[QE-users] Re?? Re?? Re?? Error happens after setting max_seconds in turbo_davidson.x

?? Tue, 20 Apr 2021 03:31:56 -0700

Dear Iurii,


Thanks for your suggestion. As the HPC of our University is used to run this 
calculation, I will check it with our IT service about the disc spece. Thanks.


Best,
Weijie Zhou&nbsp;




----------------------------------------------------------------
Weijie Zhou
PhD student
University of Leeds
UK

------------------&nbsp;????????&nbsp;------------------
??????:                                                                         
                                               "Iurii TIMROV"                   
                                                                 
<users@lists.quantum-espresso.org&gt;;
????????:&nbsp;2021??4??19??(??????) ????6:33
??????:&nbsp;"users"<users@lists.quantum-espresso.org&gt;;

????:&nbsp;Re: [QE-users]Re?? Re?? Error happens after setting max_seconds in   
turbo_davidson.x



  
Dear Weijie,
 

 
 
For me it works using QE6.7. Please see the files here: 
 
 
https://drive.google.com/drive/folders/1U-SIOw1UHtidryhb1cJeYsgurkm2YPFM?usp=sharing
 

 
 
Check that you have enough disc space. Try on a different cluster. Do not mix 
versions of QE.
 

 
 
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: users <users-boun...@lists.quantum-espresso.org&gt; on behalf of ?? 
<508682...@qq.com&gt;
 Sent: Sunday, April 18, 2021 10:28:45 PM
 To: users
 Subject: [QE-users] Re?? Re?? Error happens after setting max_seconds in 
turbo_davidson.x &nbsp;
 
  Dear Iurii,
 
 
 Thanks for your reply. I modified my input followed with your suggestion but 
ecut is set as 40 (30 cannot make convergence), and ran the calculation using 
QE6.5. It made restart file successfully. It seems that large memory 
contributed to big value of  ecut leads to the problem. But in scf calculation, 
ecut of 40 is not good one as it lead to highest occupied/lowest unoccupied 
shitfed to 5.2276/5.4369 from 4.8298/5.6383 (ecut 80).&nbsp; 
 
 
 Besides, I tried to use QE6.7 with ecut 80, and other parameters for input 
files are same with yours.&nbsp; But new error occured when running 
turbo_davidson.x giving the error as
 
 
 Reading xml data from directory:
 
 
 &nbsp; &nbsp; 
&nbsp;../../../tmp_Mo8O26_davidson_size20_e-4_nosmearing_QE6.7/Mo_O.save/
 &nbsp; &nbsp; &nbsp;Message from routine qes_read:magnetizationType:
 &nbsp; &nbsp; &nbsp;do_magnetization: wrong number of occurrences
 &nbsp; &nbsp; &nbsp;Message from routine qexsd_readschema :
 &nbsp; &nbsp; &nbsp;error reading output_obj of xsd data file
 
 
 
&nbsp;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 
 
&nbsp;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 
 
&nbsp;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 &nbsp; &nbsp; &nbsp;Error in routine read_xml_file (4):
 &nbsp; &nbsp; &nbsp;fatal error reading xml file
 
&nbsp;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 
 
 
 
 Do you have any clue about this error? The input&amp;output files for this 
calcualtion could be accessed in
 
 
 
https://drive.google.com/drive/folders/1lJTr7WdcOf73Bk36fSxP-yHZk52iDqGS?usp=sharing&nbsp;&nbsp;
 
 
 
 
 
 Thanks,
 
 
 Weijie Zhou
  
 
 
 
  ----------------------------------------------------------------
 Weijie Zhou
 PhD student
 University of Leeds
 UK
 
 
 
 ------------------ ???????? ------------------
  ??????: "Iurii TIMROV" <users@lists.quantum-espresso.org&gt;;
 ????????:&nbsp;2021??4??17??(??????) ????10:21
 ??????:&nbsp;"users"<users@lists.quantum-espresso.org&gt;;
 
 ????:&nbsp;Re: [QE-users]Re?? Error happens after setting max_seconds in 
turbo_davidson.x
 
 
 
  
Dear Weijie,
 

 
 
I have run a test using QE6.7 and your inputs with reduced parameters on my 
workstations using 8 cores. The code works fine, the restart files are written 
successfully when the turbo_davidson.x code reached max_seconds. Below are my 
inputs, you can try them  as well.
 

