Hello again I followed your advices this time
here's what I did : downloading gromacs 4.0.7 downloading fftw 2.1.5initializing 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 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 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 />/ />/ /
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