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 successso 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.ne...@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 5.3If 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 compilationexport 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/binexport 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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