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Perlmutter (NERSC)

The Perlmutter cluster is located at NERSC.

Introduction

If you are new to this system, please see the following resources:

Preparation

Use the following commands to download the ImpactX source code:

git clone https://github.com/ECP-WarpX/impactx.git $HOME/src/impactx

On Perlmutter, you can run either on GPU nodes with fast A100 GPUs (recommended) or CPU nodes.

.. tab-set::

   .. tab-item:: A100 GPUs

      We use system software modules, add environment hints and further dependencies via the file ``$HOME/perlmutter_gpu_impactx.profile``.
      Create it now:

      .. code-block:: bash

         cp $HOME/src/impactx/docs/source/install/hpc/perlmutter-nersc/perlmutter_gpu_impactx.profile.example $HOME/perlmutter_gpu_impactx.profile

      .. dropdown:: Script Details
         :color: light
         :icon: info
         :animate: fade-in-slide-down

         .. literalinclude:: perlmutter-nersc/perlmutter_gpu_impactx.profile.example
            :language: bash

      Edit the 2nd line of this script, which sets the ``export proj=""`` variable.
      Perlmutter GPU projects must end in ``..._g``.
      For example, if you are member of the project ``m3239``, then run ``nano $HOME/perlmutter_gpu_impactx.profile`` and edit line 2 to read:

      .. code-block:: bash

         export proj="m3239_g"

      Exit the ``nano`` editor with ``Ctrl`` + ``O`` (save) and then ``Ctrl`` + ``X`` (exit).

      .. important::

         Now, and as the first step on future logins to Perlmutter, activate these environment settings:

         .. code-block:: bash

            source $HOME/perlmutter_gpu_impactx.profile

      Finally, since Perlmutter does not yet provide software modules for some of our dependencies, install them once:

      .. code-block:: bash

         bash $HOME/src/impactx/docs/source/install/hpc/perlmutter-nersc/install_gpu_dependencies.sh
         source ${CFS}/${proj%_g}/${USER}/sw/perlmutter/gpu/venvs/impactx/bin/activate

      .. dropdown:: Script Details
         :color: light
         :icon: info
         :animate: fade-in-slide-down

         .. literalinclude:: perlmutter-nersc/install_gpu_dependencies.sh
            :language: bash


   .. tab-item:: CPU Nodes

      We use system software modules, add environment hints and further dependencies via the file ``$HOME/perlmutter_cpu_impactx.profile``.
      Create it now:

      .. code-block:: bash

         cp $HOME/src/impactx/docs/source/install/hpc/perlmutter-nersc/perlmutter_cpu_impactx.profile.example $HOME/perlmutter_cpu_impactx.profile

      .. dropdown:: Script Details
         :color: light
         :icon: info
         :animate: fade-in-slide-down

         .. literalinclude:: perlmutter-nersc/perlmutter_cpu_impactx.profile.example
            :language: bash

      Edit the 2nd line of this script, which sets the ``export proj=""`` variable.
      For example, if you are member of the project ``m3239``, then run ``nano $HOME/perlmutter_cpu_impactx.profile`` and edit line 2 to read:

      .. code-block:: bash

         export proj="m3239"

      Exit the ``nano`` editor with ``Ctrl`` + ``O`` (save) and then ``Ctrl`` + ``X`` (exit).

      .. important::

         Now, and as the first step on future logins to Perlmutter, activate these environment settings:

         .. code-block:: bash

            source $HOME/perlmutter_cpu_impactx.profile

      Finally, since Perlmutter does not yet provide software modules for some of our dependencies, install them once:

      .. code-block:: bash

         bash $HOME/src/impactx/docs/source/install/hpc/perlmutter-nersc/install_cpu_dependencies.sh
         source ${CFS}/${proj}/${USER}/sw/perlmutter/cpu/venvs/impactx/bin/activate

      .. dropdown:: Script Details
         :color: light
         :icon: info
         :animate: fade-in-slide-down

         .. literalinclude:: perlmutter-nersc/install_cpu_dependencies.sh
            :language: bash

Compilation

Use the following :ref:`cmake commands <building-cmake>` to compile the application executable:

.. tab-set::

   .. tab-item:: A100 GPUs

      .. code-block:: bash

         cd $HOME/src/impactx
         rm -rf build_pm_gpu

         cmake -S . -B build_pm_gpu -DImpactX_COMPUTE=CUDA
         cmake --build build_pm_gpu -j 16

      The ImpactX application executables are now in ``$HOME/src/impactx/build_pm_gpu/bin/``.
      Additionally, the following commands will install ImpactX as a Python module:

      .. code-block:: bash

         cd $HOME/src/impactx
         rm -rf build_pm_gpu_py

         cmake -S . -B build_pm_gpu_py -DImpactX_COMPUTE=CUDA -DImpactX_APP=OFF -DImpactX_PYTHON=ON
         cmake --build build_pm_gpu_py -j 16 --target pip_install

   .. tab-item:: CPU Nodes

      .. code-block:: bash

         cd $HOME/src/impactx
         rm -rf build_pm_cpu

         cmake -S . -B build_pm_cpu -DImpactX_COMPUTE=OMP
         cmake --build build_pm_cpu -j 16

