PyTorch/2.2.0-rocm-5.6.1-python-3.10-singularity-exampleVenv-20240315 (PyTorch-2.2.0-rocm-5.6.1-python-3.10-singularity-exampleVenv-20240315.eb)
Install with the EasyBuild-user module in partition/container:
module load LUMI partition/container EasyBuild-user
eb PyTorch-2.2.0-rocm-5.6.1-python-3.10-singularity-exampleVenv-20240315.eb
To access module help after installation use module spider PyTorch/2.2.0-rocm-5.6.1-python-3.10-singularity-exampleVenv-20240315.
EasyConfig:
# Developed by Kurt Lust and Mihkel Tiks for LUMI
#DOC Contains PyTorch 2.2.0 with torchaudio 2.2.0, torchdata 0.7.1+cpu, torchtext 0.17.0+cpu,
#DOC torchvision 0.17.0 GPU version, DeepSpeed 0.12.3, flash-attention 2.0.4 and
#DOC xformers 0.0.25+8dd471d.d20240209, on Python 3.10 and ROCm 5.6.1.
#DOC The container also fully assists the procedure to add extra packages in a Python virtual environment.
#DOC
#DOC As an example of how installation in the virtual environment can be automated through EasyBuild,
#DOC torchmetrics and pytorch-lightning are installed in the virtual environment.
#DOC
#DOC This version works with $WITH_CONDA, $WITH_VENV and $WITH_CONDA_VENV for initialisation of the
#DOC conda / Python venv / or both environments respectively.
#DOC
#DOC This environment is experimental and only meant as an example of what can be done, but may
#DOC not be fully functional for everybody. Most users should use the non-exampleVenv versions.
easyblock = 'MakeCp'
local_c_rocm_version = '5.6.1'
local_c_python_mm = '3.10'
local_c_PyTorch_version = '2.2.0'
local_dockerhash = '7392c9d4dcf7'
local_c_DeepSpeed_version = '0.12.3'
local_c_flashattention_version = '2.0.4'
local_c_xformers_version = '0.0.25+8dd471d.d20240209'
local_conda_env = 'pytorch'
name = 'PyTorch'
version = local_c_PyTorch_version
versionsuffix = f'-rocm-{local_c_rocm_version}-python-{local_c_python_mm}-singularity-exampleVenv-20240315'
local_sif = f'lumi-pytorch-rocm-{local_c_rocm_version}-python-{local_c_python_mm}-pytorch-v{local_c_PyTorch_version}-dockerhash-{local_dockerhash}.sif'
#local_docker = f'lumi-pytorch-rocm-{local_c_rocm_version}-python-{local_c_python_mm}-pytorch-v2.2.0.docker'
homepage = 'https://pytorch.org/'
whatis = [
'Description: PyTorch, a machine learning package',
'Keywords: PyTorch, DeepSpeed, flash-attention, xformers'
]
description = f"""
This module provides a container with PyTorch %(version)s (with torchaudio,
torchdata, torchtext and torchvision) on Python {local_c_python_mm}. It also contains
DeepSpeed {local_c_DeepSpeed_version}, flash-attention {local_c_flashattention_version} and xformers {local_c_xformers_version}.
The module defines a number of environment variables available outside the
container:
* SIF and SIFPYTORCH: The full path and name of the Singularity SIF file
to use with singularity exec etc.
* SINGULAIRTY_BINDPATH: Mounts the necessary directories from the system,
including /users, /project, /scratch and /flash so that you should be
able to use your regular directories in the container.
* RUNSCRIPTS and RUNSCRIPTSPYTORCH: The directory with some sample
runscripts.
* CONTAINERROOT: Root directory of the container installation. Alternative
for EBROOTPYTHORCH.
There are also a number of environment variables available inside the container.
These are not strictly needed though as the module already ensures that all
necessary environment variables are set to activate the Conda environment in
the container and on top of that the virtual environment for additional packages.
* WITH_CONDA: Command to execute to activate the Conda environment used for
the Python installation.
* WITH_VENV: Command to execute to activate the pre-created Python virtual
environment.
* INIT_CONDA_VENV: Command that can be used to initialise the Conda environment
and then on top of it the Python virtual environment.
Outside of the container, the following commands are available:
* start-shell: To start a bash shell in the container. Arguments can be used
to, e.g., tell it to start a command. Without arguments, the conda and Python
virtual environments will be initialised, but this is not the case as soon as
arguments are used.
* make-squashfs: Make the user-software.squashfs file that would then be mounted
in the container after reloading the module. This will enhance performance if
the extra installation in user-software contains a lot of files.
