -0,0 +1 @@
+definitions_empty.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir/definitions_kuma-l40s.yaml b/stacks/pinot-noir/definitions_kuma-l40s.yaml
new file mode 120000
index 0000000000000000000000000000000000000000..3552a78f67656b1b6647cced51cbfb18b5882f10
--- /dev/null
+++ b/stacks/pinot-noir/definitions_kuma-l40s.yaml
@@ -0,0 +1 @@
+definitions_empty.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir/definitions_kuma_h100.yaml b/stacks/pinot-noir/definitions_kuma_h100.yaml
deleted file mode 120000
index 2c65e6a4923cf87b9addc7a71f26c0e6acb0f36f..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir/definitions_kuma_h100.yaml
+++ /dev/null
@@ -1 +0,0 @@
-definitions_cuda.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir/definitions_kuma_l40s.yaml b/stacks/pinot-noir/definitions_kuma_l40s.yaml
deleted file mode 120000
index 2c65e6a4923cf87b9addc7a71f26c0e6acb0f36f..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir/definitions_kuma_l40s.yaml
+++ /dev/null
@@ -1 +0,0 @@
-definitions_cuda.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir/mirrors.yaml b/stacks/pinot-noir/mirrors.yaml
deleted file mode 100644
index 2c338aa265ca4ab7735374e44dd491d1f2c81115..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir/mirrors.yaml
+++ /dev/null
@@ -1 +0,0 @@
-mirrors: {}
diff --git a/stacks/pinot-noir/modules_acc_cuda.yaml b/stacks/pinot-noir/modules_acc_cuda.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..6baee16b9a1286c8af13e7e5ba223b08c96f2d4f
--- /dev/null
+++ b/stacks/pinot-noir/modules_acc_cuda.yaml
@@ -0,0 +1,21 @@
+modules:
+ default:
+ lmod:
+ nvhpc+mpi@24.3:
+ environment:
+ set:
+ HPCX_DIR: "{prefix}/Linux_x86_64/24.3/comm_libs/12.3/hpcx/hpcx-2.17.1"
+ OPAL_PREFIX: "${HPCX_DIR}/ompi"
+ prepend_path:
+ LD_LIBRARY_PATH: "${HPCX_DIR}/ompi/lib"
+ LD_LIBRARY_PATH: "${HPCX_DIR}/ucx/lib"
+ LD_LIBRARY_PATH: "${HPCX_DIR}/ucx/lib/ucx"
+ LD_LIBRARY_PATH: "${HPCX_DIR}/ucc/lib"
+ LD_LIBRARY_PATH: "${HPCX_DIR}/ucc/lib/ucc"
+ LD_LIBRARY_PATH: "${HPCX_DIR}/hcoll/lib"
+ LD_LIBRARY_PATH: "${HPCX_DIR}/sharp/lib"
+ LD_LIBRARY_PATH: "${HPCX_DIR}/nccl_rdma_sharp_plugin/lib"
+ PATH: "${HPCX_DIR}/ucx/bin"
+ PATH: "${HPCX_DIR}/ucc/bin"
+ PATH: "${HPCX_DIR}/hcoll/bin"
+ PATH: "${HPCX_DIR}/sharp/bin"
diff --git a/stacks/pinot-noir/modules_acc_none.yaml b/stacks/pinot-noir/modules_acc_none.yaml
new file mode 120000
index 0000000000000000000000000000000000000000..5be0f314270ddfe2b36d1716f4ea55e43bff43b4
--- /dev/null
+++ b/stacks/pinot-noir/modules_acc_none.yaml
@@ -0,0 +1 @@
+modules_empty.yaml
\ No newline at end of file
diff --git a/stacks/pinot-noir/modules.yaml b/stacks/pinot-noir/modules_common.yaml
similarity index 92%
rename from stacks/pinot-noir/modules.yaml
rename to stacks/pinot-noir/modules_common.yaml
index 38fcc67d3399d00e3662efcae31e385da1fb39ad..08558927791b43b6741f8126d6d529439f2e056c 100644
--- a/stacks/pinot-noir/modules.yaml
+++ b/stacks/pinot-noir/modules_common.yaml
@@ -3,10 +3,13 @@ modules:
enable: [lmod]
lmod:
hash_length: 0
+
core_compilers:
- gcc@11.2.1
+
hierarchy:
- mpi
+
all:
environment:
