Thanks for the suggestions !!!
"./configure gnu" followed by "make install", I am now getting another
error as follows:
make[2]: Entering directory `/opt/amber12/AmberTools/src/pbsa'
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o dsvdc.o dsvdc.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o timer.o timer.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o decomp.o decomp.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o pbsa.o pbsa.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o sa_driver.o
sa_driver.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o pb_force.o pb_force.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o np_force.o np_force.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o pb_read.o pb_read.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o pb_write.o pb_write.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o getcoor.o getcoor.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o runmd.o runmd.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o runmin.o runmin.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o egb.o egb.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o force.o force.F90
gfortran -DFFTW -DBINTRAJ -c -O0 -ffree-form -I/opt/amber12/include
-I/opt/amber12/include -o pb_init.o pb_init.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o pb_lsolver.o
pb_lsolver.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o pb_nlsolver.o
pb_nlsolver.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o pb_fddrv.o pb_fddrv.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o pb_iimdrv.o
pb_iimdrv.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o pb_exmol.o pb_exmol.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o pb_mpfrc.o pb_mpfrc.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o pb_direct.o
pb_direct.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o pb_list.o pb_list.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o pb_fftsolv.o
pb_fftsolv.F90
gfortran -DFFTW -DBINTRAJ -c -O3 -mtune=native -ffree-form
-I/opt/amber12/include -I/opt/amber12/include -o fftw3.o fftw3.F90
fftw3.F90:10: Error: Can't open included file 'fftw3.f03'
make[2]: *** [fftw3.o] Error 1
make[2]: Leaving directory `/opt/amber12/AmberTools/src/pbsa'
make[1]: *** [serial] Error 2
make[1]: Leaving directory `/opt/amber12/AmberTools/src'
make: *** [install] Error 2
I am not sure whether the error is related to our previous discussion or
entirely different thread is needed.
Re-installed the fftw3, however the error remains the same.
The config.h for your reference is as follows:
# Amber configuration file, created with: ./configure gnu
###############################################################################
# (1) Location of the installation
BASEDIR=/opt/amber12
BINDIR=/opt/amber12/bin
LIBDIR=/opt/amber12/lib
INCDIR=/opt/amber12/include
DATDIR=/opt/amber12/dat
LOGDIR=/opt/amber12/logs
###############################################################################
# (2) If you want to search additional libraries by default, add them
# to the FLIBS variable here. (External libraries can also be linked
into
# NAB programs simply by including them on the command line; libraries
# included in FLIBS are always searched.)
FLIBS= -lsff -lpbsa -lrism -lfftw3 -larpack -llapack -lblas
-L$(BASEDIR)/lib -lnetcdf -lgfortran -w
FLIBS_PTRAJ= -larpack -llapack -lblas -lgfortran -w
FLIBSF= -larpack -llapack -lblas
FLIBS_FFTW3= -lfftw3
###############################################################################
# (3) Modify any of the following if you need to change, e.g. to use gcc
# rather than cc, etc.
SHELL=/bin/sh
INSTALLTYPE=serial
BUILDAMBER=amber
# Set the C compiler, etc.
# The configure script should be fine, but if you need to hand-edit,
# here is some info:
# Example: CC-->gcc; LEX-->flex; YACC-->yacc (built in byacc)
# Note: If your lexer is "really" flex, you need to set
# LEX=flex below. For example, on some distributions,
# /usr/bin/lex is really just a pointer to /usr/bin/flex,
# so LEX=flex is necessary. In general, gcc seems to need flex.
# The compiler flags CFLAGS and CXXFLAGS should always be used.
# By contrast, *OPTFLAGS and *NOOPTFLAGS will only be used with
# certain files, and usually at compile-time but not link-time.
# Where *OPTFLAGS and *NOOPTFLAGS are requested (in Makefiles,
# makedepend and depend), they should come before CFLAGS or
# CXXFLAGS; this allows the user to override *OPTFLAGS and
# *NOOPTFLAGS using the BUILDFLAGS variable.
# AMBERBUILDFLAGS provides a hook into all stages of the build process.
# It can be used to build debug versions, invoke special features, etc.
# Example: make AMBERBUILDFLAGS='-O0 -g' sander
#
CC=gcc
CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
-DHASBZ2 $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
CNOOPTFLAGS=
COPTFLAGS=-O3 -mtune=native
AMBERCFLAGS= $(AMBERBUILDFLAGS)
CXX=g++
CPLUSPLUS=g++
CXXFLAGS= $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
CXXNOOPTFLAGS=
CXXOPTFLAGS=-O3
AMBERCXXFLAGS= $(AMBERBUILDFLAGS)
NABFLAGS= $(AMBERBUILDFLAGS)
PBSAFLAG=-DFFTW $(AMBERBUILDFLAGS)
LDFLAGS= $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
AMBERLDFLAGS=$(AMBERBUILDFLAGS)
LEX= flex
YACC= $(BINDIR)/yacc
AR= ar rv
M4= m4
RANLIB=ranlib
# Set the C-preprocessor. Code for a small preprocessor is in
# ucpp-1.3; it gets installed as $(BINDIR)/ucpp;
CPP=ucpp -l
# These variables control whether we will use compiled versions of BLAS
# and LAPACK (which are generally slower), or whether those libraries are
# already available (presumably in an optimized form).
LAPACK=install
BLAS=install
F2C=skip
# These variables determine whether builtin versions of certain components
# can be used, or whether we need to compile our own versions.
UCPP=install
C9XCOMPLEX=skip
# For Windows/cygwin, set SFX to ".exe"; for Unix/Linux leave it empty:
# Set OBJSFX to ".obj" instead of ".o" on Windows:
SFX=
OSFX=.o
MV=mv
RM=rm
CP=cp
# Information about Fortran compilation:
FC=gfortran
FFLAGS= $(LOCALFLAGS) $(CUSTOMBUILDFLAGS) -I$(INCDIR) $(NETCDFINC)
$(AMBERBUILDFLAGS)
FNOOPTFLAGS= -O0
FOPTFLAGS= -O3 -mtune=native
AMBERFFLAGS=$(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -ffree-form
LM=-lm
FPP=cpp -traditional -P
FPPFLAGS= -DBINTRAJ $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
AMBERFPPFLAGS=$(AMBERBUILDFLAGS)
FCREAL8=-fdefault-real-8
XHOME= /usr
XLIBS= -L/usr/lib/x86_64-linux-gnu -L/usr/lib64 -L/usr/lib
MAKE_XLEAP=install_xleap
NETCDF=$(BASEDIR)/include/netcdf.mod
NETCDFLIB=-L$(BASEDIR)/lib -lnetcdf
NETCDFINC=-I$(BASEDIR)/include
PNETCDF=
PNETCDFLIB=
FFTWLIB=-lfftw3
ZLIB=-lz
BZLIB=-lbz2
HASFC=yes
MTKPP=install_mtkpp
XBLAS=$(LIBDIR)/libxblas-amb.a
FFTW3=$(LIBDIR)/libfftw3.a
MDGX=yes
COMPILER=gnu
MKL=
MKL_PROCESSOR=
#CUDA Specific build flags
NVCC=
PMEMD_CU_INCLUDES=
PMEMD_CU_LIBS=
PMEMD_CU_DEFINES=
#PMEMD Specific build flags
PMEMD_F90=gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT
PMEMD_FOPTFLAGS=-O3 -mtune=native $(AMBERBUILDFLAGS)
PMEMD_CC=gcc
PMEMD_COPTFLAGS=-O3 -mtune=native -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ $(AMBERBUILDFLAGS)
PMEMD_FLIBSF=
PMEMD_LD= gfortran $(AMBERBUILDFLAGS)
LDOUT= -o
#for NAB:
MPI=
#1D-RISM
RISM=yes
#3D-RISM NAB
RISMSFF=-DRISMSFF
SFF_RISM_INTERFACE=../rism/amber_rism_interface.NAB.o
TESTRISMSFF=testrism
#3D-RISM SANDER
RISMSANDER=
SANDER_RISM_INTERFACE=
FLIBS_RISMSANDER=
TESTRISMSANDER=
#PUPIL
PUPILLIBS=-lrt -lm -lc -L${PUPIL_PATH}/lib -lPUPIL -lPUPILBlind
#Python interpreter we are using
PYTHON=/usr/bin/python2.7
Any suggestions please !!
Thank you.
-- Joshi
On Fri, Nov 1, 2013 at 2:36 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Oct 31, 2013 at 9:45 AM, David A Case <case.biomaps.rutgers.edu
> >wrote:
>
> > On Thu, Oct 31, 2013, Jason Swails wrote:
> > >
> > > cp /opt/amber12/lib64/* /opt/amber12/lib
> > >
> > > These should probably be simlinked to each other...
> >
> > They already should be symlinked to each other (see e.g. line 2364 of
> > configure2). So I'm wondering if the "cannot find -lnetcdf" has some
> other
> > origin.
> >
>
> I thought they were. The simlink must have been removed at some point if
> the OP really did see libnetcdf.a in lib64/ and not lib/. Based on the
> information we have I'm having a hard time figuring out exactly what
> happened (and what was done to cause it).
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> 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
Received on Thu Oct 31 2013 - 21:00:02 PDT
