[gmx-users] Compiling Gromacs 4.0.7 on AIX 5.3

[Sebastien Morin]

Hi Chris.

Thank you for your answer

I tried the 4.0.4 version but unfortunately, it did better but new 
errors appeared anyway

so what I test now is another version of FFTW (fftw-2.1.5.tar.gz)
and the "make" command for gromacs 4.0.7 was a success

so the question is : What will be the difference in using Gromacs if I 
use FFTW2 instead of FFTW3 ?

thanks again

-------------------
here are errors shown when compiling gromacs 4.0.7 with fftw 3.2.2 on 
AIX 5.3
-------------------
"
  cc -qlanglvl=extc89 -DHAVE_CONFIG_H -I. -I../../src 
-I/usr/include/libxml2 -I../../include 
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -I/usr/local/include -O3 
-qarch=pwr5 -qtune=pwr5 -qmaxmem=16384 -c -M gmx_sdf.c -o gmx_sdf.o
"/usr/include/stdio.h", line 497.12: 1506-343 (S) Redeclaration of 
fgetpos64 differs from previous declaration on line 296 of 
"/usr/include/stdio.h".
"/usr/include/stdio.h", line 497.12: 1506-377 (I) The type "long long*" 
of parameter 2 differs from the previous type "long*".
"/usr/include/stdio.h", line 500.12: 1506-343 (S) Redeclaration of 
fseeko64 differs from previous declaration on line 440 of 
"/usr/include/stdio.h".
"/usr/include/stdio.h", line 500.12: 1506-377 (I) The type "long long" 
of parameter 2 differs from the previous type "long".
"/usr/include/stdio.h", line 501.12: 1506-343 (S) Redeclaration of 
fsetpos64 differs from previous declaration on line 298 of 
"/usr/include/stdio.h".
"/usr/include/stdio.h", line 501.12: 1506-377 (I) The type "const long 
long*" of parameter 2 differs from the previous type "const long*".
"/usr/include/stdio.h", line 502.16: 1506-343 (S) Redeclaration of 
ftello64 differs from previous declaration on line 441 of 
"/usr/include/stdio.h".
"/usr/include/stdio.h", line 502.16: 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 800.33: 1506-343 (S) Redeclaration of 
ftruncate64 differs from previous declaration on line 798 of 
"/usr/include/unistd.h".
"/usr/include/unistd.h", line 800.33: 1506-377 (I) The type "long long" 
of parameter 2 differs from the previous type "long".
"/usr/include/unistd.h", line 836.33: 1506-343 (S) Redeclaration of 
truncate64 differs from previous declaration on line 834 of 
"/usr/include/unistd.h".
"/usr/include/unistd.h", line 836.33: 1506-377 (I) The type "long long" 
of parameter 2 differs from the previous type "long".
"/usr/include/unistd.h", line 853.33: 1506-343 (S) Redeclaration of 
pread64 differs from previous declaration on line 850 of 
"/usr/include/unistd.h".
"/usr/include/unistd.h", line 853.33: 1506-377 (I) The type "long long" 
of parameter 4 differs from the previous type "long".
"/usr/include/unistd.h", line 854.33: 1506-343 (S) Redeclaration of 
pwrite64 differs from previous declaration on line 851 of 
"/usr/include/unistd.h".
"/usr/include/unistd.h", line 854.33: 1506-377 (I) The type "long long" 
of parameter 4 differs from the previous type "long".
"/usr/include/unistd.h", line 921.25: 1506-343 (S) Redeclaration of 
fclear64 differs from previous declaration on line 918 of 
"/usr/include/unistd.h".
"/usr/include/unistd.h", line 921.25: 1506-050 (I) Return type "long 
long" in redeclaration is not compatible with the previous return type 
"long".
"/usr/include/unistd.h", line 921.25: 1506-377 (I) The type "long long" 
of parameter 2 differs from the previous type "long".
"/usr/include/unistd.h", line 922.25: 1506-343 (S) Redeclaration of 
fsync_range64 differs from previous declaration on line 919 of 
"/usr/include/unistd.h".
"/usr/include/unistd.h", line 922.25: 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.



