I am adapting a fortran mpi program from sequential to parallel writing for certain types of files. It uses netcdf 4.3.3.1/hdf5 1.8.9 parallel. I use intel compiler version 14.0.3.174.
When all reads/writes are done it is time to close the files. At this point, the simulations does not continue anymore. So all calls are waiting. When I check the call stack from each processor I can see the master root is different compared to the rest of them.
Mpi Master processor call stack:
__sched_yield, FP=7ffc6aa978b0
opal_progress, FP=7ffc6aa978d0
ompi_request_default_wait_all, FP=7ffc6aa97940
ompi_coll_tuned_sendrecv_actual, FP=7ffc6aa979e0
ompi_coll_tuned_barrier_intra_recursivedoubling, FP=7ffc6aa97a40
PMPI_Barrier, FP=7ffc6aa97a60
H5AC_rsp__dist_md_write__flush, FP=7ffc6aa97af0
H5AC_flush, FP=7ffc6aa97b20
H5F_flush, FP=7ffc6aa97b50
H5F_flush_mounts, FP=7ffc6aa97b80
H5Fflush, FP=7ffc6aa97ba0
NC4_close, FP=7ffc6aa97be0
nc_close, FP=7ffc6aa97c00
restclo, FP=7ffc6aa98660
driver, FP=7ffc6aaa5ef0
main, FP=7ffc6aaa5f90
__libc_start_main, FP=7ffc6aaa6050
_start,
Remaining processors call stack:
__sched_yield, FP=7fffe330cdd0
opal_progress, FP=7fffe330cdf0
ompi_request_default_wait, FP=7fffe330ce50
ompi_coll_tuned_bcast_intra_generic, FP=7fffe330cf30
ompi_coll_tuned_bcast_intra_binomial, FP=7fffe330cf90
ompi_coll_tuned_bcast_intra_dec_fixed, FP=7fffe330cfb0
mca_coll_sync_bcast, FP=7fffe330cff0
PMPI_Bcast, FP=7fffe330d030
mca_io_romio_dist_MPI_File_set_size, FP=7fffe330d080
PMPI_File_set_size, FP=7fffe330d0a0
H5FD_mpio_truncate, FP=7fffe330d0c0
H5FD_truncate, FP=7fffe330d0f0
H5F_dest, FP=7fffe330d110
H5F_try_close, FP=7fffe330d340
H5F_close, FP=7fffe330d360
H5I_dec_ref, FP=7fffe330d370
H5I_dec_app_ref, FP=7fffe330d380
H5Fclose, FP=7fffe330d3a0
NC4_close, FP=7fffe330d3e0
nc_close, FP=7fffe330d400
RESTCOM`restclo, FP=7fffe330de60
driver, FP=7fffe331b6f0
main, FP=7fffe331b7f0
__libc_start_main, FP=7fffe331b8b0
_start,
I do realize one call stack contain bcast an the other a barrier. This might cause a deadlock. Yet I do not foresee how to continue from here. If a mpi call is not properly done (e.g only called in 1 proc), I would expect an error message instead of such behaviour.
Update: the source code is around 100k lines.
The files are opened this way:
cmode = ior(NF90_NOCLOBBER,NF90_NETCDF4)
cmode = ior(cmode, NF90_MPIIO)
CALL ipslnc( NF90_CREATE(fname,cmode=cmode,ncid=ncfid, comm=MPI_COMM, info=MPI_INFO))
And closed as:
iret = NF90_CLOSE(ncfid)
