Cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)

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Cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)

Postby nkxirainbow » Wed Jul 22, 2009 9:34 am

Dear Professor:
I am very glad of using Yambo.
I use fedora 10 of 64 bit.
I met a problem. I follows the instruction to try to run the example. I have obtained the "ns.bd1 ns.wf" files in ./doc/sample/example/bulk_silicon/SAVE directory. However, I got an error "cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)" when I run "yambo" in the ./doc/sample/example/bulk_silicon dictionary.
By the way, I received the password for the SVN repository. Where does the Yambo need the password? When I compile and run yambo, there is no need to input the password.
Can you give me any hlep?
Thank you very much :)


Hui Wang
Nankai University, China.
Hui Wang
Nankai Universty, China
nkxirainbow@gmail.com
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Re: Cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)

Postby Daniele Varsano » Wed Jul 22, 2009 10:18 am

Dear Hui Wang,
the problem you are encountering: "cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)" it is
probably due the fact that you have the database in netcdf format, while your source is compiled
without linking this library. If this is the reason you have to compile netcdf library and link them
when you compile yambo. You can find instructions on how to do that in the yambo web-page at this
link.
Regarding your second question:
If you downloaded yambo from the download page of the website you don't' need any password,
the password is needed if you want to download it from the SVN repository which contains
the latest revsion of the code.

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

Postby nkxirainbow » Wed Jul 22, 2009 2:50 pm

Dear Daniele:
Thanks a lot for your answer:)
I try to configure with the input "./configure --with-netcdf=/home/raman/accessory-soft/netCDF/lib/". But I still get the previous problem:/
I have attach the output of configure(configure.out) and make all(make.out).
My compiler is g95 and mpif90.The architecture is fedora 10 with 64-bit.
The problems occur compiling in serial and in parallel, and the version of Yambo is "yambo-3.2.1-r.448".

Thanks a lot:)
Hui Wang
Nankai Universty, China
nkxirainbow@gmail.com
nkxirainbow
 
Posts: 11
Joined: Wed Jul 22, 2009 6:12 am

Re: Cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)

Postby andrea marini » Wed Jul 22, 2009 3:04 pm

nkxirainbow wrote:Dear Daniele:
Thanks a lot for your answer:)
I try to configure with the input "./configure --with-netcdf=/home/raman/accessory-soft/netCDF/lib/". But I still get the previous problem:/
I have attach the output of configure(configure.out) and make all(make.out).
My compiler is g95 and mpif90.The architecture is fedora 10 with 64-bit.
The problems occur compiling in serial and in parallel, and the version of Yambo is "yambo-3.2.1-r.448".

Thanks a lot:)


Dear Hui Wang,

there is no file appearing as an attachment. Try to zip/tar the files before uploading. Moreover please add also the config/report and config/setup files.

Andrea
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
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Re: Cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)

Postby Daniele Varsano » Wed Jul 22, 2009 3:08 pm

Anyway check at the end of your configure procedure if the netcdf box is marked.
Moreover, typing ./configure -h you can see that the options
--with-netcdf-include=<path>
Path of the NetCDF include directory
--with-netcdf-lib=<path>
Path of the NetCDF lib directory

are required.

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

Postby myrta gruning » Wed Jul 22, 2009 3:09 pm

Dear Hui Wang,

somehow I cannot see the attached files. Anyway the correct configure command (check ./configure --help) should be:

NETCDFHOME=/home/raman/accessory-soft/netCDF/
./configure FC=ifort CC=icc --with-netcdf-include=$NETCDFHOME/include --with-netcdf-lib=$NETCDFHOME/lib

At the end you get a report of the configuration. And you should get a cross corresponding to NETCDF like that

Code: Select all
# [X ] NETCDF/Large Files


Note as well that netcdf is quite "nasty". Usually you need to compile it with the same compiler as the program. :roll:

cheers
m
Dr Myrta GrĂ¼ning
Atomistic Simulation Centre
Queen's University Belfast - Northern Ireland

http://www.researcherid.com/rid/B-1515-2009
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Re: Cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)

Postby nkxirainbow » Thu Jul 23, 2009 4:03 am

Dear Daniele, Andrea and Dr Myrta GrĂ¼ning

Thank you very much. :) I follow you instruction and configure again smoothly. :D
And I am very glad that I run the yambo in ./doc/sample/bulk_silicon successfully. :lol:

I do not change the configure file and I input ./configure --with-netcdf-include=/home/raman/accessory-soft/netcdf/include/ --with-netcdf-lib=/home/raman/accessory-soft/netcdf/lib/ --with-iotk=/home/raman/espresso-4.0.4/iotk/ --with-p2y=4.0. I hope it may help others :roll:

Once again, Thanks a lot :P
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Hui wang
Nankai University,China
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Nankai Universty, China
nkxirainbow@gmail.com
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