Troubles with 5.1 and netcdf-v3

[chwolf]

Hi guys,

I tried my best all day sifting through forum posts but I couldn't get it to work.

Setup: Yambo 5.1, Centos 7, Intel 19 (bit older system).

I compiled Yambo with ./compile FC=ifort CC=icc and the compilation goes OK but when running something more difficult than the setup (yambo -i) I get the error related to some netcdf variable reported previously.

So I tried

./configure FC=ifort CC=icc --enable-netcdf-v3, which runs OK, but during compilation the first error is

\t[netcdf-c-4.7.4] installation
chmod: cannot access ‘/usr/local/yambo-5.1/src/lib/external/intel/mpiifort/v3/serial/lib*/*netcdf*a’: No such file or directory
\t[netcdf-fortran-4.5.3] download

which is correct because:

ls /usr/local/yambo-5.1/src/lib/external/intel/mpiifort/v3/serial/lib/
libhdf5.a libhdf5_fortran.la libhdf5_hl_fortran.a libhdf5hl_fortran.la libhdf5.la
libhdf5_fortran.a libhdf5_hl.a libhdf5hl_fortran.a libhdf5_hl.la libhdf5.settings

and later

[src/tools] libtools.a (lib)
make[2]: *** [/usr/local/yambo-5.1/src/config/mk/local/rules.mk:9: mod_pars.o] Error 1
mod_pars.f90(26): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [NETCDF]
[driver] yambo (checking work to be done)
yambo linking failed. Check log/compile_yambo.log
mod_pars.f90(26): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [NETCDF]
make[1]: *** [config/mk/global/actions/compile_yambo.mk:42: yambo] Error 1
yambo build failed


Interestingly there is also no netcdf version that looks like a version 3, because the version downloaded by yambo is netcdf-c-4.7.4 (is that right?) but inside the netcdf folders everything looks ok.

Has anyone encountered and solved this problem...? Any help is greatly appreciated!

Chris

[chwolf]

PS: the config.log

[Daniele Varsano]

Dear Christoph,

there is no need to use the netcdf-3 and you can safely use the netcdf version downloaded by Yambo.
Can you post what kind od problem you are facing with your calculations? Often, netcdf error are due to other problem in the calculation.

Best,
Daniele

[chwolf]

Dear Daniele,

Thanks for your reply and sorry for the delay, I was traveling.

I updated my compilers to intel OneAPI 2021, just in case. After loading all modules I compiled with the following:

Code: Select all

./configure FC=mpiifort F77=mpiifort  --enable-par-linalg --with-scalapack-libs=mkl --with-blacs-libs=mkl

Compilation of the core package went smoothly. p2y works without hickup. But when calling yambo I get an error that is quite puzzling:

Code: Select all

yambo -i -V RL

[ERROR] Initialization not yet done. Use RL units in input or run initialization(base)

-i -V RL should do exactly what the error says and, as a matter of fact no yambo.in file is created (the -Q flag also does not help).

I guess even the compilation worked I did not obtain a "working" yambo - but what could cause this?