set:
@@ -40,53 +43,63 @@ modules:
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"
+
+# cuda:
+# 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"
+# 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
@@ -94,16 +107,21 @@ modules:
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:
@@ -111,12 +129,15 @@ modules:
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:
diff --git a/stacks/pinot-noir/modules_kuma-h100.yaml b/stacks/pinot-noir/modules_kuma-h100.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..8ddd771fff8e49d8a00ac2ba17096cdd8ff145ed
--- /dev/null
+++ b/stacks/pinot-noir/modules_kuma-h100.yaml
@@ -0,0 +1,19 @@
+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'
+ nvshmem:
+ environment:
+ set:
+ NVSHMEM_HCA_LIST: 'mlx5_2:1,mlx5_3:1'
+ NVSHMEM_BOOTSTRAP: MPI
diff --git a/stacks/pinot-noir/modules_kuma-l40s.yaml b/stacks/pinot-noir/modules_kuma-l40s.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..10a02d6a9cb56d2f1bcb9e66730d60c124561bda
--- /dev/null
+++ b/stacks/pinot-noir/modules_kuma-l40s.yaml
@@ -0,0 +1,19 @@
+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'
+ nvshmem:
+ environment:
+ set:
+ NVSHMEM_HCA_LIST: 'mlx5_0:1,mlx5_1:1'
+ NVSHMEM_BOOTSTRAP: MPI
diff --git a/stacks/pinot-noir/modules_kuma_h100.yaml b/stacks/pinot-noir/modules_kuma_h100.yaml
deleted file mode 100644
index 997a2e17dbd2183ee05688ae39bbc6a9be1403e4..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir/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/modules_kuma_l40s.yaml b/stacks/pinot-noir/modules_kuma_l40s.yaml
deleted file mode 100644
index 7be541da7ebaa02cccf6874f657a141d82f56541..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir/modules_kuma_l40s.yaml
+++ /dev/null
@@ -1,9 +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'
diff --git a/stacks/pinot-noir/packages.yaml b/stacks/pinot-noir/packages.yaml
deleted file mode 100644
index 01e4aa6bffd49e9caf3c243de15edba0287bd56f..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir/packages.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
-packages:
- all:
- providers:
- mpi: [openmpi, intel-oneapi-mpi]
- iconv: [libiconv]
- jpeg: [libjpeg]
- zlib-api: [zlib-ng]
- require:
- - spec: "^libiconv"
- when: "^iconv"
-
- zlib-ng:
- require: ['build_system=autotools']
diff --git a/stacks/pinot-noir/packages_acc_cuda.yaml b/stacks/pinot-noir/packages_acc_cuda.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..ae5b5aab7d61ee68b55219ed108e610755d78cdb
--- /dev/null
+++ b/stacks/pinot-noir/packages_acc_cuda.yaml
@@ -0,0 +1,82 @@
+packages:
+ all:
+ require:
+ - "~rocm"
+
+ - spec: cuda_arch={cuda_arch}
+ when: '+cuda'
+
+ - spec: '+cuda'
+ when: '%gcc'
+
+ # ---------------------------------------------------------------------------
+ cuda:
+ prefer:
+ - spec: "^gcc-runtime@{gcc_version}"
+ when: "%gcc"
+ - spec: "%gcc@{gcc_version} target={target}"
+ when: "%gcc"
+ require:
+ - '@12.4.1'
+
+ hypre:
+ require:
+ - spec: '+cuda cuda_arch={cuda_arch} +unified-memory'
+ when: '%gcc'
+
+ kokkos:
+ require:
