Commit 67c09995 authored by Spencer Bliven's avatar Spencer Bliven
Browse files

Document crYOLO/1.5.6_gpu build process

parent ab670c0c
# crYOLO
crYOLO/1.2.3 was built as a miniconda independent environment.
Subsequent versions are deployed as central conda environments.
This significantly changed the build process.
## Adding New Versions
To add a new version, first create the conda environment, as described in
Next, update files/variants with the new version and run `./build <VERSION>` to
install the modulefile
......@@ -3,14 +3,7 @@
pbuild::add_to_group 'EM'
pbuild::prep() {
source "${BUILDBLOCK_DIR}/files/config-$"
echo "prepping"
mkdir -p "$SRC_DIR"
curl -fsSLo "$SRC_DIR/" "${}"
curl -fsSLo "$SRC_DIR/cryoloBM.tgz" "${CRYOLOBM_URL:-}"
curl -fsSLo "$SRC_DIR/cryolo.tgz" "${CRYOLO_URL:-${V_MAJOR}_${V_MINOR}_${V_PATCH}/cryolo-${V}.tar.gz}"
pbuild::configure() {
......@@ -22,22 +15,6 @@ pbuild::compile() {
pbuild::install() {
mkdir -p $PREFIX
# Install conda
bash "$SRC_DIR/" -b -p $PREFIX/conda
# Create environment
$PREFIX/conda/bin/conda create -y --name crYOLO anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy
# Activate
source $PREFIX/conda/bin/activate crYOLO
# Install
pip install $SRC_DIR/cryolo.tgz
pip install $SRC_DIR/cryoloBM.tgz
# Deactivate
source deactivate
crYOLO/1.2.3 unstable cuda/9.0.176
crYOLO/1.5.6_gpu unstable anaconda/2019.07
......@@ -32,20 +32,17 @@ switch -- $shelltype {
#puts stderr "Switching crYOLO mode to [module-info mode]"
#puts stdout "{ date; echo Switching crYOLO mode to [module-info mode] ; } >> /gpfs/home/bliven_s/cryolo_mod.log;\n"
#set useflag [string map {{:} {}} $USEFLAGS]
#puts stderr "conda activate cryolo-${V_PKG}-${USEFLAGS%\n"
switch [module-info mode] {
"load" {
#puts stderr "source $PREFIX/conda/bin/activate crYOLO"
puts stdout "source $PREFIX/conda/bin/activate crYOLO;\n"
# Relies on the anaconda module being loaded since we need to update the path
puts stdout "conda activate cryolo-1.5.6-gpu;\n"
"unload" -
"remove" {
#puts stderr "source deactivate"
puts stdout "source $PREFIX/conda/bin/deactivate;\n"
puts stdout {unset $(set|sed -rn 's/^(_?conda[a-z_]*).*$/\1/pI');}
puts stdout "conda deactivate;\n"
IMPORTANT! DON'T INSTALL WITH AURISTOR. Use an OpenAFS system (e.g. pmod6)
export TMPDIR=/opt/tmp/bliven_s
CONDA_COPY_ALWAYS=1 conda env create --file cryolo.yml
conda activate cryolo
The alternate TMPDIR is required on pmod6 because /tmp is too small for pip to expand all wheel files.
name: cryolo-1.5.6-gpu
- defaults
- python=3.6
- pyqt=5
- cudnn=7.1.2
- numpy==1.14.5
- cython
- wxPython==4.0.4
- intel-openmp==2019.4
- pip
- pip:
- cryolo[gpu]==1.5.6
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