New jureca stage

atlas_controller/start_remote_server.sh

@@ -2,7 +2,7 @@
 # Start server on remote machine
 
 USER=schiffer1
-HOST=jureca11.fz-juelich.de
+HOST=jureca10.fz-juelich.de
 COMMAND='cd /p/home/jusers/schiffer1/jureca/project_jinm16/atlasui/atlas_controller/; source load_modules.sh; source venv/bin/activate; export PYTHONPATH=`pwd`:$PYTHONPATH; python atlas_controller/app.py'
 RECONNECT=60
 

atlas_controller/start_tunnel.sh

@@ -2,7 +2,7 @@
 # Start SSH tunnel
 
 USER=schiffer1
-HOST=jureca11.fz-juelich.de
+HOST=jureca10.fz-juelich.de
 RECONNECT=60
 echo "Starting SSH tunnel..."
 

atlas_server/src/static/training/predict.job.sh

-#!/bin/bash
+#!/bin/bash -ex
+
 # Load modules
 echo Loading modules...
+# Note: Purge important, surrounding atlas_controller might have a different environment. 
 module purge
-
-export SOFTWARE_STAGE=2022
-export OTHERSTAGES=/p/software/jurecadc/otherstages
 source ${HOME}/galaxy/init.sh
 export ATLAS_MODULE=atlas
-
-module use ${OTHERSTAGES} &> /dev/null
-module use ${SOFTWARE_STAGE_MODULES} &> /dev/null
-
 module load ${ATLAS_MODULE}
 echo Modules loaded
 # Use the dev packages

atlas_server/src/static/training/train.job.sh

-#!/bin/bash
+#!/bin/bash -ex
+
 # Load modules
 echo Loading modules...
+# Note: Purge important, surrounding atlas_controller might have a different environment. 
 module purge
-
-export SOFTWARE_STAGE=2022
-export OTHERSTAGES=/p/software/jurecadc/otherstages
 source ${HOME}/galaxy/init.sh
 export ATLAS_MODULE=atlas
-
-module use ${OTHERSTAGES} &> /dev/null
-module use ${SOFTWARE_STAGE_MODULES} &> /dev/null
-
 module load ${ATLAS_MODULE}
 echo Modules loaded
 # Use the dev packages
@@ -32,6 +27,10 @@ INPUT_SPACING=1
 OUTPUT_SPACING=16
 PREFIX="mask"
 
+which python
+ml atlas
+which python
+
 # Get path to TIFF images to determine shape
 IMAGE_PATTERN=`python -c "from atlas import constants; print(constants.original_path.format(brain=int('${BRAIN}'), slice=1234))"`
 echo "Image pattern: ${IMAGE_PATTERN}"

docker-compose.yml

@@ -25,6 +25,8 @@ services:
   atlas-server-mongodb:
     image: mongo:4.2.2
     restart: always
+    ports:
+      - 28017:27017
     environment:
       MONGO_INITDB_ROOT_USERNAME: root
       MONGO_INITDB_ROOT_PASSWORD: root