Merge pull request EESSI#399 from trz42/nessi-2023.06-deps-PyTorch-bu…

…ndle-CPU-only

{2023.06,2023a} dependencies for PyTorch-bundle v2.1.2

EESSI-install-software.sh

@@ -17,11 +17,6 @@ display_help() {
   echo "  --skip-cuda-install    -  disable installing a full CUDA SDK in the host_injections prefix (e.g. in CI)"
 }
 
-# Function to check if a command exists
-function command_exists() {
-    command -v "$1" >/dev/null 2>&1
-}
-
 function copy_build_log() {
     # copy specified build log to specified directory, with some context added
     build_log=${1}
@@ -159,8 +154,13 @@ fi
 #   are:
 #     - .lmod/lmodrc.lua
 #     - .lmod/SitePackage.lua
+#
 # We run scripts to create them if they don't exist or if the scripts have been
 # changed in the PR.
+#
+# (TODO do we need to change the path if we have sub-directories for
+# accelerators? And would we need different scripts for creating lua files under
+# different directories?)
 
 # Set base directory for software and for Lmod config files
 _eessi_software_path=${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
@@ -256,6 +256,12 @@ if command_exists "nvidia-smi"; then
     ${EESSI_PREFIX}/scripts/gpu_support/nvidia/link_nvidia_host_libraries.sh
 fi
 
+# Install extra software that is needed (e.g., for providing a custom ctypes
+# library when needed)
+cd ${TOPDIR}/scripts/extra
+./install_extra_packages.sh --temp-dir /tmp/temp --easystack eessi-2023.06-extra-packages.yml
+cd ${TOPDIR}
+
 # use PR patch file to determine in which easystack files stuff was added
 changed_easystacks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing') 
 if [ -z "${changed_easystacks}" ]; then

bot/build.sh

@@ -266,16 +266,20 @@ mkdir -p ${TARBALL_TMP_BUILD_STEP_DIR}
 BUILD_STEP_ARGS+=("--save" "${TARBALL_TMP_BUILD_STEP_DIR}")
 BUILD_STEP_ARGS+=("--storage" "${STORAGE}")
 # add options required to handle NVIDIA support
-BUILD_STEP_ARGS+=("--nvidia" "all")
+if command_exists "nvidia-smi"; then
+    echo "Command 'nvidia-smi' found, using available GPU"
+    BUILD_STEP_ARGS+=("--nvidia" "all")
+else
+    echo "No 'nvidia-smi' found, no available GPU but allowing overriding this check"
+    BUILD_STEP_ARGS+=("--nvidia" "install")
+fi
+# Retain location for host injections so we don't reinstall CUDA
+# (Always need to run the driver installation as available driver may change)
+
 if [[ ! -z ${SHARED_FS_PATH} ]]; then
     BUILD_STEP_ARGS+=("--host-injections" "${SHARED_FS_PATH}/host-injections")
 fi
 
-# Don't run the Lmod GPU driver check when doing builds (may not have a GPU, and it's not relevant for vanilla builds anyway)
-echo "EESSI_OVERRIDE_GPU_CHECK='${EESSI_OVERRIDE_GPU_CHECK}'"
-export EESSI_OVERRIDE_GPU_CHECK=1
-echo "EESSI_OVERRIDE_GPU_CHECK='${EESSI_OVERRIDE_GPU_CHECK}'"
-
 # create tmp file for output of build step
 build_outerr=$(mktemp build.outerr.XXXX)
 

easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml

@@ -55,3 +55,23 @@ easyconfigs:
   - PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb:
       options:
         cuda-compute-capabilities: 6.0,6.1,7.0,7.5,8.0,8.6,8.9,9.0
+  # PyTorch-bundle-CUDA's dependencies without CUDA
+  - librosa-0.10.1-foss-2023a.eb
+  - NLTK-3.8.1-foss-2023a.eb
+  - parameterized-0.9.0-GCCcore-12.3.0.eb
+  - Scalene-1.5.26-GCCcore-12.3.0.eb
+  - scikit-image-0.22.0-foss-2023a.eb
+  - SentencePiece-0.2.0-GCC-12.3.0.eb:
+      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19987
+      options:
+        from-pr: 19987
+  - libmad-0.15.1b-GCCcore-12.3.0.eb:
+      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19987
+      options:
+        from-pr: 19987
+  - SoX-14.4.2-GCCcore-12.3.0.eb:
+      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19987
+      options:
+        from-pr: 19987
+  - tensorboard-2.15.1-gfbf-2023a.eb
+  - tqdm-4.66.1-GCCcore-12.3.0.eb

