Hi all, I installed on a new machine with a fresh build of openmpi 1.6.5, and
had one successful assembly with Ray 2.3- but all subsequent attempts have
resulted in an ORTE error (below). I tried rebuilding openmpi but that did not
change the error. Any ideas on this one?
Here's the Ray command with the same inputs that ran successfully the first
time:
scott@biolinux2[Ray-2.3.0] mpiexec -n 7 Ray -o test3 -p
TaqFragment_S2_L001_R1_001.fastq TaqFragment_S2_L001_R2_001.fastq -k 31
and here's the end of the error output:
[biolinux2:05099] [[57821,1],0] ORTE_ERROR_LOG: Data unpack would read past end
of buffer in file ../../../orte/util/nidmap.c at line 398
[biolinux2:05099] [[57821,1],0] ORTE_ERROR_LOG: Data unpack would read past end
of buffer in file ../../../../../orte/mca/ess/base/ess_base_nidmap.c at line 62
[biolinux2:05099] [[57821,1],0] ORTE_ERROR_LOG: Data unpack would read past end
of buffer in file ../../../../../../orte/mca/ess/env/ess_env_module.c at line
173
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_ess_base_build_nidmap failed
--> Returned value Data unpack would read past end of buffer (-26) instead of
ORTE_SUCCESS
--------------------------------------------------------------------------
[biolinux2:05099] [[57821,1],0] ORTE_ERROR_LOG: Data unpack would read past end
of buffer in file ../../../orte/runtime/orte_init.c at line 132
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_ess_set_name failed
--> Returned value Data unpack would read past end of buffer (-26) instead of
ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_mpi_init: orte_init failed
--> Returned "Data unpack would read past end of buffer" (-26) instead of
"Success" (0)
--------------------------------------------------------------------------
*** The MPI_Init() function was called before MPI_INIT was invoked.
*** This is disallowed by the MPI standard.
*** Your MPI job will now abort.
[biolinux2:5099] Abort before MPI_INIT completed successfully; not able to
guarantee that all other processes were killed!
--------------------------------------------------------------------------
mpiexec has exited due to process rank 0 with PID 5099 on
node biolinux2 exiting improperly.
------------------------------------------------------------------------------
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