Le 15/04/2010 19:38, chris.neale at utoronto.ca a écrit :
> This worked for me on AIX 5.3 for gromacs 4.0.4, I didn't try to 
> compile any gromacs versions after that because we found that gromacs 
> runs much better on Xeons and Opterons than it runs on power6's 
> running AIX 5.3
>
> If you have a problem specific to 4.0.7 (i.e. you can compile 4.0.4 
> alright on AIX 5.3), then I'm sorry but I can not help you there.
>
> Note: be sure to modify the /scratch/cneale lines to match your system.
>
> Note: the -O5 flag makes this compilation take about 20h. You should 
> probably try without it first (~30 minute - 1h compilation), but it 
> does giev a few extra percent speed.
>
> Chris.
>
> ##serial compilation
>
> export 
> PATH=/usr/lpp/ppe.hpct/bin:/usr/vacpp/bin:.:/usr/bin:/etc:/usr/sbin:/usr/ucb:/usr/bin/X11:/sbin:/usr/java14/jre/bin:/usr/java14/bin:/usr/lpp/LoadL/full/bin:/usr/local/bin 
>
> export F77=xlf_r
> export CC=xlc_r
> export CXX=xlc++_r
> export FFLAGS="-O5 -qarch=pwr6 -qtune=pwr6"
> export CFLAGS="-O5 -qarch=pwr6 -qtune=pwr6"
> export CXXFLAGS="-O5 -qarch=pwr6 -qtune=pwr6"
> export FFTW_LOCATION=/scratch/cneale/exe/fftw-3.1.2_aix/exec
> export GROMACS_LOCATION=/scratch/cneale/exe/gromacs-4.0.4_aix/exec
> export CPPFLAGS=-I$FFTW_LOCATION/include
> export LDFLAGS=-L$FFTW_LOCATION/lib
> cd /scratch/cneale/exe/gromacs-4.0.4_aix
> mkdir exec
> ./configure --prefix=$GROMACS_LOCATION --without-motif-includes
> --without-motif-libraries --without-x --without-xml >output.configure
> 2>&1
> make >output.make 2>&1
> make install >output.make_install 2>&1
> make distclean
>
> #####################################
>
> ##parallel compilation
>
> export F77=xlf_r
> export CC=xlc_r
> export CXX=xlc++_r
> export FFLAGS="-O5 -qarch=pwr6 -qtune=pwr6"
> export CFLAGS="-O5 -qarch=pwr6 -qtune=pwr6"
> export CXXFLAGS="-O5 -qarch=pwr6 -qtune=pwr6"
> export FFTW_LOCATION=/scratch/cneale/exe/fftw-3.1.2_aix/exec
> export GROMACS_LOCATION=/scratch/cneale/exe/gromacs-4.0.4_aix/exec
> export CPPFLAGS=-I$FFTW_LOCATION/include
> export LDFLAGS=-L$FFTW_LOCATION/lib
> cd /scratch/cneale/exe/gromacs-4.0.4_aix
> echo "cn-r0-10" > ~/.rhosts
> echo localhost > ~/host.list
> for((i=2;i<=16;i++)); do
>   echo localhost >> ~/host.list
> done
> export MP_HOSTFILE=~/host.list
> ./configure --prefix=$GROMACS_LOCATION --without-motif-includes
> --without-motif-libraries --without-x --without-xml --enable-mpi
> --disable-nice --program-suffix="_mpi" CC=mpcc_r F77=mpxlf_r >
> output.configure_mpi 2>&1
> make mdrun > output.make_mpi 2>&1
> make install-mdrun > output.make_install_mpi 2>&1
> make distclean
>
>

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