 
 
Please check that you have enough disc space.
 

 
 
Greetings,
 
Iurii
 

 
 
 &nbsp;&amp;control
 
 &nbsp; &nbsp; calculation='scf'
 
 &nbsp; &nbsp; restart_mode='from_scratch',
 
 &nbsp; &nbsp; prefix='MoO'
 
 &nbsp; &nbsp; pseudo_dir = '/scratch/timrov/q-e-qe-6.7MaX-Release/pseudo/'
 
 &nbsp; &nbsp; outdir='/scratch/timrov/q-e-qe-6.7MaX-Release/tempdir/'
 
 &nbsp;/
 
 &nbsp;&amp;system
 
 &nbsp; &nbsp; a &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp; &nbsp; &nbsp; =&nbsp;  2.00000e+01
 
 &nbsp; &nbsp; ecutwfc &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp; =&nbsp;  30
 
 &nbsp; &nbsp; ibrav &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp; &nbsp; = 1
 
 &nbsp; &nbsp; nat &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp; &nbsp; &nbsp; = 34
 
 &nbsp; &nbsp; ntyp&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp; &nbsp; &nbsp; = 2
 
 &nbsp; &nbsp; nbnd&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 
&nbsp; &nbsp; &nbsp; =250
 
 &nbsp; &nbsp; tot_charge= -4
 
 &nbsp; &nbsp; assume_isolated='martyna-tuckerman'
 
