MOZYME parallel

[vvishwesh]

Just wanted a clarification. I am trying to do 1SCF calculation with MOZYME for a large protein. Can't see any evidence of multiple CPUs being used. Is the calculation single CPU only. Here are the keywords I am using 1SCF MOZYME XYZ THREADS=8

[godotalgorithm]

No, the MOZYME solver is not parallelized at all right now. The THREADS keyword is only for dense linear algebra operations (BLAS & LAPACK) used during conventional MOPAC calculations. MOZYME calculations generally have a relatively modest memory footprint, so the intended way to utilize multiple cores with MOZYME calculations is to run many independent jobs simultaneously, up to 1 job per core. Protein work often involves a combinatorial aspect (trying different ligands or binding sites), so there are often multiple independent calculations that need to be run at each stage of a study.

I have tinkered a bit with refactoring MOZYME's sparse pseudo-diagonalization algorithm, but there doesn't seem to be enough interest in it to justify more effort (i.e. I have no further work planned in the absence of a grant or contract). Prof. Gerd Rocha's group at the University of Paraiba has been independently working on adding OpenMP-based threading to the existing MOZYME implementation, and they are hoping to have it ready for integration into the open-source version of MOPAC in the next year or so.

[vvishwesh]

Thanks for the info.