Hi Justin,<div><br></div><div>try to add "#include <sys/types.h>" before the include of regex.h in sm-keywords.c.</div><div><br></div><div>Roland</div><div><br><div class="gmail_quote">On Sun, Aug 1, 2010 at 12:49 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;"><div class="im"><br>
<br>
Roland Schulz wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
look at /usr/include/regex.h line 68. What is/are the keyword before. I <br>
</blockquote>
<br></div>
Line 68 occurs very early in the file, and corresponds to:<br>
<br>
typedef off_t regoff_t;<br>
<br>
In regex.h, there are 60 lines of comments followed by:<br>
<br>
#ifndef _REGEX_H_<br>
#define _REGEX_H_<br>
<br>
#include <sys/cdefs.h><br>
<br>
/* types */<br>
typedef off_t regoff_t;<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
assume this is (re)defined in some of the GROMACS or system include files and thus breaks the regex.h. You can run the cc command line shown below with all the options from the shown folder and add -E to the command-line. This shows you were this is defined. If you can't find it send me the output of cc -E and the regex.h as PM attachment.<br>
<br>
</blockquote>
<br></div>
Adding -E to the cc command doesn't produce anything. Perhaps I've done something wrong, but if I understood you, the command should be:<br>
<br>
cc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2 -I../../../include -I/home/rdiv1001/fftw-3.0.1/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -faltivec -funroll-all-loops -std=gnu99 -mcpu=7450 -mtune=970 -MT sm_keywords.lo -MD -MP -MF .deps/sm_keywords.Tpo -c sm_keywords.c -o sm_keywords.o -E<br>
<br>
I'll send you the regex.h file off-list. Thanks for your attention.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Roland<div><div></div><div class="h5"><br>
<br>
On Fri, Jul 30, 2010 at 5:53 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
Hi,<br>
<br>
I'm trying to install the newest beta on our university's<br>
supercomputer, but I'm encountering an error during compilation.<br>
It's an aging system, so this might be somewhat difficult to solve.<br>
Here are the specs:<br>
<br>
Mac OSX 10.3<br>
2.3 GHz PowerPC 970FX processors<br>
gcc 3.3<br>
fftw 3.0.1<br>
<br>
Configuration went without a hitch, with config.log indicating all<br>
necessary headers, libraries, etc. were found.<br>
<br>
./configure --prefix=/home/rdiv1001/gromacs-4.5_beta1<br>
CPPFLAGS="-I/home/rdiv1001/fftw-3.0.1/include"<br>
LDFLAGS="-L/home/rdiv1001/fftw-3.0.1/lib"<br>
--program-suffix=_4.5_beta1 --disable-threads<br>
<br>
Compilation fails with the following:<br>
<br>
Making all in selection<br>
...<br>
/bin/sh ../../../libtool --tag=CC --mode=compile cc<br>
-DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2<br>
-I../../../include -I/home/rdiv1001/fftw-3.0.1/include -O3<br>
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -faltivec<br>
-funroll-all-loops -std=gnu99 -mcpu=7450 -mtune=970 -MT<br>
sm_keywords.lo -MD -MP -MF .deps/sm_keywords.Tpo -c -o<br>
sm_keywords.lo sm_keywords.c<br>
cc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2<br>
-I../../../include -I/home/rdiv1001/fftw-3.0.1/include -O3<br>
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -faltivec<br>
-funroll-all-loops -std=gnu99 -mcpu=7450 -mtune=970 -MT<br>
sm_keywords.lo -MD -MP -MF .deps/sm_keywords.Tpo -c sm_keywords.c -o<br>
sm_keywords.o<br>
In file included from sm_keywords.c:41:<br>
/usr/include/regex.h:68: error: parse error before "regoff_t"<br>
/usr/include/regex.h:78: error: parse error before "regoff_t"<br>
/usr/include/regex.h:124: error: parse error before "regmatch_t"<br>
make[4]: *** [sm_keywords.lo] Error 1<br>
make[3]: *** [all-recursive] Error 1<br>
make[2]: *** [all-recursive] Error 1<br>
make[1]: *** [all] Error 2<br>
make: *** [all-recursive] Error 1<br>
<br>
Any ideas for a fix?<br>
<br>
-Justin<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></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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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<br><div><div></div><div class="h5">
-- <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>
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