[Pw_forum] Error: ...excited on signal 9 (killed)

[Amar Singh]

Dear Friends,​I am trying a vc-relax on a 320 atom supercell on a 40 
processor/256 GB RAM system. As soon as the first iteration starts, run is 
terminated with following message.mpi has noticed that process rank 14 with PID 
25185 n node Linux-mix excited on signal 9 (killed).​With increasing numbers of 
processors (8 - 160), Estimated total allocated dynamic RAM is 
increasing and reached to 450 GB. But problem remains same, and run fails 
with same error message. Besides, for smaller supercells (10 - 40 atoms), this 
problem does not appear at all.Will appreciate any suggestion. Thanks Amar___
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Re: [Pw_forum] [Non-DoD Source] Re: Where to put psuedo potential for run-tests?

[Downs, Andrew S CTR USARMY ARL (US)]

Huh...ok.. making ./pseudo/ and putting it in there worked...but now the tests 
run, and every single one of them fails immediately. 

It looks like it's not trying to do anything.

Every test produces:

Different sets of data extracted from benchmark and test.
Data only in benchmark: s1,v1u,e1,t1.

What does that mean?

-Original Message-
From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf 
Of Paolo Giannozzi
Sent: Friday, December 22, 2017 3:11 PM
To: PWSCF Forum 
Subject: [Non-DoD Source] Re: [Pw_forum] Where to put psuedo potential for 
run-tests?

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On Fri, Dec 22, 2017 at 7:03 PM, Downs, Andrew S CTR USARMY ARL (US) 
 > 
wrote:



The test suite fails on 'make run-tests' stating that it can't download 
a pseudo potential with an incredibly obtuse name (who names these??)



me: Caution-http://www.quantum-espresso.org/pseudopotentials/naming-convention/ 
< Caution-http://www.quantum-espresso.org/pseudopotentials/naming-convention/ > 

Feel free to name your pseudopotentials with incredibly intelligent names



O.pz-rrkjus.UPF failed to download - do it yourself (or something to 
that effect)



likely, you have neither wget nor curl working on your system, or you do not 
have direct internet access 

 

Where should pseudo potentials be stored for the test suite?



in $ESPRESSO_PSEUDO, that normally points to the pseudo/ subdirectory


Paolo
-- 

Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, 
via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax 
+39-0432-558222



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Re: [Pw_forum] [Non-DoD Source] Re: Where to put psuedo potential for run-tests?

[Downs, Andrew S CTR USARMY ARL (US)]

I have /both/ curl and wget working, making this especially curious.  I have a 
working internet connection that was sufficient to download and then build QE 
6.2.1, I assume that's 'direct' enough.

Can I just set $ESPRESSO_PSEUDO to the directory I have the pseudo potential in?

The test suite does not appear to have a 'psuedo' directory...but I'll try 
making one and putting it in there...

Thank you.

-Original Message-
From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf 
Of Paolo Giannozzi
Sent: Friday, December 22, 2017 3:11 PM
To: PWSCF Forum 
Subject: [Non-DoD Source] Re: [Pw_forum] Where to put psuedo potential for 
run-tests?

All active links contained in this email were disabled. Please verify the 
identity of the sender, and confirm the authenticity of all links contained 
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On Fri, Dec 22, 2017 at 7:03 PM, Downs, Andrew S CTR USARMY ARL (US) 
 > 
wrote:



The test suite fails on 'make run-tests' stating that it can't download 
a pseudo potential with an incredibly obtuse name (who names these??)



me: Caution-http://www.quantum-espresso.org/pseudopotentials/naming-convention/ 
< Caution-http://www.quantum-espresso.org/pseudopotentials/naming-convention/ > 

Feel free to name your pseudopotentials with incredibly intelligent names



O.pz-rrkjus.UPF failed to download - do it yourself (or something to 
that effect)



likely, you have neither wget nor curl working on your system, or you do not 
have direct internet access 

 

Where should pseudo potentials be stored for the test suite?



in $ESPRESSO_PSEUDO, that normally points to the pseudo/ subdirectory


Paolo
-- 

Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, 
via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax 
+39-0432-558222



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Re: [Pw_forum] Where to put psuedo potential for run-tests?

