[QE-users] DFT + U phonon calculation keeps on crashing at same mode

Fri Nov 26 09:13:28 CET 2021

Dear Iurii,

Thank you so much for your help. I have restarted the calculation and it finally finished! Regarding the time limit it is usually 5 days for the cluster I am using, but I have never requested that many nodes, so there might be a shorter time limit for such computational expensive calculations, so this might be a possibility and I will ask our system administrator about it. Once more thank you so much for all of your help and the fantastic work on the hp.x code!

Best wishes,

Johannes

ISIS/Diamond/University of Exeter
________________________________
From: Iurii TIMROV <iurii.timrov at epfl.ch>
Sent: Thursday, November 25, 2021 11:42 AM
To: Meusburger, Johannes (SDC,RAL,ISIS) <Johannes.Meusburger at stfc.ac.uk>; Iurii TIMROV <iurii.timrov at epfl.ch>; Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] DFT + U phonon calculation keeps on crashing at same mode

I forgot to tell that when you restart the DFPT+U code you should specify

read_dns_bare = .true.

                   If .true. the PH code tries to read three files in the DFPT+U
                   calculation: dns_orth, dns_bare, d2ns_bare.
                   dns_orth and dns_bare are the first-order variations of
                   the occupation matrix, while d2ns_bare is the second-order
                   variation of the occupation matrix. These matrices are
                   computed only once during the DFPT+U calculation. However,
                   their calculation (especially of d2ns_bare) is computationally
                   expensive, this is why they are written to file and then can be
                   read (e.g. for restart) in order to save time.

Iurii

--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: users <users-bounces at lists.quantum-espresso.org> on behalf of Iurii TIMROV via users <users at lists.quantum-espresso.org>
Sent: Thursday, November 25, 2021 12:35:23 PM
To: Johannes Meusburger - STFC UKRI; Quantum ESPRESSO users Forum
Subject: Re: [QE-users] DFT + U phonon calculation keeps on crashing at same mode

Dear Johannes,

I do not find anything strange in your input files.

Your calculation took 1 day and 14 hours to compute the second bare derivative of the occupation matrix, which is known to be a bottleneck of DFPT+U. Then, the code arrived to

Representation # 115 mode # 117

while in total you have 213 irreducible representations. So maybe you have a 2-days time limit and hence the phonon code was just stopped because you have hit the time limit on the cluster? Can you try to restart the calculation?

Greetings,

Iurii

--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: Johannes Meusburger - STFC UKRI <Johannes.Meusburger at stfc.ac.uk>
Sent: Thursday, November 25, 2021 11:20:44 AM
To: Iurii TIMROV; Quantum ESPRESSO users Forum
Subject: Re: [QE-users] DFT + U phonon calculation keeps on crashing at same mode

Dear Iurii,

I have uploaded the files to https://drive.google.com/drive/folders/1lovw14SlqeV8C9gFeUfhl4GfcVRhXcWT?usp=sharing and am using Quantum ESPRESSO 6.7 and GCC 8.3 as compiler.

Many thanks for your help and all the best,

Johannes
________________________________
From: users <users-bounces at lists.quantum-espresso.org> on behalf of Iurii TIMROV via users <users at lists.quantum-espresso.org>
Sent: Thursday, November 25, 2021 9:34 AM
To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] DFT + U phonon calculation keeps on crashing at same mode

Dear Johannes,

Can you share your input and output files again: please put them on Google Drive and send the link. Which version of QE and compiler do you use?

Greetings,

Iurii

--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: users <users-bounces at lists.quantum-espresso.org> on behalf of Johannes Meusburger - STFC UKRI <Johannes.Meusburger at stfc.ac.uk>
Sent: Thursday, November 25, 2021 10:23:53 AM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] DFT + U phonon calculation keeps on crashing at same mode

Dear all,

I just wanted to ask if anyone knows why my calculation keeps on crashing at the same mode and could suggest a solution.

All the best and many thanks,

Johannes

ISIS/Diamond/University of Exeter
________________________________
From: Meusburger, Johannes (SDC,RAL,ISIS)
Sent: Thursday, November 4, 2021 11:13 AM
To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: DFT + U phonon calculation keeps on crashing at same mode

Dear all,

I wanted to compute the phonon frequencies for FeSO4 x 4H2O at the gamma point at the DFT + U level. However, the calculation keeps on crashing at the same mode (i.e. Representation # 115 mode # 117). ph.x does not show any error but my cluster's error file states:

cpu-bind=MASK - cn044, task  0  0 [80073]: mask 0xffffffffffffffff set
mlx5: cn053.scarf.rl.ac.uk: got completion with error:
00000000 00000000 00000000 00000000
00000000 00000000 00000000 00000000
00000019 00000000 00000000 00000000
00000000 00008813 08027c5f 678857d3
[[55717,1],192][btl_openib_component.c:3645:handle_wc] from cn053 to: cn054 error polling LP CQ with status REMOTE ACCESS ERROR status number 10 for wr_id 3f7e980 opcode 1  vendor error 136 qp_idx 0

The same calculation at the LDA level (without Hubbard U) completed without any problems.

I have attached the pw.x and ph.x input and output files for the DFT + U calculation. Any help to resolve this issue would be very much appreciated.

Many thanks and all the best,

Johannes Meusburger
ISIS/Diamond/University of Exeter

This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20211126/693e2cb7/attachment.html>