Add CUDA support #172

huebner-m · 2022-05-12T15:58:40Z

This WIP PR follows up on the work done in the Hackathons.
The following features have been implemented:

Check that NVIDIA drivers are installed on host (via nvidia-smi)
Get latest CUDA compat libs from NVIDIA website (automatically picking the correct OS version etc.)
Check that host_injections is a writable path
Install CUDA compat libs in host_injections (using the appropriate rpm or deb files and tools)
Check if CUDA is already installed as a module
Check if disk space in host_injections is sufficient to install CUDA
Install CUDA using EasyBuild
Add test based on CUDA samples to check if GPU support works
Add EasyBuild hook to tag software that depends on CUDA with the property gpu (based on https://github.com/easybuilders/JSC/blob/2022/Custom_Hooks/eb_hooks.py#L335)
Add Lmod plugin that hides software with the property gpu if CUDA is not installed

Open tasks:

Only download/install CUDA compat libs from NVIDIA website if necessary (wip, see: 2cc5ce9)
Update Lmod version to make plugin work, also see: Use properties in isVisible hook TACC/Lmod#552
Ship CUDA samples with EESSI
Ship p7zip with software layer
Tested with Debian10 container, test other OSs

Related issues:

CUDA itself is not shipped by EESSI and has to be installed on the host. The scripts perform various checks and download and install the CUDA compat libs. Modules with CUDA as a dependecy are hidden in Lmod, unless the CUDA compat libs are installed which is only done when CUDA itself is installed on the host. This aspect still has to be tested with an updated Lmod version in the EESSI compat layer.

…tead

ocaisa

Encouraging!

eb_hooks.py

ocaisa · 2022-05-12T16:02:20Z

eb_hooks.py

+        or ec_dict["toolchain"]["name"] in CUDA_ENABLED_TOOLCHAINS
+    ):
+        key = "modluafooter"
+        value = 'add_property("arch","gpu")'


I think gpu is a recognised property in Lmod so a good choice for now. Once we add AMD support it will get more complicated.

We can add a new property by extending the property table propT. To do so, we could add a file init/lmodrc.lua with a new property. This file can be loaded using the env var $LMOD_RC. Unfortunately, we do not seem to be able to add entries to arch but rather have to add a new property (or find a way to extend arch that I'm missing).

ocaisa · 2022-05-12T16:03:48Z

gpu_support/add_gpu_support.sh

+# TODO: needs more thorough testing
+os_family=$(uname | tr '[:upper:]' '[:lower:]')
+
+# Get OS version


@boegel Does EB do this already, can we hook into that?

gpu_support/add_gpu_support.sh

gpu_support/test_cuda

ocaisa · 2022-05-12T16:17:37Z

gpu_support/test_cuda

+module use /cvmfs/pilot.eessi-hpc.org/host_injections/nvidia/modules/all/
+module load CUDA
+tmp_dir=$(mktemp -d)
+cp -r $EBROOTCUDA/samples $tmp_dir


CUDA no longer ships samples, there is a plan to ship the (compiled) CUDA samples with EESSI

gpu_support/test_cuda

init/SitePackage.lua

ocaisa · 2022-05-13T08:09:35Z

There are indications that we may be allowed to ship the CUDA runtime with EESSI, that would mean we wouldn't (necessarily) need to install CUDA unless people want to actually build their own software on top of EESSI.

I would go with this PR as is right now, but in a future pilot we should make that installation optional (making another code branch that only creates the software installation directory so that the Lmod plugin will still work). In that scenario though, we will need some major tweaking to the CUDA module shipped with EESSI, it would need conditionals based on what is available on the host. We'd also probably want to shadow nvcc and friends with a nice echo script that explains what is needed to get a fully functional installation.

gpu_support/add_gpu_support.sh

init/eessi_environment_variables

Only install cuda compat libs when either they are not installed yet or they are outdated

EESSI-pilot-install-software.sh

init/eessi_environment_variables

ocaisa

I think it's time to remove the WIP label and get someone else feedback on this!

