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

Sun Aug 1 07:00:06 CEST 2010

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 <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>> 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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>>
>>
>>
>> --
>> 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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-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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