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"LOG folder" on parallel run
Posted: Tue Aug 17, 2021 8:14 pm
by Abeshipour
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
Re: "LOG folder" on parallel run
Posted: Tue Aug 31, 2021 10:36 am
by Daniele Varsano
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
Re: "LOG folder" on parallel run
Posted: Wed Sep 01, 2021 2:37 pm
by Abeshipour
Dear Daniele
Thank you a lot for your answers.
I attach config.log .
Re: "LOG folder" on parallel run
Posted: Fri Sep 03, 2021 8:50 am
by andrea.ferretti
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
Re: "LOG folder" on parallel run
Posted: Fri Sep 10, 2021 11:13 am
by Abeshipour
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.
--------------------------------------------------------------------------
Re: "LOG folder" on parallel run
Posted: Fri Sep 10, 2021 12:13 pm
by Daniele Varsano
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