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

Scott Brozell sbrozell at scripps.edu
Tue Dec 23 09:37:05 PST 2008


Hi,

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

> Here is how I am trying to build dock6 on a 64-bit system.  Same build error,
> not sure what I am doing wrong...

> make all

Where is the complete verbatim output from make all ?
It will show the command to link dock6.mpi.


> userA:~/dock6/install$ mpicc -show
> gcc -I/usr/local/mpich2mef/include -L/usr/local/mpich2mef/lib -lmpich
> -lpthread -lrt
> userA:~/dock6/install$ mpicxx -show
> g++ -I/usr/local/mpich2mef/include -L/usr/local/mpich2mef/lib -lmpichcxx
> -lmpich -lpthread -lrt

This suggests that mpicxx is not the problem
assuming that $(MPICH_HOME)/bin/mpicxx is the same mpicxx as above.

Scott

> ./configure gnu.parallel
> edit config.h
> MPICH_HOME=/usr/local/mpich2mef
> CC=          gcc -m32
> CXX=         g++ -m32
> CFLAGS=      -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX
> -I$(MPICH_HOME)/includ
> e -O2
> FC=          g77 -m32
> FFLAGS=      -O2 -fno-automatic -fno-second-underscore
> LOAD=        $(MPICH_HOME)/bin/mpicxx
> LIBS=        -lm -L/usr/local/mpich2mef/lib -lmpich -lpthread -lrt
> SFX=         .mpi
> 
> > > utils.o: In function `std::vector<PARAMETER, std::allocator<PARAMETER> 
> > > > ::_M_insert_aux(__gnu_cxx::__normal_iterator<PARAMETER*, 
> > > std::vector<PARAMETER, std::allocator<PARAMETER> > >, PARAMETER const&)':
> > > utils.cpp:(.text._ZNSt6vectorI9PARAMETERSaIS0_EE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPS0_S2_EERKS0_[std::vector<PARAMETER,
> > > std::allocator<PARAMETER> 
> > > > ::_M_insert_aux(__gnu_cxx::__normal_iterator<PARAMETER*, 
> > > std::vector<PARAMETER, std::allocator<PARAMETER> > >, PARAMETER
> > > const&)]+0x164): undefined reference to `operator new(unsigned int)'
> > > collect2: ld returned 1 exit status
> > > make[2]: *** [dock6.mpi] Error 1
> > >     
> >
> > This error is very likely due to linking C++ object files with a C
> > (ie not C++) compiler.
> > Verify that your mpicxx invokes a C++ compiler via
> > mpicxx -show
> > or similar options.
> > If you cannot resolve this then send verbose and explicit details
> > especially the command to link dock6.mpi.


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