gpu_support/add_nvidia_gpu_support.sh

gpu_support/add_amd_gpu_support.sh

ocaisa

Allow using an environment variable to skip GPU checks

gpu_support/add_nvidia_gpu_support.sh

eb_hooks.py

gpu_support/test_cuda

ocaisa · 2022-09-12T13:52:51Z

gpu_support/add_nvidia_gpu_support.sh

+  module load EasyBuild
+  # we need the --rebuild option, since the module file is shipped with EESSI
+  tmpdir=$(mktemp -d)
+  eb --rebuild --installpath-modules=${tmpdir} --installpath=${cuda_install_dir}/ CUDA-${install_cuda_version}.eb


Right now this makes testing difficult as the actual CUDA module in EESSI is not available. You might be better off here checking if the CUDA module exists and if so prefixing this command with EASYBUILD_INSTALLPATH_MODULES=${tmpdir}

ocaisa · 2022-09-12T13:53:38Z

gpu_support/add_nvidia_gpu_support.sh

+# The rpm and deb files contain the same libraries, so we just stick to the rpm version.
+# If p7zip is missing from the software layer (for whatever reason), we need to install it.
+# This has to happen in host_injections, so we check first if it is already installed there.
+module use ${cuda_install_dir}/modules/all/


Maybe do this conditionally (i.e, only if this directory exists)

ocaisa · 2022-09-12T14:10:23Z

gpu_support/add_nvidia_gpu_support.sh

+  # we need the --rebuild option, since the module file is shipped with EESSI
+  tmpdir=$(mktemp -d)
+  eb --rebuild --installpath-modules=${tmpdir} --installpath=${cuda_install_dir}/ CUDA-${install_cuda_version}.eb


Suggested change

# we need the --rebuild option, since the module file is shipped with EESSI

tmpdir=$(mktemp -d)

eb --rebuild --installpath-modules=${tmpdir} --installpath=${cuda_install_dir}/ CUDA-${install_cuda_version}.eb

# we need the --rebuild option and a random dir for the module if the module file is shipped with EESSI

if [ -f ${EESSI_SOFTWARE_PATH}/modules/all/CUDA/${install_cuda_version}.lua ]; then

tmpdir=$(mktemp -d)

extra_args="--rebuild --installpath-modules=${tmpdir}"

fi

eb ${extra_args} --installpath=${cuda_install_dir}/ CUDA-${install_cuda_version}.eb

gpu_support/test_cuda.sh

ocaisa · 2022-09-13T09:10:14Z

gpu_support/test_cuda.sh

+  echo "Cannot test CUDA, modules path does not exist, exiting now..."
+  exit 1
+fi
+module load CUDA


We should probably load the specific version of CUDA here.

gpu_support/add_nvidia_gpu_support.sh

ocaisa · 2022-09-13T09:56:21Z

For me to get this working out of the box right now I needed

diff --git a/gpu_support/add_nvidia_gpu_support.sh b/gpu_support/add_nvidia_gpu_support.sh
index 025a1be..9cf4b70 100755
--- a/gpu_support/add_nvidia_gpu_support.sh
+++ b/gpu_support/add_nvidia_gpu_support.sh
@@ -76,9 +76,12 @@ else
   fi
   # install cuda in host_injections
   module load EasyBuild
-  # we need the --rebuild option, since the module file is shipped with EESSI
-  tmpdir=$(mktemp -d)
-  eb --rebuild --installpath-modules=${tmpdir} --installpath=${cuda_install_dir}/ CUDA-${install_cuda_version}.eb
+  # we need the --rebuild option and a random dir for the module if the module file is shipped with EESSI
+  if [ -f ${EESSI_SOFTWARE_PATH}/modules/all/CUDA/${install_cuda_version}.lua ]; then
+    tmpdir=$(mktemp -d)
+    extra_args="--rebuild --installpath-modules=${tmpdir}"
+  fi
+  eb ${extra_args} --installpath=${cuda_install_dir}/ CUDA-${install_cuda_version}.eb
   ret=$?
   if [ $ret -ne 0 ]; then
     echo "CUDA installation failed, please check EasyBuild logs..."
@@ -97,6 +100,12 @@ if [[ $? -eq 0 ]]; then
   echo "p7zip module found! No need to install p7zip again, proceeding with installation of compat libraries"
 else
   # install p7zip in host_injections
+  export EASYBUILD_IGNORE_OSDEPS=1
+  export EASYBUILD_SYSROOT=${EPREFIX}
+  export EASYBUILD_RPATH=1
+  export EASYBUILD_FILTER_ENV_VARS=LD_LIBRARY_PATH
+  export EASYBUILD_FILTER_DEPS=Autoconf,Automake,Autotools,binutils,bzip2,cURL,DBus,flex,gettext,gperf,help2man,intltool,libreadline,libtool,Lua,M4,makeinfo,ncurses,util-linux,XZ,zlib
+  export EASYBUILD_MODULE_EXTENSIONS=1
   module load EasyBuild
   eb --robot --installpath=${cuda_install_dir}/ p7zip-${install_p7zip_version}.eb
   ret=$?