[Paolo Giannozzi]

On Fri, Dec 22, 2017 at 7:03 PM, Downs, Andrew S CTR USARMY ARL (US) <
andrew.s.downs3@mail.mil> wrote:

The test suite fails on 'make run-tests' stating that it can't download a
> pseudo potential with an incredibly obtuse name (who names these??)
>

me: http://www.quantum-espresso.org/pseudopotentials/naming-convention/
Feel free to name your pseudopotentials with incredibly intelligent names

O.pz-rrkjus.UPF failed to download - do it yourself (or something to that
> effect)
>

likely, you have neither wget nor curl working on your system, or you do
not have direct internet access


> Where should pseudo potentials be stored for the test suite?
>

in $ESPRESSO_PSEUDO, that normally points to the pseudo/ subdirectory

Paolo
-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] Converged SCF total energies different in 6.0/6.1/6.2

[WF]

Thanks very much for this important information.

Best regards,
Feng

>See this note in file Doc/release-notes:
>
>  * Some constants in the definition of PBE functionals were truncated to
>6 significant digits. While not a bug, this could lead to tiny
differences
>with respect to previous results and other XC implementations (r13592)
>
>More explicitly: some constants that previously were truncated to 6 digits,
are now defined with full precision. This removes minor numerical
discrepancies with the results obtained using libxc.
>
>Paolo

>On Thu, Dec 21, 2017 at 3:11 AM, WF  wrote:

>> Dear all,
>>
>> In tests a normal DFT calculations with Si, I noticed that QE 6.0 and 
>> 6.1 gives exactly same total energy with 6.0 and 6.1 (-15.75190880 
>> Ry), but with QE 6.2.1, the total energy is -15.75191309Ry. I tested 
>> this on two different machines with different compilers, the results 
>> are the same across all of them (at least to last digit). I did some 
>> tests on larger systems also and found even larger difference. This 
>> 1e-5 Ry order of difference is not negligible. Is there anything 
>> introduced in 6.2 leads to this difference? Thanks very much.
>>
>>
>>
>> Best regards,
>>
>> Feng
>>
>>
>>
>>
>> ___
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>
>
>
>--
>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ.
Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax
+39-0432-558222
> -- next part --
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--
Dr. Feng Wu
Postdoctoral researcher
Department of Chemistry and Biochemistry
University of California, Santa Cruz
Phone: 831-459-2874



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[Pw_forum] Where to put psuedo potential for run-tests?

[Downs, Andrew S CTR USARMY ARL (US)]

Hello,

I've just compiled QE 6.2.1 on my laptop, for the sake of making sure it works, 
I want to run the test suite.

The test suite fails on 'make run-tests' stating that it can't download a 
pseudo potential with an incredibly obtuse name (who names these??)

O.pz-rrkjus.UPF failed to download - do it yourself (or something to that 
effect)

So I find this file online though google, but I have no idea where it should 
go.  Where should pseudo potentials be stored for the test suite?

Thank you.

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Re: [Pw_forum] Force is fluctuating for water system

[Narendranath Ghosh]

Dear Lorenzo , Dear Seitsonen Thank you very much. Actually what I am
trying to find is to Where do the excess e- prefer to stay in my water
system ?

I have crossed 50 BFGS steps but still it could not  find the minimum.
The Force is fluctuating very much .I have applied 90 Ry with a pseudo
potential and used BLYP exchange-correlation functional from a standard
reference. (THE JOURNAL OF CHEMICAL PHYSICS 128, 214506 2008)
 any other factor that should care relaxing a system with odd number of
electrons.

