date:20180208

[Pw_forum] Memory problems with a job using PWSCF from qe-gpu

2018-02-08 Thread Reinaldo Pis Diez

Dear folks,

I've managed to compile the gpu-enabled version of PWSCF from the 
sources provided by Filippo Spiga using Portland compilers and MKL 
libraries. The node has CentOS 6.6 and 16 GB of RAM. I ran some 
small tests and results were the same than those obtained with a 
non-gpu version of qe-6.1 compiled with the GNU compilers.

When I try to test the executable with a more realistic job (a Cu 
surface made by 75 atoms with 1 to 6 carbon atoms on it) an "out of 
memory" problem occurs and the job terminates. I must say that that 
job was successfully ran on another similar node (except for the 
fact that it doesn't have a gpu card). When I use "mpirun -np 1" 
before invoking pw.x, I've got

...
  Estimated max dynamical RAM per process >   10128.95MB
  Generating pointlists ...
  new r_m :   0.0689 (alat units)  1.6647 (a.u.) for type    1
  new r_m :   0.0689 (alat units)  1.6647 (a.u.) for type    2

0: ALLOCATE: 2525186688 bytes requested; status = 2(out of memory)
/opt/pgi/linux86-64/17.4/lib/libpgf90_rpm1.so(__fort_abortx+0x17) 
[0x2b646f7f2af7]
   /opt/pgi/linux86-64/17.4/lib/libpgf90.so(__fort_abort+0x5e) 
[0x2b646f41897e]
   /opt/pgi/linux86-64/17.4/lib/libcudafor.so(+0x5ac38) [0x2b6456f6cc38]
/opt/pgi/linux86-64/17.4/lib/libcudafor.so(pgf90_dev_mod_alloc04+0xc9) 
[0x2b6456f6d70e]
   /usr/local/fspiga-qe-gpu-7e1de44/bin/pw.x() [0x5e16d7]
   /usr/local/fspiga-qe-gpu-7e1de44/bin/pw.x() [0x497953]
   /usr/local/fspiga-qe-gpu-7e1de44/bin/pw.x() [0x52b05d]
   /usr/local/fspiga-qe-gpu-7e1de44/bin/pw.x() [0x40d82c]
   /usr/local/fspiga-qe-gpu-7e1de44/bin/pw.x() [0x40d704]
   /lib64/libc.so.6(__libc_start_main+0xfd) [0x36f741ed5d]
   /usr/local/fspiga-qe-gpu-7e1de44/bin/pw.x() [0x40a1c9]
--
mpirun noticed that process rank 0 with PID 23370 on node n13 exited 
on signal 6 (Aborted).
--

When I ran the same job with "mpirun -np 8" then I've got

...
     Estimated total allocated dynamical RAM >   11048.12MB
  Generating pointlists ...
  new r_m :   0.0689 (alat units)  1.6647 (a.u.) for type    1
  new r_m :   0.0689 (alat units)  1.6647 (a.u.) for type    2
0: ALLOCATE: 315564672 bytes requested; status = 2(out of memory)
[a lot of error messages]

I cannot understand the source of the error but I guess that it has 
to do with the gpu card. Running the deviceQuery program that comes 
with CUDA I've got (among a lot of information)

Device 0: "TITAN X (Pascal)"
   CUDA Driver Version / Runtime Version  8.0 / 8.0
   CUDA Capability Major/Minor version number:    6.1
   Total amount of global memory: 12189 MBytes 
(12781158400 bytes)
   (28) Multiprocessors, (128) CUDA Cores/MP: 3584 CUDA Cores
   GPU Max Clock rate:    1531 MHz (1.53 GHz)
   Memory Clock rate: 5005 Mhz
   Memory Bus Width:  384-bit
   L2 Cache Size: 3145728 bytes

Any help is welcome. I can provide the proper input file with the 
corresponding pseudopotentials if requested.