ocaisa · 2022-09-15T15:23:25Z

The discussion today at the EESSI Community Meeting, led to the following design suggestion/comments:

According to the CUDA EULA we can distribute the CUDA runtime. It looks like this maps more or less to the lib directory under the CUDA installation, even if not the EULA essentially gives a whitelist.
We can create post install hook for the CUDA installation that replaces anything not in the whitelist with a symlink to the equivalent location under host_injections. When the host_injections path has a CUDA install, CUDA is fully capable, otherwise it is just the runtime (i.e., we only ship the runtime).
We use an EasyBuild hook so that CUDA will be downgraded to a build dependency (or simply excluded from the final module file). Our use of rpath means software built with CUDA will still work (since they will link to the runtime, which we will ship)
Lmod will need to be smart on two fronts. It will need a hook that looks at the Lmod gpu property and check for the compat library before allowing the module to load (with a helpful error if it needs to fail). For the CUDA module itself, it will also need to refuse to load it unless the symlinks inside have been resolved.
For the verification that CUDA is actually working, we will need to ship a compiled deviceQuery (or whatever), since there is no guarantee the nvcc compiler will be available.

The benefit of this approach is that we only install the CUDA SDK if the user actually wants it. It will greatly speed up the GPU support script since there will be need for any eb installations at all (by default).

Whitelisted CUDA libraries can now be shipped with EESSI. The other libraries and files are replaced with symlinks to host_injections. A compiled CUDA sample can now also be shipped with EESSI. This is relevant if users only need the runtime capabilities and not the whole CUDA suite (which would include the compilers). It is now possible to solely install the compat libs as a user and get access to the runtime environment this way. It is still possible to also install the whole CUDA suite. CUDA enabled modules with the gpu property now only load if the compat libs are installed in host_injections.

The CUDA version needed for modules are now written as envvars that will be exported into the module files. The CUDA version for which we have the current compat libs installed is saved in a txt file in ../host_injections/nvidia/latest/version.txt The lmod hook called when loading modules with the gpu property now compares these two versions and exits out if the installed version needs to be updated.

The fix for removing the temporary test dir is needed when cloning the samples from github, i.e. for CUDA > 11.6.0. Otherwise, the script call from the eb hook will get stuck.

ocaisa · 2022-12-16T10:24:55Z

gpu_support/add_nvidia_gpu_support.sh

+###############################################################################################
+# Install CUDA
+cuda_install_dir="${EESSI_SOFTWARE_PATH/versions/host_injections}"
+mkdir -p ${cuda_install_dir}
+if [ "${install_cuda}" != false ]; then
+  bash $(dirname "$BASH_SOURCE")/cuda_utils/install_cuda.sh ${install_cuda_version} ${cuda_install_dir}
+fi