+ - spec: '+cuda +cuda_lambda cuda_arch={cuda_arch} +wrapper ~openmptarget'
+ when: '%gcc'
+
+ kokkos-kernels:
+ require: ['+cuda', '+cublas', '+cusolver', '+cusparse', 'cuda_arch={cuda_arch}']
+
+ libxc:
+ require: ['+cuda', 'cuda_arch={cuda_arch}']
+
+ nvshmem:
+ require:
+ - spec: '+cuda cuda_arch={cuda_arch} +ibgda +nccl +ucx +mpi'
+
+ openmpi:
+ require: ['+cuda', 'cuda_arch={cuda_arch}', 'fabrics=hcoll']
+
+ papi:
+ require: ['+nvml', '+infiniband', '+cuda']
+
+ paraview:
+ require: ['~cuda']
+
+ petsc:
+ require:
+ - spec: '+cuda cuda_arch={cuda_arch}'
+ when: '%gcc'
+
+ py-tensorflow:
+ require:
+ - spec: '+cuda cuda_arch={cuda_arch} +nccl'
+
+ py-torch:
+ require:
+ - spec: '+cuda cuda_arch={cuda_arch} +nccl +cudnn'
+
+ python:
+ require:
+ - spec: 'target={target}'
+ when: '%gcc@{gcc_version}'
+
+ suite-sparse:
+ require:
+ - spec: '+cuda'
+ when: '@7.3.1'
+ - spec: '~cuda'
+ when: '@7.2.1'
+
+ ucc:
+ require:
+ - spec: '+cuda cuda_arch={cuda_arch} +nccl'
+
+ ucx:
+ require:
+ - spec: '+xpmem +cma +rdmacm +rc +ud +dc +verbs +ib_hw_tm +gdrcopy +cuda cuda_arch={cuda_arch} ~rocm'
diff --git a/stacks/pinot-noir/packages_acc_none.yaml b/stacks/pinot-noir/packages_acc_none.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..0aa29d8aa89378efccc88721d31443a6c52c5595
--- /dev/null
+++ b/stacks/pinot-noir/packages_acc_none.yaml
@@ -0,0 +1,3 @@
+packages:
+ all:
+ require: ['~cuda', '~rocm']
diff --git a/stacks/pinot-noir/packages_common.yaml b/stacks/pinot-noir/packages_common.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..4b636f1e928fb31053eeb8dfc59f3be76c87e94e
--- /dev/null
+++ b/stacks/pinot-noir/packages_common.yaml
@@ -0,0 +1,26 @@
+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/packages_helvetios.yaml b/stacks/pinot-noir/packages_helvetios.yaml
deleted file mode 100644
index fe0d4ad01829f0895adce34a9071fe0eb4218e18..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir/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/packages_izar.yaml b/stacks/pinot-noir/packages_izar.yaml
deleted file mode 100644
index 9ce65d95e200925fe7b5bd50d0f76c18b2f33097..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir/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/packages_jed.yaml b/stacks/pinot-noir/packages_jed.yaml
deleted file mode 100644
index 822d1e2f6b56828d7269ba821ecb27be99c9d6d2..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir/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/packages_kuma-h100.yaml b/stacks/pinot-noir/packages_kuma-h100.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..fb5764966000dd33ff469f833f1851d7fb1daeb0
--- /dev/null
+++ b/stacks/pinot-noir/packages_kuma-h100.yaml
@@ -0,0 +1,36 @@
+packages:
+ cp2k:
+ require: ['+cuda', 'cuda_arch=90']
+
+ # ---------------------------------------------------------------------------
+ # Externals
+ # ---------------------------------------------------------------------------
+ hcoll:
+ buildable: false
+ externals:
+ - spec: 'hcoll@4.8.3227'
+ prefix: /opt/mellanox/hcoll
+
