[mpich-discuss] Code works with -ppn, fails without using MPICH 3.2

[Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]]

All,

I've been evaluating different MPI stacks on our cluster and found that 
MPICH 3.2 does really well on some simple little benchmarks. It also 
runs Hello World just fine, so I decided to apply it to our climate 
model (GEOS).

However, the first time I did that, things went a bit nuts. Essentially:

> (1065) $ mpirun -np 96 ./GEOSgcm.x | & tee withoutppn.log
> srun.slurm: cluster configuration lacks support for cpu binding
> Fatal error in PMPI_Comm_create: Unknown error class, error stack:
> PMPI_Comm_create(564).................: MPI_Comm_create(MPI_COMM_WORLD, group=0x88000000, new_comm=0x106d1740) failed
> PMPI_Comm_create(541).................: 
> MPIR_Comm_create_intra(215)...........: 
> MPIR_Get_contextid_sparse_group(500)..: 
> MPIR_Allreduce_impl(764)..............: 
> MPIR_Allreduce_intra(257).............: 
> allreduce_intra_or_coll_fn(163).......: 
> MPIR_Allreduce_intra(417).............: 
> MPIDU_Complete_posted_with_error(1137): Process failed
> MPIR_Allreduce_intra(417).............: 
> MPIDU_Complete_posted_with_error(1137): Process failed
> MPIR_Allreduce_intra(268).............: 
> MPIR_Bcast_impl(1452).................: 
> MPIR_Bcast(1476)......................: 
> MPIR_Bcast_intra(1287)................: 
> MPIR_Bcast_binomial(310)..............: Failure during collective

(NOTE: The srun.slurm thing is just an error/warning we always get. 
Doesn't matter if it's MPT, Open MPI, MVAPICH2, Intel MPI...it happens.)

The thing is, it works just fine at (NX-by-NY) of 1x6 and 2x12, but once 
I go to 3x18, boom, collapse. As I am on 28-core nodes, my first thought 
was it was due to crossing nodes. But, those benchmarks I ran did just 
fine for 192 nodes, so...hmm.

Out of desperation, I finally thought, what if it was the fact that 28 
doesn't divide 96 and passed in -ppn and:

> (1068) $ mpirun -ppn 12 -np 96 ./GEOSgcm.x |& tee withppn.log
> srun.slurm: cluster configuration lacks support for cpu binding
>  
>  In MAPL_Shmem:
>      NumCores per Node =           12
>      NumNodes in use   =            8
>      Total PEs         =           96
> ...

Starts up just fine! Note that every other MPI stack (MPT, Intel MPI, 
MVAPICH2, and Open MPI) handle the non-ppn type job just fine, but it's 
possible that they are evenly distributing the processes themselves. And 
the "MAPL_Shmem" lines you see are just reporting what the process 
structure looks like. I've added some print statements including this:

    if (present(CommIn)) then
        CommCap = CommIn
    else
        CommCap = MPI_COMM_WORLD
    end if

    if (.not.present(CommIn)) then
       call mpi_init(status)
       VERIFY_(STATUS)
    end if
    write (*,*) "MPI Initialized."

So, boring, and CommIn is *not* present, so we are using MPI_COMM_WORLD, 
and mpi_init is called as one would. Now if I run:

   mpirun -np 96 ./GEOSgcm.x | grep 'MPI Init' | wc -l

to count the number initialized, multiple times, I get results like: 
40, 56, 56, 45, 68. Never consistent.

So, I'm a bit at a loss. I freely admit I might have built MPICH3 
incorrectly. It was essentially my first time. I configured with:

>  ./configure --prefix=$SWDEV/MPI/mpich/3.2/intel_17.0.4.196 \
>     --disable-wrapper-rpath CC=icc CXX=icpc FC=ifort F77=ifort \
>      --enable-fortran=all --enable-cxx | & tee configure.intel_17.0.4.196.log

which might be too vanilla for a SLURM/Infiniband cluster, but, yet, it 
works with -ppn. But maybe I need extra options to work at all times? 
--with-ibverbs? --with-slurm?

Any ideas on what's happening and what I might have done wrong?

Thanks,
Matt
-- 
Matt Thompson, SSAI, Sr Scientific Programmer/Analyst
NASA GSFC,    Global Modeling and Assimilation Office
Code 610.1,  8800 Greenbelt Rd,  Greenbelt,  MD 20771
Phone: 301-614-6712                 Fax: 301-614-6246
http://science.gsfc.nasa.gov/sed/bio/matthew.thompson
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