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Copy pathpr-check.sh
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executable file
·230 lines (185 loc) · 6.35 KB
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#!/bin/bash
# Copyright 2016 Intel Corporation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# Check readiness for pull request
set -e
# Check whether we are running on Princeton's della compute cluster.
is_della=false
if [[ $(hostname -s) == della* ]];
then
is_della=true
fi
# Set this to where brainiak example notebooks and their datasets should be stored when running.
EXAMPLE_NOTEBOOKS_DIR=docs/examples
# Check if we are running on della.princeton.edu
if [[ "$is_della" == true ]]; then
echo "Running on della, load required modules"
# Load some modules we will need on della
module load anaconda3/2023.3
# Load openmpi and turn off infiniband
# module load openmpi/gcc/2.0.2/64
module load openmpi/gcc/4.1.2
export MPICC=$(which mpicc)
export OMPI_MCA_btl="vader,self,tcp"
# Issues with pip using tmp on della
export TMPDIR=/scratch/gpfs/dmturner/tmp
fi
if [ ! -f src/brainiak/__init__.py ]
then
echo "Run "$(basename "$0")" from the root of the BrainIAK hierarchy."
exit 1
fi
basedir=$(pwd)
function create_venv_venv {
python3 -m venv ../$1
}
function activate_venv_venv {
source ../$1/bin/activate
}
function deactivate_venv_venv {
deactivate
}
function remove_venv_venv {
rm -r ../$1
}
function create_conda_venv {
conda create -n $1 --yes python=3.8
}
function activate_conda_venv {
source activate $1
# Pip may update setuptools while installing BrainIAK requirements and
# break the Conda cached package, which breaks subsequent runs.
conda install --yes -f setuptools
if [[ "$is_della" == true ]]; then
# On della, we need to set LD_LIBRARY_PATH to the conda environment libs explicitly.
# This is because when importing tensorflow the system libstd++ is picked
# up instead of the conda one. This causes subsequent GLIB version errors
# when trying to load compiled modules
export LD_LIBRARY_PATH="$CONDA_PREFIX/lib:$LD_LIBRARY_PATH"
fi
}
function deactivate_conda_venv {
if [[ "$is_della" == true ]]; then
conda deactivate
else
source deactivate
fi
}
function remove_conda_venv {
conda env remove -n $1 --yes
}
function exit_with_error {
echo $1 >&2
exit 1
}
function exit_with_error_and_venv {
$deactivate_venv
cd $basedir
$remove_venv $venv
exit_with_error "$1"
}
if [ -z "$IGNORE_CONDA" ] && [ "$(which conda)" ]
then
export PYTHONNOUSERSITE=True
create_venv=create_conda_venv
activate_venv=activate_conda_venv
deactivate_venv=deactivate_conda_venv
remove_venv=remove_conda_venv
#ignore_installed="--ignore-installed"
else
create_venv=create_venv_venv
activate_venv=activate_venv_venv
deactivate_venv=deactivate_venv_venv
remove_venv=remove_venv_venv
fi
# Check if running in an sdist
if git ls-files --error-unmatch pr-check.sh 2> /dev/null
then
git clean -Xf .
else
sdist_mode="--sdist-mode"
fi
venv=$(mktemp -u brainiak_pr_venv_XXXXX) || \
exit_with_error "mktemp -u error"
$create_venv $venv || {
exit_with_error "Virtual environment creation failed."
}
$activate_venv $venv || {
$remove_venv $venv
exit_with_error "Virtual environment activation failed."
}
if [[ "$is_della" == true ]]; then
# We need to fetch any data needed for running notebook examples
# Update our data cache with any download_data.sh scripts found in the repo
BRAINIAK_EXAMPLES_DATA_CACHE_DIR=/scratch/gpfs/dmturner/brainiak_tests/brainiak-example-data
echo "Copying download_data.sh scripts to brainiak-example-data cache"
rsync -av --prune-empty-dirs --include="*/" --include="download_data.sh" --exclude="*" $EXAMPLE_NOTEBOOKS_DIR/ $BRAINIAK_EXAMPLES_DATA_CACHE_DIR/
# Download any data, this should only trigger downloads for new datasets since download_data.sh should check if the data exists.
echo "Executing download_data scripts in cache directory"
pushd .
cd $BRAINIAK_EXAMPLES_DATA_CACHE_DIR
bash download_data.sh
popd
echo "Updating the working repo with any data downloaded into the cache"
rsync -av $BRAINIAK_EXAMPLES_DATA_CACHE_DIR/ $EXAMPLE_NOTEBOOKS_DIR/
# Skip upgrading pip, this was causing failures on della, not sure why.
# Install mpi4py first, no cache director
pip install mpi4py --no-cache-dir || \
exit_with_error_and_venv "Failed to install mpi4py."
else
python3 -m pip install -U pip || \
exit_with_error_and_venv "Failed to update Pip."
fi
# install brainiak in editable mode (required for testing)
# Install with all dependencies (testing, documentation, examples, etc.)
python3 -m pip install $ignore_installed -U \
-v --config-settings=cmake.verbose=true --config-settings=logging.level=INFO \
-e .[all] || \
exit_with_error_and_venv "Failed to install BrainIAK."
# static analysis, skip on della for now, failing for numpy 1.20 typing issues I think
if [[ "$is_della" == false ]]; then
./run-checks.sh || exit_with_error_and_venv "run-checks failed"
fi
# run tests
if [[ "$is_della" == true ]]; then
echo "Running on della head node, need to request time on a compute node"
export BRAINIAKDEV_MPI_COMMAND=srun
salloc -t 03:00:00 -N 1 -n 16 sh run-tests.sh $sdist_mode || \
exit_with_error_and_venv "run-tests failed"
else
./run-tests.sh $sdist_mode || \
exit_with_error_and_venv "run-tests failed"
fi
# build documentation, only if not della
if [[ "$is_della" == true ]]; then
echo "Skipping docs build on della"
else
cd docs
if [ ! -z $SLURM_NODELIST ]
then
if [[ "$is_della" == true ]]; then
make_wrapper="srun -t 00:30:00 -N 1 -n 4 "
else
make_wrapper="srun -n 1"
fi
fi
$make_wrapper make || {
cd -
exit_with_error_and_venv "make docs failed"
}
cd -
fi
$deactivate_venv
$remove_venv $venv
echo "pr-check finished successfully."