[QE-users] Re： Re： Re： Error happens after setting max_seconds in turbo_davidson.x
飘
508682179 at qq.com
Tue Apr 20 12:30:38 CEST 2021
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
----------------------------------------------------------------
Weijie Zhou
PhD student
University of Leeds
UK
------------------ 原始邮件 ------------------
发件人: "Iurii TIMROV" <users at lists.quantum-espresso.org>;
发送时间: 2021年4月19日(星期一) 晚上6:33
收件人: "users"<users at lists.quantum-espresso.org>;
主题: 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-bounces at lists.quantum-espresso.org> on behalf of 飘 <508682179 at qq.com>
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
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).
Besides, I tried to use QE6.7 with ecut 80, and other parameters for input files are same with yours. But new error occured when running turbo_davidson.x giving the error as
Reading xml data from directory:
../../../tmp_Mo8O26_davidson_size20_e-4_nosmearing_QE6.7/Mo_O.save/
Message from routine qes_read:magnetizationType:
do_magnetization: wrong number of occurrences
Message from routine qexsd_readschema :
error reading output_obj of xsd data file
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine read_xml_file (4):
fatal error reading xml file
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Do you have any clue about this error? The input&output files for this calcualtion could be accessed in
https://drive.google.com/drive/folders/1lJTr7WdcOf73Bk36fSxP-yHZk52iDqGS?usp=sharing
Thanks,
Weijie Zhou
----------------------------------------------------------------
Weijie Zhou
PhD student
University of Leeds
UK
------------------ 原始邮件 ------------------
发件人: "Iurii TIMROV" <users at lists.quantum-espresso.org>;
发送时间: 2021年4月17日(星期六) 晚上10:21
收件人: "users"<users at lists.quantum-espresso.org>;
主题: 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
&control
calculation='scf'
restart_mode='from_scratch',
prefix='MoO'
pseudo_dir = '/scratch/timrov/q-e-qe-6.7MaX-Release/pseudo/'
outdir='/scratch/timrov/q-e-qe-6.7MaX-Release/tempdir/'
/
&system
a = 2.00000e+01
ecutwfc = 30
ibrav = 1
nat = 34
ntyp = 2
nbnd =250
tot_charge= -4
assume_isolated='martyna-tuckerman'
/
&electrons
conv_thr = 1.0d-8
/
ATOMIC_SPECIES
Mo 95.94 Mo.upf
O 15.999 O.upf
ATOMIC_POSITIONS {angstrom}
Mo 0.011800 -0.882450 -2.732125
Mo 0.210675 -2.315000 1.646750
Mo 1.961325 -2.892175 -1.042350
Mo -1.743275 -0.383075 -0.047150
O 0.170525 -1.302200 -0.431375
O 1.833025 -2.939550 0.887000
O 1.668550 -1.814000 -2.603400
O 0.852375 -4.156450 -1.364525
O 3.494400 -3.581575 -1.331675
O -1.164775 -0.859925 1.754125
O -1.326825 0.320475 -1.821825
O -2.853125 0.892925 0.413600
O -2.723075 -1.719050 -0.429725
O -0.880150 -3.578800 1.175650
O 0.468325 -2.590150 3.305325
O 0.158250 -0.119825 -4.231600
O -1.075000 -2.186500 -3.000775
Mo -0.011825 0.882450 2.732100
Mo -0.210700 2.315000 -1.646775
Mo -1.961350 2.892175 1.042325
Mo 1.743275 0.383075 0.047100
O -0.170550 1.302225 0.431325
O -1.833050 2.939575 -0.887025
O -1.668550 1.814000 2.603375
O -0.852375 4.156450 1.364475
O -3.494400 3.581575 1.331650
O 1.164750 0.859950 -1.754175
O 1.326800 -0.320450 1.821775
O 2.853125 -0.892925 -0.413625
O 2.723075 1.719050 0.429700
O 0.880125 3.578800 -1.175675
O -0.468325 2.590150 -3.305350
O -0.158275 0.119850 4.231575
O 1.075000 2.186500 3.000725
K_POINTS {gamma}
&lr_input
prefix = 'MoO',
outdir = '/scratch/timrov/q-e-qe-6.7MaX-Release/tempdir/',
restart = .false.
max_seconds = 600
/
&lr_dav
if_dft_spectrum= .false.
num_eign = 6,
num_init = 12,
num_basis_max = 40,
residue_conv_thr = 1.0D-4,
start = 0.0,
finish = 6,
step = 2.0D-4,
broadening = 0.005,
reference = 0.5,
p_nbnd_occ = 8,
p_nbnd_virt = 8,
poor_of_ram = .false.
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-bounces at lists.quantum-espresso.org> on behalf of 飘 <508682179 at qq.com>
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
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
------------------ 原始邮件 ------------------
发件人: "Iurii TIMROV" <users at lists.quantum-espresso.org>;
发送时间: 2021年4月16日(星期五) 下午5:34
收件人: "users"<users at lists.quantum-espresso.org>;
主题: 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-bounces at lists.quantum-espresso.org> on behalf of 飘 <508682179 at qq.com>
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
Dear Iurii,
Thanks for your reply and reminder. I am using QE 6.5. And you can see the input & 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
------------------ 原始邮件 ------------------
发件人: "Iurii TIMROV" <users at lists.quantum-espresso.org>;
发送时间: 2021年4月11日(星期天) 下午5:23
收件人: "users"<users at lists.quantum-espresso.org>;
主题: 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-bounces at lists.quantum-espresso.org> on behalf of 飘 <508682179 at qq.com>
Sent: Sunday, April 11, 2021 3:47:21 AM
To: users
Subject: [QE-users] Error happens after setting max_seconds in turbo_davidson.x
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:
&lr_input
prefix='Mo_O',
outdir='../../../tmp_Mo8O26_davidson_size20_e-4_nosmearing_T2'
restart=.false.
max_seconds = 144000,
/
&lr_dav
if_dft_spectrum= .false.
num_eign = 16,
num_init = 32,
num_basis_max = 80,
residue_conv_thr = 1.0D-4,
start = 0.0,
finish = 6,
step = 2.0D-4,
broadening = 0.005,
reference = 0.5,
p_nbnd_occ = 8,
p_nbnd_virt = 8,
poor_of_ram = .false.
poor_of_ram2 = .true.
But error happened at the end of calculation (max_second is reached) when writing data for restart. The error message:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine diropn (22):
error opening ../../../tmp_Mo8O26_davidson_size20_e-4_nosmearing_T2/Mo_O.restart_davidson_vec_b.3
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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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