[gmx-users] Compiling Gromacs 4.0.7 on AIX 5.3

Tue Apr 20 14:12:19 CEST 2010

Hello again

I followed your advices this time

here's what I did :

downloading gromacs 4.0.7
downloading fftw 2.1.5

initializing environment variables (modified to fit my configuration 
(pwr5) :

export LDFLAGS='-L/usr/local/lib'
export CPPFLAGS='-I/usr/local/include'

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=pwr5 -qtune=pwr5"
export CFLAGS="-O5 -qarch=pwr5 -qtune=pwr5"
export CXXFLAGS="-O5 -qarch=pwr5 -qtune=pwr5"

for FFTW :

./configure --enable-threads --enable-float
make
make install

(that's OK, installed in /usr/local/lib and /usr/local/include)

for Gromacs :

./configure --with-fft=fftw2

(that's OK)

make

unfortunately, the result is :
...
"nb_kernel333.h", line 101.1: 1506-282 (S) The type of the parameters 
must be specified in a prototype.
"nb_kernel334.h", line 63.1: 1506-033 (S) Function F77_FUNC_ is not 
valid. Function cannot return a function.
"nb_kernel334.h", line 63.1: 1506-282 (S) The type of the parameters 
must be specified in a prototype.
"nb_kernel334.h", line 101.1: 1506-033 (S) Function F77_FUNC_ is not 
valid. Function cannot return a function.
"nb_kernel334.h", line 101.1: 1506-282 (S) The type of the parameters 
must be specified in a prototype.
"nb_kernel400.h", line 63.1: 1506-033 (S) Function F77_FUNC_ is not 
valid. Function cannot return a function.
"nb_kernel400.h", line 63.1: 1506-282 (S) The type of the parameters 
must be specified in a prototype.
"nb_kernel400.h", line 101.1: 1506-033 (S) Function F77_FUNC_ is not 
valid. Function cannot return a function.
"nb_kernel400.h", line 101.1: 1506-282 (S) The type of the parameters 
must be specified in a prototype.
"nb_kernel410.h", line 63.1: 1506-033 (S) Function F77_FUNC_ is not 
valid. Function cannot return a function.
"nb_kernel410.h", line 63.1: 1506-282 (S) The type of the parameters 
must be specified in a prototype.
"nb_kernel410.h", line 101.1: 1506-033 (S) Function F77_FUNC_ is not 
valid. Function cannot return a function.
"nb_kernel410.h", line 101.1: 1506-282 (S) The type of the parameters 
must be specified in a prototype.
"nb_kernel420.h", line 63.1: 1506-033 (S) Function F77_FUNC_ is not 
valid. Function cannot return a function.
"nb_kernel420.h", line 63.1: 1506-282 (S) The type of the parameters 
must be specified in a prototype.
"nb_kernel420.h", line 63.1: 1506-343 (S) Redeclaration of F77_FUNC_ 
differs from previous declaration on line 101 of "nb_kernel410.h".
"nb_kernel420.h", line 63.1: 1506-050 (I) Return type 
"void(int*,int*,int*,int*,int*,float*,float*,int*,float*,float*,float*,float*,float*,float*,float*,int*,int*,float*,float*,float*,float*,float*,float*,float*,float*,int*,int*,void*,int*,int*)" 
in redeclaration is not compatible with the previous return type 
"void(int*,int*,int*,int*,int*,float*,float*,int*,float*,float*,float*,float*,float*,float*,float*,int*,int*,float*,float*,float*,float*,float*,float*,float*,float*,int*,int*,void*,int*,int*,float*)".
"nb_kernel420.h", line 100.1: 1506-033 (S) Function F77_FUNC_ is not 
valid. Function cannot return a function.
"nb_kernel420.h", line 100.1: 1506-282 (S) The type of the parameters 
must be specified in a prototype.
"nb_kernel430.h", line 63.1: 1506-033 (S) Function F77_FUNC_ is not 
valid. Function cannot return a function.
"nb_kernel430.h", line 63.1: 1506-282 (S) The type of the parameters 
must be specified in a prototype.
"nb_kernel430.h", line 101.1: 1506-033 (S) Function F77_FUNC_ is not 
valid. Function cannot return a function.
"nb_kernel430.h", line 101.1: 1506-282 (S) The type of the parameters 
must be specified in a prototype.
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.
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 don't really know how to do this :-(

Le 16/04/2010 20:43, Chris Neale a écrit :
> Dear Sebastien:
>
> Perhaps it's obvious, but can you confirm that you used the 
> compilation options that I posted? My suggestion was not so much that 
> you should try to compile 4.0.4 but that you should try the options 
> that I posted. So if you used your original compilation commands with 
> gromacs version 4.0.4 then I am not surprised that it also failed to 
> compile... please go back and attempt with the commands that I provided.
>
> If, however, you did try those options (and on v4.0.4) then I am sorry 
> to say that I'm no expert at compilation -- a previous colleague 
> worked out that AIX compillation for me and I'm just passing along 
> what worked for me.
>
> Regarding the fftw question, I am sorry but that too I can not answer.
>
> Chris.
>
> -- original message --
>
> 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 
> <http://lists.gromacs.org/mailman/listinfo/gmx-users> 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
> />/
> />/ /

-------------- next part --------------
A non-text attachment was scrubbed...
Name: sebastien_morin.vcf
Type: text/x-vcard
Size: 357 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100420/aaf7849f/attachment.vcf>