*Dr. Narendra Nath Ghosh*

*Research Associate*

*University of Gour  Banga*

*Malda-732102*

*India*

*Phone No : 09126667601*


On Fri, Dec 22, 2017 at 2:07 AM, Ari P Seitsonen 
wrote:

>
> Dear Narendra Nath Ghosh,
>
>   Adding to Lorenzo's answer, a small note: You seem to have an odd number
> of electrons but you do not specify 'nspin = 2' - are you sure that this is
> what you intended to do (physically)? 70 Ry with a pseudo potential à la
> Troullier-Martins for oxygen, it might be at the lower limit (it depends on
> the core radii, usually I would go for 80-90 Ry minimum). And, do you know
> if the electron gets localised or remains delocalised - this is an open
> question to my knowledge, and might well depend on the kind of
> exchange-correlation functional used (GGA like BLYP probably delocalise it
> - with the highest occupied orbital in the conduction band - and hybrid
> functionals might localise it).
>
> Greetings from Helsinki/Finland,
>
>apsi
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=
> -=*=-=*=-=*=-=*=-
>   Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
> Ecole Normale Supérieure (ENS), Département de Chimie, Paris
> Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935
>
>
>
> On Tue, 19 Dec 2017, Narendranath Ghosh wrote:
>
> Dear all
>>
>> I am relaxing a system of 128 water molecule with extra electron.The
>> force is fluctuating even after bfgs
>> steps   =  48.
>>
>>
>>
>> Input:
>>
>> 
>>   calculation='relax',
>>   outdir='/share_home/hpc/NEGATIVE_HYDRATED_ELECTRON/OUTPUT',
>>   prefix='water-128-negative',
>>   pseudo_dir='/share_home/hpc/RESEARCH_SCHOLAR/HYDRATED-ELECTRON/pseudo',
>>   verbosity='high',
>>   restart_mode='restart',
>> /
>> 
>>   ibrav=0,
>>   celldm(1)=29.8576727681d0,
>>   nat=384,
>>   tot_charge=-1,
>>   ntyp=2,
>>   ecutwfc=70,
>>   ecutrho=280,
>>   input_dft='BLYP',
>>   occupations='smearing',
>>   degauss=0.05d0,
>> /
>> 
>>   mixing_beta=0.500d0,
>>   electron_maxstep=500,
>> /
>> 
>> /
>> ATOMIC_SPECIES
>>  O  16.0d0   O.blyp-mt.UPF
>>  H  1.0079d0 H.blyp-vbc.UPF
>>
>> K_POINTS {automatic}
>>   1 1 1 0 0 0
>> CELL_PARAMETERS {alat}
>>   1.d0  0.d0  0.d0
>>   0.d0  1.d0  0.d0
>>   0.d0  0.d0  1.d0
>>
>> Output
>>
>> Total force = 0.030447 Total SCF correction = 0.001115
>>  Total force = 0.033732 Total SCF correction = 0.000223
>>  Total force = 0.042921 Total SCF correction = 0.000171
>>  Total force = 0.032971 Total SCF correction = 0.000165
>>  Total force = 0.032983 Total SCF correction = 0.000266
>>  Total force = 0.036132 Total SCF correction = 0.000252
>>Total force = 0.040191 Total SCF correction = 0.000833
>>  Total force = 0.032897 Total SCF correction = 0.001663
>>  Total force = 0.025425 Total SCF correction = 0.000288
>>  Total force = 0.019869 Total SCF correction = 0.000279
>>  Total force = 0.020382 Total SCF correction = 0.000102
>>  Total force = 0.025164 Total SCF correction = 0.000109
>>  Total force = 0.027580 Total SCF correction = 0.000141
>>  Total force = 0.026211 Total SCF correction = 0.000188
>>  Total force = 0.023574 Total SCF correction = 0.000139
>>  Total force = 0.024877 Total SCF correction = 0.000103
>>  Total force = 0.027597 Total SCF correction = 0.000131
>>  Total force = 0.027563 Total SCF correction = 0.000169
>>  Total force = 0.023015 Total SCF correction = 0.000195
>>  Total force = 0.02 Total SCF correction = 0.000109
>>  Total force = 0.021345 Total SCF correction = 0.92
>>  Total force = 0.023793 Total SCF correction = 0.000129
>>  Total force = 0.024400 Total SCF correction = 0.000145
>>  Total force = 0.025073 Total SCF correction = 0.000243
>>  Total force = 0.022300 Total SCF correction = 0.000376
>>  Total force = 0.020060 Total SCF correction = 0.97
>>  Total force = 0.021991 Total SCF correction = 0.000134
>>  Total force = 0.022541 Total SCF