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
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Received on Thu Jan 13 2011 - 15:30:05 PST
