inizialization and databases

Concerns any physical issues arising during the setup step (-i option). This includes problems with symmetries, k/q-point sets, and so on. For technical problems (running in parallel, etc), refer to the Technical forum.

Moderator: Daniele Varsano

Re: inizialization and databases

Postby claudio » Tue May 24, 2011 3:45 pm

Dear Sam

may you put on the forum the file

config/setup

inside your yambo folder

thanks
Cla
Claudio Attaccalite
Institut Neel, CNRS/UJF ABINEEL group
25 rue des Martyrs BP 166, Bâtiment D
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Re: inizialization and databases

Postby Daniele Varsano » Tue May 24, 2011 3:47 pm

Dear Sam,
Yambo and libnecdf should be compiled with the same compiler,
please check that this is the case.

Cheers,

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/
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Re: inizialization and databases

Postby samazadi » Tue May 24, 2011 4:06 pm

Dear Claudio and Daniele

Attached file is config/setup file.
To install libnetcdf I used "Synaptic Package Manager" of Ubuntu.
Thanks in advance.

Ciao
Sam
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*******************************************
Sam Azadi
Institute of Physical Chemistry and
Center for Computational Sciences
Johannes Gutenberg University Mainz
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D-55128 Mainz
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azadi@uni-mainz.de
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Re: inizialization and databases

Postby myrta gruning » Wed May 25, 2011 10:30 am

Hallo Sam

It is just a guess, but maybe you can try to edit the setup by modyfing the line

lnetcdf = -L/usr/local/lib -lnetcdff -lnetcdf

(or lnetcdf = -L/usr/local/lib -lnetcdf -lnetcdff)

Good luck,
m
Dr Myrta Grüning
Atomistic Simulation Centre
Queen's University Belfast - Northern Ireland

http://www.researcherid.com/rid/B-1515-2009
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Re: inizialization and databases

Postby samazadi » Thu May 26, 2011 7:14 pm

Dear Myrta

Thanks for your guess, it fixed the problem of compiling but when I run "yambo" after "p2y -N":

yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)

Cheers
Sam
*******************************************
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Institute of Physical Chemistry and
Center for Computational Sciences
Johannes Gutenberg University Mainz
Staudinger Weg 9
D-55128 Mainz
Germany
azadi@uni-mainz.de
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Re: inizialization and databases

Postby Daniele Varsano » Fri May 27, 2011 3:23 pm

Dear Sam,
may be it is a stupid comment,
anyway, are you running yambo in the right directory?
which means, in the directory you are running yambo there is
the SAVE directory when you type ls.

Next, if there is the SAVE directory,
the contained files are named ns.db1 etc..? or s.db1?
I ask this in order to understand if it is a netcdf related problem

Cheers,

Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
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Re: inizialization and databases

Postby samazadi » Fri May 27, 2011 5:42 pm

Dear Daniele

I appreciate any comment.
Yes. I do. I run yambo in the directory which there is SAVE directory.
In the SAVE directory there are two "ns.db1" and "ns.wf" binary files successfully created by "p2y -N":

************************************************************
<---> [01] P(W) 2 Y(ambo) Ver. 4.0
<---> DBs path set to .
<---> Index file set to data-file.xml
<---> Header/K-points/Energies...done
<---> Cell data...done
<---> Atomic data...done
<---> Symmetries...[SI no]...[I yes]...[-I no]...[TR yes]
<---> [WARNING]GGA not supported: switching to PZ. PW XC string is: SLA PW PBE PBE
<---> XC functional...Perdew & Zunger (xc)
<---> K-points mesh...done
<---> RL vectors...done
<---> IGK arrays...done
<---> Energies...done
<---> :: Electrons : 16.00000
<---> :: Temperature [ev]: 0.000000
<---> :: Lattice factors [a.u.]: 6.517587 5.644401 5.140017
<---> :: K-points : 32
<---> :: Bands : 40
<---> :: Spinor components : 1
<---> :: Spin polarizations : 1
<---> :: Spin orbit coupling : no
<---> :: Symmetries [spatial]: 1
<---> :: [T-rev]: yes
<---> :: Max WF components : 1496
<---> :: RL vectors (WF): 1998
<---> :: RL vectors (CHARGE): 1998
<---> :: XC potential : Perdew & Zunger (xc)
<---> :: Atomic species : 1
<---> :: Max atoms/species : 16
<---> == Writing DB1 ...done ==
<---> == DB2 (wavefunctions) ...done ==
**********************************************************

The point is when I don't use "-lnetcdff" flag in setup file ,
in the [Linking yambo] part of compiling yambo stops with errors which I posted at previous emails.
But when I use "-lnetcdff" flag as Myrta suggested there is no error in compiling but there is warning:

>>>[Linking yambo]<<<
make[1]: Entering directory `/home/sam/espresso-4.2.1/yambo-copy/driver'
/home/sam/espresso-4.2.1/yambo-copy/driver/driver.c: In function ‘main’:
/home/sam/espresso-4.2.1/yambo-copy/driver/driver.c:311: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result

make[1]: Leaving directory `/home/sam/espresso-4.2.1/yambo-copy/driver'


Cheers
Sam
*******************************************
Sam Azadi
Institute of Physical Chemistry and
Center for Computational Sciences
Johannes Gutenberg University Mainz
Staudinger Weg 9
D-55128 Mainz
Germany
azadi@uni-mainz.de
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Re: inizialization and databases

Postby andrea marini » Mon May 30, 2011 7:53 am

Dear Sam,

I fear we will continue walking around the problem without spotting it. Let's go step by step. The point is that, as far as I understand, you managed to link yambo with netcdf but, nevrtheless, yambo does not seem to be capable of reading the NETCDF databases. And this is quite strange. So, please, confirm me that you can actually compile the simple program (check it by hand, do not trust the config.log)

Code: Select all
 
program main
use netcdf
end


Then, if this is the case, add the option "--enable-msgs-comps=no" to the configure and run
Code: Select all
> make yambo >& COMPILE.txt


Then attach to your post the COMPILE.txt

Cheers

Andrea
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
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Re: inizialization and databases

Postby claudio » Mon May 30, 2011 8:04 am

Dear Sam

just another comment: yambo works perfectly without NetCDF,
if you do not need to transfer yambo databases between different machines you do not need NetCDF

cla
Claudio Attaccalite
Institut Neel, CNRS/UJF ABINEEL group
25 rue des Martyrs BP 166, Bâtiment D
38042 Grenoble cedex 9 France
web site: http://www.attaccalite.com
Freely download scientific books from: http://www.freescience.info
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Re: inizialization and databases

Postby samazadi » Mon May 30, 2011 1:07 pm

Dear Claudio

I tried to use yambo without NetCDF. I did:

./configure --with-iotk=/home/sam/espresso-4.2.1/iotk --with-p2y=4.0 --disable-netcdf-LFS
make all

it compiled successfully, but there is same problem in running yambo (after " p2y -N "):

yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)

Would you please tell me how can I compile without NetCDF ?
Thanks in advance.

Cheers
Sam
*******************************************
Sam Azadi
Institute of Physical Chemistry and
Center for Computational Sciences
Johannes Gutenberg University Mainz
Staudinger Weg 9
D-55128 Mainz
Germany
azadi@uni-mainz.de
+49/(0)6131/39-26844
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