Cheers guys, On Mon, Apr 23, 2012 at 5:33 PM, Christoph Junghans <[email protected]> wrote: > Hi Sikandar, > > you are correct! > > Threads make use of the shared memory nature of the system and hence > data is not communicated. > > I guess it would be possible to replace the thread class with a > mpi-based class, but I am not sure how much work it is. > Maybe Konstantin can comment on this! > > Cheers, > > Christoph > > > Am 23. April 2012 08:31 schrieb Sikandar Mashayak <[email protected]>: >> Hi >> >> As per my understanding, votca applications are thread enabled allowing >> us to use multiple cores on the same machine. Since, the implementation >> is based on the shared memory, I am not sure if we can use it on HPC >> to make use of multiple nodes, which require implementation based on the >> distributed memory. >> >> Please correct me, if I am missing anything. >> >> Thanks >> Sikandar >>
Threads are limited to shared memory architectures and VOTCA is based on threads, thus, you're right. Adding MPI as a communication interface is in principle possible. However, I don't see a practical application and feel free to correct me here: - VOTCA uses a simple parallelization over time frames, i.e., if you wanted to analyze a trajectory, you could also split it up into chunks of the size "frames/cores" and you'd be able to compute your quantities in a "trivially parallel" way - on a current server node with 8-12 cores, this runs already into IO limits: in order to use all CPU power, you want to decrease IO (little input data) and increase FLOPS (complicated inner calculation loops); if your actual calculation is too simple, VOTCA will be limited by transferring data from the disk to the memory (IO limit); this is what I observe most of the time - if you were to generalize this approach to more heterogeneous architectures (Threads+MPI), you'd be hitting fast-interconnect limits Do you have a minimal example that you'd like to be sped up? The first step would be to make sure that your calculation is limited by the CPU. Best Konstantin -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
