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MECCA development in accelerators - KPP Fortran to CUDA source-to-source pre-processor
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README.md

MECCA - KPP Fortran to CUDA source-to-source pre-processor

Disclaimer: This software is in alpha-test mode, equivalent to the MESSy red 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

1. Requirements:

Software: CUDA compiler and python are required for the pre-processor.

Hardware: CUDA compatible GPU (Fermi, Kepler, Pascal, Volta, or later).

2. Installation:

There are two files required to enable using the GPUs: f2c_alpha.py and kpp_integrate_cuda_prototype.cu.

The files have to be available in the messy/util directory. No additional changes are required.

Note: MESSy has to be linked with the -lcudart and -lstdc++ flags. For example, you can append it to the SPEC_NETCDF_LIB variable in the configuration file (under config/mh-XXXX).

3. Running the MECCA Fortran to CUDA source-to-source pre-processor:

You have to enter the ./messy/util 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.f90
  • messy/smcl/messy_cmn_photol_mem.f90
  • messy/smcl/messy_main_constants_mem.f90
  • messy/util/kpp_integrate_cuda_prototype.cu
  • messy/smcl/specific.mk
  • messy/smcl/Makefile.m

If any of these files is missing or not configured as in the MESSy release, the preprocessor will stop with an error message.

4. Running EMAC with GPU MECCA and improving performance:

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.

NVIDIA Multi-Process Service

To run multiple CPU processes per GPU, the Multi-process service (MPS) provided by NVIDIA can be used.

Warning: Memory Protection

Volta MPS client processes have fully isolated GPU address spaces. Pre-Volta MPS client processes allocate memory from different partitions of the same GPU virtual address space. As a result:

  • An out-of-range write in a CUDA Kernel can modify the CUDA-accessible memory state of another process, and will not trigger an error.
  • An out-of-range read in a CUDA Kernel can access CUDA-accessible memory modified by another process, and will not trigger an error, leading to undefined behavior.

5. Unit testing

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

6. References

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: http://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: 10.1109/TPDS.2019.2918798 URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=8723098&isnumber=4359390

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