Let's break this into separate script (and PR) since it will be needed by #212

You also need to check the exit code on the creation of cuda_install_dir since this may fail

ocaisa · 2022-12-16T10:27:34Z

gpu_support/add_nvidia_gpu_support.sh

+  bash $(dirname "$BASH_SOURCE")/cuda_utils/install_cuda.sh ${install_cuda_version} ${cuda_install_dir}
+fi
+###############################################################################################
+# Prepare installation of CUDA compat libraries, i.e. install p7zip if it is missing


You can drop stuff related to p7zip because of #212 (and that also means we can drop prepare_cuda_compatlibs.sh entirely)

ocaisa · 2022-12-16T10:30:47Z

gpu_support/add_nvidia_gpu_support.sh

+# Otherwise, give up
+bash $(dirname "$BASH_SOURCE")/cuda_utils/install_cuda_compatlibs_loop.sh ${cuda_install_dir} ${install_cuda_version}
+
+cuda_version_file="/cvmfs/pilot.eessi-hpc.org/host_injections/nvidia/latest/version.txt"


Suggested change

cuda_version_file="/cvmfs/pilot.eessi-hpc.org/host_injections/nvidia/latest/version.txt"

cuda_version_file="/cvmfs/pilot.eessi-hpc.org/host_injections/nvidia/latest/eessi_compat_version.txt"

I also think that this creation should be part of install_cuda_compatlibs_loop.sh and we should put the supported CUDA version in there according to the compat libs, not the version we need (will help us to avoid unnecessary updates in the future).

ocaisa · 2022-12-16T10:31:39Z

gpu_support/cuda_utils/install_cuda.sh

+install_cuda_version=$1
+cuda_install_dir=$2
+
+# TODO: Can we do a trimmed install?


This is done now via your hook

ocaisa · 2022-12-16T10:34:10Z

gpu_support/cuda_utils/install_cuda.sh

+#!/bin/bash
+
+install_cuda_version=$1
+cuda_install_dir=$2


General CUDA installation is done via #212 now so I don't think you need this argument. This script is only about installing the CUDA package under host_injections...but changing the name of the script to reflect that is probably a good idea.

ocaisa · 2022-12-16T10:36:27Z

gpu_support/cuda_utils/install_cuda.sh

+# This is only relevant for users, the shipped CUDA installation will
+# always be in versions instead of host_injections and have symlinks pointing
+# to host_injections for everything we're not allowed to ship
+if [ -f ${cuda_install_dir}/software/CUDA/${install_cuda_version}/EULA.txt ]; then


The if/else is still good, except we should be checking under the host_injections path. This will allow us to skip any check on available space etc.

You should construct cuda_install_dir rather than take it as an argument

Also, we should allow for a forced installation to override this check

It prefer the we ship the EULA text so I think we should check for an expected broken symlink here:

if [[ -L "${cuda_install_dir}/software/CUDA/bin/nvcc" && -e "${cuda_install_dir}/software/CUDA/bin/nvcc" ]]; then

ocaisa · 2022-12-16T10:42:26Z

gpu_support/cuda_utils/install_cuda.sh

+  avail_space=$(df --output=avail ${cuda_install_dir}/ | tail -n 1 | awk '{print $1}')
+  if (( ${avail_space} < 16000000 )); then
+    echo "Need more disk space to install CUDA, exiting now..."
+    exit 1


This is a tricky one, we need space for sources, space for the build, space for the install but people can choose where to put all these. I guess we leave it as is for now, but allow people to set an envvar to override this check (and tell them that envvar in the error message)

ocaisa · 2022-12-16T10:43:56Z

gpu_support/cuda_utils/install_cuda.sh

+  # install cuda in host_injections
+  module load EasyBuild
+  # we need the --rebuild option and a random dir for the module if the module file is shipped with EESSI
+  if [ -f ${EESSI_SOFTWARE_PATH}/modules/all/CUDA/${install_cuda_version}.lua ]; then


If this script is standalone, we'll need to guarantee EESSI_SOFTWARE_PATH is defined.

ocaisa · 2022-12-16T10:45:20Z

gpu_support/cuda_utils/install_cuda.sh

+    extra_args="--rebuild --installpath-modules=${tmpdir}"
+  fi
+  eb ${extra_args} --installpath=${cuda_install_dir}/ CUDA-${install_cuda_version}.eb
+  ret=$?


