Marcin,
If you are interested, I can send you the R examples I use to test
things offline.
-- bennet
On Mon, Jun 4, 2018 at 4:17 PM, marcin.krotkiewski
<marcin.krotkiew...@gmail.com> wrote:
> huh. This code also runs, but it also only displays 4 connect / disconnect
> messages. I should add that the test R script shows 4 connect, but 8
> disconnect messages. Looks like a bug to me, but where? I guess we will try
> to contact R forums and ask there.
>
> Bennet: I tried to use doMPI + startMPIcluster / closeCluster. In this case
> I get a warning about fork being used:
>
> --------------------------------------------------------------------------
> A process has executed an operation involving a call to the
> "fork()" system call to create a child process. Open MPI is currently
> operating in a condition that could result in memory corruption or
> other system errors; your job may hang, crash, or produce silent
> data corruption. The use of fork() (or system() or other calls that
> create child processes) is strongly discouraged.
>
> The process that invoked fork was:
>
> Local host: [[36000,2],1] (PID 23617)
>
> If you are *absolutely sure* that your application will successfully
> and correctly survive a call to fork(), you may disable this warning
> by setting the mpi_warn_on_fork MCA parameter to 0.
> --------------------------------------------------------------------------
>
> And the process hangs as well - no change.
>
> Marcin
>
>
>
> On 06/04/2018 05:27 PM, r...@open-mpi.org wrote:
>
> It might call disconnect more than once if it creates multiple
> communicators. Here’s another test case for that behavior:
>
>
>
>
>
> On Jun 4, 2018, at 7:08 AM, Bennet Fauber <ben...@umich.edu> wrote:
>
> Just out of curiosity, but would using Rmpi and/or doMPI help in any way?
>
> -- bennet
>
>
> On Mon, Jun 4, 2018 at 10:00 AM, marcin.krotkiewski
> <marcin.krotkiew...@gmail.com> wrote:
>
> Thanks, Ralph!
>
> Your code finishes normally, I guess then the reason might be lying in R.
> Running the R code with -mca pmix_base_verbose 1 i see that each rank calls
> ext2x:client disconnect twice (each PID prints the line twice)
>
> [...]
> 3 slaves are spawned successfully. 0 failed.
> [localhost.localdomain:11659] ext2x:client disconnect
> [localhost.localdomain:11661] ext2x:client disconnect
> [localhost.localdomain:11658] ext2x:client disconnect
> [localhost.localdomain:11646] ext2x:client disconnect
> [localhost.localdomain:11658] ext2x:client disconnect
> [localhost.localdomain:11659] ext2x:client disconnect
> [localhost.localdomain:11661] ext2x:client disconnect
> [localhost.localdomain:11646] ext2x:client disconnect
>
> In your example it's only called once per process.
>
> Do you have any suspicion where the second call comes from? Might this be
> the reason for the hang?
>
> Thanks!
>
> Marcin
>
>
> On 06/04/2018 03:16 PM, r...@open-mpi.org wrote:
>
> Try running the attached example dynamic code - if that works, then it
> likely is something to do with how R operates.
>
>
>
>
>
> 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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