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

[Dustin M. <dus...@gm...>]

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