[gmx-users] Re: Gromacs3.3 Compilation on IBM powerpc

Tue Mar 14 03:53:34 CET 2006

Dear Erik:

The last error is just "configure:6705: error: cannot compute sizeof (int), 77"

Xie Yinghong

> Find the _last_ error in config.log, and check what the compiler said  
> about it.

> Cheers,

> Erik

On Mar 14, 2006, at 2:11 AM, Yinghong wrote:

> Dear Erik:
>
> I have carefully read through config.log file, and I found out some  
> possible problems for compilation failure, could you please help me  
> to locate the real reason and solution?
>
> As I think, maybe this error is from xlc, but it seemed much  
> related to "conftest.c" file, which was reported for several times  
> as errors.
>
> How should I deal it with? By the way, I have passed through the  
> compilation of single version. The following errors were from MPI  
> compilation. Of course, I only added a "--enable-mpi" flag when  
> compling MPI version, as described in the last email.
>
>
> config.log:
> ...
> ...
> ...
> ## ----------- ##
> ## Core tests. ##
> ## ----------- ##
> ...
> ...
> configure:2586: checking for C compiler version
> configure:2589: xlc --version </dev/null >&5
> xlc: 1501-216 command option --version is not recognized - passed  
> to ld
> ...
> ...
> ...
> configure:2806: checking whether we are using the GNU C compiler
> configure:2830: xlc -c -O3 -qarch=pwr4 -qtune=pwr4 -qansialias -w - 
> I/afs/ipp-garching.mpg.de/home/x/xieyh/fftw_213/include conftest.c >&5
> "conftest.c", line 20.14: 1506-275 (S) Unexpected text me encountered.
> "conftest.c", line 20.8: 1506-045 (S) Undeclared identifier choke.
> configure:2836: $? = 1
> configure: failed program was:
> | /* confdefs.h.  */
> |
> | #define PACKAGE_NAME "GROMACS"
> | #define PACKAGE_TARNAME "gromacs"
> | #define PACKAGE_VERSION "3.3"
> | #define PACKAGE_STRING "GROMACS 3.3"
> | #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
> | #define PACKAGE "gromacs"
> | #define VERSION "3.3"
> | #define GMX_SOFTWARE_SQRT
> | #define BUILD_TIME "Mon Mar 13 08:13:33 NFT 2006"
> | #define BUILD_USER "xieyh at psi24"
> | #define BUILD_MACHINE "AIX 2 0010594A4C00"
> | /* end confdefs.h.  */
> |
> | int
> | main ()
> | {
> | #ifndef __GNUC__
> |        choke me
> | #endif
> |
> |   ;
> |   return 0;
> | }
>
> configure:2889: xlc -c -g -I/afs/ipp-garching.mpg.de/home/x/xieyh/ 
> fftw_213/include conftest.c >&5
> configure:2895: $? = 0
> configure:2899: test -z
>                          || test ! -s conftest.err
> ...
> ...
> configure:3061: xlc -c -O3 -qarch=pwr4 -qtune=pwr4 -qansialias -w - 
> I/afs/ipp-garching.mpg.de/home/x/xieyh/fftw_213/include conftest.c >&5
> "conftest.c", line 2.3: 1506-166 (S) Definition of function choke  
> requires parentheses.
> "conftest.c", line 2.9: 1506-046 (S) Syntax error.
> configure:3067: $? = 1
> configure: failed program was:
> | #ifndef __cplusplus
> |   choke me
> | #endif
> ...
> ...
> configure:4775: mpcc -E -I/afs/ipp-garching.mpg.de/home/x/xieyh/ 
> fftw_213/include conftest.c
> "conftest.c", line 18.10: 1506-296 (S) #include file  
> <ac_nonexistent.h> not found.
> ...
> ...
> | #include <stdio.h>
> | #include <stdlib.h>
> | #ifdef F77_DUMMY_MAIN
> |
> | #  ifdef __cplusplus
> |      extern "C"
> | #  endif
> |    int F77_DUMMY_MAIN() { return 1; }
> |
> | #endif
> | int
> | main ()
> | {
> |
> |   FILE *f = fopen ("conftest.val", "w");
> |   if (! f)
> |     exit (1);
> |   if (((long) (sizeof (int))) < 0)
> |     {
> |       long i = longval ();
> |       if (i != ((long) (sizeof (int))))
> |       exit (1);
> |       fprintf (f, "%ld\n", i);
> |     }
> |   else
> |     {
> |       unsigned long i = ulongval ();
> |       if (i != ((long) (sizeof (int))))
> |       exit (1);
> |       fprintf (f, "%lu\n", i);
> |     }
> |   exit (ferror (f) || fclose (f) != 0);
> |
> |   ;
> |   return 0;
> | }
> configure:6705: error: cannot compute sizeof (int), 77
> See `config.log' for more details.
>
>
>
> Xie Yinghong
>
>
>> Hi,
>>
>> Check config.log for the actual error. You might also want to make
>> sure that you can compile a small MPI test program.
>>
>> Cheers,
>>
>> Erik
>>
>> On Mar 13, 2006, at 8:52 PM, Yinghong wrote:
>>
>>> Dear users:
>>>
>>> I have successfully installed fftw2.1.3 and single version
>>> Gromacs3.3 on IBM powerpc Aix5.2.0.0 with the following
>>> environmental variables:
>>>
>>> setenv CC xlc
>>> setenv MPICC mpcc
>>> setenv F77 xlf
>>> setenv CXX xlC
>>> setenv CPPFLAGS -I.../fftw_213/include
>>> setenv LDFLAGS -L.../fftw_213/lib
>>> setenv CFLAGS "-O3 -qarch=pwr4 -qtune=pwr4 -qansialias -w"
>>> setenv FFLAGS "-O3 -qarch=pwr4 -qtune=pwr4 -qansialias -qstrict -w"
>>> Now, I would like to compile the parallel version of Gromacs3.3,
>>> and I did it as the follows:
>>> 1. make disclean;
>>> 2. ./configure --prefix=$HOME/gromacs33 --exec-prefix=$HOME/
>>> gromacs33 --enable-float --disable-fortran --disable-largefile --
>>> without-x --disable-
>>> vectorized-sqrt --with-fft=fftw2 --enable-mpi --program-suffix=_mpi
>>>
>>> It is worthy noting that the all parameters for ./configure are the
>>> same as perviously successful single version, except that "--enable-
>>> mpi --program-suffix=_mpi" is added in compiling MPI version.
>>> However, compilation can not pass because of the following reason.
>>> If anybody encountered such an error, could you give me some
>>> suggestion? How to deal with it? Any help will be extermely
>>> appreciately.
>>>
>>> ...
>>> ...
>>> checking for style of include used by make... GNU
>>> checking dependency style of xlc... none
>>> checking for mpxlc... mpcc
>>> checking whether the MPI cc command works... yes
>>> checking how to run the C preprocessor... mpcc -E
>>> ******************************************
>>> * Using CFLAGS from environment variable *
>>> ******************************************
>>> checking whether byte ordering is bigendian... yes
>>> checking for egrep... grep -E
>>> checking for ANSI C header files... no
>>> checking for sys/types.h... yes
>>> checking for sys/stat.h... yes
>>> checking for stdlib.h... yes
>>> checking for string.h... yes
>>> checking for memory.h... yes
>>> checking for strings.h... yes
>>> checking for inttypes.h... yes
>>> checking for stdint.h... yes
>>> checking for unistd.h... yes
>>> checking for int... yes
>>> checking size of int... configure: error: cannot compute sizeof
>>> (int), 77
>>> See `config.log' for more details.
>
>
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