Thanks in advance

Reinaldo Pis Diez
Center of Inorganic Chemistry
Natl Univ of La Plata
Argentina
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Crash with Environ-0.2

2018-02-08 Thread Oliviero Andreussi

Dear Dr. Huu Chuong Nguyën (Bob),

Thank you very much for investigating the problem further and reporting the 
bug. I will look at the problem and if the incompatibility is easy to fix, I 
will let you know and will forward the patches as soon as possible. Thank you 
again.

Best,

Oliviero Andreussi
--
Department of Physics
University of North Texas
Email: oliviero.andreu...@unt.edu
Skype: olivieroandreussi
Web: https://sites.google.com/site/olivieroandreussi

From: pw_forum-boun...@pwscf.org  on behalf of Huu 
Chuong Nguyën 
Sent: Thursday, February 8, 2018 2:19:00 PM
To: pw_forum@pwscf.org
Subject: Re: [Pw_forum] Crash with Environ-0.2

Hi,


I found that if I comment the line

!vdw_corr = Grimme-D2, ! DFT-D2 dispersion correction
it works!

There may be some issues between  DFT-D2 and environ-0.2

Best regards,



Dr. Huu Chuong Nguyën (Bob)

Postdoc Researcher - Group of Prof. Núria López

Institute of Chemical Research of Catalonia (ICIQ)
The Barcelona Institute of Science and Technology

Av. Països Catalans 16 - 43007 Tarragona (Spain)

PB-12 Huu Chuong Nguyën - PERSONAL

hngu...@iciq.es - www.iciq.es


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] How to set variables when get symmetry operation # N not allowed?

2018-02-08 Thread Paolo Giannozzi

There are no symmetries with fractional translations. Problem solved.

Paolo

On Thu, Feb 8, 2018 at 5:30 PM, Arena Konta  wrote:

> Dear prof. Paolo Giannozzi
>
> Thank you for quick response. Please, clarify me: I set variable
> "use_all_frac=.true." and option "verbosity='high'" and get output showed
> below. Hoverwer, I am still unable to find the right values of frac. trans
> (n=1?) I have to calculate phonons,
> so i need to set right k-mesh.
>
>  8 Sym. Ops., with inversion, found
>
>
> sfrac. trans.
>
>   isym =  1 identity
>
>  cryst.   s( 1) = ( 1  0  0  )
>   ( 0  1  0  )
>   ( 0  0  1  )
>
>  cart.s( 1) = (  1.000  0.000  0.000 )
>   (  0.000  1.000  0.000 )
>   (  0.000  0.000  1.000 )
>
>
>   isym =  2 180 deg rotation - cart. axis [0,0,1]
>
>  cryst.   s( 2) = (-1  0  0  )
>   ( 0 -1  0  )
>   (-1 -1  1  )
>
>  cart.s( 2) = ( -1.000  0.000  0.000 )
>   (  0.000 -1.000  0.000 )
>   (  0.000  0.000  1.000 )
>
>
>   isym =  3  90 deg rotation - cart. axis [0,0,-1]
>
>  cryst.   s( 3) = ( 0 -1  0  )
>   ( 1  0  0  )
>   ( 0 -1  1  )
>
>  cart.s( 3) = (  0.000  1.000  0.000 )
>   ( -1.000  0.000  0.000 )
>   (  0.000  0.000  1.000 )
>
>
>   isym =  4  90 deg rotation - cart. axis [0,0,1]
>
>  cryst.   s( 4) = ( 0  1  0  )
>   (-1  0  0  )
>   (-1  0  1  )
>
>  cart.s( 4) = (  0.000 -1.000  0.000 )
>   (  1.000  0.000  0.000 )
>   (  0.000  0.000  1.000 )
>
>
>   isym =  5 inversion
>
>  cryst.   s( 5) = (-1  0  0  )
>   ( 0 -1  0  )
>   ( 0  0 -1  )
>
>  cart.s( 5) = ( -1.000  0.000  0.000 )
>   (  0.000 -1.000  0.000 )
>   (  0.000  0.000 -1.000 )
>
>
>   isym =  6 inv. 180 deg rotation - cart. axis [0,0,1]
>
>  cryst.   s( 6) = ( 1  0  0  )
>   ( 0  1  0  )
>   ( 1  1 -1  )
>
>  cart.s( 6) = (  1.000  0.000  0.000 )
>   (  0.000  1.000  0.000 )
>   (  0.000  0.000 -1.000 )
>
>
>   isym =  7 inv.  90 deg rotation - cart. axis [0,0,-1]
>
>  cryst.   s( 7) = ( 0  1  0  )
>   (-1  0  0  )
>   ( 0  1 -1  )
>
>  cart.s( 7) = (  0.000 -1.000  0.000 )
>   (  1.000  0.000  0.000 )
>   (  0.000  0.000 -1.000 )
>
>
>   isym =  8 inv.  90 deg rotation - cart. axis [0,0,1]
>
>  cryst.   s( 8) = ( 0 -1  0  )
>   ( 1  0  0  )
>   ( 1  0 -1  )
>
>  cart.s( 8) = (  0.000  1.000  0.000 )
>   ( -1.000  0.000  0.000 )
>   (  0.000  0.000 -1.000 )
>
>
> Thank you in avdance.
> Arena Konta
>
>
> 
> *
>
> Set variable "use_all_frac=.true." and option "verbosity='high'". This will
> find and print all symmetries and associated fractional translations. If a
> fractional translation along a crystal axis is 1/n, with n integer, the FFT
> dimension along that axis must contain a factor n. If you do not need
> hybrid functionals or phonons, just set variable "use_all_frac=.true."
>
> Paolo
>
>
>
>
>
> 2018-02-07 20:18 GMT+01:00 Arena Konta :
>
>> Hi All,
>>
>> I read Troubleshooting and found out that "you can force your FFT grid to be 
>> commensurate with fractional translation (set variables nr1, nr2, nr3 to 
>> suitable values)". How to do this for the crystal structure presented below? 
>> I have tried to this for various k-mesh, but every time I get 6 symmetry 
>> operations are not compatible with FFT grid:
>>  warning: symmetry operation # 2 not compatible with FFT grid.
>>   -1 0 0
>>0 -1 0
>>   -1 -1 1
>>  warning: symmetry operation # 3 not compatible with FFT grid.
>>0 -1 0
>>

