Hi Hai,
Sorry for the slow response, I had to start over setting up the
environment, configuring, and 'make install' to get all the details of the
error. This might be way more information than necessary or useful; if so,
I apologize.
I started by loading module files for cray-netCDF and fftw3. Then as per
instructions from the configure help I ran:
> ./configure -nofftw3 -noX11 --with-netcdf /opt/cray/pe/netcdf/
4.4.1.1/cray/8.3 --skip-python cray
this ran successfully with lots of "OK"s and said configuration successful.
Then I ran:
> source amber.sh
> make install
which ran for a long time displaying all sorts of things I didn't
understand, completed amber tools, just starts amber and reaches the error:
Installation of AmberTools17 serial (cray) is complete at Thu Sep 14
16:51:30 CDT 2017.
make[1]: Leaving directory '/p/home/tschutt7/Software/
amber16/AmberTools/src'
make[1]: Entering directory '/p/home/tschutt7/Software/amber16/src'
Starting installation of Amber16 (serial) at Thu Sep 14 16:51:30 CDT 2017.
cd pmemd && make install
make[2]: Entering directory '/p/home/tschutt7/Software/amber16/src/pmemd'
make -C src/ install
make[3]: Entering directory '/p/home/tschutt7/Software/
amber16/src/pmemd/src'
ftn -DBINTRAJ -DEMIL -DFFTW_FFT -h noomp -emf -I/opt/cray/pe/netcdf/
4.4.1.1/cray/8.3//include -c gbl_constants.F90
ftn -DBINTRAJ -DEMIL -DFFTW_FFT -h noomp -emf -I/opt/cray/pe/netcdf/
4.4.1.1/cray/8.3//include -c gbl_datatypes.F90
ftn -DBINTRAJ -DEMIL -DFFTW_FFT -h noomp -emf -I/opt/cray/pe/netcdf/
4.4.1.1/cray/8.3//include -c state_info.F90
ftn -DBINTRAJ -DEMIL -DFFTW_FFT -h noomp -emf -I/opt/cray/pe/netcdf/
4.4.1.1/cray/8.3//include -c file_io_dat.F90
ftn -DBINTRAJ -DEMIL -DFFTW_FFT -h noomp -emf -I/opt/cray/pe/netcdf/
4.4.1.1/cray/8.3//include -c pmemd_lib.F90
ftn -DBINTRAJ -DEMIL -DFFTW_FFT -h noomp -emf -I/opt/cray/pe/netcdf/
4.4.1.1/cray/8.3//include -c parallel_dat.F90
module parallel_dat_mod
^
ftn-855 crayftn: ERROR PARALLEL_DAT_MOD, File = parallel_dat.F90, Line =
11, Column = 8
The compiler has detected errors in module "PARALLEL_DAT_MOD". No module
information file will be created for this module.
/*precision setting for SPDP, DPDP, SPSP*/
^
ftn-100 crayftn: ERROR PARALLEL_DAT_MOD, File = parallel_dat.F90, Line =
18, Column = 1
This statement must begin with a label, a keyword, or an identifier.
Cray Fortran : Version 8.5.7 (20170117205456_0ba2aebdef39707eeacb0698e4e05a
28a8a8b4d5)
Cray Fortran : Thu Sep 14, 2017 16:51:31
Cray Fortran : Compile time: 0.0120 seconds
Cray Fortran : 487 source lines
Cray Fortran : 2 errors, 0 warnings, 0 other messages, 0 ansi
Cray Fortran : "explain ftn-message number" gives more information about
each message.
Makefile:165: recipe for target 'parallel_dat.o' failed
make[3]: *** [parallel_dat.o] Error 1
make[3]: Leaving directory '/p/home/tschutt7/Software/amber16/src/pmemd/src'
Makefile:21: recipe for target 'serial' failed
make[2]: *** [serial] Error 2
make[2]: Leaving directory '/p/home/tschutt7/Software/amber16/src/pmemd'
Makefile:27: recipe for target 'serial' failed
make[1]: *** [serial] Error 2
make[1]: Leaving directory '/p/home/tschutt7/Software/amber16/src'
Makefile:7: recipe for target 'install' failed
make: *** [install] Error 2
Alternatively, when I try and use the gnu or intel compilers I can't get
past the configuration step. I swap out all the environment modules for
each respectively but the NetCDF fails as indicated here:
Checking NetCDF...
Using bundled NetCDF library.
Starting NetCDF build.
Configuring NetCDF C interface (may be time-consuming)...
Compiling the NetCDF C interface (may be time-consuming)...
Error: NetCDF C compile failed.
Check /p/home/tschutt7/Software/Try2amber16/amber16/
AmberTools/src/netcdf-4.3.0/netcdf.c.compile.log
for errors.
Configure failed due to the errors above!
So that's when I started asking for help and I've included Alan, from the
HPC helpdesk here in this email chain now. He's the one who knows computers
and compilers way better than me and came across the link object files
thing. Alan, what was the full error when you tried to install?
-Tim
On Thu, Sep 14, 2017 at 3:39 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Sep 14 2017 - 15:30:03 PDT