+ 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/packages_kuma-l40s.yaml b/stacks/pinot-noir/packages_kuma-l40s.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..31774ed2def2ea16cf24f23f73f2c199664b324e
--- /dev/null
+++ b/stacks/pinot-noir/packages_kuma-l40s.yaml
@@ -0,0 +1,40 @@
+packages:
+ # ---------------------------------------------------------------------------
+ cp2k:
+ require: ['~cuda']
+
+ dbcsr:
+ require: ['~cuda']
+
+ # ---------------------------------------------------------------------------
+ # Externals
+ # ---------------------------------------------------------------------------
+ hcoll:
+ buildable: false
+ externals:
+ - spec: 'hcoll@4.8.3227'
+ prefix: /opt/mellanox/hcoll
+
+ 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/packages_kuma_h100.yaml b/stacks/pinot-noir/packages_kuma_h100.yaml
deleted file mode 100644
index 281c15220290598dbe1e9d38ffc6a9268089bce4..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir/packages_kuma_h100.yaml
+++ /dev/null
@@ -1,82 +0,0 @@
-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'
-
- nvshmem:
- require:
- - spec: '+cuda cuda_arch=90 +ibgda +nccl +ucx +mpi'
-
- 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@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/packages_kuma_l40s.yaml b/stacks/pinot-noir/packages_kuma_l40s.yaml
deleted file mode 100644
index a1b6aef1ba3ec155b9dedcdc3825c7206f3222f0..0000000000000000000000000000000000000000
--- a/stacks/pinot-noir/packages_kuma_l40s.yaml
+++ /dev/null
@@ -1,82 +0,0 @@
-packages:
- all:
- target: ["zen4"]
- require:
- - "~rocm"
-
- - spec: cuda_arch=89 target=zen4
- when: '+cuda'
-
- - spec: '+cuda'
- when: '%gcc'
-
- # ---------------------------------------------------------------------------
- hypre:
- require:
- - spec: '+cuda cuda_arch=89 +unified-memory'
- when: '%gcc'
-
- kokkos:
- require:
- - spec: '+cuda cuda_arch=89 +cuda_uvm +wrapper ~openmptarget'
- when: '%gcc'
-
- nvshmem:
- require:
- - spec: '+cuda cuda_arch=89 +ibgda +nccl +ucx +mpi'
-
- openmpi:
- require:
- - spec: '+cuda cuda_arch=89 target=zen4'
-
- 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'
-
- 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=89 ~rocm target=zen4'
-
- # ---------------------------------------------------------------------------
- # 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/packages_stack.yaml b/stacks/pinot-noir/packages_stack.yaml
index 65bebbff72b75fc05be003c6c16492fbf27e07a0..cc7f0d9ec5782f741b30617d0e389f6a6ea7e99d 100644
--- a/stacks/pinot-noir/packages_stack.yaml
+++ b/stacks/pinot-noir/packages_stack.yaml
@@ -1,19 +1,27 @@
packages:
all:
- providers:
- mpi: [openmpi, intel-oneapi-mpi]
- iconv: [libiconv]
- jpeg: [libjpeg]
- zlib-api: [zlib-ng]
+ target: ["{target}"]
+ prefer: ['target={target}']
+
require:
- spec: '+ipo'
when: '%gcc'
+ - spec: '^netlib-scalapack'
+ when: '%gcc ^scalapack'
+
# ----------------------------------------------------------------------------
# Requirements
# ----------------------------------------------------------------------------
adios2:
- require: ['+kokkos']
+ require: ['+kokkos', '+mgard']
+
+ apr:
