[gmx-users] Sanity error in cpp while intalling FFTW

sharada sharada at ccmb.res.in
Thu Nov 2 13:11:44 CET 2006 

Hello Erik,

Thank you for suggesting the idea. I have got the required help from 
FFTW authors. I could load the Gromacs successfully. I have even done a 
test run (pdb2gmx - mdrun) on my protein in water. However I am unable 
to finally visualise the animation of the dynamics run using ngmx. It 
says command not found. Why is it giving me this error when all the 
other programs are working ? I could't locate the link for this program 
in any folder. Where is it installed ? My  configure,make,make install 
and make links didnot give any errors ! Kindly guide me. Thanks in advance.

sharada


Erik Lindahl wrote:

> Hi,
>
> First, since this is an FFTW-related issue you will probably get 
> better help by asking the FFTW authors.
>
> Looking in config.log, the script is trying to preprocess the test program
>
> /* confdefs.h.  */
> #define PACKAGE_NAME "fftw"
> #define PACKAGE_TARNAME "fftw"
> #define PACKAGE_VERSION "3.1.2"
> #define PACKAGE_STRING "fftw 3.1.2"
> #define PACKAGE_BUGREPORT "fftw at fftw.org <mailto:fftw at fftw.org>"
> #define PACKAGE "fftw"
> #define VERSION "3.1.2"
> #define FFTW_SINGLE 1
> #define BENCHFFT_SINGLE 1
> /* end confdefs.h.  */
> #ifdef __STDC__
> # include <limits.h>
> #else
> # include <assert.h>
> #endif
>
>
> using the command gcc -std=gnu99 -E  conftest.c
>
> but gets the error message
>
> In file included from /usr/include/bits/posix1_lim.h:130,
>                  from /usr/include/limits.h:144,
>                  from 
> /usr/lib/gcc-lib/i386-redhat-linux/3.2.3/include/limits.h:132,
>                  from 
> /usr/lib/gcc-lib/i386-redhat-linux/3.2.3/include/syslimits.h:7,
>                  from 
> /usr/lib/gcc-lib/i386-redhat-linux/3.2.3/include/limits.h:11,
>                  from conftest.c:13:
> /usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or 
> directory
>
>
> <limits.h> is mandatory for ANSI C99, so there is something wrong with 
> your operating system/compiler installation.
>
> Cheers,
>
> Erik
>
>
>
>
>
> On Oct 17, 2006, at 1:43 PM, sharada wrote:
>
>>
>>
>>
>> Hi gromacs users,
>>
>> I am trying to install gromacs on Linux. While installing the fftw 
>> module , I am getting the following error
>> at the ./configure stage:
>>
>> [root at Sharada fftw-3.1.2]# ./configure --enable-float 
>> --enable-threads --enable-sse
>>
>> checking for a BSD-compatible install... /usr/bin/install -c
>> checking whether build environment is sane... yes
>> checking for gawk... gawk
>> checking whether make sets $(MAKE)... yes
>> checking whether to enable maintainer-specific portions of 
>> Makefiles... no
>> checking build system type... i686-pc-linux-gnu
>> checking host system type... i686-pc-linux-gnu
>> checking for gcc... gcc
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ISO C89... none needed
>> checking for style of include used by make... GNU
>> checking dependency style of gcc... gcc3
>> checking for C compiler vendor... gnu
>> checking for gcc option to accept ISO C99... -std=gnu99
>> checking for gcc -std=gnu99 option to accept ISO Standard C... 
>> (cached) -std=gnu99
>> checking for a BSD-compatible install... /usr/bin/install -c
>> checking whether ln -s works... yes
>> checking whether make sets $(MAKE)... (cached) yes
>> checking for a sed that does not truncate output... /bin/sed
>> checking for grep that handles long lines and -e... /bin/grep
>> checking for egrep... /bin/grep -E
>> checking for ld used by gcc -std=gnu99... /usr/bin/ld
>> checking if the linker (/usr/bin/ld) is GNU ld... yes
>> checking for /usr/bin/ld option to reload object files... -r
>> checking for BSD-compatible nm... /usr/bin/nm -B
>> checking how to recognise dependent libraries... pass_all
>> checking how to run the C preprocessor... /lib/cpp
>> configure: error: C preprocessor "/lib/cpp" fails sanity check
>> See `config.log' for more details.
>>
>> what does the error trying to tell me ? cpp is linked to 
>> /usr/bin/cpp. I am installing from the root account. can any body 
>> help ?  I am attaching the config.log file alongwith.  Thanks in advance.
>>
>> regards,
>> sharada
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>> <config.log>
>> _______________________________________________
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>
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