Let's import the bash functions defined in utils.sh and use them throughout (where appropriate)

ocaisa · 2022-12-16T10:47:20Z

@huebner-m Let's branch out a separate PR for the script to install CUDA under host_injections

ocaisa · 2022-12-16T10:51:48Z

gpu_support/cuda_utils/install_cuda_compatlibs.sh

+if [ -w /cvmfs/pilot.eessi-hpc.org/host_injections ]; then
+  mkdir -p ${host_injections_dir}
+else
+  echo "Cannot write to eessi host_injections space, exiting now..." >&2


Let's start using utils.sh here

ocaisa · 2022-12-16T10:56:26Z

gpu_support/cuda_utils/install_cuda_compatlibs.sh

+fi
+cd ${host_injections_dir}
+
+# Check if our target CUDA is satisfied by what is installed already


Do we know what our target CUDA version is at this point. And if the nvidia-smi result is good enough, what then? I guess we should check that this version comes from an installation of the compat-libs otherwise we still need to install compat libs.

If the supported CUDA version is new enough and comes from an EESSI installation of the CUDA compat libs, we can already exit gracefully.

We should leverage the contents of /cvmfs/pilot.eessi-hpc.org/host_injections/nvidia/latest/eessi_compat_version.txt here

ocaisa · 2022-12-16T10:59:44Z

gpu_support/cuda_utils/install_cuda_compatlibs.sh

@@ -0,0 +1,92 @@
+#!/bin/bash


Shouldn't this be a compat layer bash?

It's fine as is, as long as the first thing we do is source the EESSI environment

gpu_support/cuda_utils/install_cuda_compatlibs.sh

ocaisa · 2022-12-16T11:00:46Z

gpu_support/cuda_utils/install_cuda_compatlibs.sh

+  # p7zip is installed under host_injections for now, make that known to the environment
+  if [ -d ${cuda_install_dir}/modules/all ]; then
+    module use ${cuda_install_dir}/modules/all/
+  fi


You can drop this

ocaisa · 2022-12-16T11:32:47Z

gpu_support/cuda_utils/install_cuda_compatlibs.sh

+fi
+
+# Create the space to host the libraries
+mkdir -p ${host_injection_linker_dir}


We should always check exit codes on our commands, seems like a function that does that for us is needed

ocaisa · 2022-12-16T11:33:22Z

gpu_support/cuda_utils/install_cuda_compatlibs_loop.sh

+      if [ -d ${cuda_install_dir}/modules/all ]; then
+        module use ${cuda_install_dir}/modules/all/
+      else
+        echo "Cannot load CUDA, modules path does not exist, exiting now..."
+        exit 1
+      fi


Drop this, no need for the module use, CUDA-Samples is shipped with EESSI. Our Lmod hook should cause the load of (a specific version of) CUDA-Samples (not CUDA since we only deal with compat libs here) to fail unless the compat libs are in place (i.e. Lmod should ensure the existence of /cvmfs/pilot.eessi-hpc.org/host_injections/nvidia/latest/eessi_compat_version.txt)

ocaisa · 2022-12-16T11:34:52Z

gpu_support/cuda_utils/install_cuda_compatlibs_loop.sh

+        exit 1
+      else
+        echo "Successfully loaded CUDA, you are good to go! :)"
+        echo "  - To build CUDA enabled modules use ${EESSI_SOFTWARE_PATH/versions/host_injections} as your EasyBuild prefix"


This is not required, then can build where they like (but it is a very sensible location!)

ocaisa · 2022-12-16T11:41:39Z

gpu_support/cuda_utils/prepare_cuda_compatlibs.sh

@@ -0,0 +1,31 @@
+#!/bin/bash


This script can be dropped

ocaisa · 2022-12-16T11:42:48Z

gpu_support/cuda_utils/test_cuda.sh

@@ -0,0 +1,82 @@
+#!/bin/bash


This script can be greatly simplified, just load CUDA-Samples and see does deviceQuery run

