craylabs/ncar_ml_eke

Repository for paper -- Using Machine Learning at Scale in HPC Simulations with SmartSim: An Application to Ocean Climate Modeling

Using Machine Learning at Scale in HPC Simulations with SmartSim

This project is code for the paper: Using Machine Learning at Scale in HPC Simulations with SmartSim

Reproduction

We strove to make this project as reproducible as possible. If you find any places where reproducibility is lacking or could be improved, please file an issue to let us know.

Installation

Below are the steps to install the various components needed to reproduce the results in the paper for the ML-EKE parameterization with SmartSim

Clone

First, clone the repository with the MOM6 submodule

git clone --recursive https://github.com/CrayLabs/NCAR_ML_EKE.git

Install SmartSim

See documentation for full build instructions if necessary

Update: Please use SmartRedis 0.2.0 and SmartSim 0.3.2 if available (Release: July 30, 2021) Otherwise, use branch develop for both libraries.

pip install smartsim==0.3.1 # 0.3.2 if available
export CUDNN_LIBRARY=/path/to/cudnn/library
export CUDNN_INCLUDE_DIR=/path/to/cudnn.h
smart --device gpu --no_tf # just build the PyTorch backend. Use -v for verbose mode

Install and Build SmartRedis

Build SmartRedis from source to compile into MOM6

Modules used in paper

Currently Loaded Modulefiles:
  1) modules/3.2.11.4                                    14) Base-opts/2.4.142-7.0.3.0_42.11__g8f27585.ari
  2) craype-network-aries                                15) cray-mpich/7.7.18.1
  3) nodestat/2.3.89-7.0.3.0_33.12__g8645157.ari         16) dws/3.0.36-7.0.3.0_65.9__g6985c90.ari
  4) sdb/3.3.818-7.0.3.0_26.26__g8ad6d1f.ari             17) craype/2.7.10.1
  5) udreg/2.3.2-7.0.3.0_36.21__g5f0d670.ari             18) cray-libsci/20.09.1
  6) ugni/6.0.14.0-7.0.3.0_25.20__gdac08a5.ari           19) pmi/5.0.17
  7) gni-headers/5.0.12.0-7.0.3.0_37.17__gd0d73fe.ari    20) atp/3.13.1
  8) dmapp/7.1.1-7.0.3.0_38.29__g93a7e9f.ari             21) rca/2.2.20-7.0.3.0_24.22__g8e3fb5b.ari
  9) xpmem/2.2.27-7.0.3.0_47.2__gada73ac.ari             22) perftools-base/21.05.0
 10) llm/21.4.632-7.0.3.0_44.6__gf148da5.ari             23) PrgEnv-gnu/6.0.10
 11) nodehealth/5.6.28-7.0.3.0_75.26__g742816f.ari       24) cray-netcdf/4.7.4.4
 12) system-config/3.6.3181-7.0.3.0_50.1__g4e5190fd.ari  25) cray-hdf5/1.12.0.4
 13) slurm/20.11.5-1                                     26) gcc/8.3.0

See documentation for full build instructions if necessary

Note: There is a env file in MOM6/build/gnu that specifies the programming environment we built with. Specifically, we used the GNU toolchain with gcc 8.3.1.

IMPORTANT: Source the env script before building anything (if you are on a Cray or HPC system with modules)

git clone https://www.github.com/CrayLabs/SmartRedis.git smartredis
cd smartredis
# checkout the 0.2.0 tag if available otherwise use develop
make lib
export SMARTREDIS_INSTALL_PATH=$(pwd)/install

Build MOM6

Assuming you checked out the repository, built and installed SmartSim and SmartRedis, you now need to build MOM6.

Follow the Getting Started portion of the MOM6-examples wiki for compiling and running the MOM6-SIS2 coupled model. Please be sure to replace the MOM6 directory from this repository in MOM6-examples/src/MOM6

In the Downloading input data section, make sure to download the OM4_025, obs, and CORE directories.

Download the SmartSim-MOM6 input data

We host and include the input data we used to run MOM6 along with pre-trained models and scripts we used for the paper.

To download the data, either at the DOI link at the top of the repo or here

Download the data into MOM6/INPUT. The MOM6 input dataset pretrained models and scripts for the SmartSim workload are all included. Replace the hidden .datasets symlink to the directory where you downloaded the MOM6 input data.

Copy the executable built previously into the MOM6 directory.

Run

Before running the SmartSim driver script, be sure that the computational setup described by the script suits your system.

This script assumes launching on a slurm cluster with at least

• 228 CPU nodes with 96 cpus (including hyperthreads)
• 16 nodes with P100 GPUs and 36 cpu cores (including hyperthreads)

This can be changed to suit your system with the parameters listed below

To run the exact same experiment as our paper, increase the time in both batch jobs and the number of days to 10 years. This is hopefully obvious how to do in the script.

Once configured, the entire workload can be executed with

# make sure python environment with SmartSim installed is active
cd driver
python driver.py

Note: this will submit two batch allocations to the scheduler of large size if configurations are not changed. To add account or other information please consult the SmartSim API Docs

Results

When the workload is run successfully, there will be a AI-EKE-MOM6 directory with all of the output from each ensemble member. Included are timings in each MOM_<ensemble_number>.out which look like

(SmartRedis put tensor)               0.003483      0.019676      0.010159      0.003618  0.000    41     0   909
(SmartRedis run model)                0.946908      2.807891      1.943015      0.462866  0.008    41     0   909
(SmartRedis unpack tensor )           0.001292      0.011080      0.001756      0.000605  0.000    41     0   909

You can use these to examine the overall timings of each operation that uses SmartRedis inside MOM6

Variants

Below are some variants that can be run for examining different configurations or for different systems

Reference Simulation

The compare the SmartSim approach vs the MEKE paramterization, change the line in MOM6/OM4_025/MOM_override from

EKE_SOURCE='sr' to EKE_SOURCE='prog'

Then comment out the parts of the driver script that create and launch the database. Once commented out, you can run the driver script as normal and the MOM6 simulations will be executed with the MEKE paramterization instead of the Smartsim approach.

CPU-only Machines

If you don't have GPU nodes, don't worry, we have you covered. Follow the instructions to install SmartSim for CPU. We include a pre-trained model for CPU inference as well. To use the CPU model, change the line in MOM6/OM4_025/MOM_override from

SMARTREDIS_MODEL='ncar_ml_eke.gpu.pt' to SMARTREDIS_MODEL='ncar_ml_eke.pt'

both models are included in the input data directory you downloaded earlier.

Contributors

The collaboration was a joint effort between Hewlett Packard Enterprise (HPE), National Center for Atmosheric Research (NCAR), and the University of Victoria (U Vic)

Contributors in no particular order

• Andrew Shao (U Vic)
• Sam Partee (HPE)
• Alessandro Rigazzi (HPE)
• Scott Bachman (NCAR)
• Gustavo Marques (NCAR)
• Matthew Ellis (HPE)

ncar_ml_eke's Issues

Update instructions for MOM6 data

The instructions presume that some of the more fundamental MOM6 input data for the OM4_025 configuration were pre-downloaded on disk (note this is separate from the data that is archived on zenodo). Currently the .datasets symlink points to a certain user (me) who no longer has access to the system.

We need to update the instructions to explain how to download and link the inputs on a brand new platform.