From 2050a89364e6bc7c45c8a7e75187180bcba09336 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Sun, 5 May 2024 14:08:51 +0200 Subject: [PATCH 1/7] {2023.06}[foss/2023a] cuDNN v8.9.2.26 --- .../pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml index 3018901ca9..e948a2e55d 100644 --- a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml +++ b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml @@ -26,3 +26,4 @@ easyconfigs: # from-commit: ae2fc38307b56ae7ac12dff95c9d07404e1a8530 # trying from-pr as an alternative from-pr: 20379 + - cuDNN-8.9.2.26-CUDA-12.1.1.eb From 1f0206f56a6ce9a3797d7c8e60402de7390289b7 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Sun, 5 May 2024 19:00:41 +0200 Subject: [PATCH 2/7] add post sanitycheck hook for cuDNN --- eb_hooks.py | 57 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/eb_hooks.py b/eb_hooks.py index 199dab8e54..44877103ea 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -688,6 +688,62 @@ def post_sanitycheck_cuda(self, *args, **kwargs): raise EasyBuildError("CUDA-specific hook triggered for non-CUDA easyconfig?!") +def post_sanitycheck_cuDNN(self, *args, **kwargs): + """ + Remove files from cuDNN installation that we are not allowed to ship, + and replace them with a symlink to a corresponding installation under host_injections. + """ + if self.name == 'cuDNN': + print_msg("Replacing files in cuDNN installation that we can not ship with symlinks to host_injections...") + + allowlist = ['LICENSE'] + + # read cuDNN LICENSE, construct allowlist based on section 2.6 that specifies list of files that can be shipped + license_path = os.path.join(self.installdir, 'LICENSE') + search_string = "2. Distribution. The following portions of the SDK are distributable under the Agreement:" + with open(license_path) as infile: + for line in infile: + if line.strip().startswidth(search_string): + # remove search string, split into words, remove trailing + # dots '.' and only retain words starting with a dot '.' + distributable = line[len(search_string):] + for word in distributable.split(): + if word[0] == '.': + allowlist.append(word.rstrip('.')) + + allowlist = sorted(set(allowlist)) + self.log.info("Allowlist for files in cuDNN installation that can be redistributed: " + ', '.join(allowlist)) + + # iterate over all files in the CUDA installation directory + for dir_path, _, files in os.walk(self.installdir): + for filename in files: + full_path = os.path.join(dir_path, filename) + # we only really care about real files, i.e. not symlinks + if not os.path.islink(full_path): + # check if the current file is part of the allowlist + basename = filename.split('.')[0] + if '.' in filename: + extension = '.' + filename.split('.')[1] + if basename in allowlist: + self.log.debug("%s is found in allowlist, so keeping it: %s", basename, full_path) + elif '.' in filename and extension in allowlist: + self.log.debug("%s is found in allowlist, so keeping it: %s", extension, full_path) + else: + self.log.debug("%s is not found in allowlist, so replacing it with symlink: %s", + filename, full_path) + # if it is not in the allowlist, delete the file and create a symlink to host_injections + host_inj_path = full_path.replace('versions', 'host_injections') + # make sure source and target of symlink are not the same + if full_path == host_inj_path: + raise EasyBuildError("Source (%s) and target (%s) are the same location, are you sure you " + "are using this hook for a NESSI installation?", + full_path, host_inj_path) + remove_file(full_path) + symlink(host_inj_path, full_path) + else: + raise EasyBuildError("cuDNN-specific hook triggered for non-cuDNN easyconfig?!") + + def inject_gpu_property(ec): """ Add 'gpu' property, via modluafooter easyconfig parameter @@ -768,4 +824,5 @@ def inject_gpu_property(ec): POST_SANITYCHECK_HOOKS = { 'CUDA': post_sanitycheck_cuda, + 'cuDNN': post_sanitycheck_cuDNN, } From 889ee40a9e4422b20249faa77638127db8d8f1e4 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Sun, 5 May 2024 20:12:45 +0200 Subject: [PATCH 3/7] fix function name typo --- eb_hooks.