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

[David Perel]

} From gmx-users-bounces at gromacs.org  Tue Dec 27 19:25:23 2011
} Subject: Re: [gmx-users] Compile error : libgmx.so: undefined reference to
}  `pthread_setaffinity_np'
} 
} 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.

Thanks. I'll try a GCC > 4.1, and also disabling threading in the GCC 3.4.6
build.

} 
} -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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