      The ImpactX application executables are now in ``$HOME/src/impactx/build_pm_cpu/bin/``.
      Additionally, the following commands will install ImpactX as a Python module:

      .. code-block:: bash

         rm -rf build_pm_cpu_py

         cmake -S . -B build_pm_cpu_py -DImpactX_COMPUTE=OMP -DImpactX_APP=OFF -DImpactX_PYTHON=ON
         cmake --build build_pm_cpu_py -j 16 --target pip_install

Now, you can :ref:`submit Perlmutter compute jobs <running-cpp-perlmutter>` for ImpactX :ref:`Python (PICMI) scripts <usage-picmi>` (:ref:`example scripts <usage-examples>`). Or, you can use the ImpactX executables to submit Perlmutter jobs (:ref:`example inputs <usage-examples>`). For executables, you can reference their location in your :ref:`job script <running-cpp-perlmutter>` or copy them to a location in $PSCRATCH.

Update ImpactX & Dependencies

If you already installed ImpactX in the past and want to update it, start by getting the latest source code:

cd $HOME/src/impactx

# read the output of this command - does it look ok?
git status

# get the latest ImpactX source code
git fetch
git pull

# read the output of these commands - do they look ok?
git status
git log # press q to exit

And, if needed,

As a last step, clean the build directory rm -rf $HOME/src/impactx/build_pm_* and rebuild ImpactX.

Running

.. tab-set::

   .. tab-item:: A100 (40GB) GPUs

      The batch script below can be used to run a ImpactX simulation on multiple nodes (change ``-N`` accordingly) on the supercomputer Perlmutter at NERSC.
      This partition as up to `1536 nodes <https://docs.nersc.gov/systems/perlmutter/architecture/>`__.

      Replace descriptions between chevrons ``<>`` by relevant values, for instance ``<input file>`` could be ``plasma_mirror_inputs``.
      Note that we run one MPI rank per GPU.

      .. literalinclude:: perlmutter-nersc/perlmutter_gpu.sbatch
         :language: bash
         :caption: You can copy this file from ``$HOME/src/impactx/docs/source/install/hpc/perlmutter-nersc/perlmutter_gpu.sbatch``.

      To run a simulation, copy the lines above to a file ``perlmutter_gpu.sbatch`` and run

      .. code-block:: bash

         sbatch perlmutter_gpu.sbatch

      to submit the job.


   .. tab-item:: A100 (80GB) GPUs

      Perlmutter has `256 nodes <https://docs.nersc.gov/systems/perlmutter/architecture/>`__ that provide 80 GB HBM per A100 GPU.
      In the A100 (40GB) batch script, replace ``-C gpu`` with ``-C gpu&hbm80g`` to use these large-memory GPUs.


   .. tab-item:: CPU Nodes

      The Perlmutter CPU partition as up to `3072 nodes <https://docs.nersc.gov/systems/perlmutter/architecture/>`__, each with 2x AMD EPYC 7763 CPUs.

      .. literalinclude:: perlmutter-nersc/perlmutter_cpu.sbatch
         :language: bash
         :caption: You can copy this file from ``$HOME/src/impactx/docs/source/install/hpc/perlmutter-nersc/perlmutter_cpu.sbatch``.

Post-Processing

For post-processing, most users use Python via NERSC's Jupyter service (documentation).

As a one-time preparatory setup, log into Perlmutter via SSH and do not source the ImpactX profile script above. Create your own Conda environment and Jupyter kernel for post-processing:

module load python

conda config --set auto_activate_base false

# create conda environment
rm -rf $HOME/.conda/envs/impactx-pm-postproc
conda create --yes -n impactx-pm-postproc -c conda-forge mamba conda-libmamba-solver
conda activate impactx-pm-postproc
conda config --set solver libmamba
mamba install --yes -c conda-forge python ipykernel ipympl matplotlib numpy pandas yt openpmd-viewer openpmd-api h5py fast-histogram dask dask-jobqueue pyarrow

# create Jupyter kernel
rm -rf $HOME/.local/share/jupyter/kernels/impactx-pm-postproc/
python -m ipykernel install --user --name impactx-pm-postproc --display-name ImpactX-PM-PostProcessing
echo -e '#!/bin/bash\nmodule load python\nsource activate impactx-pm-postproc\nexec "$@"' > $HOME/.local/share/jupyter/kernels/impactx-pm-postproc/kernel-helper.sh
chmod a+rx $HOME/.local/share/jupyter/kernels/impactx-pm-postproc/kernel-helper.sh
KERNEL_STR=$(jq '.argv |= ["{resource_dir}/kernel-helper.sh"] + .' $HOME/.local/share/jupyter/kernels/impactx-pm-postproc/kernel.json | jq '.argv[1] = "python"')
echo ${KERNEL_STR} | jq > $HOME/.local/share/jupyter/kernels/impactx-pm-postproc/kernel.json

exit

When opening a Jupyter notebook on https://jupyter.nersc.gov, just select ImpactX-PM-PostProcessing from the list of available kernels on the top right of the notebook.

Additional software can be installed later on, e.g., in a Jupyter cell using !mamba install -y -c conda-forge .... Software that is not available via conda can be installed via !python -m pip install ....