Hi Justin, try to add "#include <sys/types.h>" before the include of regex.h in sm-keywords.c.
Roland On Sun, Aug 1, 2010 at 12:49 AM, Justin A. Lemkul <[email protected]> wrote: > > > Roland Schulz wrote: > >> Hi, >> >> look at /usr/include/regex.h line 68. What is/are the keyword before. I >> > > Line 68 occurs very early in the file, and corresponds to: > > typedef off_t regoff_t; > > In regex.h, there are 60 lines of comments followed by: > > #ifndef _REGEX_H_ > #define _REGEX_H_ > > #include <sys/cdefs.h> > > /* types */ > typedef off_t regoff_t; > > > 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. >> >> > 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: > > 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 > > I'll send you the regex.h file off-list. Thanks for your attention. > > -Justin > > Roland >> >> >> On Fri, Jul 30, 2010 at 5:53 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> Hi, >> >> I'm trying to install the newest beta on our university's >> supercomputer, but I'm encountering an error during compilation. >> It's an aging system, so this might be somewhat difficult to solve. >> Here are the specs: >> >> Mac OSX 10.3 >> 2.3 GHz PowerPC 970FX processors >> gcc 3.3 >> fftw 3.0.1 >> >> Configuration went without a hitch, with config.log indicating all >> necessary headers, libraries, etc. were found. >> >> ./configure --prefix=/home/rdiv1001/gromacs-4.5_beta1 >> CPPFLAGS="-I/home/rdiv1001/fftw-3.0.1/include" >> LDFLAGS="-L/home/rdiv1001/fftw-3.0.1/lib" >> --program-suffix=_4.5_beta1 --disable-threads >> >> Compilation fails with the following: >> >> Making all in selection >> ... >> /bin/sh ../../../libtool --tag=CC --mode=compile 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 -o >> sm_keywords.lo sm_keywords.c >> 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 >> In file included from sm_keywords.c:41: >> /usr/include/regex.h:68: error: parse error before "regoff_t" >> /usr/include/regex.h:78: error: parse error before "regoff_t" >> /usr/include/regex.h:124: error: parse error before "regmatch_t" >> make[4]: *** [sm_keywords.lo] Error 1 >> make[3]: *** [all-recursive] Error 1 >> make[2]: *** [all-recursive] Error 1 >> make[1]: *** [all] Error 2 >> make: *** [all-recursive] Error 1 >> >> Any ideas for a fix? >> >> -Justin >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected] >> <mailto:[email protected]>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov <http://cmb.ornl.gov >> > >> >> 865-241-1537, ORNL PO BOX 2008 MS6309 >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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