<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><br><br>--- On <b>Thu, 13/8/09, st <i><y1gao@ucsd.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: st <y1gao@ucsd.edu><br>Subject: [gmx-users] problem installing gromacs<br>To: gmx-users@gromacs.org<br>Date: Thursday, 13 August, 2009, 1:42 AM<br><br><div id="yiv2114306933">
<div><font face="Calibri">Hi There,</font></div>
<div><font face="Calibri"></font> </div>
<div><font face="Calibri">I have some problems</font><font face="Calibri">
installing gromacs on the linux server. </font></div>
<div><font face="Calibri"></font> </div>
<div><font face="Calibri">fftw installed with no error, but when I install
gromacs,</font></div>
<div><font face="Calibri">I got the following error:</font></div>
<div><font face="Calibri">*****************************************</font></div>
<div><font face="Calibri">/bin/sh ../../libtool --tag=CC --mode=link
cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -L/home/y1gao/soft/fftw/lib -o grompp
grompp.o libgmxpreprocess_d.la ../mdlib/l<br>cc -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops -o .libs/grompp
grompp.o -L/home/y1gao/soft/fftw/lib ./.libs/libgmxpreprocess_d.a
-L/usr/X11R6/lib ../mdlib/.libs/libmd_d.so /n<br>_d.so -lnsl -lfftw3 -lm -lSM
-lICE -lX11 -Wl,--rpath
-Wl,/home/y1gao/soft/gromacs//lib<br>../mdlib/.libs/libmd_d.so: undefined
reference to `__libm_sse2_sincos'<br>../mdlib/.libs/libmd_d.so: undefined
reference to `__libm_sse2_log'<br>../mdlib/.libs/libmd_d.so: undefined reference
to `_intel_fast_memcpy'<br>collect2: ld returned 1 exit status<br>make[3]: ***
[grompp] Error 1<br>make[3]: Leaving directory
`/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src/kernel'<br>make[2]:
*** [all-recursive] Error 1<br>make[2]: Leaving directory
`/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src'<br>make[1]: ***
[all] Error 2<br>make[1]: Leaving directory
`/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src'<br>make: ***
[all-recursive] Error 1<br></font><font face="Calibri">*******************************************</font></div>
<div><font face="Calibri"></font> </div>
<div><font face="Calibri">I used the combinations of the following fftw and
gromacs:</font></div>
<div><font face="Calibri">fftw 3.2.1; fftw3.2.2</font></div>
<div><font face="Calibri">gromacs 3.3.3; gromacs 4.0.4</font></div>
<div><font face="Calibri"></font> </div>
<div><font face="Calibri">gcc version 3.4.6</font></div>
<div> <br><br><br>try with make links after make install of gromacs. probably this may help....<br>good luck<br><br><br></div>
<div><font face="Calibri">The command I used are:</font></div>
<div><font face="Calibri">*************************</font></div>
<div><font face="Calibri">To install fftw:</font></div>
<div><font face="Calibri"> $ ./configure
--enable-threads --enable-sse2 -prefix
/home/y1gao/soft/fftw/lib</font></div>
<div><font face="Calibri"> $ make</font></div>
<div><font face="Calibri">$ make install</font></div>
<div><font face="Calibri"></font> </div>
<div><font face="Calibri">To install gromacs:</font></div>
<div><font face="Calibri">$ ./configure --enable-shared
LDFLAGS='-L/home/y1gao/soft/fftw/lib' CPPFLAGS='-I/home/y1gao/soft/fftw/include'
--enable-double --prefix=/home/y1gao/soft/gromacs/</font></div>
<div><font face="Calibri">$ make</font></div>
<div><font face="Calibri">$ make install</font></div>
<div><font face="Calibri">( error comes out here)</font></div>
<div><font face="Calibri"></font> </div>
<div><font face="Calibri">*************************</font></div>
<div><font face="Calibri"></font> </div>
<div><font face="Calibri">Could anyone help me find a way out? Thanks in
advance.</font></div>
<div><font face="Calibri"></font> </div>
<div><font face="Calibri">Stone</font></div>
<div><font face="Calibri"></font> </div></div><br>-----Inline Attachment Follows-----<br><br><div class="plainMail">_______________________________________________<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php"
target="_blank">http://www.gromacs.org/mailing_lists/users.php</a></div></blockquote></td></tr></table><br>
<!--1--><hr size=1></hr> Love Cricket? Check out live scores, photos, video highlights and more. <a href="http://in.rd.yahoo.com/tagline_cricket_2/*http://cricket.yahoo.com" target="_blank"> Click here</a>.