Try running the attached example dynamic code - if that works, then it likely is something to do with how R operates.
simple_spawn.c
Description: Binary data
> On Jun 4, 2018, at 3:43 AM, marcin.krotkiewski <marcin.krotkiew...@gmail.com>
> wrote:
>
> Hi,
>
> I have some problems running R + Rmpi with OpenMPI 3.1.0 + PMIx 2.1.1. A
> simple R script, which starts a few tasks, hangs at the end on diconnect.
> Here is the script:
>
> library(parallel)
> numWorkers <- as.numeric(Sys.getenv("SLURM_NTASKS")) - 1
> myCluster <- makeCluster(numWorkers, type = "MPI")
> stopCluster(myCluster)
>
> And here is how I run it:
>
> SLURM_NTASKS=5 mpirun -np 1 -mca pml ^yalla -mca mtl ^mxm -mca coll ^hcoll R
> --slave < mk.R
>
> Notice -np 1 - this is apparently how you start Rmpi jobs: ranks are spawned
> by R dynamically inside the script. So I ran into a number of issues here:
>
> 1. with HPCX it seems that dynamic starting of ranks is not supported, hence
> I had to turn off all of yalla/mxm/hcoll
>
> --------------------------------------------------------------------------
> Your application has invoked an MPI function that is not supported in
> this environment.
>
> MPI function: MPI_Comm_spawn
> Reason: the Yalla (MXM) PML does not support MPI dynamic process
> functionality
> --------------------------------------------------------------------------
>
> 2. when I do that, the program does create a 'cluster' and starts the ranks,
> but hangs in PMIx at MPI Disconnect. Here is the top of the trace from gdb:
>
> #0 0x00007f66b1e1e995 in pthread_cond_wait@@GLIBC_2.3.2 () from
> /lib64/libpthread.so.0
> #1 0x00007f669eaeba5b in PMIx_Disconnect (procs=procs@entry=0x2e25d20,
> nprocs=nprocs@entry=10, info=info@entry=0x0, ninfo=ninfo@entry=0) at
> client/pmix_client_connect.c:232
> #2 0x00007f669ed6239c in ext2x_disconnect (procs=0x7ffd58322440) at
> ext2x_client.c:1432
> #3 0x00007f66a13bc286 in ompi_dpm_disconnect (comm=0x2cc0810) at
> dpm/dpm.c:596
> #4 0x00007f66a13e8668 in PMPI_Comm_disconnect (comm=0x2cbe058) at
> pcomm_disconnect.c:67
> #5 0x00007f66a16799e9 in mpi_comm_disconnect () from
> /cluster/software/R-packages/3.5/Rmpi/libs/Rmpi.so
> #6 0x00007f66b2563de5 in do_dotcall () from
> /cluster/software/R/3.5.0/lib64/R/lib/libR.so
> #7 0x00007f66b25a207b in bcEval () from
> /cluster/software/R/3.5.0/lib64/R/lib/libR.so
> #8 0x00007f66b25b0fd0 in Rf_eval.localalias.34 () from
> /cluster/software/R/3.5.0/lib64/R/lib/libR.so
> #9 0x00007f66b25b2c62 in R_execClosure () from
> /cluster/software/R/3.5.0/lib64/R/lib/libR.so
>
> Might this also be related to the dynamic rank creation in R?
>
> Thanks!
>
> Marcin
>
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