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A read-only Git copy of the OpenBenchmarking.org test profiles.
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mrbayes test does not scale with CPUs because it is not being built with an MPI tool chain and mpi config option #289

Open ColinIanKing opened 1 year ago

ColinIanKing commented 1 year ago

the install.sh script currently does not enable MPI and so when it is run with mpiexec it just runs on a single thread. A possible fix is:

tar -zxvf MrBayes-3.2.7a.tar.gz
cd MrBayes-3.2.7a
env MPICC=mpicc ./configure --with-mpi
make
echo $? > ~/install-exit-status

Note:

  1. one needs to set MPICC and use --with-mpi with ./configure
  2. on small memory systems make -j $NUM_CPU_CORES can OOM kill the build with MPI builds, so best to build it with one CPU

Also when running with just a few CPUs I've hit bugs with mrbayes and weird memory allocation issues being reported (from src/utils.c) during MPI runs:

      WARNING: Reallocation of zero size attempted. This is probably a bug. Problems may follow.
      WARNING: Reallocation of zero size attempted. This is probably a bug. Problems may follow.

..so I'm not sure if this is a scalable test case :-( As it stands, the test is not scaled onto the number of CPUs. I've run it on 1..24 cpus and don't see any scaling in performance because it's not built with a MPI toolchain.