[gmx-users] Compiling Gromacs 4.0.7 on AIX 5.3

Tue Apr 20 14:20:50 CEST 2010

I've never worked with such architecture, but I do remember seeing a few posts 
in the past, some of which may be useful.  Perhaps this one will hold some clues:

http://lists.gromacs.org/pipermail/gmx-users/2007-April/027074.html

Sorry I can't provide much more than this, but I thought I'd at least mention it.

-Justin

Sebastien Morin wrote:
> 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 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
>> />/
>> />/ /
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================