[gmx-users] Compile error : libgmx.so: undefined reference to `pthread_setaffinity_np'

[Justin A. Lemkul]

David Perel wrote:
> Hello gmx-users --
>  
>  The following error occurs during compilation of Gromacs 4.5.5 :
> 
>   4.5.5/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so: undefined reference to `pthread_setaffinity_np'
> 
>  There was an exchange on this problem on the gmx-users list on 21/09/2011,
>  but apparently no solution.
> 
>  OS 	: RHEL 4
> 
>  CPU 	: Dual-Core AMD Opteron Processor 2220
> 
>  gcc	: 3.4.6 20060404 (Red Hat 3.4.6-11)
> 

This is a very old GCC.  I suspect if you want to use threading, you will need a 
newer version.  Alternatively, you can disable threads during configuration.

-Justin

>  glibc 	: glibc-2.3.4-2.54
> 
>  The following is from the configure script :
> 
> 	FFTW=/afs/cad/hpc/amd/opt/fftw/3.3/gnu3
> 
> 	INSTALL_DIR=/some/dir
> 	CPPFLAGS="-I$FFTW/include"
> 	LDFLAGS="-L$FFTW/lib"
> 	
> 	time ./configure \
> 	    CPPFLAGS="$CPPFLAGS" \
> 	    LDFLAGS="$LDFLAGS" \
> 	    --prefix=$INSTALL_DIR \
> 	    --with-fft=fftw3 \
> 	    2>&1 | tee -a CONFIGURE.log
> 
>  Any suggestions on how to resolve this problem would be greatly appreciated.
> 
>  Thanks.
> 
> ___________
> David Perel
> IST University Computing Systems (UCS)
> New Jersey Institute of Technology
> davidp at njit.edu

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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