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Update and fix conda environment construction script #262

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merged 4 commits into from
Mar 24, 2022
Merged

Update and fix conda environment construction script #262

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402189d
Update and fix conda environment construction script
bwohlberg Mar 23, 2022
32e070c
Merge branch 'main' into brendt/conda
bwohlberg Mar 24, 2022
c35925e
Bug fix
bwohlberg Mar 24, 2022
96b2043
Improve instructions
bwohlberg Mar 24, 2022
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12 changes: 4 additions & 8 deletions misc/conda/README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -19,19 +19,15 @@ To install miniconda in ``/opt/conda`` do
./install_conda.sh -y /opt/conda


To create a conda environment called ``py38scico`` with default Python version (3.8) and without GPU support
To create a conda environment called ``py39`` with default Python version (3.9) and without GPU support

::

./make_conda_env.sh -y -e py38scico
./make_conda_env.sh -y -e py39


To include GPU support, add the ``-g`` flag

::

./make_conda_env.sh -y -g -e py38scico

To include GPU support, follow the `jax installation instructions <https://github.com/google/jax#pip-installation-gpu-cuda>`__ after
running this script and activating the environment created by it.


Caveats
Expand Down
67 changes: 22 additions & 45 deletions misc/conda/make_conda_env.sh
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Expand Up @@ -21,23 +21,17 @@ fi


SCRIPT=$(basename $0)
REPOPATH=$(realpath $(dirname $0))
USAGE=$(cat <<-EOF
Usage: $SCRIPT [-h] [-y] [-g] [-p python_version] [-c cuda_version]
[-e env_name] [-j jaxlib_url]
Usage: $SCRIPT [-h] [-y] [-g] [-p python_version] [-e env_name]
[-h] Display usage information
[-y] Do not ask for confirmation
[-g] Install jaxlib with GPU support
[-c] CUDA version without decimals (e.g. specify 11.0 as 110)
[-p python_version] Specify Python version (e.g. 3.8)
[-p python_version] Specify Python version (e.g. 3.9)
[-e env_name] Specify conda environment name
[-j jaxlib_url] Specify URL for jaxlib pip install
EOF
)

JAXURL=https://storage.googleapis.com/jax-releases/jax_releases.html
AGREE=no
GPU=no
CUVER=""
PYVER="3.9"
ENVNM=py$(echo $PYVER | sed -e 's/\.//g')

Expand All @@ -58,21 +52,18 @@ EOF


OPTIND=1
while getopts ":hygc:p:e:j:" opt; do
while getopts ":hyp:e:" opt; do
case $opt in
c|p|e|j) if [ -z "$OPTARG" ] || [ "${OPTARG:0:1}" = "-" ] ; then
p|e) if [ -z "$OPTARG" ] || [ "${OPTARG:0:1}" = "-" ] ; then
echo "Error: option -$opt requires an argument" >&2
echo "$USAGE" >&2
exit 2
fi
;;&
h) echo "$USAGE"; exit 0;;
y) AGREE=yes;;
g) GPU=yes;;
c) CUVER=$OPTARG;;
p) PYVER=$OPTARG;;
e) ENVNM=$OPTARG;;
j) JAXURL=$OPTARG;;
:) echo "Error: option -$OPTARG requires an argument" >&2
echo "$USAGE" >&2
exit 2
Expand Down Expand Up @@ -127,25 +118,16 @@ if [ "$OS" == "Darwin" ]; then
fi
fi

if [ "$GPU" == "yes" ] && [ "$CUVER" == "" ]; then
if [ "$(which nvcc)" == "" ]; then
echo "Error: GPU-enabled jaxlib requested but CUDA version not"\
"specified and could not be automatically determined" >&2
exit 9
else
CUVER=$(nvcc --version | grep -o 'release [0-9][0-9]*\.[[0-9][0-9]*' \
| sed -e 's/release //' -e 's/\.//')
fi
fi

JLVER=$($SED -n 's/^jaxlib==\([0-9\.]\)/\1/p' requirements.txt)
JXVER=$($SED -n 's/^jax==\([0-9\.]\)/\1/p' requirements.txt)
JLVER=$($SED -n 's/^jaxlib>=\([0-9\.]*\).*/\1/p' \
$REPOPATH/../../requirements.txt)
JXVER=$($SED -n 's/^jax>=\([0-9\.]*\).*/\1/p' \
$REPOPATH/../../requirements.txt)

CONDAHOME=$(conda info --base)
ENVDIR=$CONDAHOME/envs/$ENVNM
if [ -d "$ENVDIR" ]; then
echo "Error: environment $ENVNM already exists"
exit 10
exit 9
fi

if [ "$AGREE" == "no" ]; then
Expand All @@ -154,7 +136,7 @@ if [ "$AGREE" == "no" ]; then
read -r -p "$RSTR" CNFRM
if [ "$CNFRM" != 'y' ] && [ "$CNFRM" != 'Y' ]; then
echo "Cancelling environment creation"
exit 11
exit 10
fi
else
echo "Creating conda environment $ENVNM with Python $PYVER"
Expand All @@ -172,7 +154,6 @@ if [ "$OS" == "Darwin" ]; then
else
ALLREQUIRE=$(mktemp -t condaenv_XXXXXX.txt)
fi
REPOPATH=$(realpath $(dirname $0))
for req in $REQUIRE; do
pthreq="$REPOPATH/../../$req"
cat $pthreq >> $ALLREQUIRE
Expand Down Expand Up @@ -223,21 +204,8 @@ if [ "$(which ffmpeg)" = '' ]; then
conda install $CONDA_FLAGS ffmpeg
fi

# Install jaxlib and jax, with jaxlib version depending on requested
# GPU support
if [ "$GPU" == "yes" ]; then
pip install --upgrade jax==$JXVER jaxlib==$JLVER+cuda$CUVER -f $JAXURL
retval=$?
if [ $retval -ne 0 ]; then
echo "Error: jaxlib installation failed"
exit 12
fi
else
pip install --upgrade jaxlib==$JLVER jax==$JXVER
echo "Jax installed without GPU support. To avoid warning messages,"
echo "add the following to your .bashrc or .bash_aliases file"
echo " export JAX_PLATFORM_NAME=cpu"
fi
# Install jaxlib and jax
pip install --upgrade jaxlib==$JLVER jax==$JXVER

# Install other packages that require installation via pip
pip install $NOCONDA
Expand All @@ -251,9 +219,18 @@ if [ "$(which dpkg 2>/dev/null)" ]; then
fi
fi

echo
echo "Activate the conda environment with the command"
echo " conda activate $ENVNM"
echo "The environment can be deactivated with the command"
echo " conda deactivate"
echo
echo "Jax installed without GPU support. To avoid warning messages,"
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This means if GPU support is required then you should not use this script?

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No, it means that manual action is required after use of the script. I had assumed that this was implied by the following sentence "To include GPU support ...", but perhaps it's not as clear as I had thought?

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It was not clear to me. Let's make it more clear.

Also in the .rst file we could make it something like To include GPU support, follow the jax installation instructions after running the installation script.

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Done.

echo "add the following to your .bashrc or .bash_aliases file"
echo " export JAX_PLATFORM_NAME=cpu"
echo "To include GPU support, see instructions at"
echo " https://github.com/google/jax#pip-installation-gpu-cuda"
echo "for additional steps required after running this script and"
echo "activating the environment created by it."

exit 0