Code: Select all

# [VER] 5.1
#
# Legend: [E]=external library [C]=internal lib to be compiled [I]=internal lib already compiled [X]=used [-]=not used
# 
# - GENERAL CONFIGURATIONS -
# 
# [SYS] linux@x86_64
# [SRC] /usr/local/yambo-5.1/src
# [BRN] master
# [CMP] /usr/local/yambo-5.1/src
# [TGT] /usr/local/yambo-5.1/src
# [BIN] /usr/local/yambo-5.1/src/bin
# [LIB] /usr/local/yambo-5.1/src/lib/external
#
# [EDITOR] vim
# [ MAKE ] make
#
# [-] Double precision
# [X] Keep object files
# [X] Run-Time timing profile 
# [-] Run-Time memory profile 
#
# - SCRIPTS -
#
# [-] YDB: Yambo DataBase
# [-] YAMBOpy: Yambo Python scripts
# 
# - PARALLEL/CUDA SUPPORT -
#
# [-] CUDA
# [E] MPI
# [-] OpenMP
# 
# - I/O -
#
# [-]: Parallel I/O  
# [C]: HDF5 
# [C]: NETCDF Large Files Support enabled, Version 4
# [-]: Parallel NETCDF 
# [-]: Parallel HDF5  
# 
# - LIBRARIES - 
#
# [-] FUTILE  :  
#                  
# [-] YAML    :  
#                  
# [C] IOTK    : /usr/local/yambo-5.1/src/lib/external/intel/mpiifort/lib/libiotk.a (QE hdf5-support)
#                 -I/usr/local/yambo-5.1/src/lib/external/intel/mpiifort/include/
# [-] ETSF_IO :  
#                  
# [C] NETCDF  : /usr/local/yambo-5.1/src/lib/external/intel/mpiifort/v4/serial/lib/libnetcdff.a /usr/local/yambo-5.1/src/lib/external/intel/mpiifort/v4/serial/lib/libnetcdf.a 
#                 -I/usr/local/yambo-5.1/src/lib/external/intel/mpiifort/v4/serial/include -I/usr/local/yambo-5.1/src/lib/external/intel/mpiifort/v4/serial/include 
# [C] HDF5    : /usr/local/yambo-5.1/src/lib/external/intel/mpiifort/v4/serial/lib/libhdf5_hl_fortran.a /usr/local/yambo-5.1/src/lib/external/intel/mpiifort/v4/serial/lib/libhdf5_fortran.a /usr/local/yambo-5.1/src/lib/external/intel/mpiifort/v4/serial/lib/libhdf5_hl.a /usr/local/yambo-5.1/src/lib/external/intel/mpiifort/v4/serial/lib/libhdf5.a -lz -lm -ldl -lcurl
#                 -I/usr/local/yambo-5.1/src/lib/external/intel/mpiifort/v4/serial/include
#
# > MATH: (FFTW MKL) 
#
# [E] FFT       : -L/usr/local/intel/oneapi/mkl/latest/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm
#                 
# [E] BLAS      : -L/usr/local/intel/oneapi/mkl/latest/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm
# [E] LAPACK    : 
# [E] SCALAPACK : -L/usr/local/intel/oneapi/mkl/latest/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 
# [E] BLACS     : -L/usr/local/intel/oneapi/mkl/latest/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64
# [-] PETSC     :  
#                  
# [-] SLEPC     :  
#                  
#
# > OTHERs
#
# [C] LibXC     : /usr/local/yambo-5.1/src/lib/external/intel/mpiifort/lib/libxcf90.a /usr/local/yambo-5.1/src/lib/external/intel/mpiifort/lib/libxcf03.a  /usr/local/yambo-5.1/src/lib/external/intel/mpiifort/lib/libxc.a
#                 -I/usr/local/yambo-5.1/src/lib/external/intel/mpiifort/include
# [E] MPI       : -L/usr/local/intel/oneapi/mpi/latest/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /usr/local/intel/oneapi/mpi/latest/lib/release -Xlinker -rpath -Xlinker /usr/local/intel/oneapi/mpi/latest/lib -lmpifort -lmpi -ldl -lrt -lpthread 
#                 -I/usr/local/intel/oneapi/mpi/latest/include 
#
# - COMPILERS -
#
# FC kind = intel mpiifort for the Intel(R) MPI Library 2021.6 for Linux*
# MPI kind= Intel(R) MPI Library 2021.6 for Linux* OS
#
# [ CPP ] gcc -E -P -D_HDF5_LIB -D_HDF5_IO -D_MPI -D_FFTW -D_FFTW_OMP  -D_SCALAPACK     -D_TIMING     -D_P2Y_QEXSD_HDF5
# [ FPP ] fpp -free -P -D_HDF5_LIB -D_HDF5_IO -D_MPI -D_FFTW -D_FFTW_OMP  -D_SCALAPACK     -D_TIMING    
# [ CC  ] mpiicc -O2 -std=gnu99 -D_C_US -D_FORTRAN_US
# [ FC  ] mpiifort -assume bscc -O3 -g -ip      
# [ FCUF] -assume bscc -O0 -g   
# [ F77 ] mpiifort -assume bscc -O3 -g -ip   
# [ F77U] -assume bscc -O0 -g   
# [Cmain] -nofor-main
#
# You can modify compilers and flags by editing the file "config/setup"

[chwolf]

okay, seems like it just failed to launch any editor... it seems to be working now.

Thanks for your help so far, I am sure I will be back soon!

Chris

[Daniele Varsano]

Dear Christoph,

I'm glad it is working. Do not hesitate to post for any problem you encounter.
Best,
Daniele