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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Received on Thu Sep 14 2017 - 14:00:03 PDT