 &nbsp;/
 
 &nbsp;&amp;electrons
 
 &nbsp; &nbsp; conv_thr =&nbsp; 1.0d-8
 
 &nbsp;/
 
 ATOMIC_SPECIES
 
 Mo&nbsp; 95.94&nbsp; &nbsp; Mo.upf
 
 O&nbsp; 15.999&nbsp; &nbsp; O.upf
 
 ATOMIC_POSITIONS {angstrom}
 
 Mo&nbsp; &nbsp; &nbsp; 0.011800&nbsp; -0.882450&nbsp; -2.732125
 
 Mo&nbsp; &nbsp; &nbsp; 0.210675&nbsp; -2.315000 &nbsp; 1.646750
 
 Mo&nbsp; &nbsp; &nbsp; 1.961325&nbsp; -2.892175&nbsp; -1.042350
 
 Mo &nbsp; &nbsp; -1.743275&nbsp; -0.383075&nbsp; -0.047150
 
 O &nbsp; &nbsp; &nbsp; 0.170525&nbsp; -1.302200&nbsp; -0.431375
 
 O &nbsp; &nbsp; &nbsp; 1.833025&nbsp; -2.939550 &nbsp; 0.887000
 
 O &nbsp; &nbsp; &nbsp; 1.668550&nbsp; -1.814000&nbsp; -2.603400
 
 O &nbsp; &nbsp; &nbsp; 0.852375&nbsp; -4.156450&nbsp; -1.364525
 
 O &nbsp; &nbsp; &nbsp; 3.494400&nbsp; -3.581575&nbsp; -1.331675
 
 O&nbsp; &nbsp; &nbsp; -1.164775&nbsp; -0.859925 &nbsp; 1.754125
 
 O&nbsp; &nbsp; &nbsp; -1.326825 &nbsp; 0.320475&nbsp; -1.821825
 
 O&nbsp; &nbsp; &nbsp; -2.853125 &nbsp; 0.892925 &nbsp; 0.413600
 
 O&nbsp; &nbsp; &nbsp; -2.723075&nbsp; -1.719050&nbsp; -0.429725
 
 O&nbsp; &nbsp; &nbsp; -0.880150&nbsp; -3.578800 &nbsp; 1.175650
 
 O &nbsp; &nbsp; &nbsp; 0.468325&nbsp; -2.590150 &nbsp; 3.305325
 
 O &nbsp; &nbsp; &nbsp; 0.158250&nbsp; -0.119825&nbsp; -4.231600
 
 O&nbsp; &nbsp; &nbsp; -1.075000&nbsp; -2.186500&nbsp; -3.000775
 
 Mo &nbsp; &nbsp; -0.011825 &nbsp; 0.882450 &nbsp; 2.732100
 
 Mo &nbsp; &nbsp; -0.210700 &nbsp; 2.315000&nbsp; -1.646775
 
 Mo &nbsp; &nbsp; -1.961350 &nbsp; 2.892175 &nbsp; 1.042325
 
 Mo&nbsp; &nbsp; &nbsp; 1.743275 &nbsp; 0.383075 &nbsp; 0.047100
 
 O&nbsp; &nbsp; &nbsp; -0.170550 &nbsp; 1.302225 &nbsp; 0.431325
 
 O&nbsp; &nbsp; &nbsp; -1.833050 &nbsp; 2.939575&nbsp; -0.887025
 
 O&nbsp; &nbsp; &nbsp; -1.668550 &nbsp; 1.814000 &nbsp; 2.603375
 
 O&nbsp; &nbsp; &nbsp; -0.852375 &nbsp; 4.156450 &nbsp; 1.364475
 
 O&nbsp; &nbsp; &nbsp; -3.494400 &nbsp; 3.581575 &nbsp; 1.331650
 
 O &nbsp; &nbsp; &nbsp; 1.164750 &nbsp; 0.859950&nbsp; -1.754175
 
 O &nbsp; &nbsp; &nbsp; 1.326800&nbsp; -0.320450 &nbsp; 1.821775
 
 O &nbsp; &nbsp; &nbsp; 2.853125&nbsp; -0.892925&nbsp; -0.413625
 
 O &nbsp; &nbsp; &nbsp; 2.723075 &nbsp; 1.719050 &nbsp; 0.429700
 
 O &nbsp; &nbsp; &nbsp; 0.880125 &nbsp; 3.578800&nbsp; -1.175675
 
 O&nbsp; &nbsp; &nbsp; -0.468325 &nbsp; 2.590150&nbsp; -3.305350
 
 O&nbsp; &nbsp; &nbsp; -0.158275 &nbsp; 0.119850 &nbsp; 4.231575
 
 O &nbsp; &nbsp; &nbsp; 1.075000 &nbsp; 2.186500 &nbsp; 3.000725
 
 K_POINTS {gamma}
 
 
 
 
 
 
 
 &nbsp;&amp;lr_input
 
 &nbsp; prefix = 'MoO',
 
 &nbsp; outdir = '/scratch/timrov/q-e-qe-6.7MaX-Release/tempdir/',
 
 &nbsp; restart = .false.
 
 &nbsp; max_seconds = 600
 
 &nbsp;/
 
 &nbsp;&amp;lr_dav
 
 &nbsp; if_dft_spectrum= .false.
 
 &nbsp; num_eign = 6,
 
 &nbsp; num_init = 12,
 
 &nbsp; num_basis_max = 40,
 
 &nbsp; residue_conv_thr = 1.0D-4,
 
 &nbsp; start&nbsp; = 0.0,
 
 &nbsp; finish = 6,
 
 &nbsp; step &nbsp; = 2.0D-4,
 
 &nbsp; broadening = 0.005,
 
 &nbsp; reference = 0.5,
 
 &nbsp; p_nbnd_occ&nbsp; = 8,
 
 &nbsp; p_nbnd_virt = 8,
 
 &nbsp; poor_of_ram&nbsp; = .false.
 
 &nbsp; poor_of_ram2 = .true.
 
 
 
 /
 

 
     --
 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-boun...@lists.quantum-espresso.org&gt; on behalf of ?? 
<508682...@qq.com&gt;
 Sent: Friday, April 16, 2021 8:03:37 PM
 To: users
 Subject: [QE-users] Re?? Error happens after setting max_seconds in 
turbo_davidson.x &nbsp;
 
  Dear Iurii,
 
 
 I used  example 8 of TDDFPT for testing restart work under QE6.5 and it works 
fine as well. So I am afraid it is not the version problem.
 
 
 Best, 
   Weijie Zhou
 
 
 
 
 
 
  ----------------------------------------------------------------
 Weijie Zhou
 PhD student
 University of Leeds
 UK
 
 
 
 
 ------------------ ???????? ------------------
  ??????: "Iurii TIMROV" <users@lists.quantum-espresso.org&gt;;
 ????????:&nbsp;2021??4??16??(??????) ????5:34
 ??????:&nbsp;"users"<users@lists.quantum-espresso.org&gt;;
 
 ????:&nbsp;Re: [QE-users]RE?? Error happens after setting max_seconds in 
turbo_davidson.x
 
 
 
  
Dear Weijie,
 
 I made a quick test using example 8 of TDDFPT and the restart works fine. 
Therefore, try to use QE6.7 and try example 8. If it works for you, then try it 
for your system (for the sake of testing reduce the cutoff, num_eign, num_init, 
max_seconds). 
 

