process-uc1-integration

docker (folder)

Contains everything needed to build the docker image.

mount-sshfs-snetdn.sh

To use locally only in to mount snetdn via sshfs, e.g. for uploading files. This is not used in the actual process-uc1-execution-script-sshfs.sh.

process-uc1-execution-script-sshfs.sh

Script that prepares the VM, launches the docker container for the usecase and cleans up resources after termination.

VM preparation:

• Install sshfs
• Config sshfs
• Creates target mount dir /mnt/snedtn
• Mounts target mount dir with lobcder

Launch docker container:

• Mounts /mnt/snedtn/camelyon17 from host to /process-uc1/data/camelyon17 in container
• Run bin/cnn --config-file etc/config.ini extract
• Results saved to snedtn : snetdn/uc1-results

Resource cleanup:

• Unmounts target mount dir (just to be sure, might flush cache)

install_mount-fstab-lobcder.sh (deprecated)

Script that installs davfs2 or, creates mount target dir, creates webdav secrets file for lobcder credentials, creates fstab entry and mounts target dir.

This script is not used in the cloud (or VM), but is rather meant to run locally to mount lobcder.

process-uc1-execution-script-davfs.sh (deprecated)

Script that prepares the VM, launches the docker container for the usecase and cleans up resources after termination.

VM preparation:

• Install davfs2
• Creates entry for lobcder credentaisl in /etc/davfs2/secrets
• Creates target mount dir /mnt/lobcder
• Mounts target mount dir with lobcder

Launch docker container:

• Mounts /mnt/lobcder/snedtn/camelyon17 from host to /process-uc1/data/camelyon17 in container
• Run bin/cnn --config-file etc/config.ini extract
• Results saved to lobcder : snetdn/uc1-results

Resource cleanup:

• Unmounts target mount dir (in order to to force cash to be flushed and written to remote resource)

Copy camelyon dataset files to snedtn via sshfs

Copy camelyon17 files from nas4 to snedtn via sshfs. Filenaes provided via stdnin (one filename per line).

#cd to a dir with images
$ cd /mnt/nas4/datasets/ToReadme/CAMELYON17/centre_0
#copy images provided via stdnin to snetdn. Use Ctrl+D to mark end of input.
$ awk '{print $1}' | xargs -n 1 -I '{}' cp -v '{}' /mnt/snedtn/camelyon17/centre_0

E.g. provide the following imagenames via stdin. One line per imagename:

• patient_005_node_1.tif
• patient_006_node_0.tif
• patient_012_node_0.tif
• patient_018_node_2.tif
• patient_019_node_2.tif
• patient_017_node_4.tif

Then do:

$ Enter
$ Ctrl+D

After files have been copied compare md5 checksum

Pass the filenames to compare to stdin. One filename per line.

awk '{print $1}' | xargs -n 1 -I '{}' bash -c $'md5sum=$(md5sum {} | awk \'{ print $1 }\'); md5sum_other=$(md5sum /mnt/snedtn/camelyon17/centre_0/{} | awk \'{ print $1 }\'); if [ $md5sum != $md5sum_other ]; then echo "md5 does not match: {}"; else echo "{} match: $md5sum"; fi'

$ Enter
$ Ctrl+D

Run script on VM (147.213.76.127)

Copy private key for snedtn sshfs from local to VM

Make sure to also provide the correct private key for the VM.

$ scp -i ~/.ssh/id_rsa_linux ~/.ssh/id_rsa_process_uc1 [email protected]:/home/ubuntu/.ssh/

Connect to VM

Make sure to provide the correct private key.

$ ssh -i ~/.ssh/id_rsa_linux [email protected]

Clone this project from git

$ cd ~/
$ git clone https://github.com/ieggel/process-uc1-integration.git

Test Run execution script on VM

Consider using byobu in order to continue running the process even when quitting ssh session.

$ byobu

Then execute with sshfs:

$ cd /home/ubuntu/process-uc1-integration
$ ./process-uc1-execution-script-sshfs.sh

OR with webdav (depreacted):

$ cd /home/ubuntu/process-uc1-integration
$ ./process-uc1-execution-script-davfs.sh