[gmx-users] Re: Gromacs-4.0.2: Compilation problem on IBM P690 Regatta System

[Suman Chakrabarty]

I have solved the reported problem by adding --disable-largefile to
the configure options. Now the non-parallel version compiles and
installs fine. What is the file size limit now? Is it 2 GB?

But now I have problem with the parallel (MPI) version. When I issue
the command:
./configure --prefix=/home/hpcscratch/csdsuman/Gromacs/GMX402
--disable-largefile --enable-mpi --disable-nice
--program-suffix="_mpi"

It ends with the following error:
checking whether byte ordering is bigendian... yes
checking for int... yes
checking size of int... configure: error: cannot compute sizeof (int)
See `config.log' for more details.

Can anybody suggest what should I look for in the config.log file and
how to go about solving it? Thanks.


Regards,
Suman Chakrabarty.

On Tue, Nov 18, 2008 at 12:38 AM, Suman Chakrabarty
<suman at sscu.iisc.ernet.in> wrote:
> Dear all,
>
> this is the first time I have experienced any problem with Gromacs
> compilation! Of course till now I have been using simple desktop PCs
> (both 32 bit and 64 bit) with regular Linux OS (Fedora, Ubuntu etc.).
> Now I tried to compile gromacs-4.0.2 on a parallel environment of IBM
> P690 Regatta System with AIX (build system type from configuration
> log: powerpc-ibm-aix5.2.0.0).
>
> I have compiled the FFTW library myself successfully and added the
> required flags before compiling gromacs. configure works without any
> error. But "make" ends prematurely with the following errors:
>
> =======================================================================
>
>  cc -qlanglvl=ansi -DHAVE_CONFIG_H -I. -I../../src -I../../include
> -DGMXLIBDIR=\"/home/phd/02/csdsuman/Gromacs/GMX402/share/top\"
> -I/home/phd/02/csdsuman/FFTW/FFTW320/include -O3 -qarch=pwr4
> -qtune=pwr4 -qmaxmem=16384 -c -M gmx_sdf.c -o gmx_sdf.o
> "/usr/include/stdio.h", line 487.12: 1506-343 (S) Redeclaration of
> fgetpos64 differs from previous declaration on line 296 of
> "/usr/include/stdio.h".
> "/usr/include/stdio.h", line 487.12: 1506-377 (I) The type "long
> long*" of parameter 2 differs from the previous type "long*".
> "/usr/include/stdio.h", line 490.12: 1506-343 (S) Redeclaration of
> fseeko64 differs from previous declaration on line 427 of
> "/usr/include/stdio.h".
> "/usr/include/stdio.h", line 490.12: 1506-377 (I) The type "long long"
> of parameter 2 differs from the previous type "long".
> "/usr/include/stdio.h", line 491.12: 1506-343 (S) Redeclaration of
> fsetpos64 differs from previous declaration on line 298 of
> "/usr/include/stdio.h".
> "/usr/include/stdio.h", line 491.12: 1506-377 (I) The type "const long
> long*" of parameter 2 differs from the previous type "const long*".
> "/usr/include/stdio.h", line 492.16: 1506-343 (S) Redeclaration of
> ftello64 differs from previous declaration on line 428 of
> "/usr/include/stdio.h".
> "/usr/include/stdio.h", line 492.16: 1506-050 (I) Return type "long
> long" in redeclaration is not compatible with the previous return type
> "long".
> "/usr/include/unistd.h", line 171.17: 1506-343 (S) Redeclaration of
> lseek64 differs from previous declaration on line 169 of
> "/usr/include/unistd.h".
> "/usr/include/unistd.h", line 171.17: 1506-050 (I) Return type "long
> long" in redeclaration is not compatible with the previous return type
> "long".
> "/usr/include/unistd.h", line 171.17: 1506-377 (I) The type "long
> long" of parameter 2 differs from the previous type "long".
> "/usr/include/sys/lockf.h", line 64.20: 1506-343 (S) Redeclaration of
> lockf64 differs from previous declaration on line 62 of
> "/usr/include/sys/lockf.h".
> "/usr/include/sys/lockf.h", line 64.20: 1506-377 (I) The type "long
> long" of parameter 3 differs from the previous type "long".
> "/usr/include/unistd.h", line 815.33: 1506-343 (S) Redeclaration of
> ftruncate64 differs from previous declaration on line 813 of
> "/usr/include/unistd.h".
> "/usr/include/unistd.h", line 815.33: 1506-377 (I) The type "long
> long" of parameter 2 differs from the previous type "long".
> "/usr/include/unistd.h", line 833.33: 1506-343 (S) Redeclaration of
> truncate64 differs from previous declaration on line 831 of
> "/usr/include/unistd.h".
> "/usr/include/unistd.h", line 833.33: 1506-377 (I) The type "long
> long" of parameter 2 differs from the previous type "long".
> "/usr/include/unistd.h", line 850.33: 1506-343 (S) Redeclaration of
> pread64 differs from previous declaration on line 847 of
> "/usr/include/unistd.h".
> "/usr/include/unistd.h", line 850.33: 1506-377 (I) The type "long
> long" of parameter 4 differs from the previous type "long".
> "/usr/include/unistd.h", line 851.33: 1506-343 (S) Redeclaration of
> pwrite64 differs from previous declaration on line 848 of
> "/usr/include/unistd.h".
> "/usr/include/unistd.h", line 851.33: 1506-377 (I) The type "long
> long" of parameter 4 differs from the previous type "long".
> "/usr/include/unistd.h", line 918.25: 1506-343 (S) Redeclaration of
> fclear64 differs from previous declaration on line 915 of
> "/usr/include/unistd.h".
> "/usr/include/unistd.h", line 918.25: 1506-050 (I) Return type "long
> long" in redeclaration is not compatible with the previous return type
> "long".
> "/usr/include/unistd.h", line 918.25: 1506-377 (I) The type "long
> long" of parameter 2 differs from the previous type "long".
> "/usr/include/unistd.h", line 919.25: 1506-343 (S) Redeclaration of
> fsync_range64 differs from previous declaration on line 916 of
> "/usr/include/unistd.h".
> "/usr/include/unistd.h", line 919.25: 1506-377 (I) The type "long
> long" of parameter 3 differs from the previous type "long".
> make: 1254-004 The error code from the last command is 1.
>
>
> Stop.
> make: 1254-004 The error code from the last command is 1.
>
>
> Stop.
> make: 1254-004 The error code from the last command is 2.
>
>
> Stop.
> make: 1254-004 The error code from the last command is 1.
>
>
> Stop.
> ==========================================================================
>
> I had attempted to attach the config.log file along with the full screen
> output of configure and make, but the size limit of the list did not
> allow me to do so. Please let me know if you need any further details
> for the troubleshooting. Any help/suggestion will be much appreciated.
>
>
> Thanks,
> Suman Chakrabarty.
>
>
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