Compilation error in yambo-5.0.3

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

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

Forum rules
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
andrea.ferretti
Posts: 184
Joined: Fri Jan 31, 2014 11:13 am

Re: Compilation error in yambo-5.0.3

Post by andrea.ferretti » Tue Sep 14, 2021 5:59 pm

for completeness, here is an older post from another user
viewtopic.php?t=1891
who found a similar problem.

There the solution seems to involve using "--enable-netcdf-v3"
(which shouldn't be really used, but perhaps it is worth a try)

Andrea
Andrea Ferretti, PhD
CNR-NANO-S3 and MaX Centre
via Campi 213/A, 41125, Modena, Italy
Tel: +39 059 2055322; Skype: andrea_ferretti
URL: http://www.nano.cnr.it

Bramhachari Khamari
Posts: 86
Joined: Wed Oct 23, 2019 5:52 am

Re: Compilation error in yambo-5.0.3

Post by Bramhachari Khamari » Wed Sep 15, 2021 6:02 am

Dear Sir,
Thank you for the reply. In the link provided the problem is solved using "--enable-netcdf-v3". However comipling in this manner yambo_rt does not work as suggested by Davide sir. I am lokking to run real time simulation (yambo_rt). Any other suggestion is welcome. Just to confirm when you say netcdf-v4 wht does that mean?

i) Is it netcdf-c-4.7.4.tar.gz or netcdf-fortran-4.5.3.tar.gz
ii) Is it both
ii) how to add netcdf and hdf5 with intel in configuring yambo.

Regards,
Bramhachari Khamari
Post Doctoral Fellow
Department of Physics
IIT Kanpur, India.

andrea.ferretti
Posts: 184
Joined: Fri Jan 31, 2014 11:13 am

Re: Compilation error in yambo-5.0.3

Post by andrea.ferretti » Sat Sep 18, 2021 4:23 pm

Dear Bramchari,

netcdf-v4 means the standard format of netcdf more or less since version 4.x (of netcdf), which is based on hdf5.
You don't have to specify anything at netcdf compile time.

Concerning yambo, you need both netcdf-c and netcdf-fortran. hdf5 is also a requirement to compile netcdf-c.
Below is an example of configure flags to link external netcdf, netcdff and hdf5 libs.

take care
Andrea

Code: Select all

MKLROOT=/opt/intel/compilers_and_libraries_2020.0.166/linux/mkl

./configure \
  FC=ifort \
  CC=icc \
  --with-fft-libs="-mkl" \
  --with-blas-libs="-L$MKLROOT -lmkl_intel_lp64  -lmkl_sequential -lmkl_core " \
  --with-lapack-libs="-L$MKLROOT -lmkl_intel_lp64  -lmkl_sequential -lmkl_core " \
  --with-scalapack-libs="-L$MKLROOT -lmkl_scalapack_lp64 " \
  --with-blacs-libs="-L$MKLROOT -lmkl_blacs_intelmpi_lp64 " \
  --with-iotk-path="/opt/iotk/y1.2.2-intel" \
  --with-libxc-path="/opt/libxc/2.2.3-intel" \
  --with-hdf5-path="/opt/hdf5/1.12.0-intel" \
  --with-netcdf-path="/opt/netcdf/4.7.4-hdf5-intel" \
  --with-netcdff-path="/opt/netcdff/4.5.2-hdf5-intel" \
  --enable-open-mp \
  --enable-time-profile \
  --enable-memory-profile \
  --enable-msgs-comps
Andrea Ferretti, PhD
CNR-NANO-S3 and MaX Centre
via Campi 213/A, 41125, Modena, Italy
Tel: +39 059 2055322; Skype: andrea_ferretti
URL: http://www.nano.cnr.it

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