Embedded Files
General Information
We highly encourage all school participants to prepare for the hands-on sessions by installing some prerequisites. We advise to do the following before school starts:
Have a working Python3 installation and make sure it includes the numpy.
Prepare your system by checking the installation instructions for each code below.
The WebNucleo and Talys codes are provided also in the form of a pre-compiled docker image. If you wish to use them via Docker please refer to the official website for installation instructions.
NOTE: All hands-on sessions will take place at the Biomedical and Physical Science (BPS) building, room 1400, across from FRIB.
OMEGA
Installation Instructions
Create a directory where you want to download the codes.
Go to that directory with a terminal and clone the GitHub repository:
git clone https://github.com/NuGrid/NuPyCEE.git
From the same directory which contains the cloned NuPyCEE directory, you can import the codes in Python mode by typing:
from NuPyCEE import omega
from NuPyCEE import sygma
from NuPyCEE import stellab
If you prefer to import the NuPyCEE codes from anywhere else within your workspace, you have to update your Python path using a terminal:
export PYTHONPATH="your_path_to_before_NuPyCEE:$PYTHONPATH"
All export commands should be put into your bash file to load it automatically each time you open a terminal.
Find below the links to the repositories used during the session
https://github.com/NuGrid/NuPyCEE.git
https://github.com/becot85/JINAPyCee
https://github.com/tomtrueman/Frontiers-Summer-School
Instructions on how to run them again can be found in this README file.
WebNucleo
Installation Instructions
Installation instructions and more information about the WebNucleo code can be found at the following link.
You can work on WebNucleo using the pre-compiled docker image. Docker installation instructions and more information can be found here.
Alternatively, you can choose to install the libraries and the WebNucleo code directly on your PC/laptop by yourself.
Talys
Installation Instructions
Installation via Docker
As an alternative to the usual installation described above, you can use the pre-compiled docker image prepared exclusively for the school at https://hub.docker.com/r/skowrons/talys on DockerHub.
Install Docker following the directions on this website
To pull the talys open a terminal and do docker pull skowrons/talys:v1.96
Download the setup.sh from here, make it executable using the command chmod u+x setup.sh, and run it as ./setup.sh
Once the setup is done it will create a running Talys container with an attached docker volume to store your files and print the following message
Talys container running; stopping and removing it...Done!
Talys volume already exists.
Starting Talys container... Done!
You can access the container by typing docker exec -it talys bash
To copy files to the container use the cp command as docker cp yourFile.txt talys:/workdir
To copy files from the container use the cp command as docker cp talys:/workdir/output.txt /your/directory
The running docker mounts a virtual volume at /workdir which will persist even after the docker is relaunched with the setup.sh script, thus please use that directory to do your calculations.
Installation via script
Download TALYS-1.96 (Make sure you have enough space ~ 1.5Gb)
Uncompress downloaded file
tar –xvf talys.tar
Navigate to the Talys folder and find the talys.setup file
Open the file with an editor
Set the first two variables to your system specifications
compiler='gfortran'
Thome = path/to/directory (where you like to have the talys executable)
Run the installation ./talys.setup (it might result in several warning messages)
If the installation is successful you should get the following message
The TALYS setup has been completed.
You will find a talys executable in your "path/to/directory" directory.
You are all set to run the sample problems in the samples directory with the verified script.
Verification
cd samples
./verify (it will take some time)
Frequent troubles and solutions
Ensure that the verify file has the correct path to the Talys executable. To find the path do which talys then copy and paste it in the verify file line 11 (e.g. talys=${/usr/local/bin/} )
Ensure that all directories have execute permission and that all files in the Talys directory have read and write permission. If not, do chmod -R u+rwX talys
Ensure that Talys setup can read the nuclear structure database.
This is done in the subroutine source/machine.f.
If talys.setup has failed to replace the path to the Talys directory in the machine.f do it by editing line 34.
If the talys.setup does not work, you can follow the instructions for manual installation from page 24 of the Talys manual.
If any of the aforementioned steps don't work please contact us either via e-mail or in person before the day of the session.
Bayesian Uncertainty Quantification Methods
Installation Instructions
The Bayesian Uncertainty Quantification hands-on session will require a Jupyter notebook.
Advanced Scientific Computing and Statistics Network https://github.com/ascsn/bayesianprimer
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