Tiger Team Projects
The following enumeration provides an overview of collaborations between members of the bwHPC-S5 team and scientists, i.e. tiger teams. To apply for support by a tiger team, click
Wave optic simulations using COMSOL and MATLAB with distributed memory
The goal of this computational project was the optimization of a micro-optical device. An optical model was implemented in COMSOL using the wave optics module and the frequency domain interface, which solves the electric field that a light source elicits inside an optical structure. In the end the optimization had to be controlled with an optimization algorithm and an objective function implemented in MATLAB. MATLAB calls COMSOL in an optimization loop and receives the results to find the best optical design.
Several opportunities were investigated to implement the interaction of the two programs on the bwForCluster NEMO and to distribute the calculation over multiple nodes. As a boundary condition, only one license of the floating network licenses of COMSOL could be used during the optimization step. However, the availability of this license was not guaranteed for subsequent requests, i.e. releasing the license and reacquiring it did not always succeed.
To circumvent this problem, a for-loop of job submissions via a shell script was used. This solution submited a COMSOL and a MATLAB job per iteration. A job array could not be used because the individual jobs interact with each other. The submission of multiple jobs slowed down the calculations. Therefore, in a second step, the individual iterations were consolidated into a for-loop within a single job submission and variables were passed to the job environment to take the dependencies into account.
As a final optimization, the control loop of the NEMO job submission was parametrized with the nodes and number of cores. COMSOL was called in a loop by MATLAB and started on the cluster each time. This variant has the advantage of controlling everything with the MATLAB job and saving computational time as well as conserving the COMSOL network license during the time of calculation.
Members of the Tiger Team: IMTEK - Laboratory for Biomedical Microtechnology (Marie Theresa Alt, Marta Timon), HPC Competence Center ENM (Freiburg)