+ # https://issues.apache.org/jira/browse/SVN-4813
+ require: ['@1.6.2']
+
+ arpack-ng:
+ prefer: ['+mpi']
boost:
prefer: ['~mpi']
@@ -24,25 +32,55 @@ packages:
'+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: '@12.4.0'
- 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: ['+slepc']
+ require: ['@0.8.0', '+slepc']
+
+ ffmpeg:
+ require: ['+libx264']
fftw:
prefer: ['+mpi', '+openmp']
+ gettext:
+ require: ['+libxml2', '+xz']
+
gnuplot:
- require:
- - spec: '@5.4.10'
+ require: ['@5.4.10', '+cairo']
hdf5:
prefer:
- - spec: '+mpi'
- spec: '@1.14.3'
require:
- spec: '+hl +threadsafe +szip +cxx +fortran'
@@ -56,79 +94,212 @@ packages:
intel-oneapi-mkl:
prefer: ['~cluster']
+ julia:
+ require: ['@1.10.4']
+
kokkos:
- prefer: ['+openmp', '+numactl', '+memkind', '+threads',
- '+aggressive_vectorization']
+ require: ['+numactl', '+memkind', '+serial',
+ '+openmp', '~openmptarget',
+ '~threads', '~sycl',
+ '+aggressive_vectorization', '@4.3.01']
+
+ kokkos-kernels:
+ require: ['@4.3.01', '+openmp', '~threads', '~ipo']
- kokkos-kernel:
- prefer: ['+openmp', '+threads']
+ kokkos-nvcc-wrapper:
+ prefer: ['@4.3.01']
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']
+ 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'
- llvm:
- prefer: ['~clang']
+ 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:
- prefer: ['threads=pthreads symbol_suffix=none ~ilp64']
+ require: ['build_system=makefile']
+ prefer: ['threads=openmp', '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'
+ require: ['@5.0.3',
+ 'fabrics=ofi,ucc,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:
- - spec: '+hypre +mumps +saws +scalapack +mpi +suite-sparse +kokkos'
+ require: ['+hypre', '+mumps', '+saws', '+scalapack', '+mpi', '+suite-sparse', '+kokkos', '+openmp']
python:
require:
- - spec: '+ssl +tkinter'
+ - 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']
+ require: ['+mpi', '~mkl']
py-torch:
- require: ['+mpi']
+ 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: ['+mpi', '+openmp', '~gipaw', '+scalapack', '+libxc', '~ipo']
+ prefer: ['hdf5=parallel']
+
+ rust:
+ require: ['+dev']
scotch:
prefer: ['~mpi']
+ sirius:
+ prefer: ['+fortran', '~elpa', '+wannier90']
+
+ slepc:
+ require:
+ - spec: '^arpack-ng +mpi'
+
+ spades:
+ require: ['~ipo']
+
suite-sparse:
require:
- - spec: '+graphblas'
+ - '+graphblas'
+ - one_of: ['@7.3.1', '@7.2.1']
+ prefer: ['@7.3.1']
tk:
require: ['+xft', '+xss']
ucx:
+ require: ['@1.17.0', '+rdmacm', '+rc', '+dc', '+ud', '+cma', '+verbs']
+
+ vtk:
require:
- - spec: '+rdmacm +rc +dc +ud +cma +verbs'
+ - spec: '~python ++mpi +xdmf +ffmpeg'
+
+ xmlto:
+ require: ['@0.0.29']
# ----------------------------------------------------------------------------
# System dependencies
@@ -139,6 +310,18 @@ packages:
- 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:
@@ -157,7 +340,6 @@ packages:
- spec: 'slurm@23-11-7-1'
prefix: /usr
-
# ----------------------------------------------------------------------------
# Externals
# ----------------------------------------------------------------------------
diff --git a/stacks/pinot-noir/spack.yaml b/stacks/pinot-noir/spack.yaml
