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

[Justin A. Lemkul]

Suman Chakrabarty wrote:
> 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.

Please read this post from the archives, and the subsequent responses:

http://www.gromacs.org/pipermail/gmx-users/2008-November/037935.html

-Justin

> 
> 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.
>>
>>
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>>
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================