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Hello Erik,<br>
<br>
Thank you for suggesting the idea. I have got the required help from
FFTW authors. I could load the Gromacs successfully. I have even done a
test run (pdb2gmx - mdrun) on my protein in water. However I am unable
to finally visualise the animation of the dynamics run using ngmx. It
says command not found. Why is it giving me this error when all the
other programs are working ? I could't locate the link for this program
in any folder. Where is it installed ? My configure,make,make install
and make links didnot give any errors ! Kindly guide me. Thanks in
advance.<br>
<br>
sharada<br>
<br>
<br>
Erik Lindahl wrote:<br>
<blockquote type="cite"
cite="mid76CBF514-78C0-4FA6-9826-55E652821AFA@cbr.su.se">Hi,
<div><br class="khtml-block-placeholder">
</div>
<div>First, since this is an FFTW-related issue you will probably get
better help by asking the FFTW authors.</div>
<div><br class="khtml-block-placeholder">
</div>
<div>Looking in config.log, the script is trying to preprocess the
test program</div>
<div><br class="khtml-block-placeholder">
</div>
<div>/* confdefs.h. */</div>
<div>#define PACKAGE_NAME "fftw"</div>
<div>#define PACKAGE_TARNAME "fftw"</div>
<div>#define PACKAGE_VERSION "3.1.2"</div>
<div>#define PACKAGE_STRING "fftw 3.1.2"</div>
<div>#define PACKAGE_BUGREPORT "<a href="mailto:fftw@fftw.org">fftw@fftw.org</a>"</div>
<div>#define PACKAGE "fftw"</div>
<div>#define VERSION "3.1.2"</div>
<div>#define FFTW_SINGLE 1</div>
<div>#define BENCHFFT_SINGLE 1</div>
<div>/* end confdefs.h. */</div>
<div>#ifdef __STDC__</div>
<div># include <limits.h></div>
<div>#else</div>
<div># include <assert.h></div>
<div>#endif</div>
<div><br class="khtml-block-placeholder">
</div>
<div><br class="khtml-block-placeholder">
</div>
<div>using the command gcc -std=gnu99 -E conftest.c</div>
<div><br class="khtml-block-placeholder">
</div>
<div>but gets the error message</div>
<div><br class="khtml-block-placeholder">
</div>
<div>In file included from /usr/include/bits/posix1_lim.h:130,</div>
<div> from /usr/include/limits.h:144,</div>
<div> from
/usr/lib/gcc-lib/i386-redhat-linux/3.2.3/include/limits.h:132,</div>
<div> from
/usr/lib/gcc-lib/i386-redhat-linux/3.2.3/include/syslimits.h:7,</div>
<div> from
/usr/lib/gcc-lib/i386-redhat-linux/3.2.3/include/limits.h:11,</div>
<div> from conftest.c:13:</div>
<div>/usr/include/bits/local_lim.h:36:26: linux/limits.h: No such
file or directory</div>
<div><br class="khtml-block-placeholder">
</div>
<div><br class="khtml-block-placeholder">
</div>
<div><limits.h> is mandatory for ANSI C99, so there is
something wrong with your operating system/compiler installation.</div>
<div><br class="khtml-block-placeholder">
</div>
<div>Cheers,</div>
<div><br class="khtml-block-placeholder">
</div>
<div>Erik</div>
<div><br class="khtml-block-placeholder">
</div>
<div><br class="khtml-block-placeholder">
</div>
<div><br class="khtml-block-placeholder">
</div>
<div><br class="khtml-block-placeholder">
</div>
<div><br>
<div>
<div>On Oct 17, 2006, at 1:43 PM, sharada wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite"><br>
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<br>
Hi gromacs users,<br>
<br>
I am trying to install gromacs on Linux. While installing the fftw
module , I am getting the following error<br>
at the ./configure stage:<br>
<br>
<span style="font-style: italic;">[root@Sharada fftw-3.1.2]#
./configure --enable-float --enable-threads --enable-sse</span><br
style="font-style: italic;">
<br style="font-style: italic;">
<span style="font-style: italic;">checking for a
BSD-compatible install... /usr/bin/install -c</span><br
style="font-style: italic;">
<span style="font-style: italic;">checking whether build
environment is sane... yes</span><br style="font-style: italic;">
<span style="font-style: italic;">checking for gawk... gawk</span><br
style="font-style: italic;">
<span style="font-style: italic;">checking whether make sets
$(MAKE)... yes</span><br style="font-style: italic;">
<span style="font-style: italic;">checking whether to enable
