<br><br><div class="gmail_quote">On Wed, Sep 21, 2011 at 9:01 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#FFFFFF" text="#000000"><div><div></div><div class="h5">
On 21/09/2011 7:27 PM, zhongjin wrote:
<blockquote type="cite">
<table border="0" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td style="font:inherit" valign="top">
<div><font style="background-color:#cce8cf">Dear GMX users:</font></div>
<div><font style="background-color:#cce8cf">While I am installing gmx4.5.5, an error occured after "make" command :</font></div>
<div>cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -pthread -I./include -o .libs/grompp grompp.o -L/home/hzj1000/software/fftw/lib ./.libs/libgmxpreprocess.so /home/hzj1000/gromacs-4.5.5/src/mdlib/.libs/libmd.so
../mdlib/.libs/libmd.so /home/hzj1000/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so ../gmxlib/.libs/libgmx.so -ldl -lnsl -lm -Wl,--rpath -Wl,/home/hzj1000/software/GMX/gromacs4.5.5/lib<br>
/home/hzj1000/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so: undefined reference to `pthread_setaffinity_np'<br>
collect2: ld returned 1 exit status<br>
make[3]: *** [grompp] Error 1<br>
make[3]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src/kernel'<br>
make[2]: *** [all-recursive] Error 1<br>
make[2]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src'<br>
make[1]: *** [all] Error 2<br>
make[1]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src'</div>
<div> <br>
</div>
</td>
</tr>
</tbody>
</table>
</blockquote>
<br></div></div>
This shouldn't happen. What compiler and hardware? configure or CMake? What command lines?<br></div></blockquote><div><br></div><div>Please also add: Which Unix? Is it Linux? Distribution? What libc version? </div><div>
<br></div><div>Roland</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div bgcolor="#FFFFFF" text="#000000"><font color="#888888">
<br>
Mark<br>
</font></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>