index 4450501f931976ff7626285308a5700d39fdbc5a..1b9bdd5145b2cd53f59a21ea5c6d784020a2102d 100644
--- a/stacks/pinot-noir/spack.yaml
+++ b/stacks/pinot-noir/spack.yaml
@@ -3,11 +3,13 @@ spack:
- compiler_definitions.yaml
- packages_stack.yaml
+ - packages_accel.yaml
- packages_env.yaml
- modules_stack.yaml
- modules_env.yaml
+ - definitions_accel.yaml
- definitions_env.yaml
- config_stack.yaml
@@ -23,7 +25,7 @@ spack:
- intel-oneapi-mpi@2021.12.1
- blas_gcc:
- - openblas@0.3.26
+ - openblas@0.3.27
- blas_oneapi:
- intel-oneapi-mkl@2024.1.0
@@ -39,8 +41,8 @@ spack:
# -------------------------------------------------------------------------
- core_codes:
- bzip2
- - cmake
- - emacs +tls
+ - cmake +ncurses
+ - emacs
- fastqc
- fio
- git
@@ -48,24 +50,27 @@ spack:
- gmp
- gnuplot
- gzip
- - imagemagick +ghostscript
- intel-oneapi-advisor
- intel-oneapi-inspector
- intel-oneapi-vtune
- libarchive
+ - libgd
- libjpeg-turbo
- libpng
- libtiff
- libxml2
+ - likwid
- lmod
- mpfr
- neovim
- - ninja
+ #- ninja
+ - papi
- parallel
- picard
- rclone
- - rust
- sbt
+ - squashfs
+ - squashfs-mount
- sratoolkit
- subversion
- tar
@@ -80,43 +85,42 @@ spack:
# Serial codes
# -------------------------------------------------------------------------
- serial_codes:
- - bwa
- - fftw +openmp ~mpi
- - fftw ~openmp ~mpi
- - eigen
+ - fftw +openmp ~~mpi
+ - fftw ~~openmp ~~mpi
- gsl
- - hdf5@1.14.1 ~mpi
- - hisat2
+ - hdf5@1.14.3 ~~mpi
- htslib
- intel-oneapi-tbb
- jasper
- - kallisto ^hdf5 ~mpi
+ - kallisto ^hdf5 ~~mpi
- kokkos
- kokkos-kernels
- mafft
- metis
- muscle
- - netcdf-c~mpi ^hdf5~mpi
- - netcdf-fortran ^netcdf-c ~mpi ^hdf5 ~mpi
- - nfft ^fftw~mpi~openmp
+ - netcdf-c ~~mpi
+ - netcdf-fortran ^netcdf-c ~~mpi
+ - nfft ^fftw~~mpi~~openmp
- python
- - scotch ~mpi
+ - scotch ~~mpi
- star
- subread
- - unblur ^fftw~mpi~openmp
+ - unblur ^fftw~~mpi ~~openmp
- voropp
- gcc_serial_codes:
- - cistem ^fftw~mpi
- - ctffind ^fftw ~mpi
- - ffmpeg +libx264
+ - bwa
+ - eigen
+ - ffmpeg
- glpk+gmp
- hwloc
- intel-oneapi-mkl
- libxc
- - ncview ^hdf5 ~mpi ^netcdf-c ~mpi ~parallel-netcdf
+ - qperf
+ - ncview ^netcdf-c ~~mpi ~parallel-netcdf
- sox
- stacks
+ - xgboost
- oneapi_serial_codes:
- abaqus@2023
@@ -129,16 +133,18 @@ spack:
- cuda_serial_codes: []
+ - cuda_mpi_codes: []
+
# -------------------------------------------------------------------------
# Blas dependent codes
# -------------------------------------------------------------------------
- blas_codes:
- - arpack-ng ~mpi
+ - arpack-ng ~~mpi
- superlu
- suite-sparse
- gcc_blas_codes:
- - armadillo +hdf5 ^arpack-ng ~mpi ^hdf5 ~mpi
+ - armadillo +hdf5 ^arpack-ng ~~mpi ^hdf5 ~~mpi
- octave
# -------------------------------------------------------------------------
@@ -188,111 +194,120 @@ spack:
- snakemake
- python_blas_codes:
- - boost ~mpi
- #- 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
- - py-macs2
+ - py-macs3
- py-matplotlib
- py-numpy
- py-opt-einsum
- py-pandas
- py-pybigwig
- py-xarray
- - valgrind
+ - valgrind ~~mpi
- gcc_python_codes:
- blast-plus