* unmake-squashfs: Unpack the user-software.squashfs file into the user-software
subdirectory of $CONTAINERROOT to enable installing additional packages.
Inside the container, the following scripts are available in /runscripts
(and can be checked or edited outside the container in $CONTAINERROOT/runscripts):
* conda-python-simple: Start Python in the conda + Python venv environment.
* conda-python-distributed: Example script that can be used to start Python
in a distributed way compatible with the needs of PyTorch. You should pass
the Python commands to be executed with the options that the python executable
would take.
* get-master: A script used by conda-python-distributed.
Note that any change that you make to files in $CONTAINERROOT will be fully erased
whenever you reinstall the container with EasyBuild so backup all changes or
additions!
"""
docurls = [
'DeepSpeed web site: https://www.deepspeed.ai/'
]
toolchain = SYSTEM
sources = [
{
'filename': local_sif,
'extract_cmd': '/bin/cp -L %s .'
},
# {
# 'filename': local_docker,
# 'extract_cmd': '/bin/cp -L %s .'
# },
]
skipsteps = ['build']
files_to_copy = [
([local_sif], '.'),
# ([local_docker], 'share/docker-defs/')
]
#
# Code for scripts in the bin subdirectory
#
local_bin_start_shell = """
#!/bin/bash -e
# Run application
if [[ -f "/.singularity.d/Singularity" ]]
then
# In a singularity container, just in case a user would add this to the path.
exec bash "\$@"
else
# Not yet in the container
singularity exec \$SIFPYTORCH bash "\$@"
fi
"""
local_bin_make_squashfs = """
#!/bin/bash -e
if [[ -f "/.singularity.d/Singularity" ]]
then
# In a singularity container, just in case a user would add this to the path.
>&2 echo 'The make-squashfs command should not be run in the container.'
exit 1
fi
cd "%(installdir)s"
if [[ ! -d "user-software" ]]
then
>&2 echo -e 'The \$CONTAINERROOT/user-software subdirectory does not exist, so there is nothing to put into the SquashFS file.'
exit 2
fi
if [[ -f "user-software.squashfs" ]]
then
>&2 echo -e '\$CONTAINERROOT/user-software.squashfs already exists. Please remove the file by' \
'\\nhand if you are sure you wish to proceed and re-run the make-squashfs command.'
exit 3
fi
mksquashfs user-software user-software.squashfs -processors 1 -no-progress |& grep -v Unrecognised
echo -e '\\nCreated \$CONTAINERROOT/user-software.squashfs from \$CONTAINERROOT/user-software.' \
'\\nYou need to reload the PyTorch module to ensure that the software is now mounted' \
'\\nfrom \$CONTAINERROOT/user-software.squashfs. Note that /user-software in the' \
'\\ncontainer will then be a read-only directory.' \
'\\nAfter reloading the module, you can also remove the \$CONTAINERROOT/user-software' \
'\\nsubdirectory if you so wish.\\n'
"""
local_bin_unmake_squashfs = """
#!/bin/bash -e
if [[ -f "/.singularity.d/Singularity" ]]
then
# In a singularity container, just in case a user would add this to the path.
>&2 echo 'The unmake-squashfs command should not be run in the container.'
exit 1
fi
cd "%(installdir)s"
if [[ ! -f "user-software.squashfs" ]]
then
>&2 echo -e '\$CONTAINERROOT/user-software.squashfs does not exist so cannot uncompress it.'
exit 2
fi
if [[ -d "user-software" ]]
then
>&2 echo -e 'The \$CONTAINERROOT/user-software subdirectory already exists. Please remove this directory by hand' \
'(rm -r \$CONTAINERROOT/user-software) if you are sure you wish to proceed and re-run the unmake-squashfs command.'
exit 3
fi
unsquashfs -d ./user-software user-software.squashfs
echo -e '\\nCreated \$CONTAINERROOT/user-software subdirectory from \$CONTAINERROOT/user-software.squasfs.' \
'\\nYou need to reload the PyTorch module to ensure that the software is now mounted from the' \
'\\n\$CONTAINERROOT/user-software directory and can now write to /user-software in the container.' \
'\\nYou can then also remove the \$CONTAINERROOT/user-software.squashfs file if you so wish.\\n'
"""
#
# Code for scripts in the runscript subdirectory
#
local_runscript_init_conda_venv=f"""