Re: [Pw_forum] pdos of MoS2

2018-02-08 Thread Dr. Thomas Brumme

Dear B. S. Bushan,

the pDOS is created via projection of the eigenfunctions on the atomic  
orbitals given
in the pseudopotential as those states are included in the  
calculation. You're using
pseudos with semicore states. Thus, for, e.g., Mo there are the 4s 4p  
4d 5s 5p states.
If you look at the energies for which you find states, you'll see that  
the states for
wfc#1 and wfc#3 are lower in energy than those for #2 and #4. All  
these informations
are usually printed at the beginning of the output of projwfc.x.

Cheerio

Thomas


Zitat von B S Bhushan :

> Dear Experts,
>
> I have calculated the pdos of MoS2 sheet... Where, I have observed two s
> orbitals and two p orbital pdos files for Mo. The no. of pdos files for d
> orbital is only one, though.
> The electron configuration of Mo is [Kr] 5s1 4d5. Then, How am I getting
> two s and two p pdos files ???
>
> The input scripts and the screen shot have been attached with  the mail.
>
> Awaiting your suggestions,
>
> Sincerely,
> B S Bhushan,
> Ph.D Scholar,
> ABV - Indian Institute of Information Technology and Management, Gwalior,
> India.

-- 
Dr. rer. nat. Thomas Brumme
Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
Leipzig University
Phillipp-Rosenthal-Strasse 31
04103 Leipzig

Tel:  +49 (0)341 97 36456

email: thomas.bru...@uni-leipzig.de

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] How to set variables when get symmetry operation # N not allowed?

2018-02-08 Thread Arena Konta

Dear prof. Paolo Giannozzi

Thank you for quick response. Please, clarify me: I set variable
"use_all_frac=.true." and option "verbosity='high'" and get output showed
below. Hoverwer, I am still unable to find the right values of frac. trans
(n=1?) I have to calculate phonons,
so i need to set right k-mesh.

