How to restart a unfinished GW calculation

Various technical topics such as parallelism and efficiency, netCDF problems, the Yambo code structure itself, are posted here.

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

Bramhachari Khamari
Posts: 23
Joined: Wed Oct 23, 2019 5:52 am

How to restart a unfinished GW calculation

Post by Bramhachari Khamari » Fri Feb 28, 2020 2:21 pm

Dear Developers,
Within a particular time period if a GW calculation does not finish, Can we restart it from where it stopped or one needs to do the calculation from the scratch again. If we can restart, help me how to do it.


Regards,
Bramhachari Khamari
Bramhachari Khamari
Post Doctoral Fellow
Department of Physics
IIT Kanpur, India.

User avatar
Daniele Varsano
Posts: 2416
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: How to restart a unfinished GW calculation

Post by Daniele Varsano » Fri Feb 28, 2020 3:03 pm

Dear Bramhachari ,
it depends on what step the job did stop. If yambo was calculating the screening just relaunch your calculation and yambo will restart from the point it crashed. If it stopped when the screening was already computed unfortunately at the moment it is not possible to restart and the suggestion is to split your QP calculations in different runs, ie splitting the QPkrange in different jobs and finally merge the produced databases using the ypp utility (be careful to not overwrite the databases, you can either rename them or putting in different directories using the -J yambo option).

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/

Bramhachari Khamari
Posts: 23
Joined: Wed Oct 23, 2019 5:52 am

Re: How to restart a unfinished GW calculation

Post by Bramhachari Khamari » Sat Feb 29, 2020 7:21 am

Dear Sir,
Thank you for the reply. Suppose I run two sets (two different jobs) of calculations by splitting the Qpkrange. I do not know how to merge the two different datatbases coming from the two different calculations. Could you mention the complete command using the ypp which can do this.

Regards,
Bramhachari Khamari
Bramhachari Khamari
Post Doctoral Fellow
Department of Physics
IIT Kanpur, India.

User avatar
Daniele Varsano
Posts: 2416
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: How to restart a unfinished GW calculation

Post by Daniele Varsano » Sat Feb 29, 2020 9:20 am

Dear Bramhachari,
you need first to generate the ypp input file (ypp -h for a short help) by using the command line:

Code: Select all

ypp -q m 
Next, you need to edit the ypp.in file with the following syntax:

Code: Select all

%Actions_and_names             # [QPDB] Format is "what"|"OP"|"prefactor"|"DB"|. OP can be +/-/x(only for Z)
"E" |"+" |"1" |"DB1" |
"E" |"+" |"1" |"DB2" |
%
Where you substitute the DB1 and DB2 with the name of the QP databases file you want to merge or the path where they are found.
Finally, run ypp to perform the operation, a new database containing the merged data will becreated.
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/

haseebphysics1
Posts: 136
Joined: Sat Aug 17, 2019 2:48 pm

Re: How to restart a unfinished GW calculation

Post by haseebphysics1 » Sat May 16, 2020 12:29 pm

Dear developers,

I hope all of you are well!

One of my calculations, dielectric screening for BSE was running for 13 days and due to storage issues, it stopped without any error, I want to know that can I restart the calculation from the same point? If yes, then kindly guide the way to do so.



Thanks,
Haseeb Ahmad
MS - Physics,
LUMS - Pakistan

User avatar
Daniele Varsano
Posts: 2416
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: How to restart a unfinished GW calculation

Post by Daniele Varsano » Sat May 16, 2020 3:53 pm

Dear Haseeb,
if the calculation stops when calculating the dielectric screening (ndb.pp_frafmnet*) just relaunch your calculation and Yambo will continue from the last q point it was calculating. If it stopped during the GW convolution instead it will start from scratch (the convolution). In this case, it is useful to split the calculation of the QP into several runs and merge the QP databases at the end using the ypp utility.
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/

Zafer Kandemir
Posts: 5
Joined: Wed May 06, 2020 9:43 am
Contact:

Re: How to restart a unfinished GW calculation

Post by Zafer Kandemir » Wed Jun 03, 2020 10:56 am

Dear developers,

My GW calculation stopped due to bad termination error. It had done all the calculations as you can see them in screenshot of terminals (from 1 to 169). Can I restart this calculation? Thanks.

Best regards

--
Zafer Kandemir
Postdoctoral Researcher - Theoretical Physicist
Mechanical Engineering Department
Eskisehir Technical University
26555 Tepebasi-ESKISEHIR/TURKEY
----------------------------------------
You do not have the required permissions to view the files attached to this post.
-------------------
Zafer Kandemir
Postdoctoral Researcher (Theoretical Physicist)
Mechanical Engineering Department
Eskisehir Technical University
26555 Tepebasi-ESKISEHIR/TURKEY
(PhD Physics - Izmir Institute of Technology)

User avatar
Daniele Varsano
Posts: 2416
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: How to restart a unfinished GW calculation

Post by Daniele Varsano » Wed Jun 03, 2020 5:09 pm

Dear Zafer,
from the screenshot, you attached it seems that you successfully calculated the screening. When running the calculation again, yambo will read the screening and it will proceed to the QP calculation. Do you know the reason why yambo stopped, time limit or other reason?
In order to understand the reason why yambo stopped, you can upload your input, report and log file (you need to rename them with an allowed suffix e.g. .txt, or compress in a zip file) as we can have a look and see what went wrong.

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/

Zafer Kandemir
Posts: 5
Joined: Wed May 06, 2020 9:43 am
Contact:

Re: How to restart a unfinished GW calculation

Post by Zafer Kandemir » Thu Jun 04, 2020 1:38 pm

Dear Sir,
Thank you for replying. I know the reason. Yambo stopped due to out of memory. I attached the screenshots of the last 30 lines of r and l files. When I start this calculation again, new r-* and l-* files are generated with suffix *_01. Will the yambo read IP*.dat and ndb.* files? Is it correct?

Best regards.
You do not have the required permissions to view the files attached to this post.
-------------------
Zafer Kandemir
Postdoctoral Researcher (Theoretical Physicist)
Mechanical Engineering Department
Eskisehir Technical University
26555 Tepebasi-ESKISEHIR/TURKEY
(PhD Physics - Izmir Institute of Technology)

User avatar
Daniele Varsano
Posts: 2416
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: How to restart a unfinished GW calculation

Post by Daniele Varsano » Thu Jun 04, 2020 3:08 pm

Dear Zafer Kandemir,
it seems yambo read the databases and it is going forward.
You can check this looking at the report when database are read they are indicated with [RD], while they are written are indicated with [WR].

In general, please post the entire files and not the png. You can do by renaming them e.g. with a .txt suffix.
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/

Post Reply