"LOG folder" on parallel run

You can post here problems arising when using the latest 5.0 reslease of Yambo. Issues as parallelization strategy, performance issues and other technical aspects realted to the new release.

Moderators: Davide Sangalli, andrea marini, Daniele Varsano, andrea.ferretti, myrta gruning, Conor Hogan

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Abeshipour
Posts: 11
Joined: Mon Mar 22, 2021 10:45 am

"LOG folder" on parallel run

Post by Abeshipour » Tue Aug 17, 2021 8:14 pm

Dear all,

I am a newcomer to Yambo code, thus, I have some questions as follows

1.when I run Yambo code in the parallel space, the "Log folder" has not been created for me and, there are some output files as much as the requested cores.

Note that I followed Yambo's tutorial for parallel running.


2.can we run the first step of BSE calculations, i.e., Static screening, in the parallel space?

Best regards
Aref
Aref. Abeshipour
MSc student at chamran university of Ahvaz, Iran
https://scu.ac.ir/

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Daniele Varsano
Posts: 3070
Joined: Tue Mar 17, 2009 2:23 pm
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Re: "LOG folder" on parallel run

Post by Daniele Varsano » Tue Aug 31, 2021 10:36 am

Dear Aref,
1.when I run Yambo code in the parallel space, the "Log folder" has not been created for me and, there are some output files as much as the requested cores.
This means that the parallel compilation was not successful, you need to check your MPI environment. You can find some info on what went wrong in the config.log file. If you cannot spot them, please post your config.log file.
2.can we run the first step of BSE calculations, i.e., Static screening, in the parallel space?
Yes, all the run level can be run in parallel.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

Abeshipour
Posts: 11
Joined: Mon Mar 22, 2021 10:45 am

Re: "LOG folder" on parallel run

Post by Abeshipour » Wed Sep 01, 2021 2:37 pm

Dear Daniele
Thank you a lot for your answers.
I attach config.log .
You do not have the required permissions to view the files attached to this post.
Aref. Abeshipour
MSc student at chamran university of Ahvaz, Iran
https://scu.ac.ir/

andrea.ferretti
Posts: 195
Joined: Fri Jan 31, 2014 11:13 am

Re: "LOG folder" on parallel run

Post by andrea.ferretti » Fri Sep 03, 2021 8:50 am

Dear Aref,

at first sight I am not able to spot major problems in your config.log file.
Still, as already mention by Daniele, there could be inconsistencies in the compilation.

A few things to check are:
* is your parallel environment properly installed and working ? i.e., are you able to run
a simple test program in parallel using the very same compilers selected by yambo configure ?
(have a look at ~yambo/config/report)
* which mpilauncher are you using ? (mpirun ? is it consistent with the parallel compilation
you have done ? e.g, if you type `which mpirun` where does it come from ? same folders
as mpifort and mpicc, etc...)

take care
Andrea
Andrea Ferretti, PhD
CNR-NANO-S3 and MaX Centre
via Campi 213/A, 41125, Modena, Italy
Tel: +39 059 2055322; Skype: andrea_ferretti
URL: http://www.nano.cnr.it

Abeshipour
Posts: 11
Joined: Mon Mar 22, 2021 10:45 am

Re: "LOG folder" on parallel run

Post by Abeshipour » Fri Sep 10, 2021 11:13 am

Hello Andrea

Thanks for the tips

I reinstalled Yambo in parallel. But when I use " p2y ", I get the following error. Somehow it does not read the " XML " file. If possible, guide me to where the problem is. I attach the required files

Kind regards,
Aref

Code: Select all

ubuntu@arefabeshipour:~/hBN$ /home/ubuntu/yambo-5.0.3/bin/p2y
--------------------------------------------------------------------------
[[62131,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:

Module: OpenFabrics (openib)
  Host: arefabeshipour

Another transport will be used instead, although this may result in
lower performance.

NOTE: You can disable this warning by setting the MCA parameter
btl_base_warn_component_unused to 0.
--------------------------------------------------------------------------


 ___ __  _____  __ __  _____   _____
|   Y  ||  _  ||  Y  ||  _  \ |  _  |
|   |  ||. |  ||.    ||. |  / |. |  |
 \_  _/ |. _  ||.\_/ ||. _  \ |. |  |
  |: |  |: |  ||: |  ||: |   \|: |  |
  |::|  |:.|:.||:.|:.||::.   /|::.  |
  `--"  `-- --"`-- --"`-----" `-----"


 <---> DBs path set to : .
 <---> detected QE data format : unknown
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     Error in routine p2y_init (1):
     QE format not recognised/compatible (was wf_collect set to true?)
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 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.
--------------------------------------------------------------------------
You do not have the required permissions to view the files attached to this post.
Aref. Abeshipour
MSc student at chamran university of Ahvaz, Iran
https://scu.ac.ir/

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Daniele Varsano
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Re: "LOG folder" on parallel run

Post by Daniele Varsano » Fri Sep 10, 2021 12:13 pm

Dear Aref,

in which directory are you running the p2y?
You need to enter in the .save directory created by QE where the data-file-schema.xml file is present.

Best,

Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

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