[gpaw-users] _gpaw.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _gfortran_concat_string

[Jens Jørgen Mortensen]

On 11/01/2017 03:52 PM, HM Li via gpaw-users wrote:
> Dear.
>
> I have tried to install gpaw-1.3.0, the install has shown successful, 
> but when running, it shows:

How did you install GPAW?  What OS are you on?

Jens Jørgen

>
> =============================
>
>  ./gpaw
> Traceback (most recent call last):
>   File "./gpaw", line 2, in <module>
>     from gpaw.cli.main import main
>   File 
> "/home/longjun01/.local/lib/python3.6/site-packages/gpaw/__init__.py", 
> line 242, in <module>
>     from gpaw.calculator import GPAW
>   File 
> "/home/longjun01/.local/lib/python3.6/site-packages/gpaw/calculator.py", 
> line 11, in <module>
>     import gpaw.mpi as mpi
>   File 
> "/home/longjun01/.local/lib/python3.6/site-packages/gpaw/mpi/__init__.py", 
> line 16, in <module>
>     from gpaw.utilities import is_contiguous
>   File 
> "/home/longjun01/.local/lib/python3.6/site-packages/gpaw/utilities/__init__.py", 
> line 13, in <module>
>     import _gpaw
> ImportError: 
> /home/longjun01/.local/lib/python3.6/site-packages/_gpaw.cpython-36m-x86_64-linux-gnu.so: 
> undefined symbol: _gfortran_concat_string
>
> =============================
>
> The scalapack and lapack are builded with Intel compiler(13.0.0, gcc 
> 4.4.7).
>
> Part of customize.py:
>
> =============================
>
> #define_macros = 'GPAW_NO_UNDERSCORE_LAPACK'
> opt_string = '-lgfortran'
> extra_compile_args =['-std=c99', opt_string]
> # compiler = 'gcc'
> mpicompiler = 'mpicc'  # use None if you don't want to build a 
> gpaw-python
> mpilinker = 'mpicc '+opt_string
> # platform_id = ''
> scalapack = False
> #True
>
> library_dirs += 
> ['/home/longjun01/local/lib','/home/longjun01/xc-2.0.1/lib']
>
> # Use ScaLAPACK:
> # Warning! At least scalapack 2.0.1 is required!
> # See https://trac.fysik.dtu.dk/projects/gpaw/ticket/230
> define_macros += [('GPAW_NO_UNDERSCORE_LAPACK', '1')]
> define_macros += [('GPAW_NO_UNDERSCORE_BLAS', '1')]
> if scalapack:
>     libraries += ['scalapack']
> #                  'blacsCinit',
> #                  'blacs-openmpi']
> #    define_macros += [('GPAW_NO_UNDERSCORE_SCALAPACK', '0')]
>     define_macros += [('GPAW_NO_UNDERSCORE_CBLACS', '1')]
>     define_macros += [('GPAW_NO_UNDERSCORE_CSCALAPACK', '1')]
>
> libraries += ['lapack', 'blas', 'xc']
> # LibXC:
> # In order to link libxc installed in a non-standard location
> # (e.g.: configure --prefix=/home/user/libxc-2.0.1-1), use:
>
> # - static linking:
> if 0:
>     include_dirs += ['/home/longjun01/libxc-2.0.1/include']
>     extra_link_args += ['/home/longjun01/libxc-2.0.1/lib/libxc.a']
>     if 'xc' in libraries:
>         libraries.remove('xc')
>
> # - dynamic linking (requires rpath or setting LD_LIBRARY_PATH at 
> runtime):
> if 0:
>     include_dirs += ['/home/longjun01/libxc-2.0.1/include']
>     library_dirs += ['/home/longjun01/libxc-2.0.1/lib']
>     # You can use rpath to avoid changing LD_LIBRARY_PATH:
>     # extra_link_args += ['-Wl,-rpath=/home/user/libxc-2.0.1-1/lib']
>     if 'xc' not in libraries:
>         libraries.append('xc')
>
> =============================
>
> [longjun01 at ln3%th2 ~]$ echo $LD_LIBRARY_PATH
> /home/longjun01/xc-2.0.1/lib:/home/longjun01/local/lib:/opt/python3.6/lib
> [longjun01 at ln3%th2 ~]$ grep _gfortran_concat_string ~/local/lib/*.a
> Binary file /home/longjun01/local/lib/liblapack.a matches
>
> Thank you very much.
>
>
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