Fail to run IP calculations in parallel

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Joined: Tue Nov 07, 2023 1:53 pm

Fail to run IP calculations in parallel

Post by Jessie » Thu Nov 23, 2023 8:57 am

Dear all,

I was trying to follow the steps in the tutorial ... n_parallel to run an IP calculation in parallel, but it has failed. I also tried to run an RPA calculation and the same error occured. Here is the error information in the log files

Code: Select all

P1: [ERROR] STOP signal received while in[04] Dipoles
P1: [ERROR] Writing File ./IP_mpi8//ndb.dipoles; Variable  NOT DEFINED; NetCDF: Parallel operation on file opened for non-parallel access
and the error information on my screen:

Code: Select all

MPI_ABORT was invoked on rank 4 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
[localhost.localdomain:42104] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[localhost.localdomain:42104] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[localhost.localdomain:42104] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
The version of my yambo code is MPI+HDF5_MPI_IO - Ver. 5.1.0 and the code was installed by conda. The task has been run in the following steps:

1. yambo
2. yambo -o c -V par -F
(However, in this step, I didn't find variables named "X_Threads" and "DIP_Threads" which are mentioned in the tutorial webpage above, so I didn't change any variables about parallel in the input file.)
3. mpirun -np 8 yambo -F &

Could you give me some instructions to solve this error? Thanks.

Best regards,
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Postgraduate student
Department of Materials Science
Fudan University

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Daniele Varsano
Posts: 3926
Joined: Tue Mar 17, 2009 2:23 pm

Re: Fail to run IP calculations in parallel

Post by Daniele Varsano » Thu Nov 23, 2023 9:06 am

Dear Jessie,

it seems you have an I/O problem. It could be related to some conflict with the used parallel compiler and the mpirun you are using to launch the job.
In any case, I suggest you to update to the latest version of the code and try again. If the problem persists we will insoect it in more details.
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale

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