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

[David Perel]

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)

 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