#
# Source this file to initialize both the Conda environment and
# predefined virtual environment in the container.
#
# This script is still useful to initialise the environment when the
# module is not loaded, e.g., to execute commands in the `postinstallcmds` section.
#
source /opt/miniconda3/bin/activate {local_conda_env}
source /user-software/venv/{local_conda_env}/bin/activate
"""
local_runscript_python_simple="""
#!/bin/bash -e
# Start conda environment inside the container
# eval "\$WITH_CONDA_VENV"
# Run application
python "\$@"
"""
local_runscript_python_distributed="""
#!/bin/bash -e
# Make sure GPUs are up
if [ \$SLURM_LOCALID -eq 0 ] ; then
rocm-smi
fi
sleep 2
# MIOPEN needs some initialisation for the cache as the default location
# does not work on LUMI as Lustre does not provide the necessary features.
export MIOPEN_USER_DB_PATH="/tmp/\$(whoami)-miopen-cache-\$SLURM_NODEID"
export MIOPEN_CUSTOM_CACHE_DIR=\$MIOPEN_USER_DB_PATH
# Set MIOpen cache to a temporary folder.
if [ \$SLURM_LOCALID -eq 0 ] ; then
rm -rf \$MIOPEN_USER_DB_PATH
mkdir -p \$MIOPEN_USER_DB_PATH
fi
sleep 2
# Set interfaces to be used by RCCL.
# This is needed as otherwise RCCL tries to use a network interface it has
# noa ccess to on LUMI.
export NCCL_SOCKET_IFNAME=hsn0,hsn1,hsn2,hsn3
export NCCL_NET_GDR_LEVEL=3
# Set ROCR_VISIBLE_DEVICES so that each task uses the proper GPU
export ROCR_VISIBLE_DEVICES=\$SLURM_LOCALID
# Report affinity to check
echo "Rank \$SLURM_PROCID --> \$(taskset -p \$\$); GPU \$ROCR_VISIBLE_DEVICES"
# The usual PyTorch initialisations (also needed on NVIDIA)
# Note that since we fix the port ID it is not possible to run, e.g., two
# instances via this script using half a node each.
export MASTER_ADDR=\$(/runscripts/get-master "\$SLURM_NODELIST")
export MASTER_PORT=29500
export WORLD_SIZE=\$SLURM_NPROCS
export RANK=\$SLURM_PROCID
# Run application
python "\$@"
"""
local_runscript_get_master="""
#!/usr/bin/env python3
# This way of starting Python should work both on LUMI and in the container, though
# this script is really meant to be used in the container.
import argparse
def get_parser():
parser = argparse.ArgumentParser(description="Extract master node name from Slurm node list",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("nodelist", help="Slurm nodelist")
return parser
if __name__ == '__main__':
parser = get_parser()
args = parser.parse_args()
first_nodelist = args.nodelist.split(',')[0]
if '[' in first_nodelist:
a = first_nodelist.split('[')
first_node = a[0] + a[1].split('-')[0]
else:
first_node = first_nodelist
print(first_node)
"""
#
# An example of how some installations can be further automated.
# The empty line at the end is important because of the way we generate the file
# for use in the container.
#
# You can outcomment this (or delete this) if you also delete the matching lines
# in postinstallcmds.
#
local_pip_requirements = """
torchmetrics
pytorch-lightning
"""
#
# Now install does scripts and do further preparations of the container.
#
local_singularity_bind = '/var/spool/slurmd,/opt/cray,/usr/lib64/libcxi.so.1,/usr/lib64/libjansson.so.4,' + \
'%(installdir)s/runscripts:/runscripts,' + \
'/pfs,/scratch,/projappl,/project,/flash,/appl'
postinstallcmds = [
# Install the scripts in the bin subdirectory
'mkdir -p %(installdir)s/bin',
f'cat >%(installdir)s/bin/start-shell <<EOF {local_bin_start_shell}EOF',
'chmod a+x %(installdir)s/bin/start-shell',
f'cat >%(installdir)s/bin/make-squashfs <<EOF {local_bin_make_squashfs}EOF',
'chmod a+x %(installdir)s/bin/make-squashfs',
f'cat >%(installdir)s/bin/unmake-squashfs <<EOF {local_bin_unmake_squashfs}EOF',
'chmod a+x %(installdir)s/bin/unmake-squashfs',
# Install the runscripts
'mkdir -p %(installdir)s/runscripts',
f'cat >%(installdir)s/runscripts/init-conda-venv <<EOF {local_runscript_init_conda_venv}EOF',
'chmod a-x %(installdir)s/runscripts/init-conda-venv',
f'cat >%(installdir)s/runscripts/conda-python-simple <<EOF {local_runscript_python_simple}EOF',
'chmod a+x %(installdir)s/runscripts/conda-python-simple',
f'cat >%(installdir)s/runscripts/conda-python-distributed <<EOF {local_runscript_python_distributed}EOF',
'chmod a+x %(installdir)s/runscripts/conda-python-distributed',
f'cat >%(installdir)s/runscripts/get-master <<EOF {local_runscript_get_master}EOF',
