Users

Clara2 - a classical radiation simulation running in parallel

This is a start of a wiki page, that might help users.

If you use clara2 for the first time and want to run it on hypnos, just do the following:

1. Follow our github instructions to get the source code, or in short:

# create general Clara2 work directory and enter it
mkdir Clara2
cd Clara2

# get source code from git hub (own repo)
git clone git@github.com:<YourUserName>/clara2.git
cd clara2

# add remote link to our source code 
git remote add mainline git@github.com:ComputationalRadiationPhysics/clara2.git

# update the remote link and pull all changes
git fetch mainline
git pull --rebase mainline master

2. create a runs directory next to your source code:

# go back to Clara2 folder
cd ..

# create runs folder
mkdir runs

3. copy source code into simulation directory

# copy source code for simulation
cp -r clara2/src runs/001_first_test_run

4. set up simulation

# go to simulation directory
cd runs/001_first_run

# set up job using default
./prepare_job.sh
# --> choose 1) MPI

5. run simulation and wait till it is finished:

# submit job
qsub submit.sh

# wait till simulation is finished

6. process simulation data:

# collect spectral data from all traces
./process_data

# load python with matplotlib
module load python/2.7.5

# plot data (axis not correct)
# Adjustments to the path where this tool is located might be necessary!
../../clara2/tools/plotRadiation my_spectrum_all_000.dat