Problem w/ libxc in compilation

[Zahra Taghipour]

Dear Developers and Users,
Hello,

I am trying to install Yambo-4-0-1-rev.89 on Mac OS.X Yosemite version 10.10.4. with gcc47 and fortran on my laptop.
It does configure OK, but when I try to make interfaces I get the error message below:
.
.
Error: Unclassifiable statement at (1)
libxc.f90:107.7:

end function xc_f90_ ## info_number
1
Error: Expecting END INTERFACE statement at (1)
libxc.f90:109.28:

integer function xc_f90_ ## info_kind(info)
1
Internal Error at (1):
insert_bbt(): Duplicate key found!
make[4]: *** [libxc_la-libxc.lo] Error 1
make[3]: *** [install] Error 2
make[2]: *** [install-recursive] Error 1
make[1]: *** [package-ready-stamp] Error 2
make: *** [libs] Error 2

I noticed that others have encountered the same problem. I did try to use "make clean_all" before ./configure. I also have specified my path correctly.
It seems there is some problem with livxc or the preprocessor which I do not know how to solve.
You could find config.log, attached.

I really appreciate if you could help me solve this.

Thank you,
Zahra Taghipour
PhD student at University of New Mexico, USA

[andrea.ferretti]

Dear Zahra,

I think the problem is related to the C precompiled not being able to deal with
the concatenation operator (##).
In order to sort it out, you need to specify some flags to the configure command.
In particular, in my case (OSX 10.9.5) a set of flags like the following seem to work:

Code: Select all

./configure \
    CPP="cpp-4.2 -E" \
    CPPFLAGS="-P -ansi" \
    FCCPP="cpp-4.2 -E" \
   --enable-iotk \
   [...]

take care
Andrea

[Zahra Taghipour]

Andrea,

Thank you for your response.

Unfortunately, I still get the same error. I have tested all different flags and Variables for defining my compilers, though.

I also tried to MAKE YAMBO in Quantum Espresso folder! I get the error : " *** F90 is not defined; please define F90 or edit make.sys"! Although, I specify F90 as FORTRAN clearly!

The errors I get both in MAKE YAMBO seem to be related to F90, which I do not have any idea how to fix!
I would really appreciate any help on this.

Thank You,
Zahra
Research Assistant,
UNM, USA

[andrea.ferretti]

Hi Zahra,

some suggestions:

* the compilation of yambo through quantum espresso is somehow more difficult since it has more
constraints. In a difficult case I would definitely go for a self-standing compilation of yambo
* whenever you try a different set of compilation flags, remember to do a make clean_all
(and, if the problems is with libxc, check that lib/libxc just contains Makefile.loc;
if the libxc tar ball has already been expanded, showing up ad lib/libxc/libxc_xxx, configuration
flags are not updated and so the same error appears... all of this is avoided by making clean_all)
* proceed systematically and post relevant config.log files if you need further support

Andrea

[Zahra Taghipour]

Andrea,

I did ./Configure with the compilation flags you had posted, again. But, this time I used CPP="cpp-mp-4.5 -E" and FCCPP="cpp-mp-4.5 -E" instead, and it worked like a charm!!
Thank you so much for your help.

Zahra

[andrea.ferretti]

great, enjoy!
Andrea

[Zahra Taghipour]

Andrea,
Hello,

Since I managed to compile Yambo, I realized all of my input files have been built "Serial" and I was unable to run my codes in parallel.
So, I ran " make clean_all" and re_compile again. Now I continuously receive this error:
{
Fatal Error: Cannot read module file 'netcdf.mod' opened at (1), because it was created by a different version of GNU Fortran
make[1]: *** [mod_pars.o] Error 1
make: *** [yambo] Error 2
}
The error seems clear. But I do not know how to solve it.
I have attached the "config.log", just in case.
I would really appreciate if you could help me on this.

Yours,
Zahra

[andrea.ferretti]

Dear Zahra,

the error you get

Code: Select all

Fatal Error: Cannot read module file 'netcdf.mod' opened at (1), because it was created by a different version of GNU Fortran

means that you are trying to use .mod files from the netcdf library that have been compiled using a different compiler (or version of the compiler)

according to your config.log file, you have configured using these flags

Code: Select all

./configure CPP=cpp-mp-4.7 -E FCCPP=cpp-mp-4.7 -E CPPFLAGS=-P -ansi --enable-iotk --with-netcdf-lib=/opt/local/lib --with-netcdf-include=/opt/local/include

the error you get is probably related to the use of the netcdf lib installed in /opt/local.
If you simply drop both --with-netcdf-lib and --with-netcdf-include yambo will compile its own copy of netcdf, sorting out the problem.
Otherwise, you need to specify a netcdf library that has been compiled (i) with fortran support and (ii) using the same fortran compiler you are using

Andrea

[Zahra Taghipour]

Andrea,

Thank you for the response.

In fact, I added the "--with-netcdf-lib/include" lines after I got this error!
I thought I'd better install the NETCDF myself and introduce its LIB_PATH. However, I still get the same error.

I checked my compiler using " fortran -v". It seems I got gcc47 at the moment. I do not know where this discrepency comes from regarding different compilers!
Moreover, I have checked "nc-config --fc" and it is empty! (" "). So, I do not know which fortran compiler NETCDF is using!:/

Is there any specific way that I could re_install and compile all of them with the same/known compiler?!

Best,
Zahra

[andrea.ferretti]

Hi Zahra,

if you added --with-netcdf-lib/include *after* you got the error (meaning before you were using the internal netcdf),
I think it means that your yambo source tree has not been properly cleaned.
I would suggest to start from scratch, make clean_all, check no libnetcdf* files are in yambo/lib and
no *.mod files are in yambo/include...
then, if you compile by using the internal netcdf lib (i.e. no netcdf flags specified what-so-ever), the code should not complain...

Andrea