- - caffe +python
+ - cistem ^fftw~~mpi
+ - ctffind ^fftw ~~mpi
- gatk
- - gdb +tui +source-highlight +xz
+ - hisat2
+ - imagemagick +ghostscript
- julia+openlibm
- - libgd
- mesa
- mummer
- node-js
- - openbabel +python ^boost ~mpi
- - r
+ - rust
- spades
- - xgboost
- 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 ^hdf5 ~mpi
- - py-pymol
+ - py-h5py ~~mpi
+ - py-pymol ^hdf5~mpi
- py-scikit-learn
- py-scipy
- - py-statsmodels
+ #- py-statsmodels
- py-theano
+ - r
# -------------------------------------------------------------------------
# Parallel codes
# -------------------------------------------------------------------------
- mpi_codes:
- - fftw +mpi +openmp
- - hdf5@1.14.3 +mpi
+ - fftw ++mpi +openmp
+ - hdf5@1.14.3 ++mpi
- openfoam-org +metis
- osu-micro-benchmarks +graphing
- parmetis
- phylobayesmpi
- - py-mpi4py
- - scotch +mpi
+ - 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
+ - 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
+ #- quantum-espresso ++mpi +scalapack +gipaw
+ - quantum-espresso
- gcc_mpi_blas_codes:
- - gmsh +mpi +eigen +openmp +hdf5 ~fltk ~opencascade ~med ^mmg ~vtk
+ - 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
- - yambo +mpi io=iotk,etsf-io
+ - trilinos
+ - vtk
+ - yambo ++mpi io=iotk,etsf-io
- mpi_blas_python_codes:
- - boost +mpi
+ - boost ++mpi
- cgal
- - iq-tree@1.6.12+mpi
- - neuron +mpi +python
- - petsc@3.21.1
+ - iq-tree@1.6.12++mpi
+ - neuron ++mpi +python
+ - petsc
- plumed
- py-petsc4py
- slepc
+ - sirius
- gcc_mpi_blas_python_codes:
- # - eman2 +mpi
+ # - eman2 ++mpi
- adios2
- - cp2k +mpi +plumed +openmp smm=blas
+ - cp2k ++mpi +plumed +openmp smm=blas
# - fenics +parmetis +hdf5 +scotch +suite-sparse ~vtk ~trilinos
- fenics-dolfinx
- - gromacs +mpi +plumed
+ - gromacs ++mpi +plumed
- lammps
- opencv
- openfoam +metis
- - paraview +shared +python +hdf5 ~osmesa +opengl2 +egl
+ - paraview@5.12.0 +shared +python +hdf5 +opengl2
- py-fenics-dolfinx
- - py-h5py +mpi
- - py-horovod
+ - py-h5py ++mpi
+ # - py-horovod cannot resolve dependencies with pytorch
- py-keras
- py-tensorflow
- py-torch
- py-torchvision
- relion ~mklfft
- topaz
- - vtk
# -------------------------------------------------------------------------
# External packages
@@ -392,11 +407,22 @@ spack:
- [$^mpi_gcc]
- [$%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]
@@ -405,16 +431,16 @@ spack:
- matrix:
- [$mpi_blas_python_codes]
+ - [$^python_gcc]
- [$^blas_gcc]
- [$^mpi_gcc]
- - [$^python_gcc]
- [$%compiler_gcc]
- matrix:
- [$gcc_mpi_blas_python_codes]
+ - [$^python_gcc]
- [$^blas_gcc]
- [$^mpi_gcc]
- - [$^python_gcc]
- [$%compiler_gcc]
# --------------------------------------------------------------------------
@@ -455,6 +481,12 @@ spack:
- [$^mpi_oneapi]
- [$%compiler_oneapi]
+ - matrix:
+ - [$mpi_python_codes]
+ - [$^python_oneapi]
+ - [$^mpi_oneapi]
+ - [$%compiler_oneapi]
+
- matrix:
- [$mpi_blas_codes]
- [$^blas_oneapi]
@@ -463,9 +495,9 @@ spack:
- matrix:
- [$mpi_blas_python_codes]
+ - [$^python_oneapi]
- [$^blas_oneapi]
- [$^mpi_oneapi]
- - [$^python_oneapi]
- [$%compiler_oneapi]
view: false