[QE-users] Problem with Parallelization of Hp.x
Jamie Holber
holber at umich.edu
Fri Dec 2 22:47:33 CET 2022
That makes sense.
Thanks for your help.
Jamie
> On Dec 2, 2022, at 1:23 PM, Iurii TIMROV <iurii.timrov at epfl.ch> wrote:
>
> > In regards to the DFT+U+V I was following this line from the paper "for the sake of activating the Hubbard-related machinery (in the DFT+U+V case, there is no need to initialize V, instead initialize U for O(2p)).” Does this refer to something else?
>
> Actually this is not correct, sorry! One needs to specify at least one V to activate the DFT+U+V machinery.
>
> > If I output each HP runs to different output directories, how would I recombine the results at the end?
>
> You need to copy all files back to the same temporary folder and run the last step with compute_hp=.true. (Please check the exemples in the HP folder of Quantum ESPRESSO).
>
> HTH
>
> 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: Jamie Holber <holber at umich.edu>
> Sent: Friday, December 2, 2022 5:58:39 PM
> To: Iurii TIMROV
> Cc: Quantum ESPRESSO users Forum
> Subject: Re: [QE-users] Problem with Parallelization of Hp.x
>
> Hi Iurii,
>
> Thanks for the quick resolution!
>
> In regards to the DFT+U+V I was following this line from the paper "for the sake of activating the Hubbard-related machinery (in the DFT+U+V case, there is no need to initialize V, instead initialize U for O(2p)).” Does this refer to something else?
>
> If I output each HP runs to different output directories, how would I recombine the results at the end?
>
> Best,
> Jamie
>
>> On Dec 2, 2022, at 11:44 AM, Iurii TIMROV <iurii.timrov at epfl.ch <mailto:iurii.timrov at epfl.ch>> wrote:
>>
>> Dear Jamie,
>>
>> First of all, please note that you are not performing the DFT+U+V calculation but DFT+U because you specified this:
>> HUBBARD {ortho-atomic}
>> U Fe1-3d 1e-10
>> U Fe2-3d 1e-10
>> U Mn1-3d 1e-10
>> U Mn2-3d 1e-10
>> U O-2p 1e-10
>>
>> The pw.x code will perform DFT+U+V only if it detects at least one V parameter in the input. So you should specify e.g. this:
>> HUBBARD {ortho-atomic}
>> U Fe1-3d 1e-10
>> U Fe2-3d 1e-10
>> U Mn1-3d 1e-10
>> U Mn2-3d 1e-10
>> V Fe1-3d O-2p 1 5 1e-10
>>
>> I specified some random couple: 1st and 5th atom. The HP code will consider all O atoms as Hubbard atoms and will perturb non-equivalent O atoms.
>>
>> Now, coming to your problem. Your calculations crash because you are using the same temporary directory for all calculations: outdir='outdir/'. So independent HP calculations write and read to/from the same folder and this creates a mess. Instead, for each independent calculation you need to use a separate temporary directory, e.g. outdir1, outdir2, etc. So once you performed the ground-state calculation using pw.x, just copy outdir to outdir1, outdir2, ... and run independent HP calculations simultaneously:
>> HP run 1 : perturb_only_atom(5) = .true. -> outdir1
>> HP run 2 : perturb_only_atom(6) = .true. -> outdir2
>> ...
>>
>> HTH
>>
>> 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 <http://people.epfl.ch/265334>
>> From: Jamie Holber <holber at umich.edu <mailto:holber at umich.edu>>
>> Sent: Friday, December 2, 2022 5:04:00 PM
>> To: Iurii TIMROV
>> Cc: Quantum ESPRESSO users Forum
>> Subject: Re: [QE-users] Problem with Parallelization of Hp.x
>>
>> Just uploaded.
>>
>> Thanks,
>> Jamie
>>
>>> On Dec 2, 2022, at 10:56 AM, Iurii TIMROV <iurii.timrov at epfl.ch <mailto:iurii.timrov at epfl.ch>> wrote:
>>>
>>> Thanks! Could you upload please also the input and output files of the pw.x calculations?
>>>
>>> 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 <http://people.epfl.ch/265334>
>>>
>>> From: Jamie Holber <holber at umich.edu <mailto:holber at umich.edu>>
>>> Sent: Friday, December 2, 2022 4:45:13 PM
>>> To: Iurii TIMROV; Quantum ESPRESSO users Forum
>>> Subject: Re: [QE-users] Problem with Parallelization of Hp.x
>>>
>>> Hi Iurii,
>>>
>>> Thanks for the response. I don’t believe it is a problem with disc space because when I run the hp calculations in serial or I run hp.x calculations at the same time with different outdir they run successfully.