'chmod a+x %(installdir)s/runscripts/get-master',
# Create the virtual environment and space for other software installations that
# can then be packaged.
'mkdir -p %(installdir)s/user-software/venv',
# For the next command, we don't need all the bind mounts yet, just the user-software one is enough.
f'singularity exec --bind %(installdir)s/user-software:/user-software %(installdir)s/{local_sif} bash -c \'$WITH_CONDA ; cd /user-software/venv ; python -m venv --system-site-packages {local_conda_env}\'',
#
# Example of how to automate installation of Python packages that simply install with pip.
# EasyBuild may fail to produce a proper error though if the installation through the singularity
# command fails as it does not propagate error codes.
#
# We first create a requirements.txt file that we then use in the container to install the packages.
# The problem we are facing here is that the module is not yet available, so all bindings have to be
# cone by hand and the singularity command is a bit more comples. Finally we use the make-squashfs script
# to generate a SquashFS file from the software that we have just installed. Finally we remove the
# user-software subdirectory to instead use the SquashFS file in the container.
#
f'cat >%(installdir)s/user-software/venv/requirements.txt <<EOF {local_pip_requirements}EOF',
f'singularity exec --bind {local_singularity_bind} --bind %(installdir)s/user-software:/user-software %(installdir)s/{local_sif} bash -c \'source /runscripts/init-conda-venv ; cd /user-software/venv ; pip install -r requirements.txt\'',
'%(installdir)s/bin/make-squashfs',
'/bin/rm -rf %(installdir)s/user-software',
]
sanity_check_paths = {
# We deliberately don't check for local_sif as the user is allowed to remove that file
# but may still want to regenerate the module which would then fail in the sanity check.
#'files': [f'share/docker-defs/{local_docker}'],
'files': [],
'dirs': ['runscripts'],
}
modextravars = {
# SIF variables currently set by a function via modluafooter.
#'SIF': '%(installdir)s/' + local_sif,
#'SIFPYTORCH': '%(installdir)s/' + local_sif,
'CONTAINERROOT': '%(installdir)s',
'RUNSCRIPTS': '%(installdir)s/runscripts',
'RUNSCRIPTSPYTORCH': '%(installdir)s/runscripts',
#'SINGULARITY_BIND': local_singularity_bind,
#
# The following two lines inject the environment variables WITH_VENV and WITH_CONDA_VENV into
# the container that have a similar function as WITH_CONDA: the first one is the command to
# activate the Python virtrual environment defined by default and the second one activates
# both the conda and Python virtual environments, with the latter environment built on top of the
# former.
#
'SINGULARITYENV_WITH_VENV': f'source /user-software/venv/{local_conda_env}/bin/activate',
'SINGULARITYENV_WITH_CONDA_VENV': 'source /runscripts/init-conda-venv',
#
# The following lines inject environment variables into the container that
# basically have the same effect as activating the conda environment and Python
# virtual environment. When these are defined in the module, WITH_CONDA, WITH_VENV or
# WITGH_CONDA_VENV are not really needed.
#
'SINGULARITYENV_PREPEND_PATH': '/runscripts:/user-software/venv/pytorch/bin:/opt/miniconda3/envs/pytorch/bin:/opt/miniconda3/condabin',
'SINGULARITYENV_CONDA_DEFAULT_ENV': 'pytorch',
'SINGULARITYENV_CONDA_EXE': '/opt/miniconda3/bin/conda',
'SINGULARITYENV_CONDA_PREFIX': '/opt/miniconda3/envs/pytorch',
#'SINGULARITYENV_CONDA_PYTHON_EXE': '/opt/miniconda3/bin/python', # This Python should not be used as-is. Instead the wrapper from the Python venv should be used.
'SINGULARITYENV_VIRTUAL_ENV': '/user-software/venv/pytorch',
}
modluafooter = f"""
-- Call a routine to set the various environment variables.
create_container_vars( '{local_sif}', 'PyTorch', '%(installdir)s', '{local_singularity_bind}' )
"""
moduleclass = 'devel'