eb_hooks.py

@@ -6,6 +6,7 @@
 import easybuild.tools.environment as env
 from easybuild.easyblocks.generic.configuremake import obtain_config_guess
 from easybuild.framework.easyconfig.constants import EASYCONFIG_CONSTANTS
+from easybuild.easyblocks.python import EXTS_FILTER_PYTHON_PACKAGES
 from easybuild.tools.build_log import EasyBuildError, print_msg
 from easybuild.tools.config import build_option, update_build_option
 from easybuild.tools.filetools import apply_regex_substitutions, copy_file, remove_file, symlink, which
@@ -311,6 +312,31 @@ def parse_hook_qt5_check_qtwebengine_disable(ec, eprefix):
         raise EasyBuildError("Qt5-specific hook triggered for non-Qt5 easyconfig?!")
 
 
+
+def parse_hook_sentencepiece_disable_tcmalloc_aarch64(ec, eprefix):
+    """
+    Disable using TC_Malloc on 'aarch64/generic'
+    """
+    cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+    if ec.name == 'SentencePiece' and ec.version in ['0.2.0']:
+        if cpu_target == CPU_TARGET_AARCH64_GENERIC:
+            print_msg("parse_hook for SentencePiece: OLD '%s'", ec['components'])
+            new_components = []
+            for item in ec['components']:
+                if item[2]['easyblock'] == 'CMakeMake':
+                    new_item = item[2]
+                    new_item['configopts'] = '-DSPM_ENABLE_TCMALLOC=OFF'
+                    new_components.append((item[0], item[1], new_item))
+                else:
+                    new_components.append(item)
+            ec['components'] = new_components
+            print_msg("parse_hook for SentencePiece: NEW '%s'", ec['components'])
+        else:
+            print_msg("parse_hook for SentencePiece on %s -> leaving configopts unchanged", cpu_target)
+    else:
+        raise EasyBuildError("SentencePiece-specific hook triggered for non-SentencePiece easyconfig?!")
+
+
 def parse_hook_ucx_eprefix(ec, eprefix):
     """Make UCX aware of compatibility layer via additional configuration options."""
     if ec.name == 'UCX':
@@ -349,6 +375,30 @@ def parse_hook_lammps_remove_deps_for_CI_aarch64(ec, *args, **kwargs):
         raise EasyBuildError("LAMMPS-specific hook triggered for non-LAMMPS easyconfig?!")
 
 
+def parse_hook_librosa_custom_ctypes(ec, *args, **kwargs):
+    """
+    Add exts_filter to soundfile extension in exts_list
+    """
+    if ec.name == 'librosa' and ec.version in ('0.10.1',):
+        ec_dict = ec.asdict()
+        eessi_software_path = get_eessi_envvar('EESSI_SOFTWARE_PATH')
+        custom_ctypes_path = os.path.join(eessi_software_path, "software", "custom_ctypes", "1.2")
+        ebpythonprefixes = "EBPYTHONPREFIXES=%s" % custom_ctypes_path
+        exts_list_new = []
+        for item in ec_dict['exts_list']:
+            if item[0] == 'soundfile':
+                ext_dict = item[2]
+                ext_dict['exts_filter'] = (ebpythonprefixes + ' ' + EXTS_FILTER_PYTHON_PACKAGES[0],
+                                           EXTS_FILTER_PYTHON_PACKAGES[1])
+                exts_list_new.append((item[0], item[1], ext_dict))
+            else:
+                exts_list_new.append(item)
+        ec['exts_list'] = exts_list_new
+        print_msg("New exts_list: '%s'", ec['exts_list'])
+    else:
+        raise EasyBuildError("librosa/0.10.1-specific hook triggered for non-librosa/0.10.1 easyconfig?!")
+
+
 def pre_prepare_hook_highway_handle_test_compilation_issues(self, *args, **kwargs):
     """
     Solve issues with compiling or running the tests on both
@@ -852,17 +902,49 @@ def inject_gpu_property(ec):
     return ec
 
