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

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

Thank you! Will explore the FAQ section too.

On Wednesday, February 24, 2016, Thomas Hrabe <th...@gm...> wrote:

> Please go to
>
> pytom.org -> Documentation -> Guide & Tutorials -> FAQ and search for the
>
> LD_PRELOAD
>
> part.
>
> I think this MPI bug was previously fixed with setting LD_PRELOAD to your
> libmpi.so .
>
> Use locate libmpi.so to find it. If locate does not give you the location
> of the library, the paths.csh file in pytom/bin should list one of the
> directories in LD_LIBRARY_PATH where libmpi.so is.
>
> Thomas
>
>
> On Feb 24, 2016, at 2:37 PM, Kanika Khanna <kk...@uc...
> <javascript:_e(%7B%7D,'cvml','kk...@uc...');>> wrote:
>
> 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...
> <javascript:_e(%7B%7D,'cvml','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
>>
>
>
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