netCDF problem with rev 14 : LFS support absent?

Various technical topics such as parallelism and efficiency, netCDF problems, the Yambo code structure itself, are posted here.

Moderators: Daniele Varsano, andrea.ferretti, andrea marini, Conor Hogan, myrta gruning

Re: netCDF problem with rev 14 : LFS support absent?

Postby marco.govoni » Tue Nov 16, 2010 11:22 am

Further details:
This is the end of ndb.kindx for a well-behaved run (well-behaved in the sense that everything works normally: r_setup is created, no largedb needed since this is a coarse grid, no netcdf error, classic netcdf offset)
Code: Select all
-bash-3.2$ ncdump ndb.kindx |tail
    15, 15, 15, 15, 15, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9,
    9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 15, 15, 15, 15, 15, 15, 15, 15,
    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 9, 9, 9,
    15, 15, 15, 15, 15, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9,
    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 15,
    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 15, 15, 15, 15, 15, 15,
    15, 15, 15, 15, 15, 15, 8, 15, 15, 8 ;
}

Now I post the end of ndb.kindx for the guilty run, whose errors I have already reported in the previous posts (just to remind: no netcdf error produced after rev 16, run ends at 95% wrongly without producing readable errors, this is a large file written with 64 offset)
Code: Select all
-bash-3.2$ ncdump ndb.kindx |tail
    6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
    6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6,
    6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1,
    1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
    6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6,
    6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
    1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
    6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6,
    6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1,
    1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
    1, 1, 1, 1, 1, 1, 1

As you can see from the comparison, something is wrong and the file is not created correctly. Indeed io_disconnect was never called for this run by ioQINDX as my prints showed you.

Marco
Marco Govoni
Physics Department, University of Modena and Reggio Emilia (Italy)
marco.govoni
 
Posts: 35
Joined: Thu May 21, 2009 3:46 pm

Re: netCDF problem with rev 14 : LFS support absent?

Postby feffeficus » Tue Nov 16, 2010 2:41 pm

I jump into the discussion to attach also my own personal error, I presume to be strictly related (and already posted here previously, and not resolved: http://www.yambo-code.org/forum/viewtopic.php?f=14&t=252

I've compiled rev14 on sp6 like that
Code: Select all
module load gnuplot/3.7.1-ibm tar/1.14-ibm vim/7.2 xdiff/3.4 xl/10.1  make/3.81
module load fftw/3.2.2--xl--10.1 QuantumESPRESSO/4.1
module load zlib/1.2.5--xl--10.1 szlib/2.1--xl--10.1
module load hdf5/1.8.4_ser--xl--10.1  netcdf/4.0.1--xl--10.1

export CPP=cpp
export CC=xlc_r
export F77=xlf_r
export FC=xlf90_r
export FCFLAGS='-O2 -q64 -qstrict -qarch=pwr6 -qtune=pwr6 -qmaxmem=-1
-qsuffix=f=f -qalias=intptr -qwarn64'

./configure --with-fftw=/cineca/prod/libraries/fftw/3.2.2/xl--10.1/
--with-netcdf-lib=/cineca/prod/libraries/netcdf/4.0.1/xl--10.1/lib
--with-netcdf-include=/cineca/prod/libraries/netcdf/4.0.1/xl--10.1/include
--with-p2y=4.0
--with-iotk=/cineca/prod/build/applications/QuantumESPRESSO/4.1/xl--10.1/BA_WORK/QuantumESPRESSO-4.1/iotk
--build=powerpc-ibm --enable-largedb


Yambo seems to work, until, when calculating these b****y GW corrections, stops with:

Code: Select all
[ERROR] STOP signal received while in :[09] Dynamic Dielectric Matrix (PPA)
[ERROR][NetCDF] NetCDF: One or more variable sizes violate format constraints


And this NETCDF ERRROR occurs periodically in other several romantic moments.
I'm not blaming anyone, I would like only to report the problem.

May I instill the doubt: could it be related not to yambo, but to some *wierd* netcdf installation from Cineca?

!! new motorbike tires for who will fix the problem !!!
feffeficus
 
Posts: 31
Joined: Tue Apr 07, 2009 4:39 pm

Re: netCDF problem with rev 14 : LFS support absent?

Postby andrea marini » Tue Nov 16, 2010 2:50 pm

feffeficus wrote:!! new motorbike tires for who will fix the problem !!!


It is a CINECA problem. Nothing to do with Yambo :mrgreen: So, where are my new tyres ? :lol:

Seriously. In all these cases the is only one way. If I can reproduce the error on my linux box I can solve it with no big effort. If the problem appears ONLY on Cineca and not always ... well... it happened me in the past and I could not find any solution. Simply these errors disappeared after a major code/compiler/platform upgrade.

I am working on the Marco's problem. Feffe, in your case, you should send me the GS input files and the Yambo input files. I can try first to reproduce the error on my linux box.

Send me an E-mail with these informations and I will see what I can do.

Andrea
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
User avatar
andrea marini
 
Posts: 447
Joined: Mon Mar 16, 2009 4:27 pm

Re: netCDF problem with rev 14 : LFS support absent?

Postby feffeficus » Tue Nov 16, 2010 2:55 pm

I see.

OK. I will prepare the mail.

which brand? yamaha??
Federico Iori - LSI - Ecole Polytechnique (Palaiseau) France - http://www.etsf.polytechnique.fr
feffeficus
 
Posts: 31
Joined: Tue Apr 07, 2009 4:39 pm

Re: netCDF problem with rev 14 : LFS support absent?

Postby andrea marini » Tue Nov 16, 2010 3:04 pm

feffeficus wrote:which brand? yamaha??


Of the tyres ?!?! Pirelli, please! And my bike is an Honda, not a Yamaha :evil:
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
User avatar
andrea marini
 
Posts: 447
Joined: Mon Mar 16, 2009 4:27 pm

Previous

Return to Technical Issues

Who is online

Users browsing this forum: No registered users and 1 guest