Charm++ parallel programming system

[Ronak Buch <rabuch2 AT illinois.edu>]

Hi Mert,

You should be able to build NAMD by running NAMD's ./config script (CUDA is not used by default, you can also add --without-cuda to be explicit about it). You should be able to consult the NAMD documentation for any further questions you have.

Thanks,

Ronak

On 10/28/21 18:12, mert gölcük wrote:

Hi Sam,

Thanks for the fast response, I am so grateful. "./build charm++ ofi-linux-x86_64 smp -j12 --with-production" worked for me. Now, I am trying to build NAMD-2.14 without CUDA. Do you have any suggestions? 

Kind regards

Mert

Sam White <white67 AT illinois.edu>, 29 Eki 2021 Cum, 00:01 tarihinde şunu yazdı:

Hi Mert,

It looks like you are trying to build Charm++ on top of MPI. We generally prefer use of libfabric (OFI) as the most performant communication substrate to build Charm++ on Intel OmniPath network systems. To do that, build Charm++ with the following:

./build charm++ ofi-linux-x86_64 smp -j12 --with-production

If you do want to try an MPI build, then I think there is an inconsistency in your compiler modules and build command. It looks like you are trying to use Intel MPI with the GCC v10.2.0 compilers module loaded. I think the IMPI wrapper for GCC is properly named "mpicpc" on systems that support such configurations. So you can either try building with Intel MPI and GCC like this:

MPICXX=mpicpc ./build charm++ mpi-linux-x86_64 smp -j12 --with-production

Or with Intel MPI and the Intel compilers module loaded using:

MPICXX=mpiicpc ./build charm++ mpi-linux-x86_64 smp -j12 --with-production


Thanks, let us know if you run into any issues,
Sam

On Thu, Oct 28, 2021 at 2:14 PM mert gölcük <mertgolcuk AT gmail.com> wrote:

Dear developers,

I am trying to compile charm++ and NAMD on SUPERMUC-NG Supercomputers. NAMD is already installed on the Supermuc computers, but it is not working efficiently and fast when I compare it with the Stampede2. The architecture of both systems is the same. I attached the out file and input files. I couldn't solve the problem. Could you please help me with this issue?

Kind regards,

Mert Golcuk

System Specs;

CPU: 2x Intel Skylake Xeon Platinum 8174 

Network: Intel OmniPath

OS: SUSE Linux Enterprise Server 15 SP1

      --

Mert GÖLCÜK

Istanbul Technical University-PhD. Student at Molecular Biology-Genetics and Biotechnology Department

phone: +90 538 254 6464

e-mail: mertgolcuk AT gmail.com / golcuk AT itu.edu.tr