the sequence of my actions was
patch -p0 -N < bugfix.all.at15
./apply_bugfix.x.a11 bugfix.1to17.tar.bz2
compiling of serial and parallel, with 'make clean' command after each step
python AT15_Amber11.py
and then ld linking will fail without additional flag(-s).
2011/8/24 Jason Swails <jason.swails.gmail.com>
> Make sure all bug fixes are applied. If this is the recent patch
> bugfix.1to17.tar.bz2, then you also need to fully patch AmberTools 1.5 (the
> Amber 11 patch should print out a message to that extent). There were
> changes to configure necessary to the new pmemd.cuda patch.
>
> HTH,
> Jason
> >
> > The solution was (applying after the configuration with -cuda flag)
> > uname -a | grep 'fc14.x86_64' >/dev/null 2>&1
> > if [ $? -eq 0 ]; then
> > echo
> > echo DM PATCH2 on a11
> > echo -n "Patching $AMBERHOME/src/config.h "
> > sed -i 's[PMEMD_CU_LIBS=-L$(CUDA_HOME)/lib64
> > -L$(CUDA_HOME)/lib[PMEMD_CU_LIBS=-L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib
> > -L/usr/lib64 -lstdc++[' $AMBERHOME/src/config.h
> > echo
> > fi
> >
> > --
> > Sincerely,
> > Dmitry Mukha
> > Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Sincerely,
Dmitry Mukha
Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 24 2011 - 06:00:05 PDT
