Q dependence of exciton eigenvalues
Moderators: Davide Sangalli, andrea.ferretti, myrta gruning, andrea marini, Daniele Varsano, Conor Hogan
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Re: Q dependence of exciton eigenvalues
Dear all,
In the folder where I performed BSE computations I don't have the ndb.BS_PAR_Q1 database.
I have for Q=1:
ndb.BS_diago_Q1 and ndb.BS_Q1_CPU_x (where x goes from 1 to 119 in my case)
How can I obtain the ndb.BS_PAR_Q1 database?
Best,
Davide
In the folder where I performed BSE computations I don't have the ndb.BS_PAR_Q1 database.
I have for Q=1:
ndb.BS_diago_Q1 and ndb.BS_Q1_CPU_x (where x goes from 1 to 119 in my case)
How can I obtain the ndb.BS_PAR_Q1 database?
Best,
Davide
-----------------------------------------------------
Assistant Professor
Polytech - Paris-Saclay University
C2N, CNRS
10 Bd Thomas Gobert
91120 Palaiseau
Assistant Professor
Polytech - Paris-Saclay University
C2N, CNRS
10 Bd Thomas Gobert
91120 Palaiseau
- Daniele Varsano
- Posts: 3816
- Joined: Tue Mar 17, 2009 2:23 pm
- Contact:
Re: Q dependence of exciton eigenvalues
Dear Davide,
please sign your post with your affiliation, it is a rule of the forum and you can do once for all filling the signature in the user profile.
The BS database are CPU dependent. You can either use just 1CPU (but this could be prohibitive), or you need to use the parallel I/O.
In order to do so you need to compile the code using in the configure the command:
--enable-hdf5-par-io
I never used it, but if I'm not wrong this should do the job, maybe other expert on parallel I/O can add more or correct me.
Best,
Daniele
please sign your post with your affiliation, it is a rule of the forum and you can do once for all filling the signature in the user profile.
The BS database are CPU dependent. You can either use just 1CPU (but this could be prohibitive), or you need to use the parallel I/O.
In order to do so you need to compile the code using in the configure the command:
--enable-hdf5-par-io
I never used it, but if I'm not wrong this should do the job, maybe other expert on parallel I/O can add more or correct me.
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/
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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- Posts: 71
- Joined: Sat Jun 06, 2020 10:43 am
Re: Q dependence of exciton eigenvalues
Dear Daniele,
Sorry, I forgot to put the affiliation.
I have done as suggested by Fulvio: I re-compiled Yambo (more precisely version 5.0.4) with the option: -enable-hdf5-par-io
The p2y works and also the initialization of the SAVE database.
However when I run the GW step, it crushes. I am sending in attachment the input, output, the LOG and the error of my machine.
It seems it has some problems with the HDF5 after he finishes with dipoles. What's going wrong?
Best,
Davide
-----------------------------------------------------
Post-doctoral fellow
Institut des NanoSciences de Paris
Sorbonne Université, CNRS
4 place Jussieu,
75252 PARIS Cedex 05
Sorry, I forgot to put the affiliation.
I have done as suggested by Fulvio: I re-compiled Yambo (more precisely version 5.0.4) with the option: -enable-hdf5-par-io
The p2y works and also the initialization of the SAVE database.
However when I run the GW step, it crushes. I am sending in attachment the input, output, the LOG and the error of my machine.
It seems it has some problems with the HDF5 after he finishes with dipoles. What's going wrong?
Best,
Davide
-----------------------------------------------------
Post-doctoral fellow
Institut des NanoSciences de Paris
Sorbonne Université, CNRS
4 place Jussieu,
75252 PARIS Cedex 05
You do not have the required permissions to view the files attached to this post.
-----------------------------------------------------
Assistant Professor
Polytech - Paris-Saclay University
C2N, CNRS
10 Bd Thomas Gobert
91120 Palaiseau
Assistant Professor
Polytech - Paris-Saclay University
C2N, CNRS
10 Bd Thomas Gobert
91120 Palaiseau
- Daniele Varsano
- Posts: 3816
- Joined: Tue Mar 17, 2009 2:23 pm
- Contact:
Re: Q dependence of exciton eigenvalues
Dear David,
this seems an error from the H5FScache.c :
honestly I do not have a clue on what is happening here, someone else maybe has more experience and can provide some hints.
Mot probably not related to you problem please note that in your script the intel/mkl module is not loaded:
Next, I had a look to our input and I suggest you to not use the terminator for X as it is memory intensive and does not save much, while the terminator on G is highly suggested.
Best,
Daniele
this seems an error from the H5FScache.c :
Code: Select all
yambo: H5FScache.c:1100: H5FS__cache_sinfo_deserialize: Assertion `old_tot_space == fspace->tot_space' failed.,
Mot probably not related to you problem please note that in your script the intel/mkl module is not loaded:
Code: Select all
ERROR: Unable to locate a modulefile for 'intel-mkl/2020.5'
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/
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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- Joined: Sat Jun 06, 2020 10:43 am
Re: Q dependence of exciton eigenvalues
Dear Daniele,
Thanks for your suggestions. Should I write something in the compilation topic or should I wait here if somebody has an answer?
