Sterllerator Related Tools

This jupyter notebook shows how to open the Beams3D and BMW output and plot the magnetic fields. It is found that both of them generates the same magnetic field.

BMW

Installation on SCOREC machines (rhel9)

Note: To find the RHEL version of the machine you are on, you can use the following command:

    cat /etc/redhat-release

This is the recommended way of BMW installation since most of the SCOREC machines are now RHEL9. This process only works on RHEL 9 machines of SCOREC and was tested on 13th June 2024. Some modules may change in the future.

1. Go to your intended installation directory with cd (/lore/<username>/ recommended, see more details about space management here) and clone the repository:

    git clone https://github.com/ORNL-Fusion/Stellarator-Tools.git

2. Enter the directory and create a build directory:

    cd Stellarator-Tools
    mkdir build
    cd build

3. Load necessary modules: (ignore the warnings)

   module use /opt/scorec/spack/rhel9/v0201_4/lmod/linux-rhel9-x86_64/Core/
   module load gcc/12.3.0-iil3lno mpich/4.1.1-xpoyz4t cuda/12.1.1-zxa4msk
   module load cmake 
   module load netcdf-c netcdf-fortran openblas netlib-scalapack

4. Run cmake with the following command:

    cmake -B ./ -S ../ -DBUILD_BMW=ON -DBUILD_MAKEGRID=ON -DCMAKE_INSTALL_PREFIX=/lore/<username>/BMW

Change the installation directory as per your requirement. 5. Build and install:

    make -j4
    make install

6. To use the installed xmbw and mgrid, the shared library paths need to be updated. Execute the following export commands before using them.

    export LD_LIBRARY_PATH=$OPENBLAS_RHEL9_ROOT/lib:$LD_LIBRARY_PATH
    export LD_LIBRARY_PATH=$NETLIB_SCALAPACK_RHEL9_ROOT/lib:$LD_LIBRARY_PATH
    export LD_LIBRARY_PATH=$NETCDF_FORTRAN_RHEL9_ROOT/lib:$LD_LIBRARY_PATH
    export LD_LIBRARY_PATH=$NETCDF_C_RHEL9_ROOT/lib:$LD_LIBRARY_PATH

Note: Every time you want to use xmbw or mgrid on a new terminal, you need to export the shared library paths after loading the necessary modules(step 3).

Installation on SCOREC machines (rhel7)

This GitHub reporsiory contains the source code and brief installation guide of BMW: BMW.

Note: Direct compilation did not work for me. I used Stellarator-Tools supplied by ORNL-Fusion.

1. Clone the repository:

    git clone https://github.com/ORNL-Fusion/Stellarator-Tools.git

2. Go the the directory and create a build directory:

    cd Stellarator-Tools
    mkdir build
    cd build

3. Load the necessary modules:

    module unuse /opt/scorec/spack/lmod/linux-rhel7-x86_64/Core
    module use /opt/scorec/spack/v0201_4/lmod/linux-rhel7-x86_64/Core
    module load gcc/11.2.0-zcqgw mpich/4.1.1-6p32n

    module load netcdf-c cmake netcdf-fortran openblas netlib-scalapack

4. Run cmake: You can also follow the ccmake method from the repository README. But I recommend the following:

     cmake -B ./build -S ./ -DBUILD_BMW=ON -DCMAKE_INSTALL_PREFIX=/lore/<yourUsername>/BMW

5. Build and install:

    make -j4 install

or

    make -j4

This will create the bmw executable in the bin directory of the installation directory.

6. Update the shared libraries (xbmw will keep printing error messages until it finds all the shared libraries): (These directories may change depending on the modules loaded for installation)

    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/scorec/spack/v0201_4/install/linux-rhel7-x86_64/gcc-11.2.0/openblas-0.3.23-4kpgzbwtvvnf4m4f6rqvyclh2khpfepb/lib
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/scorec/spack/v0201_4/install/linux-rhel7-x86_64/gcc-11.2.0/netlib-scalapack-2.2.0-w3lmjdvbshpvqiihwxm2fygyjyzu275t/lib
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/scorec/spack/v0201_4/install/linux-rhel7-x86_64/gcc-11.2.0/netcdf-c-4.9.2-hzgyaz36ol6aqb4o3ne3xjabccpxjlo4/lib
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/scorec/spack/v0201_4/install/linux-rhel7-x86_64/gcc-11.2.0/netcdf-fortran-4.6.0-hwoxscrowy6gh75n5ypnlr3btfver36x/lib

Usage of BMW: Run a case from VMEC Equillibria

There can be two kinds of use cases for bmw: the coil generated magnetic filed is considered or they are not considered. If you don’t need the coil generated magnetic field, you just need the wout_...nc file and follow the steps below.

