Hi Justin,<div><br></div><div>I checked carefully. The make command also gave the same error as pasted below. How should I deal this error?</div><div><br></div><div><div>at' follow</div><div>.libs/libxdrf.o:libxdrf.c:(.text+0x31e3): undefined reference to `_xdr_int'</div>
<div>.libs/libxdrf.o:libxdrf.c:(.text+0x340b): undefined reference to `_xdr_int'</div><div>.libs/libxdrf.o:libxdrf.c:(.text+0x35a6): undefined reference to `_xdr_int'</div><div>.libs/libxdrf.o:libxdrf.c:(.text+0x3785): undefined reference to `_xdr_int'</div>
<div>.libs/libxdrf.o:libxdrf.c:(.text+0x3a01): undefined reference to `_xdr_int'</div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0xeb): undefined reference to `_xdr_float</div><div>'</div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x126): undefined reference to `_xdr_doub</div>
<div>le'</div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x161): undefined reference to `_xdr_int'</div><div><br></div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x1ec): undefined reference to `_xdr_u_ch</div><div>
ar'</div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x22f): undefined reference to `_xdr_u_ch</div><div>ar'</div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x265): undefined reference to `_xdr_u_ch</div><div>ar'</div>
<div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x293): undefined reference to `_xdr_u_ch</div><div>ar'</div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x2bf): undefined reference to `_xdr_u_ch</div><div>ar'</div><div>
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x309): undefined reference to `_xdr_u_sh</div><div>ort'</div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x3c4): undefined reference to `_xdr_doub</div><div>le'</div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x3ed): undefined reference to `_xdr_vect</div>
<div>or'</div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x518): undefined reference to `_xdr_int'</div><div><br></div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x56c): undefined reference to `_xdr_int'</div>
<div><br></div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x5e1): undefined reference to `_xdr_int'</div><div><br></div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x60e): undefined reference to `_xdr_int'</div><div>
<br></div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x63b): undefined reference to `_xdr_int'</div><div><br></div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x668): more undefined references to `_xd</div><div>r_int' follow</div>
<div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x764): undefined reference to `_xdr_doub</div><div>le'</div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x7bd): undefined reference to `_xdr_floa</div><div>t'</div><div>
.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x7d4): undefined reference to `_xdr_vect</div><div>or'</div><div>.libs/gmxfio_xdr.o:gmxfio_xdr.c:(.text+0x823): undefined reference to `_xdr_stri</div><div>ng'</div><div>Creating library file: .libs/libgmx.dll.a</div>
<div>collect2: ld returned 1 exit status</div><div>make[4]: *** [<a href="http://libgmx.la">libgmx.la</a>] Error 1</div><div>make[4]: Leaving directory `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s</div><div>rc/gmxlib'</div>
<div>make[3]: *** [all-recursive] Error 1</div><div>make[3]: Leaving directory `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s</div><div>rc/gmxlib'</div><div>make[2]: *** [all-recursive] Error 1</div><div>make[2]: Leaving directory `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s</div>
<div>rc'</div><div>make[1]: *** [all] Error 2</div><div>make[1]: Leaving directory `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s</div><div>rc'</div><div>make: *** [all-recursive] Error 1</div><br><div class="gmail_quote">
On Wed, Mar 30, 2011 at 1:54 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>
Monisha Hajra wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Hi All,<br>
<br>
I am installing GROMACS using cygwin.<br>
<br>
I am following the steps as mentioned :<br>
<a href="http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO" target="_blank">http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO</a><br>
<br></div>
*no 5, make install command give the following error in the end :*<br>
<br>
</blockquote>
<br>
What was your configuration command? Did "make" work properly? It's odd that "make install" fails if "make" works. Do you have proper permissions to install in this directory? Configuration and compilation are done locally, but installation (if left at default settings) is system-wide.<br>
<br>
The actual error message is above what you have posted here.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
ng'<br>
Creating library file: .libs/libgmx.dll.a<br>
collect2: ld returned 1 exit status<br></div>
make[3]: *** [<a href="http://libgmx.la" target="_blank">libgmx.la</a> <<a href="http://libgmx.la" target="_blank">http://libgmx.la</a>>] Error 1<div class="im"><br>
make[3]: Leaving directory `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s<br>
rc/gmxlib'<br>
make[2]: *** [install-recursive] Error 1<br>
make[2]: Leaving directory `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s<br>
rc/gmxlib'<br>
make[1]: *** [install-recursive] Error 1<br>
make[1]: Leaving directory `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s<br>
rc'<br>
make: *** [install-recursive] Error 1<br>
<br></div>
and* make links command gives the following error:*<br>
*<br>
</blockquote>
<br>
Certainly "make links" will fail if the actual installation failed.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
*<div class="im"><br>
*<br>
$ make links<br>
cd /usr/local/gromacs/bin && programs=`ls` && cd /usr/local/bin && \<br>
for i in $programs; do \<br>
(test ! -f $i && ln -s /usr/local/gromacs/bin/$i . ; exit 0); \<br>
done<br>
/bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory<br>
make: *** [links] Error 1<br>
<br>
Can anyone de-code thsi error and help me how should I successfully proceed for the same. <br>
Thanks in advance.<br>
<br></div>
Monisha *<br>
<br>
<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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