So what is the original error without editing anything? I am a bit confused.
Hai
On Thu, Sep 14, 2017 at 4:30 PM Timothy Schutt <tschutt.mymail.mines.edu>
wrote:
> Hi!
>
> I'm trying to install amber16 on a new HPC system and have been trying a
> wide variety of compilers and environment modules with no success yet. Any
> tips or advice you might be able to give for a CRAY XC40/50 system? I asked
> the HPC helpdesk here for help and they struggled as well saying:
>
>
>
> "I reached a dead-end, as shown below.
>
> module swap PrgEnv-cray PrgEnv-intel
> module unload intel
> export INTEL_VERSION=17.0.1.132
> module load intel/${INTEL_VERSION}
> # Intel compiler affected by which gcc/g++ that it finds export
> GNU_VERSION=6.3.0 module load gcc/${GNU_VERSION} export
> COMPILER_VERSION=$INTEL_VERSION export COMPILER_TYPE=intel
>
> module load fftw/3.3.4.11
> module load cray-netcdf/4.4.1.1
> module load cray-hdf5/1.10.0.1
>
> export CRAYPE_LINK_TYPE=dynamic
>
> export MKL_HOME=$MKLROOT
>
> export AMBERHOME=
>
> ./configure -nofftw3 -noX11 --with-netcdf $NETCDF_DIR cray install patches
> y install python y
>
> source ${AMBERHOME}/amber.sh
>
> Edit ${AMBERHOME}/AmberTools/src/config.h
> Change from
> FREEFORMAT_FLAG= -f free
> Change to
> FREEFORMAT_FLAG= -free
> Change from
> FFLAGS= -fPIC -h noomp -emf $(LOCALFLAGS) $(CUSTOMBUILDFLAGS) -I$(INCDIR)
> $(NETCDFINC)
> -I/opt/intel/compilers_and_libraries_2017.1.132/linux/mkl/include
> $(AMBERBUILDFLAGS) Change to (no -emf) FFLAGS= -fPIC -h noomp $(LOCALFLAGS)
> $(CUSTOMBUILDFLAGS) -I$(INCDIR) $(NETCDFINC) -I/opt/intel/compilers_and_
> libraries_2017.1.132/linux/mkl/include $(AMBERBUILDFLAGS)
>
> Edit ${AMBERHOME}/AmberTools/src/cpptraj/config.h
> Different line, same change, "-f free" => "-free" and remove "-emf"
>
> The problem with the above is, perhaps, that the developers are confusing
> the Cray compiler with the Cray wrappers that can wrap the Intel compiler.
>
> make install 2>&1 | tee install2.log
>
> make[3]: Entering directory '/p/home/scheinin/tschutt7/
> amber16/AmberTools/src/mmpbsa_py'
> /p/home/scheinin/tschutt7/amber16/bin/nab -o
> /p/home/scheinin/tschutt7/amber16/bin/mmpbsa_py_nabnmode
> mmpbsa_entropy.nab
> ld: cannot find -lpbsa
> Makefile:12: recipe for target '/p/home/scheinin/tschutt7/
> amber16/bin/mmpbsa_py_nabnmode' failed
>
> cd ./AmberTools/src/pbsa
> make libpbsa.a
>
> cd ${AMBERHOME}
> cp ./AmberTools/src/pbsa/libpbsa.a lib/
>
> make install 2>&1 | tee install2.log
>
> ftn -h noomp -emf -o /p/home/scheinin/tschutt7/amber16/bin/pmemd
> gbl_constants.o gbl_datatypes.o state_info.o [ ... much more ]
>
> defineTopo.C:(.text+0xac9): undefined reference to `std::basic_ostream >&
> std::operator<< >(std::basic_ostream >&, char const*)'
> [ ... and many, many more errors ]
>
> This is crazy, I do not see any solution. "ftn" is being used to link
> object files built with C++. That will not work.
>
> Please contact the Amber developers."
>
>
>
> Thanks! Please let me know if you have any ideas how to get this installed
> correctly, and Sorry I'm such a noob at troubleshooting these kinds of
> things. Thanks!
>
> -Tim
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>
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Received on Thu Sep 14 2017 - 14:00:04 PDT