Best,
Davide
Thanks for your suggestions. Should I write something in the compilation topic or should I wait here if somebody has an answer?
Best,
Davide
-----------------------------------------------------
Assistant Professor
Polytech - Paris-Saclay University
C2N, CNRS
10 Bd Thomas Gobert
91120 Palaiseau
Assistant Professor
Polytech - Paris-Saclay University
C2N, CNRS
10 Bd Thomas Gobert
91120 Palaiseau
- Daniele Varsano
- Posts: 3816
- Joined: Tue Mar 17, 2009 2:23 pm
- Contact:
Re: Q dependence of exciton eigenvalues
Dear Davide,
I'm not 100% sure this is a compilation issue. Let's hope that someone has a clue.
What you can do in the meanwhile is to calculate the dipoles without the parallel netcdf support and the BSE using it, in this way we can see if it is a particular problem of the dipole section.
Best,
Daniele
I'm not 100% sure this is a compilation issue. Let's hope that someone has a clue.
What you can do in the meanwhile is to calculate the dipoles without the parallel netcdf support and the BSE using it, in this way we can see if it is a particular problem of the dipole section.
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/
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/
- Davide Sangalli
- Posts: 614
- Joined: Tue May 29, 2012 4:49 pm
- Location: Via Salaria Km 29.3, CP 10, 00016, Monterotondo Stazione, Italy
- Contact:
Re: Q dependence of exciton eigenvalues
Dear all,
hard to say from the files.
Looking at the log file the job is interrupted when trying to write the ndb.dipoles database.
Can you check if the database was created and what it contains?
Also, maybe in one of the log files there is a specific error message
Tray to run
The error message I see is a general HDF5 message.
Attach the config/report file from your compilation as well.
D.
hard to say from the files.
Looking at the log file the job is interrupted when trying to write the ndb.dipoles database.
Can you check if the database was created and what it contains?
Also, maybe in one of the log files there is a specific error message
Tray to run
Code: Select all
$ grep ERROR LOG/l-*
Attach the config/report file from your compilation as well.
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/
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Re: Q dependence of exciton eigenvalues
Dear Davide,
So:
1) In my folder "g0w0" I have the dipole database "ndb.dipoles". If I do "ncdump -h ndb.dipoles" I get:
2) By doing "grep ERROR LOG/l-*" I get:
And this is for all the others cpus except for the first one apparently.
3) I am attaching the report file
Best,
Davide
So:
1) In my folder "g0w0" I have the dipole database "ndb.dipoles". If I do "ncdump -h ndb.dipoles" I get:
Code: Select all
ncdump: ndb.dipoles: ndb.dipoles: NetCDF: HDF error
Code: Select all
LOG/l-g0w0_HF_and_locXC_gw0_rim_cut_em1d_ppa_CPU_100:P100-r4i6n29: [ERROR] STOP signal received while in[05] Dipoles
LOG/l-g0w0_HF_and_locXC_gw0_rim_cut_em1d_ppa_CPU_100:P100-r4i6n29: [ERROR] Writing File ./g0w0//ndb.dipoles; Variable NOT DEFINED; NetCDF: HDF error
LOG/l-g0w0_HF_and_locXC_gw0_rim_cut_em1d_ppa_CPU_101:P101-r4i6n30: [ERROR] STOP signal received while in[05] Dipoles
3) I am attaching the report file
Best,
Davide
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-----------------------------------------------------
Assistant Professor
Polytech - Paris-Saclay University
C2N, CNRS
10 Bd Thomas Gobert
91120 Palaiseau
Assistant Professor
Polytech - Paris-Saclay University
C2N, CNRS
10 Bd Thomas Gobert
91120 Palaiseau
- Davide Sangalli
- Posts: 614
- Joined: Tue May 29, 2012 4:49 pm
- Location: Via Salaria Km 29.3, CP 10, 00016, Monterotondo Stazione, Italy
- Contact:
Re: Q dependence of exciton eigenvalues
It looks like it is the issue with asynchronous I/O
Try to replace the file with the one attached and recompile yambo.
Best,
D.
Try to replace the file
Code: Select all
src/dipoles/DIPOLE_IO.F
Best,
D.
You do not have the required permissions to view the files attached to this post.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/
-
- Posts: 71
- Joined: Sat Jun 06, 2020 10:43 am
Re: Q dependence of exciton eigenvalues
Dear Davide,
Thank you very much! Now everything works and I finally have also the ndb.BS_PAR* database
Best,
Davide
Thank you very much! Now everything works and I finally have also the ndb.BS_PAR* database
Best,
Davide
-----------------------------------------------------
Assistant Professor
Polytech - Paris-Saclay University
C2N, CNRS
10 Bd Thomas Gobert
91120 Palaiseau
Assistant Professor
Polytech - Paris-Saclay University
C2N, CNRS
10 Bd Thomas Gobert
91120 Palaiseau