Merge pull request #12 from ADACS-Australia/pawsey_testing

Pawsey testing

Author: cjproud

.gitignore

@@ -26,3 +26,6 @@ profiling.md
 /docs/build
 /docs/doctrees
 example_data/
+build/
+scripts/epochs.txt
+scripts/mean.txt

README.md

@@ -110,6 +110,13 @@ This will run the viewer using the images within the default ``results`` directo
 ./run_robbie_viewer.sh -p path_to_dir
 ```
 
+When plotting large images, it is recommended to also specify an RA and DEC position, as well as a size in coordinate units, to cutout a portion of the image for plotting.
+For example, if we want to plot an image with centre position of RA 335°, DEC -15° and size of 5°:
+
+```
+./run_robbie_viewer.sh path_to_dir 335 -15 5
+```
+
 ## Credit
 If you use Robbie as part of your work, please cite [Hancock et al. 2018](http://adsabs.harvard.edu/abs/2019A%26C....27...23H), and link to this repository.
 

docker/Dockerfile

@@ -20,4 +20,5 @@ RUN pip install -r requirements.txt && \
     python setup.py install && \
     rm -rf /tmp/build
 
+#  set env
 ENV HOME=/tmp

docker/build_docker_arm.sh

@@ -3,6 +3,6 @@ cd ..
 version=$(robbie_version.sh)
 
 # build the container and update tag
-docker buildx build . --platform linux/amd64 -f docker/Dockerfile -t "paulhancock/robbie-next:${version}" && \
+docker buildx build . --platform linux/amd64 --no-cache -f docker/Dockerfile -t "paulhancock/robbie-next:${version}" && \
 docker tag paulhancock/robbie-next:${version} paulhancock/robbie-next:latest
 cd -

nextflow.config

@@ -42,6 +42,8 @@ timeline.enabled = true
 report.enabled = true
 dag.enabled = true
 
+// get hostname
+host = "$HOSTNAME".split('-')[0]
 
 profiles {
     local {
@@ -102,12 +104,14 @@ profiles {
       }
     }
 }
-if ( "\$HOSTNAME".startsWith("garrawarla") ) {
+
+if ( host == "garrawarla") ) {
   // Set up container
   process.module = 'singularity/3.7.4'
   singularity {
     enabled = true
     envWhitelist = 'SINGULARITY_BINDPATH, SINGULARITYENV_LD_LIBRARY_PATH'
+    runOptions = '--bind $HOME:/$HOME'
   }
   params.containerDir = '/pawsey/mwa/singularity'
 

robbie.nf

@@ -177,7 +177,7 @@ process download_gleam_catalogue {
     try:
       cat.write(data_load.REF_CAT, format='fits')
       os.symlink(data_load.REF_CAT, "GLEAM_ref_cat.fits")
-    except PermissionError:
+    except OSError:
       # No permission so dump it here
       cat.write("GLEAM_ref_cat.fits", format='fits')
   """
@@ -553,7 +553,7 @@ process reproject_images {
   """
   echo ${task.process} on \${HOSTNAME}
   mkdir reprojected_images
-  ls *Epoch* > temp_epochs.txt
+  ls *.fits | grep -v "mean_image" > temp_epochs.txt
   ls *mean_image.* > temp_mean.txt
   reprojection.py --epochs temp_epochs.txt --mean temp_mean.txt --reproj_dir reprojected_images
   """
@@ -588,6 +588,7 @@ workflow {
     image_ch = fits_warp.out
     image_bkg_rms = fits_warp.out.concat(bane_raw.out.map{ it -> [it[0], [it[1..2]]]}).groupTuple().map{ it -> [ it[0], it[1][0], it[1][1][0][1]]}
   }
+
   make_mean_image( image_ch.map{ it -> it[1] }.collect() )
   make_sky_coverage( image_ch.map{ it -> it[1] }.collect() )
   bane_mean_image( make_mean_image.out[0] )

robbie_viewer_server/Dockerfile

@@ -15,5 +15,3 @@ RUN pip install -r requirements.txt
 
 # EXPOSE PORTS
 EXPOSE 5006
-
-CMD bokeh serve . --args /data 

robbie_viewer_server/build_docker.sh

@@ -1,4 +1,4 @@
 #! /usr/bin/env bash
 
 # build the container and add a target
-docker build . -f ./Dockerfile -t "robbie/robbie-viewer"
+docker build . -f ./Dockerfile -t "cjproud/robbie_viewer:latest"

robbie_viewer_server/build_docker_arm.sh

@@ -1,4 +1,4 @@
 #! /usr/bin/env bash
 
 # build the container and add a target
-docker buildx build . --platform linux/amd64 -f ./Dockerfile -t "robbie/robbie-viewer"
+docker buildx build . --platform linux/amd64 -f ./Dockerfile -t "cjproud/robbie_viewer:latest"