 
+
+def pre_module_hook(self, *args, **kwargs):
+    """Main pre-module-check hook: trigger custom functions based on software name."""
+    if self.name in PRE_MODULE_HOOKS:
+        PRE_MODULE_HOOKS[self.name](self, *args, **kwargs)
+
+
+def pre_module_hook_librosa_augment_modluafooter(self, *args, **kwargs):
+    """
+    Add EBPYTHONPREFIXES to modluafooter
+    """
+    if self.name == 'librosa' and self.version == '0.10.1':
+        eessi_software_path = get_eessi_envvar('EESSI_SOFTWARE_PATH')
+        custom_ctypes_path = os.path.join(eessi_software_path, "software", "custom_ctypes", "1.2")
+        key = 'modluafooter'
+        values = ['prepend_path("EBPYTHONPREFIXES","%s")' % (custom_ctypes_path)]
+        print_msg("Adding '%s' to modluafooter", values[0])
+        if not key in self.cfg:
+            self.cfg[key] = '\n'.join(values)
+        else:
+            new_value = self.cfg[key]
+            for value in values:
+                if not value in new_value:
+                    new_value = '\n'.join([new_value, value])
+            self.cfg[key] = new_value
+        print_msg("Full modluafooter is '%s'", self.cfg[key])
+    else:
+        raise EasyBuildError("librosa/0.10.1-specific hook triggered for non-librosa/0.10.1 easyconfig?!")
+
+
 PARSE_HOOKS = {
     'casacore': parse_hook_casacore_disable_vectorize,
     'CGAL': parse_hook_cgal_toolchainopts_precise,
     'fontconfig': parse_hook_fontconfig_add_fonts,
     'GPAW': parse_hook_gpaw_harcoded_path,
     'ImageMagick': parse_hook_imagemagick_add_dependency,
     'LAMMPS': parse_hook_lammps_remove_deps_for_CI_aarch64,
+    'librosa': parse_hook_librosa_custom_ctypes,
     'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors,
     'Pillow-SIMD' : parse_hook_Pillow_SIMD_harcoded_paths,
     'pybind11': parse_hook_pybind11_replace_catch2,
     'Qt5': parse_hook_qt5_check_qtwebengine_disable,
+    'SentencePiece': parse_hook_sentencepiece_disable_tcmalloc_aarch64,
     'UCX': parse_hook_ucx_eprefix,
 }
 
@@ -909,3 +991,7 @@ def inject_gpu_property(ec):
     'cuDNN': post_sanitycheck_cudnn,
     'cuTENSOR': post_sanitycheck_cutensor,
 }
+
+PRE_MODULE_HOOKS = {
+    'librosa': pre_module_hook_librosa_augment_modluafooter,
+}

eessi_container.sh

@@ -477,6 +477,11 @@ if [[ ${SETUP_NVIDIA} -eq 1 ]]; then
         mkdir -p ${EESSI_USR_LOCAL_CUDA}
         BIND_PATHS="${BIND_PATHS},${EESSI_VAR_LOG}:/var/log,${EESSI_USR_LOCAL_CUDA}:/usr/local/cuda"
         [[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
+        if [[ "${NVIDIA_MODE}" == "install" ]] ; then
+            # No GPU so we need to "trick" Lmod to allow us to load CUDA modules even without a CUDA driver
+            # (this variable means EESSI_OVERRIDE_GPU_CHECK=1 will be set inside the container)
+            export SINGULARITYENV_EESSI_OVERRIDE_GPU_CHECK=1
+        fi
     fi
 fi
 

install_scripts.sh

@@ -113,6 +113,7 @@ nvidia_files=(
     eessi-2023.06-cuda-and-libraries.yml
     install_cuda_and_libraries.sh
     link_nvidia_host_libraries.sh
+    copy_nvidia_host_libraries.sh
 )
 copy_files_by_list ${TOPDIR}/scripts/gpu_support/nvidia ${INSTALL_PREFIX}/scripts/gpu_support/nvidia "${nvidia_files[@]}"
 

run_in_compat_layer_env.sh

@@ -26,12 +26,12 @@ fi
 if [ ! -z ${EESSI_VERSION_OVERRIDE} ]; then
     INPUT="export EESSI_VERSION_OVERRIDE=${EESSI_VERSION_OVERRIDE}; ${INPUT}"
 fi
-if [ ! -z ${http_proxy} ]; then
-    INPUT="export http_proxy=${http_proxy}; ${INPUT}"
-fi
 if [ ! -z ${EESSI_OVERRIDE_GPU_CHECK} ]; then
     INPUT="export EESSI_OVERRIDE_GPU_CHECK=${EESSI_OVERRIDE_GPU_CHECK}; ${INPUT}"
 fi
+if [ ! -z ${http_proxy} ]; then
+    INPUT="export http_proxy=${http_proxy}; ${INPUT}"
+fi
 if [ ! -z ${https_proxy} ]; then
     INPUT="export https_proxy=${https_proxy}; ${INPUT}"
 fi

