Yes, you should compile all of AmberTools before you try to build amber. On
top of compiling netcdf, it also places the header files and libraries in a
location that sander expects to find it ($AMBERHOME/lib, $AMBERHOME/include,
etc.). Just building netcdf without having the AmberTools configure and
Makefiles handle it makes compiling amber much more difficult.
Hope this helps,
Jason
On Thu, Jan 13, 2011 at 9:42 PM, Yubo Fan <pengpengtadie.gmail.com> wrote:
> The $AMBERHOME/lib is empty. I tried to copy all files under
> NETCDF/lib to there but still got the same error message. NETCDF was
> compiled successfully at /users/yf4/APPS/AMBER10/NETCDF and pmemd was
> also compiled successfully with netcdf. sander was successfully
> compiled without netcdf. The config.h for pmemd is:
> MATH_DEFINES =
> MATH_LIBS =
> MATH_DEFINES = -DMASSV
> #MATH_LIBS = -L/opt/apps/ibm/xlmass/6.1/lib64 -lmassvp6_64 -lmass_64
> MATH_LIBS = -L/opt/apps/ibm/xlmass/6.1/lib64 -lmassvp7_64
> DIRFRC_DEFINES = -DDIRFRC_EFS -DIRFRC_COMTRANS
> F90 = /users/yf4/UTILS/OPENMPI/1.4.3/bin/mpif90
> CC = /users/yf4/UTILS/OPENMPI/1.4.3/bin/mpicc
> LOAD = /users/yf4/UTILS/OPENMPI/1.4.3/bin/mpif90
> IBM_PROCESSOR_TYPE = pwr7
> FFT_DEFINES = -DPUBFFT
> FFT_INCLUDE =
> FFT_LIBS =
> NETCDF_HOME = /users/yf4/APPS/AMBER10/NETCDF
> NETCDF_DEFINES = -DBINTRAJ
> NETCDF_MOD = netcdf.mod
> NETCDF_LIBS = /users/yf4/APPS/AMBER10/NETCDF/lib/libnetcdf.a
> # DIRFRC_DEFINES are set in configure script!
> MPI_DEFINES = -DMPI
> MPI_INCLUDE = -I/users/yf4/UTILS/OPENMPI/1.4.3/include
> MPI_LIBS = -L/users/yf4/UTILS/OPENMPI/1.4.3/lib
>
> CPP = /opt/apps/ibm/xlf/13.1/exe/cpp -P
> CPPFLAGS =
> F90_DEFINES = -DNO_C_UNDERSCORE -DUSE_MPI_MODULE="use mpi"
>
> MODULE_SUFFIX = mod
> CPUFLAGS = -qarch=$(IBM_PROCESSOR_TYPE) -qtune=$(IBM_PROCESSOR_TYPE)
> F90FLAGS = $(CPUFLAGS) -qsuffix=f=f90 -qdpc -c
> F90_OPT_DBG = -g -O0
> F90_OPT_LO = -qmaxmem=-1
> F90_OPT_MED = -qmaxmem=-1 -O
> F90_OPT_HI = -O3 -qstrict -qhot
> F90_OPT_DFLT = $(F90_OPT_HI)
>
> CFLAGS = $(CPUFLAGS) -DNO_C_UNDERSCORE
>
> LOADFLAGS = -O3 -qdpc -qhot
> LOADLIBS = -lm
>
> I think the module has not been loaded into the compilation. Do I need
> to compile the whole package of AmberTools before I compile sander? I
> only compiled netcdf.
>
> Best,
> Yubo
>
> On Thu, Jan 13, 2011 at 5:11 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > Did netcdf compile successfully? (look for libnetcdf.a or something in
> > $AMBERHOME/lib).
> >
> > On Thu, Jan 13, 2011 at 6:01 PM, Yubo Fan <pengpengtadie.gmail.com>
> wrote:
> >
> >> Hello,
> >>
> >> When compile Amber 10 on an IBM Power7 computer, it failed with:
> >> 1501-510 Compilation successful for file _ncsu-pmd-hooks.f.
> >> touch netcdf.o
> >> /opt/apps/ibm/xlf/13.1/exe/cpp
> >> -I/users/yf4/UTILS/OPENMPI/1.4.3/include -P -DCLINK_PLAIN -DXLF90
> >> -DBINTRAJ -DMPI ncsu-umbrella.f > _ncsu-umbrella.f
> >> /users/yf4/UTILS/OPENMPI/1.4.3/bin/mpif90 -c -qfixed -O3 -qmaxmem=-1
> >> -qarch=auto -qtune=auto -qfree=f90 -o ncsu-umbrella.o
> >> _ncsu-umbrella.f
> >> "_ncsu-umbrella.f", line 63.5: 1514-219 (S) Unable to access module
> >> symbol file for module netcdf. Check path and file permissions of
> >> file. Use association not done for this module.
> >> 1501-511 Compilation failed for file _ncsu-umbrella.f.
