FRENSIE-Docker-UW-Cluster

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Dependencies/Requirements

1. Docker
2. git
3. UW HPC account
4. MCNP License - optional

Installing Dependencies

Installing Docker

1. run sudo apt-get install docker
2. run sudo groupadd docker
3. run sudo gpasswd -a $USER docker
4. restart system

Note: Steps 2-4 will allow docker to be run without superuser privileges.

Installing Git

1. run sudo apt-get install git

Getting UW HPC Account

Follow the instructions on the UW HPC website for creating an account. When requesting your account you must also request access to the frensie group. All frensie related software will be stored on the cluster at /home/group/frensie.

Building FRENSIE on UW HPC Clone (first build)

1. create a working directory where the docker files will be built (e.g. software/uw-clone)
2. move to uw-clone directory
3. clone the repository: git clone https://github.com/FRENSIE/FRENSIE-Docker-UW-Cluster.git
4. make a symbolic link to the new directory: ln -s FRENSIE-Docker-UW-Cluster src
5. make a build directory: mkdir build
6. move to the build directory: cd build
7. make a copy of the frensie-docker.sh script in the build directory: cp ../src/scripts/frensie-docker.sh .
8. open the copy of the frensie-docker.sh script and
   • set the UW_CLUSTER_USER_NAME variable to the user name on the UW cluster
   • set the UW_CLUSTER_USER_DIR variable to the user directory on the UW cluster (absolute path)
9. configure the system to build: ./frensie-docker.sh ../src to configure the Docker files
10. launch the build of FRENSIE in this environment: make (this may take a while as all of FRENSIE's software dependencies and FRENSIE will be built)

Building FRENSIE on UW HPC Clone after FRENSIE Update

1. move to the build directory
2. run make clean-docker-update (quicker) or run make clean-docker (requires full rebuild of all images, which is slow)
3. run make

Installing FRENSIE Dependencies on UW HPC

Note: Skip these steps if the dependencies have already been installed on the UW HPC cluster.

1. run cd path-to-build/frensie-update where path-to-build is the path to the FRENSIE-Docker-UW-Cluster build directory
2. run ./run-frensie-update.sh to load the frensie-update image
3. run cd /home/group/frensie/software
4. run tar -czvf frensie-deps.tar.gz
5. run scp frensie-deps.tar.gz UW_HPC_USER_NAME@ace-service-1.chtc.wisc.edu:/home/group/frensie/software/. where UW_HPC_USER_NAME is the appropriate user HPC cluster user name
6. run exit
7. run ssh -X UW_HPC_USER_NAME@ace-service-1.chtc.wisc.edu where UW_HPC_USER_NAME is the appropriate user HPC cluster user name
8. run cd /home/group/frensie/software/
9. run tar -xvf frensie-deps.tar.gz

Installing FRENSIE on UW HPC

1. run cd path-to-build/frensie-update where path-to-build is the path to the FRENSIE-Docker-UW-Cluster build directory
2. run ./run-frensie-update.sh to load the frensie-update image
3. run cd UW_CLUSTER_USER_DIR where UW_CLUSTER_USER_DIR is the appropriate UW cluster user directory
4. run cd frensie_rel or cd frensie_db depending on whether FRENSIE was built for release or for debugging
5. run tar -czvf frensie.tar.gz bin lib frensie-env.sh
6. run scp frensie.tar.gz UW_HPC_USER_NAME@ace-service-1.chtc.wisc.edu:UW_CLUSTER_USER_DIR/. where UW_HPC_USER_NAME is the appropriate HPC cluster user name and UW_CLUSTER_USER_DIR is the appropriate UW cluster user directory
7. run exit
8. run ssh -X UW_HPC_USER_NAME@ace-service-1.chtc.wisc.edu where UW_HPC_USER_NAME is the appropriate user HPC cluster user name
9. run cd UW_CLUSTER_USER_DIR where UW_CLUSTER_USER_DIR is the appropriate UW cluster user directory
10. run mkdir frensie_rel or mkdir frensie_db depending on whether FRENSIE was built for release or for debugging
11. run mv frensie.tar.gz FRENSIE_DIR/. where FRENSIE_DIR is either frensie_rel or frensie_db depnding on whether FRENSIE was built for release or for debugging
12. run cd FRENSIE_DIR/. where FRENSIE_DIR is either frensie_rel or frensie_db depnding on whether FRENSIE was built for release or for debugging
13. run tar -xvf frensie.tar.gz
14. add the following lines to your .bashrc file on the UW Cluster: if [ -r $CRIMP_ENV ] then source UW_CLUSTER_USER_DIR/FRENSIE_DIR/frensie-env.sh fi where UW_CLUSTER_USER_DIR is the appropriate UW cluster user directory and FRENSIE_DIR is either frensie_rel or frensie_db depnding on whether FRENSIE was built for release or for debugging

Other Useful Docker Commands

1. docker images: run to see which docker images that have been created
2. docker rmi -f image-id: run to remove a docker image with id image-id
3. docker rmi -f repo:tag: run to remove a docker image with alias repo:tag