[gmx-users] Another install error: gmx-4.5 beta1

[Justin A. Lemkul]

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>> 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
> 
>     ========================================
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-- 
========================================

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

========================================