Repository to create a docker image and the installation script to compile paragait and all the dependencies.
- Docker for linux
git clone https://github.com/UoMResearchIT/paragait-docker
When Docker is installed go to the previous repository:
cd paragait-docker
build the docker image:
docker build -t paragait .
Start the container from the latest paragait image, give it the name paragait and log into a bash shell:
docker run --name paragait -i -t paragait:latest /bin/bash
Run the installation script which should be in the directory:
./paragait.sh
List the available containers:
docker ps -a
The list will be something like:
| CONTAINER ID | IMAGE | COMMAND | CREATED | STATUS | PORTS | NAMES |
|---|---|---|---|---|---|---|
| ed56e6355086 | paraga it:lat est | "/bin/ba sh" | 4 seconds ago | Exited (0) 1 second ago | paraga it | |
| bb020705acab | paraga it:lat est | "/bin/ba sh" | 2 hours ago | Up 39 minutes | paraga it0.5 | |
| da76eeec88d7 | a721e4 41a9e0 | "/bin/ba sh" | 5 days ago | Exited (0) 4 days ago | paraga it0.4 | |
| 57fa0423d5e8 | 99641c 22a35c | "/bin/ba sh" | 5 days ago | Exited (0) 5 days ago | paraga it0.3 | |
| 9c1dccb36ee7 | 99641c 22a35c | "/bin/ba sh" | 5 days ago | Exited (0) 5 days ago | paraga it0.2 | |
| 1bc31ba3794d | 99641c 22a35c | "/bin/ba sh" | 6 days ago | Exited (0) 5 days ago | paraga it0.1 |
Start the container you want to interact with:
docker start paragait
and log into it:
docker attach paragait
When log on the docker image, you can run every script individually or
use the convenient script paragait.sh which will run the following
- parafem.sh
- gaitsym.sh (NOT WORKING YET)
- foam-extend.sh
- openfpci.sh
Note
To compile openFPCI, you have to use gcc<6.0 (FSI, a library needed by the project does not compile with gcc>=6.0). To realise that, the docker image is configured to use gcc4.9. Depending on your distribution or system different possibilities to achieve it are available:
on ubuntu the best way is to use the update-alternative
on archlinux, you have to install gcc5 and modify the gcc, g++ and gfortran executable to use gcc5 (be careful to save the original version to be able to put back the system in its default state)
On HPC, use the module env system. E.g.
module load gcc/4.9