} From [email protected] 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 } > [email protected] } } -- } ======================================== } } 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 } } ======================================== } -- } gmx-users mailing list [email protected] } http://lists.gromacs.org/mailman/listinfo/gmx-users } Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! } Please don't post (un)subscribe requests to the list. Use the } www interface or send it to [email protected]. } Can't post? Read http://www.gromacs.org/Support/Mailing_Lists } -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
