error compilation Yambo-4.3.2:Making modules

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

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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

error compilation Yambo-4.3.2:Making modules

Postby hongshen » Wed Mar 27, 2019 2:24 am

Dear developers and users:
I'm trying to compile yambo-4.3.2 with intel parallel studio, version 19.0.3.199 on a x86_64 machine, but something goes wrong. I manually downloaded every external lib to /yambo/lib/archive and run "./configure" followed by "make yambo". Everything goes fine until ">>>[Making modules]<<<" part. Here is my error message:

make[1]: enter directory“/home/hshen/q-e-qe-6.4/yambo-4.3.2/src/modules”
mod_pars.f90(26): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [NETCDF]
use netcdf
-----^
mod_pars.f90(87): error #6592: This symbol must be a defined parameter, an enumerator, or an argument of an inquiry function that evaluates to a compile-time constant. [NF90_REAL]
integer, parameter :: nf90_SP = nf90_real
----------------------------------^
mod_pars.f90(87): error #6404: This name does not have a type, and must have an explicit type. [NF90_REAL]
integer, parameter :: nf90_SP = nf90_real
----------------------------------^
compilation aborted for mod_pars.f90 (code 1)
make[1]: *** [mod_pars.o] error 1
make[1]: leave directory“/home/hshen/q-e-qe-6.4/yambo-4.3.2/src/modules”
make: *** [yambo] error 2

Any suggestions would be appreciated!
Thank you in advance

Shen Hong
Department of optical science engineering,
Fudan University,
China
hongshen
 
Posts: 2
Joined: Tue Mar 26, 2019 1:13 pm

Re: error compilation Yambo-4.3.2:Making modules

Postby Daniele Varsano » Wed Mar 27, 2019 9:39 am

Dear Shen Hong,
it seems there is something wrong in the netcdf path.
Note there is no need to download manually the required libraries as they are automatically downloaded and compiled during the make procedure.
In case you want to use precompiled libraries, check that the paths to the libraries are correctly set during the configuring e.g. a script like:
Code: Select all
NETCDFF_LIB="-L$LIB_PATH/netcdff/4.4.4/intel--pe-xe-2017--binary/lib -lnetcdff"
NETCDF_LIB="-L$LIB_PATH/netcdf/4.4.1/intel--pe-xe-2017--binary/lib -lnetcdf"
NETCDF_INC="$LIB_PATH/netcdf/4.4.1/intel--pe-xe-2017--binary/include"
NETCDFF_INC="$LIB_PATH/netcdff/4.4.4/intel--pe-xe-2017--binary/include"
./configure --with-netcdf-libs="$NETCDF_LIB" --with-netcdf-includedir="$NETCDF_INC" \
--with-netcdff-libs="$NETCDFF_LIB" --with-netcdff-includedir="$NETCDFF_INC"

I do not exclude that you can have then similar problem with other external libraries if the path are not correctly passed to the configure.

If you instead leave yambo to download the external libraries, the correct paths are automatically set.

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
http://www.max-centre.eu/
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Daniele Varsano
 
Posts: 1950
Joined: Tue Mar 17, 2009 2:23 pm

Re: error compilation Yambo-4.3.2:Making modules

Postby hongshen » Sun Mar 31, 2019 4:35 am

Dear Daniele,
thank you for your reply. I manually download the libraries because the network doesn't work.
I tried again by specifying the libraries through configure:
./configure --with-iotk-libs="-L/home/hshen/q-e-qe-6.4/iotk/src/libiotk.a" \
--with-iotk-path="/home/hshen/q-e-qe-6.4/iotk" \
--with-libxc-path="/home/hshen/libxc/" \
--with-fft-path=/home/software/mathlib/fftw/intelmpi/3.3.8 \
--with-netcdf-libs="-L/home/hshen/mathlib/netcdfc/lib -lnetcdf" \
--with-netcdf-includedir="-I/home/hshen/mathlib/netcdfc/include" \
--with-netcdff-includedir="-I/home/hshen/mathlib/netcdfc/include" \
--with-netcdff-libs="-L/home/hshen/mathlib/netcdfc/lib -lnetcdff" \
--with-libxc-libs='-L/home/hshen/libxc/lib/ -lxc -lxcf90' \
--with-blas-libs="-L/home/software/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" \
--with-lapack-libs="-L/home/software/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" \
--with-scalapack-libs="-L/home/software/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64 -lmkl_scalapack_lp64" \
--with-blacs-libs="-L/home/software/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64 -lmkl_blacs_intelmpi_lp64" \

it seems that yambo find netcdf libraries but not headfiles, shown on the screen during configure process:
"checking for NetCDF Library using -L/home/hshen/mathlib/netcdfc/lib -lnetcdf... yes
no
checking for internal NetCDF library... to be compiled"

the config.log file that is attached says include directory not set properly, but I'm pretty sure the directories in configure is correct.
I don't know what's going wrong, could it be some incompatibility issues?

thank you

Shen Hong
Department of optical science engineering,
Fudan University,
China
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hongshen
 
Posts: 2
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Re: error compilation Yambo-4.3.2:Making modules

Postby Daniele Varsano » Sun Mar 31, 2019 9:32 pm

Dear Shen,
when indicating the includedir option e.g.:
--with-netcdf-includedir="$NETCDF_INC" \
just set the path e.g.:
NETCDF_INC="$PATH/netcdf/4.4.1/intel--pe-xe-2017--binary/include"
without indicating the "-I/" prefix
the same for --with-netcdff-includedir

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
http://www.max-centre.eu/
User avatar
Daniele Varsano
 
Posts: 1950
Joined: Tue Mar 17, 2009 2:23 pm


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