yambo 4.2.0 - NetCDF: Variable not found

Having trouble compiling the Yambo source? Using an unusual architecture? Problems with the "configure" script? This is the place to look.

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

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If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
(2) the architecture (e.g. 64-bit IBM SP5)
(3) if the problems occur compiling in serial/in parallel
(4) the version of Yambo (revision number/major release version)
(5) the relevant compiler error message

Re: yambo 4.2.0 - NetCDF: Variable not found

Postby Daniele Varsano » Wed Nov 15, 2017 4:21 pm

Dear Kushal,
It is not clear to me your answer to Davide.
In your previous post you wrote:
I moved these files to the original SAVE and it is now reading these files but I get the following error.

and this is not allowed. You need to run yambo in the folder FixSave/SAVE

In any case if can always start from scratch by doing a qe calculation and use the p2y interface. In this case you will not have format problem.

Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
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Re: yambo 4.2.0 - NetCDF: Variable not found

Postby gyro555in » Wed Nov 15, 2017 4:27 pm

I tried both ways to be honest and the result ended up being the same. It is accessing the new wf files.
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Re: yambo 4.2.0 - NetCDF: Variable not found

Postby Davide Sangalli » Wed Nov 15, 2017 4:37 pm

Yeah, sorry for the silly question.
I just tried the hBN tutorial with the 4.2 version and it works just fine.
From the error message you get it seems there maybe a problem with the blas libraries.
Can you try to also attach the file report in the folder config generated after the compilation of yambo ?

Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
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Re: yambo 4.2.0 - NetCDF: Variable not found

Postby gyro555in » Wed Nov 15, 2017 4:51 pm

Well the compilation is done in our central cluster so I am gonna ask my admin and get back.
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Re: yambo 4.2.0 - NetCDF: Variable not found

Postby gyro555in » Thu Nov 16, 2017 1:10 pm

Here is the compilation report used on our cluster.

#
# [VER] 4.2.0 r.109
#
# - GENERAL CONFIGURATIONS -
#
# [SYS] linux@x86_64
# [SRC] /opt/install/simulation/yambo-4.2.0/yambo-git2/yambo
# [TGT] /opt/install/simulation/yambo-4.2.0/yambo-git2/yambo
# [BIN] /opt/install/simulation/yambo-4.2.0/yambo-git2/yambo/bin
# [LIB] /opt/install/simulation/yambo-4.2.0/yambo-git2/yambo/lib/external
#
# [EDITOR] vim
# [ MAKE ] make
#
# [-] Double precision
# [X] Keep object files
# [X] Run-Time timing profile
# [-] Run-Time memory profile
#
#
# - PARALLEL SUPPORT -
#
# [X] MPI
# [-] OpenMP
#
# - LIBRARIES [E=external library; I?=internal library (c=to be compiled / f=found already compiled); X=system default; -=not used;] -
#
# I/O LIBS
#
# [ E ] IOTK : /opt/install/analysis/espresso/espresso-4.3.2/S3DE/iotk/src/libiotk.a (QE qexml)
# -I/opt/install/analysis/espresso/espresso-4.3.2/S3DE/iotk/src
# [ - ] ETSF_IO :
#
# [ Ic] NETCDF : -L/opt/install/simulation/yambo-4.2.0/yambo-git2/yambo/lib/external/intel/mpifort/v3/lib -lnetcdff -L/opt/install/simulation/yambo-4.2.0/yambo-git2/yambo/lib/external/intel/mpifort/v3/lib -lnetcdf -lm (With large files support)
# -I/opt/install/simulation/yambo-4.2.0/yambo-git2/yambo/lib/external/intel/mpifort/v3/include -I/opt/install/simulation/yambo-4.2.0/yambo-git2/yambo/lib/external/intel/mpifort/v3/include
# [ - ] HDF5 :
#
#
# MATH LIBS
#
# [ Ic] FFT : -L/opt/install/simulation/yambo-4.2.0/yambo-git2/yambo/lib/external/intel/mpifort/lib -lfftw3 (Internal FFTW3)
# -I/opt/install/simulation/yambo-4.2.0/yambo-git2/yambo/lib/external/intel/mpifort/include/
# [ E ] BLAS : -lblas
# [ E ] LAPACK : -llapack
# [ - ] SCALAPACK :
# [ - ] BLACS :
# [ - ] PETSC :
#
# [ - ] SLEPC :
#
#
# OTHER LIBS
#
# [ Ic] LibXC : -L/opt/install/simulation/yambo-4.2.0/yambo-git2/yambo/lib/external/intel/mpifort/lib -lxcf90 -lxc
# -I/opt/install/simulation/yambo-4.2.0/yambo-git2/yambo/lib/external/intel/mpifort/include
# [ E ] MPI : -L/opt/pkg/mpi/openmpi/1.10.2/intel/15.2/64/opt/lib -lmpi
# -I/opt/pkg/mpi/openmpi/1.10.2/intel/15.2/64/opt/include
#
# - COMPILERS (FC kind= intel) -
#
# [ CPP ] /opt/pkg/compiler/intel/fc/15.2/bin/icpc -E -g0 -O3 -m64 -gcc-name=gcc -gxx-name=g++ -cxxlib=/opt/pkg/compiler/gnu/gcc/4.8.2/lib64 -D_MPI -D_FFTW -D_TIMING
# [ FPP ] fpp -free -P -D_MPI -D_FFTW -D_TIMING
# [ CC ] mpicc -g -O2 -D_C_US -D_FORTRAN_US
# [ FC ] mpifort -assume bscc -g -O3 -ip
# [ FCUF] -assume bscc -g -O0
# [ F77 ] mpifort -assume bscc -g -O3 -ip
# [ F77U] -assume bscc -g -O0
# [Cmain] -nofor_main
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Re: yambo 4.2.0 - NetCDF: Variable not found

