[gmx-users] Another install error: gmx-4.5 beta1
Justin A. Lemkul
jalemkul at vt.edu
Sun Aug 1 16:01:36 CEST 2010
Roland Schulz wrote:
> Hi Justin,
>
> try to add "#include <sys/types.h>" before the include of regex.h in
> sm-keywords.c.
>
Thanks, that works.
-Justin
> Roland
>
> On Sun, Aug 1, 2010 at 12:49 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> 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> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
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>
> 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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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>
>
>
> --
> 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
========================================
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