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/eb_hooks.py b/eb_hooks.py index 44877103ea..223b14455d 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -703,7 +703,7 @@ def post_sanitycheck_cuDNN(self, *args, **kwargs): search_string = "2. Distribution. The following portions of the SDK are distributable under the Agreement:" with open(license_path) as infile: for line in infile: - if line.strip().startswidth(search_string): + if line.strip().startswith(search_string): # remove search string, split into words, remove trailing # dots '.' and only retain words starting with a dot '.' distributable = line[len(search_string):] From 31c5e800f7b3955d5fb226ca20194f889a8a0e54 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Mon, 6 May 2024 17:50:04 +0200 Subject: [PATCH 4/7] add installation of cuDNN under host_injections --- EESSI-install-software.sh | 5 +- .../nvidia/install_cuDNN_host_injections.sh | 210 ++++++++++++++++++ 2 files changed, 213 insertions(+), 2 deletions(-) create mode 100755 scripts/gpu_support/nvidia/install_cuDNN_host_injections.sh diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh index 6c680571e2..a1591958d1 100755 --- a/EESSI-install-software.sh +++ b/EESSI-install-software.sh @@ -199,14 +199,15 @@ pr_diff=$(ls [0-9]*.diff | head -1) # for now, this just reinstalls all scripts. Note the most elegant, but works ${TOPDIR}/install_scripts.sh --prefix ${EESSI_PREFIX} -# Install full CUDA SDK in host_injections +# Install full CUDA SDK and cu* libraries in host_injections # Hardcode this for now, see if it works # TODO: We should make a nice yaml and loop over all CUDA versions in that yaml to figure out what to install # Allow skipping CUDA SDK install in e.g. CI environments if [ -z "${skip_cuda_install}" ] || [ ! "${skip_cuda_install}" ]; then ${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cuda_host_injections.sh -c 12.1.1 --accept-cuda-eula + ${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cudnn_host_injections.sh -c 12.1.1 -d 8.9.2.26 else - echo "Skipping installation of CUDA SDK in host_injections, since the --skip-cuda-install flag was passed" + echo "Skipping installation of CUDA SDK and cu* libraries in host_injections, since the --skip-cuda-install flag was passed" fi # Install drivers in host_injections diff --git a/scripts/gpu_support/nvidia/install_cuDNN_host_injections.sh b/scripts/gpu_support/nvidia/install_cuDNN_host_injections.sh new file mode 100755 index 0000000000..7585e51458 --- /dev/null +++ b/scripts/gpu_support/nvidia/install_cuDNN_host_injections.sh @@ -0,0 +1,210 @@ +#!/usr/bin/env bash + +# This script can be used to install cuDNN under the `.../host_injections` directory. +# This provides the parts of the cuDNN installation that cannot be redistributed as +# part of NESSI due to license limitations. While GPU-based software from NESSI will +# _run_ without these, installation of additional software that requires the cuDNN +# installation(s) under `host_injections` to be present. +# +# The `host_injections` directory is a variant symlink that by default points to +# `/opt/eessi`, unless otherwise defined in the local CVMFS configuration (see +# https://cvmfs.readthedocs.io/en/stable/cpt-repo.html#variant-symlinks). For the +# installation to be successful, this directory needs to be writeable by the user +# executing this script. + +# Initialise our bash functions +TOPDIR=$(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 " -c, --cuda-version CUDA_VERSION Specify a version of CUDA to be used" + echo " when installing cuDNN (must" + echo " have a corresponding easyconfig in the" + echo " EasyBuild release)" + echo " -d, --cudnn-version CUDNN_VERSION Specify a version of cuDNN to install (must" + echo " have a corresponding easyconfig in the" + echo " EasyBuild release)" + echo " -t, --temp-dir /path/to/tmpdir Specify a location to use for temporary" + echo " storage during the cuDNN install" + echo " (must have >10GB available)" +} + +# Initialize variables +cuda_version="" +cudnn_version="" + +# Parse command-line options +while [[ $# -gt 0 ]]; do + case "$1" in + --help) + show_help + exit 0 + ;; + -c|--cuda-version) + if [ -n "$2" ]; then + cuda_version="$2" + shift 2 + else + echo "Error: Argument required for $1" + show_help + exit 1 + fi + ;; + -d|--cudnn-version) + if [ -n "$2" ]; then + cudnn_version="$2" + shift 2 + else + echo "Error: Argument required for $1" + show_help + exit 1 + fi + ;; + -t|--temp-dir) + if [ -n "$2" ]; then + CUDA_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 + +# Make sure NESSI is initialised +check_eessi_initialised + +# Make sure the CUDA version supplied is a semantic version +is_semantic_version() { + local version=$1 + local regex='^[0-9]+\.[0-9]+\.[0-9]+$' + + if [[ $version =~ $regex ]]; then + return 0 # Return success (0) if it's a semantic version + else + return 1 # Return failure (1) if it's not a semantic version + fi +} +if ! is_semantic_version "$cuda_version"; then + show_help + error="\nYou must provide a semantic version for CUDA (e.g., 12.1.1) via the appropriate\n" + error="${error}command line option. This script is intended for use with NESSI so the 'correct'\n" + error="${error}version to provide is probably one of those available under\n" + error="${error}$EESSI_SOFTWARE_PATH/software/cuDNN\n" + fatal_error "${error}" +fi + +# As an installation location just use $EESSI_SOFTWARE_PATH but replacing `versions` with `host_injections` +cudnn_install_parent=${EESSI_SOFTWARE_PATH/versions/host_injections} + +# Only install cuDNN if specified version is not found. +# (existence of easybuild subdir implies a successful install) +if [ -d "${cudnn_install_parent}"/software/cuDNN/*-CUDA-"${cuda_version}"/easybuild ]; then + echo_green "cuDNN software found! No need to install cuDNN again." +else + # We need to be able write to the installation space so let's make sure we can + if ! create_directory_structure "${cudnn_install_parent}"/software/cuDNN ; then + fatal_error "No write permissions to directory ${cudnn_install_parent}/software/cuDNN" + fi + + # we need a directory we can use for temporary storage + if [[ -z "${CUDA_TEMP_DIR}" ]]; then + tmpdir=$(mktemp -d) + else + tmpdir="${CUDA_TEMP_DIR}"/temp + if ! mkdir "$tmpdir" ; then + fatal_error "Could not create directory ${tmpdir}" + fi + fi + + required_space_in_tmpdir=50000 + # Let's see if we have sources and build locations defined if not, we use the temporary space + if [[ -z "${EASYBUILD_BUILDPATH}" ]]; then + export EASYBUILD_BUILDPATH=${tmpdir}/build + required_space_in_tmpdir=$((required_space_in_tmpdir + 5000000)) + fi + if [[ -z "${EASYBUILD_SOURCEPATH}" ]]; then + export EASYBUILD_SOURCEPATH=${tmpdir}/sources + required_space_in_tmpdir=$((required_space_in_tmpdir + 5000000)) + fi + + # The install is pretty fat, you need lots of space for download/unpack/install (~3*5GB), + # need to do a space check before we proceed + avail_space=$(df --output=avail "${cudnn_install_parent}"/ | tail -n 1 | awk '{print $1}') + if (( avail_space < 5000000 )); then + fatal_error "Need at least 5GB disk space to install cuDNN under ${cudnn_install_parent}, exiting now..." + fi + avail_space=$(df --output=avail "${tmpdir}"/ | tail -n 1 | awk '{print $1}') + if (( avail_space < required_space_in_tmpdir )); then + error="Need at least ${required_space_in_tmpdir} disk space under ${tmpdir}.\n" + error="${error}Set the environment variable CUDA_TEMP_DIR to a location with adequate space to pass this check." + error="${error}You can alternatively set EASYBUILD_BUILDPATH and/or EASYBUILD_SOURCEPATH " + error="${error}to reduce this requirement. Exiting now..." + fatal_error "${error}" + fi + + if ! command -v "eb" &>/dev/null; then + echo_yellow "Attempting to load an EasyBuild module to do actual install" + module load EasyBuild + # There are some scenarios where this may fail + if [ $? -ne 0 ]; then + error="'eb' command not found in your environment and\n" + error="${error} module load EasyBuild\n" + error="${error}failed for some reason.