We can expand the testing from there.

ocaisa · 2022-12-16T11:52:55Z

@huebner-m Break the two compat libs scripts off into another PR, the testing script into another, the lmod hook into another and the docs into another (we can finalise those once the others are ready)

ocaisa · 2023-12-21T14:42:59Z

GPU support implemented with #434

huebner-m added 3 commits April 14, 2022 14:31

Fix dump location of check whether CUDA module is installed

caa43bf

Remove setup script, use shipped init script to set env vars etc. ins…

d7212a0

…tead

ocaisa requested changes May 12, 2022

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huebner-m added 4 commits May 13, 2022 09:21

Check return values and path existence in CUDA tests

48f4455

Check return value of eb install, improve source of other scripts

c50daa2

Use mktemp to create temporary directory to install compat libs

d4e85cc

Fix echo

590e042

ocaisa reviewed May 13, 2022

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huebner-m added 3 commits May 16, 2022 13:18

Replace explicit dir names with variables, check symlink destination

7b9bb49

Install CUDA in modified version of EESSI_SOFTWARE_PATH

01844c6

If CUDA install dir exists, add it to EESSI_MODULE_PATH

0e8861f

ocaisa reviewed May 16, 2022

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huebner-m added 2 commits May 16, 2022 17:02

Use env var to check for GPU support and add this to module path

7d6af69

Move (conditional) installation of cuda compat libs to external script

2cc5ce9

Only install cuda compat libs when either they are not installed yet or they are outdated

ocaisa reviewed May 18, 2022

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huebner-m added 2 commits May 18, 2022 15:17

Consistently use EESSI_SITE_MODULEPATH to set up GPU support for Lmod

d53e80e

Rename script to add (NVIDIA) GPU support, add dummy script for AMD GPUs

850c20e

ocaisa requested changes May 19, 2022

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Add shebang

9b2e72f

huebner-m changed the title ~~Add CUDA support [WIP]~~ Add CUDA support May 19, 2022

Add option to disable checks, enables installation on nodes w/o GPUs

5f82658

ocaisa requested changes May 19, 2022

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Allow using an environment variable to skip GPU checks

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Update list of CUDA enabled toolchains

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huebner-m added 3 commits September 13, 2022 09:59

Prepend lmod module path only if the dir actually exists

e38391b

Make printout of CUDA installation more accurate

b2a4865

Only install CUDA module in tmpdir if it's already shipped in EESSI

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huebner-m added 4 commits September 13, 2022 19:28

Load correct module env as long as p7zip is not part of software layer

8c8a227

Load CUDA version specified to for installation when testing

f90dd66

Load GCCcore module when building test executable for CUDA

a24e09c

Add EasyBuild configuration for p7zip installation

3d0ebad

huebner-m added 5 commits September 27, 2022 13:33

If EULA file exists, CUDA is inst. in host_injections + some fixes

70e5dec

Pass CUDA version from eb hook to compat lib script + fix test dir rm

d65fe30

The fix for removing the temporary test dir is needed when cloning the samples from github, i.e. for CUDA > 11.6.0. Otherwise, the script call from the eb hook will get stuck.

Update documentation and merge both Lmod load hooks

2ac2671

ocaisa mentioned this pull request Dec 16, 2022

Add CUDA support to software_layer #212

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ocaisa closed this Dec 21, 2023

	cuda_version_file="/cvmfs/pilot.eessi-hpc.org/host_injections/nvidia/latest/version.txt"
	cuda_version_file="/cvmfs/pilot.eessi-hpc.org/host_injections/nvidia/latest/eessi_compat_version.txt"

Add CUDA support #172

Add CUDA support #172

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ocaisa commented May 13, 2022 •

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ocaisa commented Sep 15, 2022 •

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ocaisa Dec 18, 2022 •

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ocaisa Dec 16, 2022 •

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