yambo-4.2.3 install

Having trouble compiling the Yambo source? Using an unusual architecture? Problems with the "configure" script? Problems in GPU architectures? This is the place to look.

Moderators: Davide Sangalli, andrea.ferretti, myrta gruning, andrea marini, Daniele Varsano, Conor Hogan, Nicola Spallanzani

Forum rules
If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
(2) the architecture (e.g. 64-bit IBM SP5)
(3) if the problems occur compiling in serial/in parallel
(4) the version of Yambo (revision number/major release version)
(5) the relevant compiler error message
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Daniele Varsano
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Re: yambo install

Post by Daniele Varsano » Thu Sep 08, 2016 12:29 pm

Dear Joydev,
But
o.eps_q1_inv_alda_dyson and o.eel_q1_inv_alda_dyson files are not created. But these last two file are created when i run it in serial mode.
This is definitely clear! Now if the output are missing it is because the code stopped for some reason. In order to spot the problem is it useful to have a look to report and log files.
In any case from your input I can see:

Code: Select all

X_all_q_CPU= "2 2 2 2" # [PARALLEL] CPUs for each role
you are assiging 2 cpus on q point and 2 on k points, but you are interest in optics, or loss spectrum for the q->0 limit, i.e.
% QpntsRXd
1 | 1 | # [Xd] Transferred momenta
%

so this can be the reason of your problem.

Try to set:

Code: Select all

X_all_q_CPU= "1 1 4 4" # [PARALLEL] CPUs for each role
and see if it works. Not having seen the report I do not know if you are dealing with a bulk or a molecule, in this case also to parallelize ok k points does not make sense.

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/

joydev de
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Joined: Wed Sep 07, 2016 11:56 am

Re: yambo install

Post by joydev de » Thu Sep 08, 2016 3:56 pm

Dear Daniele

Thank you very much.
The yambo is running in parallel mode. But when i calculating the chi response function, i have a confusion in the input file.
How i divide the total memory(suppose i have total 16 core) for the flag given below-
X_q_0_CPU= "4 4 4" # [PARALLEL] CPUs for each role
X_q_0_ROLEs= "k c v" # [PARALLEL] CPUs roles (k,c,v)
X_q_0_nCPU_invert=0 # [PARALLEL] CPUs for matrix inversion
X_finite_q_CPU= "4 4 4 4" # [PARALLEL] CPUs for each role
X_finite_q_ROLEs= "q k c v" # [PARALLEL] CPUs roles (q,k,c,v)
X_finite_q_nCPU_invert=0 # [PARALLEL] CPUs for matrix inversion

Again thank you.
regards
Joydev
joydev De

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Daniele Varsano
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Re: yambo install

Post by Daniele Varsano » Thu Sep 08, 2016 4:16 pm

Dear Joydev,

X_q_0_CPU is meant for q=0 only calculations, e.g. optics.
X_finite_q_CPU when you need to calculate dielectric matrix for al the q points (e.g. in GW calculations).
So you will never have both in the same calculation.
Adding the -V par flag in the command line to build the input, it will provide the useful variables to set.

If you have 16 cores, the product of the numbers has to be equal to 16, e.g.
X_q_0_CPU= "2 2 4"
X_q_0_ROLEs= "k c v"
X_finite_q_CPU= "1 4 2 2"
X_finite_q_ROLEs= "q k c v"
and so on.

The number you set above are allowed if you have 64 cpus in the first case or 256 in the second case.

As a tip, avoid to assign more than 1 cpu to the q role in X_finite_q_ROLEs, as then the calculation use to be unbalanced.
When assigning cpu over k points, if possible, try to set a number factor of the total number of the k points of you calculations.
In order to familiarize with the parallel strategies you can have a look to the tutorial dedicated on that:
http://www.yambo-code.org/tutorials/Parallel/index.php

Hope it helps,

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/

joydev de
Posts: 31
Joined: Wed Sep 07, 2016 11:56 am

Re: yambo parallel running

Post by joydev de » Fri Sep 09, 2016 4:21 pm

Dear Daniele,

Now i am doing the absorption calculation of c_60 using yambo. When i running this in parallel mode one error message come in yambo.error file, that is given below-

