Commit 308fd1c8 authored by bliven_s's avatar bliven_s

CrYOLO/1.6.1 modules

There are _cpu and _gpu flags available, which are selected based on
fancy modulefile code (Thanks Achim)
parent 60f98fa5
crYOLO/1.2.3 unstable cuda/9.0.176
crYOLO/1.5.6_gpu unstable anaconda/2019.07
crYOLO/1.6.1_gpu unstable anaconda/2019.07
crYOLO/1.6.1_cpu unstable anaconda/2019.07
......@@ -26,19 +26,28 @@ convolutional neural networks and utilizes the popular You Only Look Once
set shelltype [module-info shelltype]
switch -- $shelltype {
"sh" {
puts stdout "source \"\${ANACONDA_PREFIX}\"/admintools/;\n"
default {
puts stderr "Shells of type '$shelltype' are NOT supported!"
#set useflag [string map {{:} {}} $USEFLAGS]
#puts stderr "conda activate cryolo-${V_PKG}-${USEFLAGS%\n"
# Determine useflags and construct conda env name
set list [split $V "_"]
set version [lindex ${list} 0]
set useflags [lrange ${list} 1 end]
set flavour [lindex $useflags 0]
set env_to_activate [string tolower ${P}]-${version}-${flavour}
#puts stderr "P/V: $P/$V"
#puts stderr "USEFLAG: [lindex $useflags 0]"
#puts stderr "$env_to_activate"
switch [module-info mode] {
"load" {
# Relies on the anaconda module being loaded since we need to update the path
puts stdout "conda activate cryolo-1.5.6-gpu;\n"
puts stdout "conda activate $env_to_activate;\n"
"unload" -
"remove" {
......@@ -2,7 +2,8 @@
IMPORTANT! DON'T INSTALL WITH AURISTOR. Use an OpenAFS system (e.g. pmod6)
export TMPDIR=/opt/tmp/bliven_s
export TMPDIR=/opt/tmp/$USER
export XDG_CACHE_HOME=/opt/tmp/$USER/.cache
CONDA_COPY_ALWAYS=1 conda env create --file cryolo.yml
conda activate cryolo
name: cryolo-1.5.6-gpu
name: cryolo-1.6.1-cpu
- defaults
......@@ -11,4 +11,4 @@ dependencies:
- intel-openmp==2019.4
- pip
- pip:
- cryolo[gpu]==1.5.6
- cryolo[cpu]==1.6.1
name: cryolo-1.6.1-gpu
- defaults
- python=3.6
- pyqt=5
- cudnn=7.1.2
- numpy==1.14.5
- cython
- wxPython==4.0.4
- intel-openmp==2019.4
- pip
- pip:
- cryolo[gpu]==1.6.1
# simulate `conda init` type hook
# Expects CONDA_EXE and CONDA_PREFIX to be set
__conda_setup="$("${CONDA_EXE:-conda}" 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
if [ -f "${CONDA_PREFIX:?CONDA_PREFIX not set}/etc/profile.d/" ]; then
. "${CONDA_PREFIX}/etc/profile.d/"
export PATH="${CONDA_PREFIX}/bin:$PATH"
unset __conda_setup
dbgecho() {
if [[ $DEBUG_JUPYTER_WRAPPER == 1 ]]; then
echo "$1" >> $DBGLOG
DATE=$(date +%Y-%m-%dT%H:%M)
dbgecho "$DATE: $@"
# ensure that module commands are available
dbgecho "sourcing profile.bash"
source /opt/psi/config/profile.bash
dbgecho "sourcing"
source /opt/psi/Programming/anaconda/2019.07/conda/etc/profile.d/ &>> $DBGLOG
dbgecho "Running activate"
conda activate $1
# undefine module command since it causes error in the notebook when using
# shell escapes
unset -f module
exec "$@"
......@@ -57,7 +57,8 @@ switch [module-info mode] {
# but we need to prevent conflicts with a conda from a different source.
# puts stderr "DEBUG: Using conda from $P/$V\n"
puts stdout "source \"$PREFIX/conda/etc/profile.d/\";\n"
#puts stdout "source \"$PREFIX/conda/etc/profile.d/\";\n"
puts stdout "source $PREFIX/admintools/;\n"
# Activate base? No: anaconda should just provide the conda tool
#puts stdout "conda activate;\n"
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