Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval

[Kanika K. <kk...@uc...>]

Hello,

So I am trying localization with the tutorial data set itself. I did not
use the hostfile as I am running on only one host. Hence, I specified the
host and no. of CPUs as per the following command

mpirun --host 'HostName' -c 4 pytom /usr/local/pytom/bin/localization.py
'PathToJobFile'/job.xml 2 2 2

I get the following error:

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):

  opal_init failed
  --> Returned value Error (-1) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***    and potentially your MPI job)
[pordoi:29128] Local abort before MPI_INIT completed successfully; not able
to aggregate error messages, and not able to guarantee that all other
processes were killed!


On Tue, Feb 23, 2016 at 3:44 PM, Dustin Morado <dus...@gm...>
wrote:

> Hi Kanika,
>
> What was the command you ran exactly? It looks like there’s an error with
> your host file. Are you running this on a cluster, or just a workstation
> with openmpi?
>
> If it’s the latter you can simply run it like this:
> mpirun --hostfile localhost -c 8 pytomlocalization.py job.xml 2 2 2
>
> which will send one of each of the 8 chunks of the tomogram to a processor.
>
> If you are on a cluster, you might want to ask the cluster admin if
> there’s a specific submit script you need to run to have access to the
> correct default hostfile.
>
> —
> Cheers,
> Dustin
>
>
> > Thanks you for that. When I run the process with openmpi, i get the
> following
> > error message:
> > Open RTE detected a parse error in the hostfile:
> /home/kkhanna/Documents/Pytom/Bacillus_ribosome/job.xml It occured on line
> number 37 on token 1.
> > —————————————————————————————————————
> > [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file
> base/rmaps_base_support_fns.c at line 176
> > [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file rmaps_rr.c at
> line 121
> > [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file
> base/rmaps_base_map_job.c at line 379
> > [pordoi:25878] 2 more processes have sent help message help-hostfile.txt
> / parse_error
> > [pordoi:25878] Set MCA parameter "orte_base_help_aggregate" to 0 to see
> all help / error messages
>