scripts/extra/custom_ctypes-1.2.eb

@@ -0,0 +1,29 @@
+##
+# This is a contribution from the NESSI project
+# Homepage: 	https://documentation.sigma2.no
+#
+# Authors::	Thomas Roeblitz <[email protected]>
+# License::	GPL-2.0-only
+#
+##
+
+easyblock = 'Tarball'
+
+name = 'custom_ctypes'
+version = '1.2'
+
+homepage = 'https://github.com/ComputeCanada/custom_ctypes'
+description = """custum_ctypes is a small Python package to fix the discovery of libraries with Python's ctypes module. It changes the behavior of find_library to return absolute paths to shared objects rather than just the names."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://github.com/ComputeCanada/custom_ctypes/archive/refs/tags']
+sources = ['%(version)s.tar.gz']
+checksums = ['3b30ce633c6a329169f2b10ff24b8eaaeef3fa208a66cdacdb53c22f02a88d9b']
+
+sanity_check_paths = {
+    'files': ['README.md'],
+    'dirs': ['lib'],
+}
+
+moduleclass = 'lib'

scripts/extra/eessi-2023.06-extra-packages.yml

@@ -0,0 +1,2 @@
+easyconfigs:
+  - custom_ctypes-1.2.eb

scripts/extra/install_extra_packages.sh

@@ -0,0 +1,95 @@
+#!/usr/bin/env bash
+
+# This script can be used to install extra packages under ${EESSI_SOFTWARE_PATH}
+
+# some logging
+echo ">>> Running ${BASH_SOURCE}"
+
+# Initialise our bash functions
+TOPDIR=$(dirname $(realpath ${BASH_SOURCE}))
+source "${TOPDIR}"/../utils.sh
+
+# Function to display help message
+show_help() {
+    echo "Usage: $0 [OPTIONS]"
+    echo "Options:"
+    echo "  --help                           Display this help message"
+    echo "  -e, --easystack EASYSTACKFILE    Easystack file which specifies easyconfigs to be installed."
+    echo "  -t, --temp-dir /path/to/tmpdir   Specify a location to use for temporary"
+    echo "                                   storage during the installation"
+}
+
+# Initialize variables
+TEMP_DIR=
+EASYSTACK_FILE=
+
+# Parse command-line options
+while [[ $# -gt 0 ]]; do
+    case "$1" in
+        --help)
+            show_help
+            exit 0
+            ;;
+        -e|--easystack)
+            if [ -n "$2" ]; then
+                EASYSTACK_FILE="$2"
+                shift 2
+            else
+                echo "Error: Argument required for $1"
+                show_help
+                exit 1
+            fi
+            ;;
+        -t|--temp-dir)
+            if [ -n "$2" ]; then
+                TEMP_DIR="$2"
+                shift 2
+            else
+                echo "Error: Argument required for $1"
+                show_help
+                exit 1
+            fi
+            ;;
+        *)
+            show_help
+            fatal_error "Error: Unknown option: $1"
+            ;;
+    esac
+done
+
+if [[ -z ${EASYSTACK_FILE} ]]; then
+    show_help
+    fatal_error "Error: need to specify easystack file"
+fi
+
+# Make sure NESSI is initialised
+check_eessi_initialised
+
+# As an installation location just use $EESSI_SOFTWARE_PATH
+export NESSI_CVMFS_INSTALL=${EESSI_SOFTWARE_PATH}
+
+# we need a directory we can use for temporary storage
+if [[ -z "${TEMP_DIR}" ]]; then
+    tmpdir=$(mktemp -d)
+else
+    mkdir -p ${TEMP_DIR}
+    tmpdir=$(mktemp -d --tmpdir=${TEMP_DIR} extra.XXX)
+    if [[ ! -d "$tmpdir" ]] ; then
+        fatal_error "Could not create directory ${tmpdir}"
+    fi
+fi
+echo "Created temporary directory '${tmpdir}'"
+export WORKING_DIR=${tmpdir}
+
+# load EasyBuild
+ml EasyBuild
+
+# load NESSI-extend/2023.06-easybuild
+ml NESSI-extend/2023.06-easybuild
+
+eb --show-config
+
+eb --easystack ${EASYSTACK_FILE} --robot
+
+# clean up tmpdir
+rm -rf "${tmpdir}"