1. Go to the directory where you have the case files (e.g. vmec_equillibria/NCSX/free_boundary_from_vmec_wiki):

    cd vmec_equillibria/NCSX/free_boundary_from_vmec_wiki

You can create the wout_...nc file using vmec or use the provided wout_...nc file as the input to bmw.

2. Run bmw:

    /lore/<yourUsername>/BMW/bin/xbmw -num_r=100 -num_p=20 -num_z=100 -rmax=1.5 -rmin=0.9 -zmax=0.5 -zmin=-0.5 -woutf=wout_ncsx_c09r00_free_birth.nc -outf=bmw_ncsx_c09r00_out.nc

This will produce the bmw_ncsx_c09r00_out.nc file in the current directory.

4. To read the output file, you can use python and the netCDF4 library. Here in this Jupyter Notebook file, I have plotted the magnetic field from the output file. GitHub Gist for Analysis

Using Coil Generated Magnetic Field

1. Check if the coils file given in the case directory. Generally, it’s given and name as coils.xxxxx.
2. Change the ier_flag in the wout_...nc file to 0 before starting the bmw run. You can modify .nc files in python using the netCDF4 library.

    import netCDF4 as nc
    wout = nc.Dataset('wout_ncsx_c09r00_free_birth.nc', 'r')
    wout.variables['ier_flag'][:] = 0
    wout.close()

3. BMW only accepts coils file in mgrid format. So, convert the coils.xxxxx file to mgrid format using the following command:

    /lore/<yourUsername>/BMW/bin/mgrid < input_file.txt

To know how to create an input file for mgrid, check this STELLOPT MAKEGRID Tutorial. Note that their binary name is xgrid but in the BMW installation, it’s mgrid.

4. Run bmw with the mgrid file generated in the above step. In this case, you don’t have to specify the parameters for the grid since the grid is already provided by the mgrid file.

    /lore/<yourUsername>/BMW/bin/xbmw -woutf=wout_ncsx_c09r00_free_birth.nc -outf=bmw_ncsx_c09r00_out.nc -mgridf=mgrid_xxxx.nc

This will take a long time to run depending on the grid size. You can also do parallel run using mpirun and -para flag.

Beams3D

Installation on SCOREC Machines

I am not able to compile the STELLOPT tool on scorec yet. The installation instructions given in the STELLOPT README is not working.

If you have access to the PPPL clusters (e.g. stellar), they have compiled STELLOPT tools. You can use them directly.

    ssh stellar-intel
    module use /home/caoxiang/module
    module load stellopt/intel 

Learn more about it here

Using Docker Image

I used the docker image of STELOPT to run Beams3D where all the necessary tools are already installed. The docker image is available at Docker Hub.

1. Get the docker image:

    docker pull zhucaoxiang/stellopt

2. Run the docker image depending on your OS. SCOREC does not support docker yet. So, I used my own computer. You may also want to run the docker as root user since the image doesn’t support writing any file for non-root users.

    docker run -it -u root zhucaoxiang/stellopt

3. The NAG library is also needed to be installed but it is a proprietary software. A trial version(for 30 days) can be found here. Installation is very straightforward. Just follow the instructions given in the website.

According to their documentation, you can avoid NAG and use LSODE instead. Try changing the NAG flag to F in the make_debian.inc file as well as changing the INTEGRATOR flag to LSODE. If you succeed, please add in the documentation or create an issue.

4. After nag installation, add NAG to the environment using the following command:

    source /home/NAG/nll6i293bl/scripts/nagvars.sh int64 vendor dynamic

5. Then, follow the Beams3D tutorial to run Beams3D. I used the following command after editing the input file.

    xbeams3d -vmec ncsx_c09r00_free_birth -coil coils.c09r00 -vessel NCSX_wall_nbiport_acc.dat -field

6. It will create a .h5 file and it can be read by python. Magnetic field data is read in this Jupyter Notebook