Getting Started with POT3D for ISC23 SCC

Owned by Ophir Maor
Last updated: Mar 09, 2023
4 min read

Overview

Potential Magnetic Field Solution using POT3D

POT3D is a Fortran code that computes potential field solutions to approximate the solar coronal magnetic field using observed photospheric magnetic fields as a boundary condition. It can be used to generate potential field source surface (PFSS), potential field current sheet (PFCS), and open field (OF) models. It has been (and continues to be) used for numerous studies of coronal structure and dynamics. The code is highly parallelized using MPI and is GPU-accelerated using Fortran standard parallelism (do concurrent) and OpenACC, along with an option to use the NVIDIA cuSparse library. The HDF5 file format is used for input/output.

 

 

Presentation

Downloading and compiling POT3D

git clone https://github.com/predsci/POT3D

There are sample build scripts in the build_examples directory.

We start with build_examples/build_cpu_mpi-only_intel_ubuntu20.04.sh (This is for CPU-only runs).

  1. Copy and rename build_examples/build_cpu_mpi-only_intel_ubuntu20.04.sh to the POT3D package root directory:
    cp ./build_examples/build_cpu_mpi-only_intel_ubuntu20.04.sh ./rebuild.sh

  2. Build and/or load the HDF5 library.

  3. Modify the rebuild.sh script to point to the location of the HDF5 library.

  4. Execute the build script:
    ./rebuild.sh

Sample build script for Fritz:

We used modules for MPI and HDF5 on Firtz.

# MPI=openmpi-4.1.2-intel2021.4.0 MPI=intelmpi-2021.7.0 if [[ "$MPI" =~ ^intel ]]; then module load hdf5/1.10.7-impi-intel export I_MPI_F90=ifort else module load hdf5/1.10.7-ompi-intel export OMPI_MPIF90=ifort fi ################################################################# # Location of local hdf5 installed with same compiler being used for POT3D: HDF5_INCLUDE_DIR="$HDF5_ROOT/include" HDF5_LIB_DIR="$HDF5_ROOT/lib" # Fortran HDF5 library flags (these can be version dependent): HDF5_LIB_FLAGS="-lhdf5_fortran -lhdf5_hl_fortran -lhdf5 -lhdf5_hl"" ...

Sample build script for PSC:

Download HPC-X from ISC23 SCC Getting Started with Bridges-2 Cluster.

Download and install HDF5 before building POT3D.

source /jet/packages/intel/oneapi/compiler/2022.1.0/env/vars.sh source /jet/packages/intel/oneapi/mkl/2022.1.0/env/vars.sh # MPI=intelmpi MPI=hpcx if [[ "$MPI" =~ ^hpcx ]]; then module use $HOME/hpcx-2.13.1/modulefiles module load hpcx export OMPI_MPICC=icc export OMPI_MPICXX=icpc export OMPI_MPIFC=ifort export OMPI_MPIF90=ifort export FC=mpif90 else source /jet/packages/intel/oneapi/mpi/2021.6.0/env/vars.sh export FC=mpiifort fi ################################################################# # Location of local hdf5 installed with same compiler being used for POT3D: HDF5_INCLUDE_DIR="$HDF5_ROOT/include" HDF5_LIB_DIR="$HDF5_ROOT/lib" # Fortran HDF5 library flags (these can be version dependent): HDF5_LIB_FLAGS="-lhdf5_fortran -lhdf5_hl_fortran -lhdf5 -lhdf5_hl"" ...

Running an Example

The following commands will run a test case with NP MPI ranks and validate that the code is working.

NP=1 cd testsuite POT3D_HOME=$PWD/.. TEST="small" cp ${POT3D_HOME}/testsuite/${TEST}/input/* ${POT3D_HOME}/testsuite/${TEST}/run/ cd ${POT3D_HOME}/testsuite/${TEST}/run echo "Running POT3D with $NP MPI rank..." mpirun -np $NP ${POT3D_HOME}/bin/pot3d > pot3d.log echo "Done!" # Get runtime: runtime=($(tail -n 5 timing.out | head -n 1)) echo "Wall clock time: ${runtime[6]} seconds" echo " " # Validate run: ${POT3D_HOME}/scripts/pot3d_validation.sh pot3d.out ${POT3D_HOME}/testsuite/${TEST}/validation/pot3d.out

 

Task and Submission

  1. Use the input under testsuite/isc2023 folder.

  2. Run POT3D with isc2023 input on both PSC bridges-2 and FAU Fritz CPU clusters using 4 nodes.
    Experiment with number of ranks per socket/numa domains to get the best results.
    Your job should converge at 25112 steps and print outputs like below:

    ### The CG solver has converged. Iteration: 25112 Residual: 9.972489313728662E-13

  3. Profile a run.

    1. Use any of the remote clusters to run an MPI profile (such as IPM profile or any other profiler) for a run using 4 nodes with full PPN.

    2. Submit the profile as a PDF to the team's folder.

    3. In your presentation, also indicate the 3 main MPI calls that are being used and their run times, as well as the total MPI time for the test.

  4. Bonus task: Run POT3D on the PSC cluster using the V100 GPU partition.

    1. Use only 4 GPUs for the run. It is recommended to use one rank per GPU.

    2. Submit the results to the team's folder.

    3. NOTE: To compile and run POT3D with the nvfortran compiler, you must load and/or build the HDF5 library compiled with nvfortran. The code is known to work with HDF5 1.8.21 (http://portal.hdfgroup.org/display/support/HDF5+1.8.21 )

    4. An example build script for POT3D with the NVIDIA compiler can be found in build_examples/build_gpu_nv22.3_ubuntu20.04.sh

    5. Note that you do NOT need to enable the cusparse option because the test case is not set up to use the algorithm that requires cusparse. Therefore, if linking cusparse is causing difficulties, you can change the build script line POT3D_CUSPARSE=1to POT3D_CUSPARSE=0.

  5. Submission and Presentation:
    - Submit all your build scripts, run scripts, inputs, and output text files (pot3d.dat, pot3d.out, timing.out, etc.)
    - Do not submit the output HDF5 data or the source code.
    - Prepare slides for the team’s interview based on your work for this application.

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