> >> make: *** [ncsu-umbrella.o] Error 1
> >>
> >> The config.h file is shown below:
> >>
> >>
> #==============================================================================
> >> # AMBER Makefile configuration for compiler/architecture: xlf90_suse
> >> # Generated via command: ./configure_amber -openmpi xlf90_suse
> >> #
> >> # Configuration script written mainly by Joe Krahn, Scott Brozell, and
> >> # Dave Case, with contributions from lots of people.
> >>
> >>
> #==============================================================================
> >>
> >>
> >>
> #------------------------------------------------------------------------------
> >> # AMBERBUILDFLAGS provides a hook into the build process for installers;
> >> # for example, to build debug versions of the amber programs
> >> # make -e AMBERBUILDFLAGS="-DDEBUG -g"
> >>
> >>
> #------------------------------------------------------------------------------
> >> AMBERBUILDFLAGS=
> >>
> >>
> >>
> #------------------------------------------------------------------------------
> >> # LOCALFLAGS is intended for program specific modifications to the
> >> # Fortran build process and may be modified by the program's local
> makefile
> >>
> >>
> #------------------------------------------------------------------------------
> >> LOCALFLAGS=
> >>
> >>
> >>
> #------------------------------------------------------------------------------
> >> # Availability and method of delivery of math and optional libraries
> >>
> >>
> #------------------------------------------------------------------------------
> >> USE_BLASLIB=$(SOURCE_COMPILED)
> >> USE_LAPACKLIB=$(SOURCE_COMPILED)
> >>
> >>
> >>
> #------------------------------------------------------------------------------
> >> # C compiler
> >>
> >>
> #------------------------------------------------------------------------------
> >> CC= xlc
> >> CPLUSPLUS=xlC
> >> CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2
> $(AMBERBUILDFLAGS)
> >> CPPFLAGS=-DCLINK_PLAIN -DBINTRAJ
> >> -I/users/yf4/APPS/AMBER10/NETCDF/include $(AMBERBUILDFLAGS)
> >>
> >>
> >>
> #------------------------------------------------------------------------------
> >> # Fortran preprocessing and compiler.
> >> # FPPFLAGS holds the main Fortran options, such as whether MPI is used.
> >>
> >>
> #------------------------------------------------------------------------------
> >> FPPFLAGS= -I/users/yf4/UTILS/OPENMPI/1.4.3/include -P -DCLINK_PLAIN
> >> -DXLF90 -DBINTRAJ -DMPI $(AMBERBUILDFLAGS)
> >> FPP= /opt/apps/ibm/xlf/13.1/exe/cpp $(FPPFLAGS)
> >> FC= /users/yf4/UTILS/OPENMPI/1.4.3/bin/mpif90
> >> FFLAGS= -qfixed $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> >> FOPTFLAGS= -qfixed -O3 -qmaxmem=-1 -qarch=auto -qtune=auto
> >> $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> >> FREEFORMAT_FLAG= -qfree=f90
> >>
> >>
> >>
> #------------------------------------------------------------------------------
> >> # Loader:
> >>
> >>
> #------------------------------------------------------------------------------
> >> LOAD= /users/yf4/UTILS/OPENMPI/1.4.3/bin/mpif90 $(LOCALFLAGS)
> >> $(AMBERBUILDFLAGS)
> >> LOADCC= xlc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> >> LOADLIB=
> >> LM= -lm
> >> XHOME= /usr/X11R6
> >> XLIBS= -L/usr/X11R6/lib
> >>
> >>
> >>
> #------------------------------------------------------------------------------
> >> # Other stuff:
> >>
> >>
> #------------------------------------------------------------------------------
> >> .SUFFIXES: .f90
> >> EMPTY=
> >> AR=ar rvs $(EMPTY)
> >> M4=m4
> >> RANLIB=/bin/true
> >> SFX=
> >> NETCDF=/users/yf4/APPS/AMBER10/NETCDF
> >> NETCDFLIB=/users/yf4/APPS/AMBER10/NETCDF/lib/libnetcdf.a
> >> MODULEDIR=-I
> >> testsanderDIVCON=test.sander.DIVCON
> >> INCDIVCON=divcon
> >> LIBDIVCON=../dcqtp/src/qmmm/libdivcon.a
> >>
> >> # Location for executables, etc:
> >>
> >> BINDIR=/users/yf4/APPS/AMBER10/AMBER10/amber10/bin
> >> LIBDIR=/users/yf4/APPS/AMBER10/AMBER10/amber10/lib
> >> INCDIR=/users/yf4/APPS/AMBER10/AMBER10/amber10/include
> >> DATDIR=/users/yf4/APPS/AMBER10/AMBER10/amber10/dat
> >>
> >> # default rules for Fortran and C compilation:
> >>
> >> .f.o: $<
> >> $(FPP) $< > _$<
> >> $(FC) -c $(FFLAGS) -o $. _$<
> >>
> >> .c.o:
> >> $(CC) -c $(CFLAGS) $(CPPFLAGS) -o $. $<
> >>
> >>
> >> The problem looks like the compilation failed to find NETCDF.
> >>
> >> Any suggestion?
> >>
> >> Sincerely,
> >> Yubo
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Jan 13 2011 - 20:30:01 PST