 
 
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-boun...@lists.quantum-espresso.org&gt; on behalf of ?? 
<508682...@qq.com&gt;
 Sent: Monday, April 12, 2021 10:49:51 AM
 To: users
 Subject: [QE-users] RE?? Error happens after setting max_seconds in 
turbo_davidson.x &nbsp;
 
   Dear Iurii,
 
 
 Thanks for your reply and reminder. I am using QE 6.5. And you can see the 
input &amp; output files in:
 
 
 
https://drive.google.com/drive/folders/1djSkUZ2MkF0nKNntQgZJ8wt3b3IpmHs-?usp=sharing
  
 
 I am sure there is  enough space and time for writing data for restart files 
after double check.  
 
 
 
 
 Best,
 
 
 Weijie Zhou
 
 
 
 
 
 
  ----------------------------------------------------------------
 Weijie Zhou
 PhD student
 University of Leeds
 UK
 
 
 
  
 
 
 
 ------------------ ???????? ------------------
  ??????: "Iurii TIMROV" <users@lists.quantum-espresso.org&gt;;
 ????????:&nbsp;2021??4??11??(??????) ????5:23
 ??????:&nbsp;"users"<users@lists.quantum-espresso.org&gt;;
 
 ????:&nbsp;Re: [QE-users] Error happens after setting max_seconds in 
turbo_davidson.x
 
 
 
  
Please read carefully how to ask questions on the pw_forum:  
https://www.quantum-espresso.org/forum
 
 
In particular:
 
- which version of QE do you use?
 
- provide all input and output files (so that we can reproduce your problem)
 

 
 
Moreover: 
 
- make sure you have enough disc space to write the data for restart
 
- make sure that the code has enough time to write the data to disc (i.e. 
compare max_seconds with the total time of the job)
 

 
 
Once all this is clarified, the QE developers can have a closer look at your 
problem.
 

 
 
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: users <users-boun...@lists.quantum-espresso.org&gt; on behalf of ?? 
<508682...@qq.com&gt;
 Sent: Sunday, April 11, 2021 3:47:21 AM
 To: users
 Subject: [QE-users] Error happens after setting max_seconds in 
turbo_davidson.x &nbsp;
 
  Dear QE users,
 
 
 I am trying to use "restart" function for turbo Davidson calculation. So the 
"max_second" was specified in the input files of turbo_davidson.x which is 
shown as below:
 
 
  &amp;lr_input
 &nbsp; &nbsp; prefix='Mo_O',
 &nbsp; &nbsp; outdir='../../../tmp_Mo8O26_davidson_size20_e-4_nosmearing_T2'
 &nbsp; &nbsp; restart=.false.
 &nbsp; &nbsp; max_seconds = 144000,
 /
 &amp;lr_dav
 if_dft_spectrum= .false.
 num_eign = 16,
 &nbsp; num_init = 32,
 &nbsp; num_basis_max = 80,
 &nbsp; residue_conv_thr = 1.0D-4,
 &nbsp; start&nbsp; = 0.0,
 &nbsp; finish = 6,
 &nbsp; step &nbsp; = 2.0D-4,
 &nbsp; broadening = 0.005,
 &nbsp; reference = 0.5,
 &nbsp; p_nbnd_occ&nbsp; = 8,
 &nbsp; p_nbnd_virt = 8,
 &nbsp; poor_of_ram&nbsp; = .false.
 &nbsp;&nbsp; poor_of_ram2 = .true.
  
 
 But error happened at the end of calculation (max_second is reached) when 
writing data for restart. The error message: 
  
&nbsp;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 &nbsp; &nbsp; Error in routine diropn (22):
 &nbsp; &nbsp; error opening 
../../../tmp_Mo8O26_davidson_size20_e-4_nosmearing_T2/Mo_O.restart_davidson_vec_b.3
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 &nbsp;&nbsp; &nbsp; stopping ...
  
 
 It will be very appreciated if you can solve my problem for me. Thanks.
 
 
 Best,
 Weijie Zhou
 
 
 
 
 
 
 ----------------------------------------------------------------
 Weijie Zhou
 PhD student
 University of Leeds
 UK

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