[Dock-fans] dock6 parallel on 64-bit system

Scott Brozell sbrozell at scripps.edu
Tue Dec 23 13:06:27 PST 2008


Hi,

>From your dock6.64.make.log:

/usr/bin/ld: warning: i386 architecture of input file `amber_typer.o' is incompatible with i386:x86-64 output

These are the underlying problems.
And they may be resolved by adding -m32 to the link stage:
LOAD=        $(MPICH_HOME)/bin/mpicxx -m32

This is probably unnecessary but prudent:
CXX=         $(MPICH_HOME)/bin/mpicxx -m32

On Mon, 22 Dec 2008, Mary Ellen Fitzpatrick wrote:

> If I install dock6 parallel on the 64-bit system without the -m32
> compiler flag, it installs without a problem.  But I am unclear if the
> results from the test suite are accurate.

I should've mentioned that this is what I do.
I have not had problems.
I do not use Zou GB/SA score.

Scott

On Tue, 23 Dec 2008, Mary Ellen Fitzpatrick wrote:

Starting installation of 
DOCK v6.2
at Tue Dec 23 12:48:21 EST 2008.

cd ../src && make install
make[1]: Entering directory `/home/mef/dock6/src'
cd dock && make install
make[2]: Entering directory `/home/mef/dock6/src/dock'
g++ -m32 -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/usr/local/mpich2mef/include -O2 -o amber_typer.o  amber_typer.cpp
...
cd nab && make all
make[3]: Entering directory `/home/mef/dock6/src/dock/nab'
gcc -m32  -c -O3 -D_ANSI_SOURCE  molio.c
gcc -m32  -c  -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/usr/local/mpich2mef/include -O2 -o prm.o  prm.c
...
ranlib nab.a
make[3]: Leaving directory `/home/mef/dock6/src/dock/nab'
/usr/local/mpich2mef/bin/mpicxx -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I/usr/local/mpich2mef/include -O2 -o dock6.mpi amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen.o dock.o dockmol.o grid.o library_file.o master_score.o orient.o score.o simplex.o sphere.o score_solvent.o score_amber.o sasa.o score_chemgrid.o utils.o trace.o nab/nab.a -lm -L/usr/local/mpich2mef/lib -lmpich -lpthread  
/usr/bin/ld: warning: i386 architecture of input file `amber_typer.o' is incompatible with i386:x86-64 output
...
amber_typer.o: In function `AMBER_TYPER::prepare_molecule(DOCKMol&, bool, bool)':
amber_typer.cpp:(.text+0x22fb): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::assign(char const*, unsigned int)'
...


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