[gmx-users] Compiling Problems

Erik Lindahl lindahl at stanford.edu
Fri Jul 18 09:03:01 CEST 2003


Hi,

This is a known bug in the IBM system headers - just add the flag

--disable-largefile

to ./configure, and it should work.

Cheers,

Erik

On Thursday, July 17, 2003, at 11:48 PM, Dr. Alexander Pazur wrote:

> Dear GROMACS newsgroup members
>
> I wish to install GROMACS on a IBM RS6000 machine under
> AIX4.3.3. with LAM-MPI for multicomputing. I have no Fortran-
> Compiler. LAM-MPI, IBM-MASS, FFTW and LessTif are installed.
> I am logged in as root-user.
> LAM-MPI is checked with its commands and works systemwide fine.
> The GROMACS ./configure swithes are:
>
> --prefix=/people/odin/gromacs --disable-fortran --disable-float 
> --enable-
> mpi --with-x
>
> ./configure works (to message "gromacs is ready to compile").
> But "make" afterwards stops having done some tasks, here
> is the protocol (screen messages from prompt to prompt):
>
> 4:root at odin:/people/odin/gromacs/gromacs-3.1.4 # make
> Making all in src
>         cd ..  && CONFIG_FILES= CONFIG_HEADERS=src/config.h
> /bin/sh ./config.status
> config.status: creating src/config.h
> config.status: src/config.h is unchanged
>         make  all-recursive
> Making all in gmxlib
>         source='3dview.c' object='3dview.lo' libtool=yes
> depfile='.deps/3dview.Plo' tmpdepfile='.deps/3dview.TPlo'
> depmode=gcc /bin/sh ../../config/depcomp  /bin/sh
> ../../libtool --mode=compile mpicc -DHAVE_CONFIG_H -I. -I. -
> I../../src   -I../../include -
> DGMXLIBDIR=\"/people/odin/gromacs/share/top\" -
> I/usr/local/include   -c -o 3dview.lo `test -f 3dview.c ||
> echo './'`3dview.c
> mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -
> DGMXLIBDIR=\"/people/odin/gromacs/share/top\" -
> I/usr/local/include -c 3dview.c -Wp,-MD,.deps/3dview.TPlo -o
> 3dview.o
> In file included from ../../include/sysstuff.h:52,
>                  from 3dview.c:34:
> /usr/bin/../lib/gcc-lib/powerpc-ibm-aix4.3.3.0/2.9-aix43-
> 010414/include/stdio.h:448: conflicting types for `fgetpos64'
> /usr/bin/../lib/gcc-lib/powerpc-ibm-aix4.3.3.0/2.9-aix43-
> 010414/include/stdio.h:288: previous declaration of
> `fgetpos64'
> /usr/bin/../lib/gcc-lib/powerpc-ibm-aix4.3.3.0/2.9-aix43-
> 010414/include/stdio.h:451: conflicting types for `fseeko64'
> /usr/bin/../lib/gcc-lib/powerpc-ibm-aix4.3.3.0/2.9-aix43-
> 010414/include/stdio.h:394: previous declaration of `fseeko64'
> /usr/bin/../lib/gcc-lib/powerpc-ibm-aix4.3.3.0/2.9-aix43-
> 010414/include/stdio.h:452: conflicting types for `fsetpos64'
> /usr/bin/../lib/gcc-lib/powerpc-ibm-aix4.3.3.0/2.9-aix43-
> 010414/include/stdio.h:290: previous declaration of
> `fsetpos64'
> /usr/bin/../lib/gcc-lib/powerpc-ibm-aix4.3.3.0/2.9-aix43-
> 010414/include/stdio.h:453: conflicting types for `ftello64'
> /usr/bin/../lib/gcc-lib/powerpc-ibm-aix4.3.3.0/2.9-aix43-
> 010414/include/stdio.h:395: previous declaration of `ftello64'
> In file included from ../../include/sysstuff.h:56,
>                  from 3dview.c:34:
> /usr/include/unistd.h:167: conflicting types for `lseek64'
> /usr/include/unistd.h:165: previous declaration of `lseek64'
> In file included from /usr/include/unistd.h:543,
>                  from ../../include/sysstuff.h:56,
>                  from 3dview.c:34:
> /usr/include/sys/lockf.h:64: conflicting types for `lockf64'
> /usr/include/sys/lockf.h:62: previous declaration of `lockf64'
> In file included from ../../include/sysstuff.h:56,
>                  from 3dview.c:34:
> /usr/include/unistd.h:576: conflicting types for `ftruncate64'
> /usr/include/unistd.h:574: previous declaration of
> `ftruncate64'
> /usr/include/unistd.h:603: conflicting types for `truncate64'
> /usr/include/unistd.h:601: previous declaration of
> `truncate64'
> /usr/include/unistd.h:620: conflicting types for `pread64'
> /usr/include/unistd.h:617: previous declaration of `pread64'
> /usr/include/unistd.h:621: conflicting types for `pwrite64'
> /usr/include/unistd.h:618: previous declaration of `pwrite64'
> /usr/include/unistd.h:674: conflicting types for `fclear64'
> /usr/include/unistd.h:671: previous declaration of `fclear64'
> /usr/include/unistd.h:675: conflicting types for
> `fsync_range64'
> /usr/include/unistd.h:672: previous declaration of
> `fsync_range64'
> 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.
> 4:root at odin:/people/odin/gromacs/gromacs-3.1.4 #
>
> ********************************************
> Is this error known ? Can somebody help me?
> Many Thanks.
>
> Alexander Pazur
> *********************************************
>  Dr. Alexander Pazur
>  Wiss. Assistent, EDV-Systembetreuer
>  Department Biologie I der Universitaet Muenchen: Botanik
>  Menzingerstr. 67
>  D-80638 Muenchen
> *********************************************
> Tel.: 089-17861-290 / -296
> Fax.: 089-17861-185
> pazur at botanik.biologie.uni-muenchen.de
> http://www.botanik.biologie.uni-muenchen.de/pazur
>
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