[node02.local:02200] 1 more process has sent help message help-orte-odls-base.txt / orte-odls-base:could-not-kill
[node02.local:02200] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
[node02.local:02200] 1 more process has sent help message help-orte-odls-base.txt / orte-odls-base:could-not-kill
[node02.local:02200] 5 more processes have sent help message help-orte-odls-base.txt / orte-odls-base:could-not-kill
[node02.local:02200] 1 more process has sent help message help-orte-odls-base.txt / orte-odls-base:could-not-kill
[node02.local:02200] 5 more processes have sent help message help-orte-odls-base.txt / orte-odls-base:could-not-kill
[node02.local:02200] 1 more process has sent help message help-orte-odls-base.txt / orte-odls-base:could-not-kill
[node02.local:02200] 5 more processes have sent help message help-orte-odls-base.txt / orte-odls-base:could-not-kill
[node02.local:02200] 1 more process has sent help message help-orte-odls-base.txt / orte-odls-base:could-not-kill
[node02.local:02200] 2 more processes have sent help message help-orte-odls-base.txt / orte-odls-base:could-not-kill

But, in my Log file, there is no error message. I am attaching one of the log file.
My nscf input file is given below-
&CONTROL
title = "nscf"
calculation = "nscf",
prefix = "C_scf",
restart_mode = "from_scratch",
outdir = "./tmp",
pseudo_dir = "/home/joydev/pseudo/",
wf_collect = .true.
nstep = 200,
verbosity = 'high'
/
&SYSTEM
ibrav = 0,
nat = 60,
ntyp = 1,
ecutwfc = 60.00,
ecutrho = 500.00,
nbnd = 1500,
nosym = .true. ,
force_symmorphic=.true.
/
&ELECTRONS
mixing_mode = "plain",
conv_thr = 1.D-8,
mixing_beta = 0.05,
electron_maxstep = 700,
diago_thr_init = 1.0e-6
diago_full_acc = .true.
diagonalization = 'cg'
diago_cg_maxiter = 2000
/
CELL_PARAMETERS
40.00 0.0 0.0
0.00 40.00 0.0
0.00 0.00 40.00
ATOMIC_SPECIES
C 12.0107 C.pz-hgh.UPF
K_POINTS gamma
ATOMIC_POSITIONS {angstrom}
C 8.725255865 6.994671648 13.324199177
C 9.173831820 8.373986983 13.326164811
C 9.422334991 6.035853019 12.587480421
C 10.301505432 8.743144900 12.591458948
C 10.300975146 9.977437618 11.830772619
C 8.001153082 9.226514550 13.326730013
C 8.001058538 10.415317156 12.594164791
C 9.173298237 10.799141768 11.832389518
C 7.301404237 5.039745021 11.823249250
C 6.576599703 6.035948146 12.587900970
C 8.696916181 5.039819548 11.823200342
C 7.275425917 6.994775121 13.323916335
C 6.828040878 8.374158697 13.325575522
C 5.404252720 6.419019568 11.825545339
C 4.974174155 7.746418766 11.827473503
C 5.699675971 8.742860268 12.591309984
C 8.725153554 4.581312724 9.400577650
C 7.275577211 4.581668054 9.400598221
C 9.421874656 4.806393943 10.588735143
C 6.577078329 4.806200263 10.588427770
C 5.404622628 5.658979849 10.589893116
C 6.828279146 5.200989597 8.167361387
C 5.699994002 6.022410276 8.169119674
C 4.974878930 6.254942849 9.403421069
C 11.024798351 6.255405482 9.403653994
C 10.301293207 6.022443520 8.168908034
C 10.594012314 5.659517534 10.589862676
C 9.173726277 5.200374036 8.167292369
C 8.001242220 5.584231924 7.405778615
C 10.301482966 7.257348200 7.408720868
C 9.173723565 7.625329533 6.673895959
C 8.001174381 6.772505198 6.673009455
C 11.025459989 7.746504252 11.827047300
C 11.472229344 8.365518377 10.593893098
C 10.594363963 6.419349252 11.825098062
C 11.472373278 7.634262938 9.405805555
C 11.025207597 8.253887801 8.173043098
C 11.024309333 9.744337702 10.595920217
C 10.593943232 10.341693840 9.410062557
C 10.594150592 9.581613099 8.174900880
C 7.275273848 9.004196423 6.676881107
C 8.724933405 9.004467442 6.676514427
C 9.421703471 9.964068885 7.412741623
C 6.576625543 9.963594220 7.412570480
C 4.974220087 8.253337644 8.172818842
C 5.699658451 7.257148408 7.409009094
C 6.827994136 7.624906973 6.674564281
C 5.403999989 9.581368584 8.174696487
C 4.975014809 9.744194728 10.596378495
C 4.527718925 8.365220588 10.594124414
C 4.527608528 7.633843843 9.405811729
C 5.404156914 10.341684689 9.410241607
C 7.275268266 11.418484195 10.599405391
C 6.828214733 10.798317948 11.832407922
C 5.700007071 9.977008240 11.830717380
C 6.576528887 11.194944950 9.411475652
C 8.696639820 10.961641153 8.176306563
C 9.421725510 11.195058409 9.411054710
C 8.724777625 11.418961270 10.599373550
C 7.300958041 10.961528390 8.176347934
Please help me. Tell me, what is the error.
joydev De