\n" + error="${error}Please re-run this script with the 'eb' command available." + fatal_error "${error}" + fi + fi + + cudnn_easyconfig="cuDNN-${cudnn_version}-CUDA-${cuda_version}.eb" + + # Check the easyconfig file is available in the release + # (eb search always returns 0, so we need a grep to ensure a usable exit code) + eb --search ^${cudnn_easyconfig}|grep cuDNN > /dev/null 2>&1 + # Check the exit code + if [ $? -ne 0 ]; then + eb_version=$(eb --version) + available_cudnn_easyconfigs=$(eb --search ^cuDNN-*.eb|grep cuDNN) + + error="The easyconfig ${cudnn_easyconfig} was not found in EasyBuild version:\n" + error="${error} ${eb_version}\n" + error="${error}You either need to give a different version of CUDA to install _or_ \n" + error="${error}use a different version of EasyBuild for the installation.\n" + error="${error}\nThe versions of available with the current eb command are:\n" + error="${error}${available_cudnn_easyconfigs}" + fatal_error "${error}" + fi + + # We need the --rebuild option, as the cuDNN module may or may not be on the + # `MODULEPATH` yet. Even if it is, we still want to redo this installation + # since it will provide the symlinked targets for the parts of the cuDNN + # installation in the `.../versions/...` prefix + # We install the module in our `tmpdir` since we do not need the modulefile, + # we only care about providing the targets for the symlinks. + extra_args="--rebuild --installpath-modules=${tmpdir}" + + # We don't want hooks used in this install, we need a vanilla cuDNN installation + touch "$tmpdir"/none.py + # shellcheck disable=SC2086 # Intended splitting of extra_args + eb --prefix="$tmpdir" ${extra_args} --hooks="$tmpdir"/none.py --installpath="${cudnn_install_parent}"/ "${cudnn_easyconfig}" + ret=$? + if [ $ret -ne 0 ]; then + eb_last_log=$(unset EB_VERBOSE; eb --last-log) + cp -a ${eb_last_log} . + fatal_error "cuDNN installation failed, please check EasyBuild logs $(basename ${eb_last_log})..." + else + echo_green "cuDNN installation at ${cudnn_install_parent}/software/cuDNN/${cudnn_version}-CUDA-${cuda_version} succeeded!" + fi + # clean up tmpdir + rm -rf "${tmpdir}" +fi From f57b76dc53e0517f8e2ae405daedad3ee66590e4 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Wed, 15 May 2024 19:57:18 +0200 Subject: [PATCH 5/7] drop dependency on cuDNN to builddependency --- eb_hooks.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/eb_hooks.py b/eb_hooks.py index a778f8b7c1..cf1c911b23 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -768,6 +768,25 @@ def inject_gpu_property(ec): ec[key] = '\n'.join([ec_dict[key], value]) else: ec[key] = value + # Check if cuDNN is in the dependencies, if so add the 'gpu' Lmod property + if ('cuDNN' in [dep[0] for dep in iter(ec_dict['dependencies'])]): + ec.log.info("Injecting gpu as Lmod arch property and envvar with cuDNN version") + key = 'modluafooter' + value = 'add_property("arch","gpu")' + cudnn_version = 0 + for dep in iter(ec_dict['dependencies']): + # Make cuDNN a build dependency only (rpathing saves us from link errors) + if 'cuDNN' in dep[0]: + cudnn_version = dep[1] + ec_dict['dependencies'].remove(dep) + if dep not in ec_dict['builddependencies']: + ec_dict['builddependencies'].append(dep) + value = '\n'.join([value, 'setenv("EESSICUDNNVERSION","%s")' % cudnn_version]) + if key in ec_dict: + if not value in ec_dict[key]: + ec[key] = '\n'.join([ec_dict[key], value]) + else: + ec[key] = value return ec From e5f9fa719aad28a26d4e6da8925b910f9a3e360c Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Wed, 15 May 2024 20:03:17 +0200 Subject: [PATCH 6/7] Lmod hook for cuDNN --- create_lmodsitepackage.py | 29 +++++++++++++++++++++++++++-- 1 file changed, 27 insertions(+), 2 deletions(-) diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py index f9053cdf9e..5b32578d24 100755 --- a/create_lmodsitepackage.py +++ b/create_lmodsitepackage.py @@ -171,13 +171,38 @@ end end +local function eessi_cudnn_enabled_load_hook(t) + local frameStk = require("FrameStk"):singleton() + local mt = frameStk:mt() + local simpleName = string.match(t.modFullName, "(.