Postby Davide Sangalli » Thu Nov 16, 2017 2:15 pm

Ok. So blas and lapack are the only ones external.
Ask if they can re-install the code with the option
./configure --enable-int-linalg

Also I would suggest the use of the option:
--with-extlibs-path=$SOME_PATH

Yambo will install all the needed libraries there once for all and eventually re-use them in the future.

Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
http://www.ism.cnr.it/en/davide-sangalli-cv/
http://www.max-centre.eu/
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Re: yambo 4.2.0 - NetCDF: Variable not found

Postby gyro555in » Mon Nov 20, 2017 3:34 pm

Your suggestions for the configuration worked and I tested some basic input files. Thank you very much for your support.
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Re: yambo 4.2.0 - NetCDF: Variable not found

Postby Alesster » Wed Oct 17, 2018 6:34 pm

I am writing here because my problem is connected with this topic.

I use QE v6.3 and Yambo v 4.2.1
Yambo was compiled with --with-p2y-version=qexsd

I am doing simple example Silicon. When I am calculating optical properties it gives error:
[ERROR] STOP signal received while in :[04] Optics
[ERROR] File ./SAVE//ndb.dip_iR_and_P; Variable NOT DEFINED; NetCDF: HDF error

What is the problem can be?

Thank you,
Best,
Sasha
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Donostia International Physics Center (DIPC),
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Re: yambo 4.2.0 - NetCDF: Variable not found

Postby Daniele Varsano » Wed Oct 17, 2018 8:57 pm

Dear Aleksandr,

I use QE v6.3 and Yambo v 4.2.1
Yambo was compiled with --with-p2y-version=qexsd


Ok, if p2y runned smoothly, all is ok up to here.

When I am calculating optical properties it gives error:
[ERROR] STOP signal received while in :[04] Optics
[ERROR] File ./SAVE//ndb.dip_iR_and_P; Variable NOT DEFINED; NetCDF: HDF error
What is the problem can be?


Here we need to investigate, and reproduce your problem. Can you also post your config.log and ./config/setup files.
Before that please note that in your input file there is a problem:
Code: Select all
% XfnQP_E
 0.530000 | 1.000000 | 1.000000 |        # [EXTQP Xd]


There is a missing % closing the filed, it should be:
Code: Select all
% XfnQP_E
 0.530000 | 1.000000 | 1.000000 |        # [EXTQP Xd]
%

May be you can try if this solve your problem. Next please note that with these settings:
Code: Select all
FxcGRLc= 1             RL      # [TDDFT] XC-kernel RL size
NGsBlkXd= 1   


you essentially not including local field effects ant the ALDA kernel is not properly evaluated, but this is not at all the reason of the error you get.

Best,
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: yambo 4.2.0 - NetCDF: Variable not found

Postby Alesster » Thu Oct 18, 2018 5:21 pm

Dear Daniele,

Thank you for the reply.

The config.log is very huge therefore I separated it on two parts.

if p2y runned smoothly, all is ok up to here.

Yes, p2y finished correctly.

There is a missing % closing the filed

In original file % is not missing.

you essentially not including local field effects ant the ALDA kernel is not properly evaluated

This is just test calculation and it must not influence on the running process. I did such kind of runs before and it was always ok.

Best,
Sasha.
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Donostia International Physics Center (DIPC),
E-20018 Donostia, Basque Country, Spain.
http://dipc.ehu.es/
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