joydev de
Posts: 31
Joined: Wed Sep 07, 2016 11:56 am

Re: yambo install

Post by joydev de » Fri Sep 09, 2016 4:22 pm

sorry,

i forgot to attach the log file. My log file is attaching .
joydev De

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Daniele Varsano
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Re: yambo install

Post by Daniele Varsano » Fri Sep 09, 2016 4:26 pm

Dear Joydev,
the log file is not attached. Probably you have to rename it as .txt or you need to zip it.
Please post also the yambo input and the report file.
Note that the error you get does not come from yambo, but from your queue system.

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/

joydev de
Posts: 31
Joined: Wed Sep 07, 2016 11:56 am

Re: yambo install

Post by joydev de » Sat Sep 10, 2016 6:08 am

Dear Daniele,

Thank you for your quick reply.

Is there any parallelization process to convert quantum espresso to yambo interfacing.
Because, when i am calculating for periodic large system, the interfacing process takes much time.

regards
Joydev
joydev De

joydev de
Posts: 31
Joined: Wed Sep 07, 2016 11:56 am

Re: yambo install

Post by joydev de » Sat Sep 10, 2016 7:52 am

Dear Daniele,

I am doing the chi calculation of c60. But always i have got a warning message in the r_optics_chi_tddft file that rename the file name ns.kb_pp_pwscf in the SAVE directory for first calculation. After renaming the file name, i have also got a warning message that you are missing the non-locality of the pseudo potential. I don't understand the reason of warning message.

One more problem, always the job exit with an error message. Here i am attaching all the information in the tar file.

Thank you

Regards
Joydev De
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joydev De

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Daniele Varsano
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Re: yambo install

Post by Daniele Varsano » Sat Sep 10, 2016 8:15 am

Dear Joydev,
i have got a warning message in the r_optics_chi_tddft file that rename the file name ns.kb_pp_pwscf in the SAVE directory for first calculation. After renaming the file name, i have also got a warning message that you are missing the non-locality of the pseudo potential. I don't understand the reason of warning message.
Inclusion of non-local part of psuedo in dipoles calculations is time consuming and not always needed. The code just warns you on that. If you do not want to include it you need to rename the ns.kb_pp_pwscf file. Up to you to judge if it is needed or not, and see how much is cumbersome to keep it.
One more problem, always the job exit with an error message.
\
Having a look at the Log file the code exit because not able to allocate the needed memory:

Code: Select all

<01m-10s> P0055: [M  4.108 Gb] Alloc WF ( 3.725)
It looks you have 4GB per code.
In order to overcome this problem you can:
1) Use lesse cores per node, e.g. 8 core instead of 16, you will have less cpus but more RAM for each.
2) Reduce a bit the cutoff for FFT of Wave functions, this is controlled by using the FFTGvecs variable.
3) Reduced the number of bands in BndsRnXd

For the case 2-3 of course you need to check convergences and control you do not loose much accuracy.

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/

joydev de
Posts: 31
Joined: Wed Sep 07, 2016 11:56 am

Re: yambo install

Post by joydev de » Sun Sep 11, 2016 11:23 am

Dear Daniele Varsano,

Thank you.

Is there any parallel method to convert the quantum espresso file to yambo data base?
Because when i calculate for the periodic system, the p2y conversion takes much time.
If any easy method present, please tell me.

Regards
Joydev De
joydev De

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