 8 Sym. Ops., with inversion, found


sfrac. trans.

  isym =  1 identity

 cryst.   s( 1) = ( 1  0  0  )
  ( 0  1  0  )
  ( 0  0  1  )

 cart.s( 1) = (  1.000  0.000  0.000 )
  (  0.000  1.000  0.000 )
  (  0.000  0.000  1.000 )


  isym =  2 180 deg rotation - cart. axis [0,0,1]

 cryst.   s( 2) = (-1  0  0  )
  ( 0 -1  0  )
  (-1 -1  1  )

 cart.s( 2) = ( -1.000  0.000  0.000 )
  (  0.000 -1.000  0.000 )
  (  0.000  0.000  1.000 )


  isym =  3  90 deg rotation - cart. axis [0,0,-1]

 cryst.   s( 3) = ( 0 -1  0  )
  ( 1  0  0  )
  ( 0 -1  1  )

 cart.s( 3) = (  0.000  1.000  0.000 )
  ( -1.000  0.000  0.000 )
  (  0.000  0.000  1.000 )


  isym =  4  90 deg rotation - cart. axis [0,0,1]

 cryst.   s( 4) = ( 0  1  0  )
  (-1  0  0  )
  (-1  0  1  )

 cart.s( 4) = (  0.000 -1.000  0.000 )
  (  1.000  0.000  0.000 )
  (  0.000  0.000  1.000 )


  isym =  5 inversion

 cryst.   s( 5) = (-1  0  0  )
  ( 0 -1  0  )
  ( 0  0 -1  )

 cart.s( 5) = ( -1.000  0.000  0.000 )
  (  0.000 -1.000  0.000 )
  (  0.000  0.000 -1.000 )


  isym =  6 inv. 180 deg rotation - cart. axis [0,0,1]

 cryst.   s( 6) = ( 1  0  0  )
  ( 0  1  0  )
  ( 1  1 -1  )

 cart.s( 6) = (  1.000  0.000  0.000 )
  (  0.000  1.000  0.000 )
  (  0.000  0.000 -1.000 )


  isym =  7 inv.  90 deg rotation - cart. axis [0,0,-1]

 cryst.   s( 7) = ( 0  1  0  )
  (-1  0  0  )
  ( 0  1 -1  )

 cart.s( 7) = (  0.000 -1.000  0.000 )
  (  1.000  0.000  0.000 )
  (  0.000  0.000 -1.000 )


  isym =  8 inv.  90 deg rotation - cart. axis [0,0,1]

 cryst.   s( 8) = ( 0 -1  0  )
  ( 1  0  0  )
  ( 1  0 -1  )

 cart.s( 8) = (  0.000  1.000  0.000 )
  ( -1.000  0.000  0.000 )
  (  0.000  0.000 -1.000 )


Thank you in avdance.
Arena Konta


*

Set variable "use_all_frac=.true." and option "verbosity='high'". This will
find and print all symmetries and associated fractional translations. If a
fractional translation along a crystal axis is 1/n, with n integer, the FFT
dimension along that axis must contain a factor n. If you do not need
hybrid functionals or phonons, just set variable "use_all_frac=.true."

Paolo





2018-02-07 20:18 GMT+01:00 Arena Konta :

> Hi All,
>
> I read Troubleshooting and found out that "you can force your FFT grid to be 
> commensurate with fractional translation (set variables nr1, nr2, nr3 to 
> suitable values)". How to do this for the crystal structure presented below? 
> I have tried to this for various k-mesh, but every time I get 6 symmetry 
> operations are not compatible with FFT grid:
>  warning: symmetry operation # 2 not compatible with FFT grid.
>   -1 0 0
>0 -1 0
>   -1 -1 1
>  warning: symmetry operation # 3 not compatible with FFT grid.
>0 -1 0
>1 0 0
>0 -1 1
>  warning: symmetry operation # 4 not compatible with FFT grid.
>0 1 0
>   -1 0 0
>   -1 0 1
>  warning: symmetry operation # 6 not compatible with FFT grid.
>1 0 0
>0 1 0
>1 1 -1
>  warning: symmetry operation # 7 not compatible with FFT grid.
>0 1 0
>   -1 0 0
>0 1 -1
>  warning: symmetry operation #

