Disclaimer: This software is in beta-test mode, equivalent to the MESSy yellow traffic light status. No unexpected behaviour was observed under testing, and users are invited to test with their model setup. However, no express guarantee is provided for production simulations. For assistance or to report problems please contact: christoudias@cyi.ac.cy
Software: CUDA compiler and python3 are required for the pre-processor.
Hardware: CUDA compatible GPU (Fermi, Kepler, Pascal, Volta, or later).
To enable using the GPUs the file:
f2c_alpha.py and folder source
have to be available in the messy/util/medina directory.
No additional changes are required.
To install the latest version from github, go to the messy/util directory and run the command:
git clone https://github.com/CyprusInst/medina.git
Note: MESSy has to be linked with the -lcudart and -lstdc++ flags.
For example, you can append the flags to the SPEC_NETCDF_LIB variable
in the configuration file (under config/mh-XXXX).
You have to enter the ./messy/util/medina directory to execute the
preprocessor, by running “python f2c_alpha.py”. The preprocessor expects
the following files to be in place:
messy/smcl/messy_mecca_kpp.f90messy/smcl/messy_cmn_photol_mem.f90messy/smcl/messy_main_constants_mem.f90messy/util/kpp_integrate_cuda_prototype.cumessy/smcl/specific.mkmessy/smcl/Makefile.mIf any of these files is missing or not configured as in the MESSy release, the preprocessor will stop with an error message.
The following command line options are available to the user (and can be used for example to run in batch mode):
-r / --ros An integer value of the Rosenbrock solver produced [1: all (select at runtime), 2: Ros2, 3: Ros3, 4: Rodas3, 5: Rodas4]-g / --gpu An integer value of the architecture [1: FERMI, 2: KEPLER, 3: MAXWELL, 4: PASCAL]-s / --smcl MESSy smcl folder location, default: “../../smcl/”’During testing it was found that the runtime parameter NPROMA should be set
to a value not greater than 128 (preferably 64) for optimal memory allocation
and performance on the GPU.
Each CPU process that offloads to GPU requires a chunk of the GPU VRAM memory, dependent on the number of species and reaction constants in the MECCA mechanism. The number of GPUs per node and VRAM memory available in each GPU dictates the total number of CPU cores that can run simultaneously.
To run multiple CPU processes per GPU, the Multi-process service (MPS) provided by NVIDIA should be used.
A self-contained unit test is included in the ditribution. The test includes reference source files implementing a simplified chemistry mechanism and compiles, exexutes and compares the FORTRAN (using gfortran) and auto-generated CUDA versions.
The test is executed by sourcing driver.sh under the tests directory.
A utility script that compares the test solver output is also included in tests/compare.py
Alvanos, M. and Christoudias, T.: GPU-accelerated atmospheric chemical kinetics in the ECHAM/MESSy (EMAC) Earth system model (version 2.52), Geosci. Model Dev., 10, 3679-3693, https://doi.org/10.5194/gmd-10-3679-2017, 2017.
Alvanos, M. and Christoudias, T., 2017. MEDINA: MECCA Development in Accelerators – KPP Fortran to CUDA source-to-source Pre-processor. Journal of Open Research Software, 5(1), p.13. DOI: https://doi.org/10.5334/jors.158
M. Alvanos and T. Christoudias, “Accelerating Atmospheric Chemical Kinetics for Climate Simulations,” in IEEE Transactions on Parallel and Distributed Systems. DOI: https://doi.org/10.1109/TPDS.2019.2918798
Theodoros Christoudias, Timo Kirfel, Astrid Kerkweg, Domenico Taraborrelli, Georges-Emmanuel Moulard, Erwan Raffin, Victor Azizi, Gijs van den Oord, and Ben van Werkhoven. 2021. GPU Optimizations for Atmospheric Chemical Kinetics. In The International Conference on High Performance Computing in Asia-Pacific Region (HPC Asia 2021). Association for Computing Machinery, New York, NY, USA, 136–138. DOI: https://doi.org/10.1145/3432261.3439863