Compilation problem

[Khalid]

Dear Researchers,
I am very new to yambo and I am trying to install yambo in my
64 bit linux laptop
with intel 15 compilers
in parallel
yambo version: yambo-4.0.1-rev.89.
I've compiled yambo as is written in the documentation: my configuration script was:
export CC=icc
export FC=ifort
export F77=ifort
export PFC=mpiifort
export MPICC=mpiicc

export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export FCFLAGS='-O3 -xHost -ip'
export FFLAGS=-O2

export mkldir=/opt/intel/composer_xe_2015.0.090/mkl/lib/intel64
export fftwdir=/home/kim/MathLab/INTEL-FFT
export iotkdir=/home/kim/ToolBox/OpenQE/espresso-5.2.0/S3DE/iotk
export libxcdir=/home/kim/MathLab/libxc-2.2.2/BUILD

./configure \
\
--disable-debug --enable-time-profile \
--disable-open-mp --enable-3d-fft --enable-iotk --enable-netcdf --enable-etsf-io\
\
--with-blas-libs="-L$mkldir -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" \
--with-lapack-libs="-L$mkldir -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" \
--with-blacs-libs="-L$mkldir -lmkl_blacs_intelmpi_lp64" \
--with-scalapack-libs="-L$mkldir -lmkl_scalapack_lp64" \
\
--with-fft-libs="-L$fftwdir/lib -lfftw3" \
--with-fft-path=$fftwdir \
\
--with-p2y-version=5.0 \
--with-iotk-libs=$iotkdir/tools/iotk \
--with-iotk-path=$iotkdir \
--with-libxc-libs="-L$libxcdir/lib -lxc" \
--with-libxc-path=$libxcdir

and everything went perfect.

But the problem is when I tried to run yambo in a folder containing SAVE directory, (I was trying to run the tutorial given in the yambo tutorial section). It shows:



_| _| _|_| _| _| _|_|_| _|_|
_| _| _| _| _|_| _|_| _| _| _| _|
_| _|_|_|_| _| _| _| _|_|_| _| _|
_| _| _| _| _| _| _| _| _|
_| _| _| _| _| _|_|_| _|_|



<---> [01] CPU structure, Files & I/O Directoriesyambo: symbol lookup error: yambo: undefined symbol: __libm_error_support


I don't know what the problem is, I have tried many things, but the problem persists.
Please help me to solve this problem.
Thanks in advance.
Khalid
M.Sc student
BUET

[Daniele Varsano]

Dear Khalid,
it looks that there is some environment problem, you have to load module in your system?
If so be sure to have them loaded also when executing yambo.
The library that has not be found seems related to Open MPI libraries, if you are using Open-MPI, you should also add this line

Code: Select all

--enable-openmpi 

when configuring.
In any case, please post your config. log and ./config/report files, this will help to spot the problem.
Please fill your signature with your complete affiliation, you can do once for all in your user profile.
Best,
Daniele

[Khalid]

Dear Sir,
Thank you very much for your kind reply.
I did not understand about loading module. Previously I have never loaded anything.

However, I have sorted out the problem. I have run make clean and reconfigure using the previous script, but this time I have used another line

source /opt/intel/composer_xe_2015.0.090/bin/compilervars.sh intel64

And everything is working fine. Perhaps this the thing you were talking about loading module (Please pardon my lack of knowledge about linux).
But one more thing, even though now I have working yambo, what irritates me is the following message shown after running make yambo interfaces ypp

"In file included from /home/kim/ToolBox/qE/yambo-4.0.1-rev.89/driver/getopt.c(107):
/home/kim/ToolBox/qE/yambo-4.0.1-rev.89/driver/getopt.h(166): warning #1292: unknown attribute "__leaf__"
__THROW;
^
"

I have surfed the internet found something in the link: "viewtopic.php?f=1&t=980&start=10"
where it is pointed out this message is because of netcdf, I don't have any installed netcdf, so I decided to use the internal netcdf. Would that be a problem ?

I have attached my config.log and ./config/report files. And I am using intelmpi.

Thank you
Khalid
M.Sc student
Bangladesh University of Engineering and Technology

[Daniele Varsano]

Dear Khalid,

However, I have sorted out the problem. I have run make clean and reconfigure using the previous script, but this time I have used another line

Code: Select all

source /opt/intel/composer_xe_2015.0.090/bin/compilervars.sh intel64

And everything is working fine. Perhaps this the thing you were talking about loading module (Please pardon my lack of knowledge about linux).

Ok, great. Yes, if you have libraries and software organized in modules essentially loading modules means setting up the right environment, essentially what you did.

"In file included from /home/kim/ToolBox/qE/yambo-4.0.1-rev.89/driver/getopt.c(107):
/home/kim/ToolBox/qE/yambo-4.0.1-rev.89/driver/getopt.h(166): warning #1292: unknown attribute "__leaf__"
__THROW;
^
"

NO, it should be not related with netcdf, but with the c compiler, anyway it is just a warning right, is the code you compiled working?

Best,
Dnaiele