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
<[EMAIL PROTECTED]> 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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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