[3dem] problem running MPI on all threads

[Joel Meyerson]

I am unable to run Relion jobs with MPI procs on all available threads. For example, if running CTFFIND4 on our 4 core / 8 hyperthread machine, the job runs successfully with 4x MPI procs, but fails with 8x MPI procs. The error message reports: "Either request fewer slots for your application, or make more slots available for use".

One suspicion is that this problem may have arisen during compiling, so I've provided commands for "cmake" and "make" below, used when building Relion. I've also attached the output for the two commands. The system has Relion 3, Centos 7, openmpi3.

sudo cmake -DCUDA_ARCH=61 -DMPI_CXX_COMPILER=/usr/lib64/openmpi3/bin/mpicxx -DMPI_C_COMPILER=/usr/lib64/openmpi3/bin/mpicc ..

sudo make -j 8

Any suggestions on how to solve this?

Thanks,
Joel

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