[gmx-users] GROMACS compilation problem on IBM AIX

Mon Feb 3 18:43:17 CET 2003

On Mon, 2003-02-03 at 15:16, Gerrit Groenhof wrote:
> Hi Jithesh,
> 
> I am not sure, but from your benchmark it seems gromacs is not
> compiled properly. I had the same problem on an IBM SP3 (4?). changing
> the optimization from O3 to O2 did the trick. What also works is to
> change from the IBM xlc compiler to the gnu gcc compiler.
> 
And it is also very important to check that all libraries are compiled
with the same options (for hardware specifics: the processor type). If
you compile part for power3 (e.g. fftw) and part for power4 (gromacs)
your simulations will die. 

Check an option in fftw compilation, it could be that they default for
the wrong architecture.,
> Good luck,
> 
> Gerrit
> 
> 
> 
> > 
> > Hi,
> > 
> > I'm trying to compile GROMACS 3.1.4 on a cluster of IBM p630. After running the configure script successfully, I tried to 'make'. But I got the following error (please see below). 
> > 
> > As per the info from earlier posting about a similar problem, I used the disable-largefile option and it got compiled. Is there any other solution? 
> > 
> > 
> > While trying to execute the dppc benchmark I'm getting INF values for constraints..and Warning: 1-4 interaction at distance larger than 1. Is there any problem?
> > 
> > 
> > thanks & regards
> > Jithesh
> > ---------
> > log from make..
> > 
> > Making all in src
> > make all-recursive
> > Making all in gmxlib
> > cd ../.. && CONFIG_HEADERS= CONFIG_LINKS=
> > CONFIG_FILES=src/gmxlib/Makefile /bin/sh ./config.status
> > config.status: creating src/gmxlib/Makefile
> > source='3dview.c' object='3dview.lo' libtool=yes
> > depfile='.deps/3dview.Plo' tmpdepfile='.deps/3dview.TPlo'
> > depmode=aix /bin/sh ../../config/depcomp /bin/sh ../../libtool
> > --mode=compile xlc128_r -DHAVE_CONFIG_H -I. -I. -
> > I../../src -I../../include
> > -DGMXLIBDIR=\"/home/bioinfo/jithesh/GROMACS/share/gromacs/top\"
> > -I/home/bioinfo/jithes
> > h/FFTW/include -O3 -qarch=pwr4 -qtune=pwr4 -qmaxmem=16384 -c -o 3dview.lo
> > `test -f 3dview.c || echo './'`3dview.c
> > xlc128_r -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include
> > -DGMXLIBDIR=\"/home/bioinfo/jithesh/GROMACS/share/grom
> > acs/top\" -I/home/bioinfo/jithesh/FFTW/include -O3 -qarch=pwr4 -qtune=pwr4
> > -qmaxmem=16384 -c -M 3dview.c
> > "/usr/include/stdio.h", line 443.12: 1506-343 (S) Redeclaration of
> > fgetpos64 differs from previous declaration on l
> > ine 269 of "/usr/include/stdio.h".
> > "/usr/include/stdio.h", line 443.12: 1506-377 (I) The type "long long*" of
> > parameter 2 differs from the previous ty
> > pe "long*".
> > "/usr/include/stdio.h", line 446.12: 1506-343 (S) Redeclaration of
> > fseeko64 differs from previous declaration on li
> > ne 389 of "/usr/include/stdio.h".
> > "/usr/include/stdio.h", line 446.12: 1506-377 (I) The type "long long" of
> > parameter 2 differs from the previous typ
> > e "long".
> > "/usr/include/stdio.h", line 447.12: 1506-343 (S) Redeclaration of
> > fsetpos64 differs from previous declaration on l
> > ine 271 of "/usr/include/stdio.h".
> > "/usr/include/stdio.h", line 447.12: 1506-377 (I) The type "const long
> > long*" of parameter 2 differs from the previ
> > ous type "const long*".
> > "/usr/include/stdio.h", line 448.16: 1506-343 (S) Redeclaration of
> > ftello64 differs from previous declaration on li
> > ne 390 of "/usr/include/stdio.h".
> > "/usr/include/stdio.h", line 448.16: 1506-050 (I) Return type "long long"
> > in redeclaration is not compatible with t
> > he previous return type "long".
> > "/usr/include/unistd.h", line 167.17: 1506-343 (S) Redeclaration of
> > lseek64 differs from previous declaration on li
> > ne 165 of "/usr/include/unistd.h".
> > "/usr/include/unistd.h", line 167.17: 1506-050 (I) Return type "long long"
> > in redeclaration is not compatible with
> > the previous return type "long".
