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
>
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Received on Thu Jan 13 2011 - 19:00:03 PST