Re: [Pw_forum] Emax and Emin for DOS and PDOS calculation

2018-02-08 Thread Lorenzo Paulatto

On 08/02/18 12:39, Madhurya Chandel wrote:
> I have a doubt that during calculation of DOS and PDOS of any system do 
> we have to specify the Emax and Emin.
> Like in VASAP we don't have to specify the range of Emax and Emin.
> If it is required how to fix it?
> What are points we have to consider?

http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_DOS.html

> 
> Second thing The band structure calculation. We have to do it stepwise 
> like the first optimization then DOS then PDOS and then band structure 
> calculation.
> Or After optimization, we can directly calculate the band structure?

DOS and PDOS are computed from the set of k-points that were saved on 
disk during the previous SCF or NSCF/BANDS calculation.If these points 
do not provide a good sampling of the Brillouin zone, the DOS will not 
be accurate, this would be the case if you did a BANDS calculation

kind regards


> 
> With Regards
> 
> *Madhurya Chandel*
> 
> *Research Scholar
> *
> *Department of Chemistry
> *
> *BITS PILANI, GOA campus
> *
> 
> *+91-7507546773*
> 
> 
> 
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
> 

-- 
Lorenzo Paulatto - Paris
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Crash with Environ-0.2

2018-02-08 Thread Huu Chuong Nguyën

Hi,


I found that if I comment the line

!vdw_corr = Grimme-D2, ! DFT-D2 dispersion correction
it works!

There may be some issues between  DFT-D2 and environ-0.2

Best regards,



Dr. Huu Chuong Nguyën (Bob)

Postdoc Researcher - Group of Prof. Núria López

Institute of Chemical Research of Catalonia (ICIQ)
The Barcelona Institute of Science and Technology

Av. Països Catalans 16 - 43007 Tarragona (Spain)

PB-12 Huu Chuong Nguyën - PERSONAL

hngu...@iciq.es - www.iciq.es


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] pdos of MoS2

2018-02-08 Thread B S Bhushan

Dear Experts,

I have calculated the pdos of MoS2 sheet... Where, I have observed two s
orbitals and two p orbital pdos files for Mo. The no. of pdos files for d
orbital is only one, though.
The electron configuration of Mo is [Kr] 5s1 4d5. Then, How am I getting
two s and two p pdos files ???

The input scripts and the screen shot have been attached with  the mail.

Awaiting your suggestions,

Sincerely,
B S Bhushan,
Ph.D Scholar,
ABV - Indian Institute of Information Technology and Management, Gwalior,
India.


mos2_nscf.in
Description: Binary data


mos2.in
Description: Binary data


pdos_mos2.in
Description: Binary data


dos_mos2.in
Description: Binary data
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Emax and Emin for DOS and PDOS calculation

2018-02-08 Thread Madhurya Chandel

Dear All

I have a doubt that during calculation of DOS and PDOS of any system do we
have to specify the Emax and Emin.
Like in VASAP we don't have to specify the range of Emax and Emin.
If it is required how to fix it?
What are points we have to consider?

Second thing The band structure calculation. We have to do it stepwise like
the first optimization then DOS then PDOS and then band structure
calculation.
Or After optimization, we can directly calculate the band structure?

With Regards

*Madhurya Chandel*

*Research Scholar *

*Department of Chemistry *

*BITS PILANI, GOA campus*

*+91-7507546773*
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Memory problems with a job using PWSCF from qe-gpu

Re: [Pw_forum] Crash with Environ-0.2

Re: [Pw_forum] How to set variables when get symmetry operation # N not allowed?

Re: [Pw_forum] pdos of MoS2

Re: [Pw_forum] How to set variables when get symmetry operation # N not allowed?

Re: [Pw_forum] Emax and Emin for DOS and PDOS calculation

Re: [Pw_forum] Crash with Environ-0.2

[Pw_forum] pdos of MoS2

[Pw_forum] Emax and Emin for DOS and PDOS calculation

9 matches

Site Navigation

Mail list logo

Footer information