> > "/usr/include/unistd.h", line 167.17: 1506-377 (I) The type "long long" of
> > parameter 2 differs from the previous ty
> > pe "long".
> > "/usr/include/sys/lockf.h", line 50.20: 1506-343 (S) Redeclaration of
> > lockf64 differs from previous declaration on
> > line 48 of "/usr/include/sys/lockf.h".
> > "/usr/include/sys/lockf.h", line 50.20: 1506-377 (I) The type "long long"
> > of parameter 3 differs from the previous
> > type "long".
> > "/usr/include/unistd.h", line 602.33: 1506-343 (S) Redeclaration of
> > ftruncate64 differs from previous declaration o
> > n line 600 of "/usr/include/unistd.h".
> > "/usr/include/unistd.h", line 602.33: 1506-377 (I) The type "long long" of
> > parameter 2 differs from the previous ty
> > pe "long".
> > "/usr/include/unistd.h", line 629.33: 1506-343 (S) Redeclaration of
> > truncate64 differs from previous declaration on
> > line 627 of "/usr/include/unistd.h".
> > "/usr/include/unistd.h", line 629.33: 1506-377 (I) The type "long long" of
> > parameter 2 differs from the previous ty
> > pe "long".
> > "/usr/include/unistd.h", line 646.33: 1506-343 (S) Redeclaration of
> > pread64 differs from previous declaration on li
> > ne 643 of "/usr/include/unistd.h".
> > "/usr/include/unistd.h", line 646.33: 1506-377 (I) The type "long long" of
> > parameter 4 differs from the previous ty
> > pe "long".
> > line 48 of "/usr/include/sys/lockf.h".
> > "/usr/include/sys/lockf.h", line 50.20: 1506-377 (I) The type "long long"
> > of parameter 3 differs from the previous
> > type "long".
> > "/usr/include/unistd.h", line 602.33: 1506-343 (S) Redeclaration of
> > ftruncate64 differs from previous declaration o
> > n line 600 of "/usr/include/unistd.h".
> > "/usr/include/unistd.h", line 602.33: 1506-377 (I) The type "long long" of
> > parameter 2 differs from the previous ty
> > pe "long".
> > "/usr/include/unistd.h", line 629.33: 1506-343 (S) Redeclaration of
> > truncate64 differs from previous declaration on
> > line 627 of "/usr/include/unistd.h".
> > "/usr/include/unistd.h", line 629.33: 1506-377 (I) The type "long long" of
> > parameter 2 differs from the previous ty
> > pe "long".
> > "/usr/include/unistd.h", line 646.33: 1506-343 (S) Redeclaration of
> > pread64 differs from previous declaration on li
> > ne 643 of "/usr/include/unistd.h".
> > "/usr/include/unistd.h", line 646.33: 1506-377 (I) The type "long long" of
> > parameter 4 differs from the previous ty
> > pe "long".
> > "/usr/include/unistd.h", line 647.33: 1506-343 (S) Redeclaration of
> > pwrite64 differs from previous declaration on l
> > ine 644 of "/usr/include/unistd.h".
> > "/usr/include/unistd.h", line 647.33: 1506-377 (I) The type "long long" of
> > parameter 4 differs from the previous ty
> > pe "long".
> > "/usr/include/unistd.h", line 712.25: 1506-343 (S) Redeclaration of
> > fclear64 differs from previous declaration on l
> > ine 709 of "/usr/include/unistd.h".
> > "/usr/include/unistd.h", line 712.25: 1506-050 (I) Return type "long long"
> > in redeclaration is not compatible with
> > the previous return type "long".
> > "/usr/include/unistd.h", line 712.25: 1506-377 (I) The type "long long" of
> > parameter 2 differs from the previous ty
> > pe "long".
> > "/usr/include/unistd.h", line 713.25: 1506-343 (S) Redeclaration of
> > fsync_range64 differs from previous declaration
> > on line 710 of "/usr/include/unistd.h".
> > "/usr/include/unistd.h", line 713.25: 1506-377 (I) The type "long long" of
> > parameter 3 differs from the previous ty
> > pe "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.
> > 
> >  
> > 
> > 
> > 
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> > 
> > --=_MAILER_ATTACH_BOUNDARY_20032311934461714636915
> > Content-Type: text/plain; name="Makefile"
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> > --=_MAILER_ATTACH_BOUNDARY_20032311934461714636915--
> > 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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