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 <[email protected]
<mailto:[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]>
<mailto:[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> <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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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Please search the archive at http://www.gromacs.org/search before
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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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