-)/") + -- If we try to load cuDNN itself, check if the full cuDNN package was installed on the host in host_injections. + -- This is required for end users to build additional cuDNN dependent software. If the full SDK isn't present, refuse + -- to load the cuDNN module and print an informative message on how to set up GPU support for NESSI + local refer_to_docs = "For more information on how to do this, see https://www.eessi.io/docs/gpu/.\\n" + if simpleName == 'cuDNN' then + -- get the full host_injections path + local hostInjections = string.gsub(os.getenv('EESSI_SOFTWARE_PATH') or "", 'versions', 'host_injections') + -- build final path where the cuDNN software should be installed + local cudnnEasyBuildDir = hostInjections .. "/software/" .. t.modFullName .. "/easybuild" + local cudnnDirExists = isDir(cudnnEasyBuildDir) + if not cudnnDirExists then + local advice = "but while the module file exists, the actual software is not entirely shipped with NESSI " + advice = advice .. "due to licencing. You will need to install a full copy of the cuDNN package where NESSI " + advice = advice .. "can find it.\\n" + advice = advice .. refer_to_docs + LmodError("\\nYou requested to load ", simpleName, " ", advice) + end + end +end + -- Combine both functions into a single one, as we can only register one function as load hook in lmod -- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed function eessi_load_hook(t) - -- Only apply CUDA hooks if the loaded module is in the NESSI prefix - -- This avoids getting an Lmod Error when trying to load a CUDA module from a local software stack + -- Only apply CUDA and cuDNN hooks if the loaded module is in the NESSI prefix + -- This avoids getting an Lmod Error when trying to load a CUDA or cuDNN module from a local software stack if from_eessi_prefix(t) then eessi_cuda_enabled_load_hook(t) + eessi_cudnn_enabled_load_hook(t) end end From 0205e890f5810ab46836372798880b99a3e57edd Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Thu, 16 May 2024 19:50:48 +0200 Subject: [PATCH 7/7] copy cuDNN install file and fix name --- EESSI-install-software.sh | 2 +- install_scripts.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh index 4e06abf3d0..d840910516 100755 --- a/EESSI-install-software.sh +++ b/EESSI-install-software.sh @@ -205,7 +205,7 @@ ${TOPDIR}/install_scripts.sh --prefix ${EESSI_PREFIX} # Allow skipping CUDA SDK install in e.g. CI environments if [ -z "${skip_cuda_install}" ] || [ ! "${skip_cuda_install}" ]; then ${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cuda_host_injections.sh -c 12.1.1 --accept-cuda-eula - ${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cudnn_host_injections.sh -c 12.1.1 -d 8.9.2.26 + ${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cuDNN_host_injections.sh -c 12.1.1 -d 8.9.2.26 else echo "Skipping installation of CUDA SDK and cu* libraries in host_injections, since the --skip-cuda-install flag was passed" fi diff --git a/install_scripts.sh b/install_scripts.sh index 17f0b81008..8bbcb6a7bf 100755 --- a/install_scripts.sh +++ b/install_scripts.sh @@ -110,7 +110,7 @@ copy_files_by_list ${TOPDIR}/scripts ${INSTALL_PREFIX}/scripts "${script_files[@ # Copy files for the scripts/gpu_support/nvidia directory nvidia_files=( - install_cuda_host_injections.sh link_nvidia_host_libraries.sh + install_cuda_host_injections.sh install_cuDNN_host_injections.sh link_nvidia_host_libraries.sh ) copy_files_by_list ${TOPDIR}/scripts/gpu_support/nvidia ${INSTALL_PREFIX}/scripts/gpu_support/nvidia "${nvidia_files[@]}"