ACHR.cu is a General Purpose Graphical Processing Unit (GP-GPU) implementation of the popular sampling algorithm of metabolic models ACHR.
The code comes with the peer-reviewed software note ACHR.cu: GPU accelerated sampling of metabolic networks..
Sampling is the tool of choice in metabolic modeling in unbiased analysis as it allows to explore the solution space constrained by the linear bounds without necessarily assuming an objective function. As metabolic models grow in size to represent communities of bacteria and complex human tissues, sampling became less used because of the large analysis time. With ACHR.cu we can achieve at least a speed up of 10x in the sampling process.
Technically sampling is a two step process:
The generation of warmup points.
The actual sampling starting from the previously generated warmup points.
The software can be installed via cloning this repository to your local machine and compiling
VFWarmup (for step 1) and
ACHR.cu (for step 2) at their root folders.
More details can be found in the documentation.
IBM CPLEX v12.6 (free for academics)
GSL linear algebra library
MPI and OpenMP
- Nvidia GPU with sm_35 architecture and above. Check the documentation for more details on the requirements.
Have a look at the code ocean capusle to run ACHR.cu in an interactive container with a sample example. The capsule has an access to an NVIDIA GPU with all software dependencies cached.
Sampling is a two-step process:
- The generation of warmup points.
cd VFWarmup source ./install.sh make
Make sure to run source on the install script because it exports environment variables. Then test your installation:
Then you can run the generation of warmup points
mpirun -np nCores --bind-to none -x OMP_NUM_THREADS=nThreads createWarmupPts model.mps
This command allows to generate warmup points given by the user in runtime of the model in
model.mps file using dynamically load balanced
nThreads through a hybrid MPI/OpenMP.
- The actual sampling starting from the previously generated warmup points.
Quick install first.
cd ACHRcu source ./install.sh make
Also here, make sure to run source on the install script because it exports environment variables. Then, test your installation:
Then you can perform the sampling.
./ACHRCuda model.mps warmuppoints.csv nFiles nPoints nSteps
This command allows to generate the actual sampling points starting from the previously generated sampling points stored in
warmuppoints.csv to generate a total of
nFiles*nPoints with each point
nSteps to converge.
The experiments were carried out using the HPC facilities of the University of Luxembourg
The software is free ańd is licensed under the MIT license, see the file LICENSE for details.
Please report any issues to the issues page.
Code of Conduct
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.