>>>
>>> I have uploaded the hp files to the google drive linked. I attempted to run hp_atom5.in and hp_atom6.in at the same time.
>>> https://drive.google.com/drive/folders/1gRVALU0B8CLsaKBZpXzvEFAHcb5dMXZ_?usp=share_link <https://drive.google.com/drive/folders/1gRVALU0B8CLsaKBZpXzvEFAHcb5dMXZ_?usp=share_link>
>>>
>>> Thank you,
>>> Jamie
>>>
>>>> On Dec 2, 2022, at 6:04 AM, Iurii TIMROV via users <users at lists.quantum-espresso.org <mailto:users at lists.quantum-espresso.org>> wrote:
>>>>
>>>> Dear Jamie,
>>>>
>>>> The problem seems to occur when writing or reading files on a disc. Are you sure that you have enough free disc space?
>>>>
>>>> Could you provide please more details about your calculations? Please share your input and output files for all pw.x and hp.x calculations that fail (e.g. using Google Drive).
>>>>
>>>> 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 <http://people.epfl.ch/265334>
>>>> From: users <users-bounces at lists.quantum-espresso.org <mailto:users-bounces at lists.quantum-espresso.org>> on behalf of Jamie Holber <holber at umich.edu <mailto:holber at umich.edu>>
>>>> Sent: Thursday, December 1, 2022 9:03:19 PM
>>>> To: users at lists.quantum-espresso.org <mailto:users at lists.quantum-espresso.org>
>>>> Subject: [QE-users] Problem with Parallelization of Hp.x
>>>>
>>>> Hello everyone,
>>>>
>>>> I am trying to replicate the U+V calculations for LiMnFePo4 as described in Timrov, Iurii, Nicola Marzari, and Matteo Cococcioni. "HP--A code for the calculation of Hubbard parameters using density-functional perturbation theory." arXiv preprint arXiv:2203.15684 (2022). <https://arxiv.org/pdf/2203.15684.pdf> The hp files run fine when I run them one at a time. However, when I try to parallelize over different perturbed atoms by running them simultaneously as described in section 4.2 I receive errors and at least one run fails. I have tried it on two different computing cluster and they both failed, but with different error messages. I’ve included the input files/errors below. Does anyone know of a way to solve this issue?
>>>>
>>>> Input file 1:
>>>> &inputhp
>>>> prefix = 'olivine', outdir='outdir/',
>>>> nq1 = 1, nq2 = 2, nq3 = 3,
>>>> conv_thr_chi = 1.0d-7,
>>>> niter_max=250,
>>>> dist_thr = 5.D-3
>>>> perturb_only_atom(5) = .true.
>>>> /
>>>>
>>>> Input file 2:
>>>> &inputhp
>>>> prefix = 'olivine', outdir='outdir/',
>>>> nq1 = 1, nq2 = 2, nq3 = 3,
>>>> conv_thr_chi = 1.0d-7,
>>>> niter_max=250,
>>>> dist_thr = 5.D-3
>>>> perturb_only_atom(6) = .true.
>>>> /
>>>>
>>>> Errors from computing cluster 1
>>>>
>>>> Error termination. Backtrace:
>>>> At line 700 of file buffers.f90 (unit = 20, file = 'outdir/olivine.wfc1')
>>>> Fortran runtime error: File cannot be deleted
>>>>
>>>> Error termination. Backtrace:
>>>> #0 0x479784 in __buffers_MOD_close_buffer
>>>> at /home/jholber/LFP/QE_studies/copy/qe-7.1/PW/src/buffers.f90:700
>>>> #1 0x405a27 in hp_close_q_
>>>> at /home/jholber/LFP/QE_studies/copy/qe-7.1/HP/src/hp_close_q.f90:28
>>>> #2 0x4057c1 in hp_main
>>>> at /home/jholber/LFP/QE_studies/copy/qe-7.1/HP/src/hp_main.f90:143
>>>> #3 0x404fac in main
>>>> at /home/jholber/LFP/QE_studies/copy/qe-7.1/HP/src/hp_main.f90:14
>>>>
>>>> Errors from Computer clusters 2
>>>>
>>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>> Error in routine davcio (22):
>>>> error writing file "/home/holber/q-e/HP/examples/LFP/../../tempdir/HP/LFP.dwfc11"
>>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>>
>>>>
>>>> Thank you,
>>>> Jamie Holber
>>>> University of Michigan
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