Perlmutter¶

login: ssh $my_username@perlmutter-p1.nersc.gov

interactive login:

# for CPU:
salloc --partition=debug --nodes=1 --time=30:00 -C cpu

# for GPU:
salloc --partition=debug --nodes=1 --time=30:00 -C gpu

Compute time:

Check hours of compute usage at https://iris.nersc.gov/

File system:

Overview: https://docs.nersc.gov/filesystems/
home directory: $HOME
scratch directory: $SCRATCH
Check your individual disk usage with myquota
Check the group disk usage with prjquota projectID, i.e. prjquota m1795 or prjquota e3sm

Archive:

NERSC uses HPSS with the commands hsi and htar
overview: https://docs.nersc.gov/filesystems/archive/
E3SM uses zstash

Perlmutter-CPU¶

There has not yet been a release with Perlmutter-CPU, so the following applies to the release of compass v1.2.0, when it happens.

Perlmutter’s CPU and GPU nodes have different configuration options and compilers. We only support Perlmutter-CPU at this time.

config options¶

Here are the default config options added when you choose -m pm-cpu when setting up test cases or a test suite:

# The paths section describes paths that are used within the ocean core test
# cases.
[paths]

# A shared root directory where MPAS standalone data can be found
database_root = /global/cfs/cdirs/e3sm/mpas_standalonedata

# the path to the base conda environment where compass environments have
# been created
compass_envs = /global/common/software/e3sm/compass/pm-cpu/base


# Options related to deploying a compass conda environment on supported
# machines
[deploy]

# the compiler set to use for system libraries and MPAS builds
compiler = gnu

# the system MPI library to use for gnu compiler
mpi_gnu = mpich

# the base path for spack environments used by compass
spack = /global/cfs/cdirs/e3sm/software/compass/pm-cpu/spack

# whether to use the same modules for hdf5, netcdf-c, netcdf-fortran and
# pnetcdf as E3SM (spack modules are used otherwise)
use_e3sm_hdf5_netcdf = True

# The parallel section describes options related to running jobs in parallel.
# Most options in this section come from mache so here we just add or override
# some defaults
[parallel]

# cores per node on the machine
cores_per_node = 128

# threads per core (set to 1 because trying to hyperthread seems to be causing
# hanging on perlmutter)
threads_per_core = 1

Additionally, some relevant config options come from the mache package:

# The parallel section describes options related to running jobs in parallel
[parallel]

# parallel system of execution: slurm, cobalt or single_node
system = slurm

# whether to use mpirun or srun to run a task
parallel_executable = srun

# cores per node on the machine
cores_per_node = 256

# account for running diagnostics jobs
account = e3sm

# available constraint(s) (default is the first)
constraints = cpu

# quality of service (default is the first)
qos = regular, premium, debug

# Config options related to spack environments
[spack]

# whether to load modules from the spack yaml file before loading the spack
# environment
modules_before = False

# whether to load modules from the spack yaml file after loading the spack
# environment
modules_after = False

# whether the machine uses cray compilers
cray_compilers = True

Hyperthreading¶

By default, hyperthreading has been disable on Perlmutter. We had found some some issues with runs hanging in early testing that seemed to be mitigated by disabling hyperthreading. We disable hyperthreading by setting threads_per_core = 1 and reducing cores_per_node to not include the 2 hyperthreads. You can re-enable hyperthreading on Perlmutter by providing a user config file where you set threads_per_core and cores_per_node as follows:

# The parallel section describes options related to running jobs in parallel
[parallel]

# cores per node on the machine (including hyperthreading)
cores_per_node = 256

# threads per core with hyperthreading
threads_per_core = 2

Gnu on Perlmutter-CPU¶

To load the compass environment and modules, and set appropriate environment variables:

source /global/cfs/cdirs/e3sm/software/compass/pm-cpu/load_latest_compass_gnu_mpich.sh

To build the MPAS model with

make [DEBUG=true] [OPENMP=true] [ALBANY=true] gnu-cray

Jupyter notebook on remote data¶

You can run Jupyter notebooks on NERSC with direct access to scratch data as follows:

ssh -Y -L 8844:localhost:8844 MONIKER@perlmutter-p1.nersc.gov
jupyter notebook --no-browser --port 8844
# in local browser, go to:
http://localhost:8844/

Note that on NERSC, you can also use their Jupyter server, it’s really nice and grabs a compute node for you automatically on logon. You’ll need to create a python kernel from e3sm-unified following these steps (taken from https://docs.nersc.gov/connect/jupyter/). After creating the kernel, you just go to “Change Kernel” in the Jupyter notebook and you’re ready to go.

You can use one of NERSC’s default Python 3 or R kernels. If you have a Conda environment, depending on how it is installed, it may just show up in the list of kernels you can use. If not, use the following procedure to enable a custom kernel based on a Conda environment. Let’s start by assuming you are a user with username user who wants to create a Conda environment on Perlmutter and use it from Jupyter.

module load python
conda create -n myenv python=3.7 ipykernel <further-packages-to-install>
<... installation messages ...>
source activate myenv
python -m ipykernel install --user --name myenv --display-name MyEnv
   Installed kernelspec myenv in /global/u1/u/user/.local/share/jupyter/kernels/myenv

Be sure to specify what version of Python interpreter you want installed. This will create and install a JSON file called a “kernel spec” in kernel.json at the path described in the install command output.

{
    "argv": [
        "/global/homes/u/user/.conda/envs/myenv/bin/python",
        "-m",
        "ipykernel_launcher",
        "-f",
        "{connection_file}"
    ],
    "display_name": "MyEnv",
    "language": "python"
}