maintainer-specific portions of Makefiles... no</span><br
style="font-style: italic;">
<span style="font-style: italic;">checking build system
type... i686-pc-linux-gnu</span><br style="font-style: italic;">
<span style="font-style: italic;">checking host system
type... i686-pc-linux-gnu</span><br style="font-style: italic;">
<span style="font-style: italic;">checking for gcc... gcc</span><br
style="font-style: italic;">
<span style="font-style: italic;">checking for C compiler
default output file name... a.out</span><br style="font-style: italic;">
<span style="font-style: italic;">checking whether the C
compiler works... yes</span><br style="font-style: italic;">
<span style="font-style: italic;">checking whether we are
cross compiling... no</span><br style="font-style: italic;">
<span style="font-style: italic;">checking for suffix of
executables...</span><br style="font-style: italic;">
<span style="font-style: italic;">checking for suffix of
object files... o</span><br style="font-style: italic;">
<span style="font-style: italic;">checking whether we are
using the GNU C compiler... yes</span><br style="font-style: italic;">
<span style="font-style: italic;">checking whether gcc
accepts -g... yes</span><br style="font-style: italic;">
<span style="font-style: italic;">checking for gcc option to
accept ISO C89... none needed</span><br style="font-style: italic;">
<span style="font-style: italic;">checking for style of
include used by make... GNU</span><br style="font-style: italic;">
<span style="font-style: italic;">checking dependency style
of gcc... gcc3</span><br style="font-style: italic;">
<span style="font-style: italic;">checking for C compiler
vendor... gnu</span><br style="font-style: italic;">
<span style="font-style: italic;">checking for gcc option to
accept ISO C99... -std=gnu99</span><br style="font-style: italic;">
<span style="font-style: italic;">checking for gcc -std=gnu99
option to accept ISO Standard C... (cached) -std=gnu99</span><br
style="font-style: italic;">
<span style="font-style: italic;">checking for a
BSD-compatible install... /usr/bin/install -c</span><br
style="font-style: italic;">
<span style="font-style: italic;">checking whether ln -s
works... yes</span><br style="font-style: italic;">
<span style="font-style: italic;">checking whether make sets
$(MAKE)... (cached) yes</span><br style="font-style: italic;">
<span style="font-style: italic;">checking for a sed that
does not truncate output... /bin/sed</span><br
style="font-style: italic;">
<span style="font-style: italic;">checking for grep that
handles long lines and -e... /bin/grep</span><br
style="font-style: italic;">
<span style="font-style: italic;">checking for egrep...
/bin/grep -E</span><br style="font-style: italic;">
<span style="font-style: italic;">checking for ld used by gcc
-std=gnu99... /usr/bin/ld</span><br style="font-style: italic;">
<span style="font-style: italic;">checking if the linker
(/usr/bin/ld) is GNU ld... yes</span><br style="font-style: italic;">
<span style="font-style: italic;">checking for /usr/bin/ld
option to reload object files... -r</span><br
style="font-style: italic;">
<span style="font-style: italic;">checking for BSD-compatible
nm... /usr/bin/nm -B</span><br style="font-style: italic;">
<span style="font-style: italic;">checking how to recognise
dependent libraries... pass_all</span><br style="font-style: italic;">
<span style="font-style: italic;">checking how to run the C
preprocessor... /lib/cpp</span><br style="font-style: italic;">
<span style="font-style: italic;">configure: error: C
preprocessor "/lib/cpp" fails sanity check</span><br
style="font-style: italic;">
<span style="font-style: italic;">See `config.log' for more
details.<br>
<br>
</span>what does the error trying to tell me ? cpp is linked
to /usr/bin/cpp. I am installing from the root account. can any body
help ? I am attaching the config.log file alongwith. Thanks in
advance.<br>
<br>
regards,<br>
sharada<br>
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</font><span>
<div><config.log></div>
</span>
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