Thank you for the suggestions.
Unfortunately, I don't have Intel compiles right now, therefore, tried
installation with gnu.
The argument I gave to configure is: ./configure gnu
As per the David's suggestion, I make uninstall and then configured and
compiled again with the above argument.
Following is the error message I got:
Warning: Type mismatch in argument 'c' at (1); passed COMPLEX(8) to REAL(8)
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
-DHASBZ2 -I/opt/amber12/include -o cluster.o cluster.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
-DHASBZ2 -I/opt/amber12/include -o clusterLib.o clusterLib.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
-DHASBZ2 \
-o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o io.o
trajectory.o netcdf_ptraj.o parallel_ptraj.o evec.o torsion.o mask.o rms.o
display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o
thermo.o pubfft.o cluster.o clusterLib.o -L/opt/amber12/lib -lpdb -larpack
-llapack -lblas -lgfortran -w -L/opt/amber12/lib -lnetcdf -lm
/usr/bin/ld: cannot find -lnetcdf
collect2: error: ld returned 1 exit status
make[2]: *** [rdparm] Error 1
make[2]: Leaving directory `/opt/amber12/AmberTools/src/ptraj'
make[1]: *** [serial] Error 2
make[1]: Leaving directory `/opt/amber12/AmberTools/src'
make: *** [install] Error 2
The configure.h file 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
I still could not figure out where the things went wrong...
Thank you !!
-- Joshi
On Wed, Oct 30, 2013 at 7:52 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Wed, Oct 30, 2013, Dhananjay wrote:
> >
> > I got an error message while installing amber on newly installed Debian
> > 7.0.
>
> What compiler are you using? What arguments did you give to configure?
> Posting your resulting config.h file might help.
>
> Also, had you compiled earlier with and different compiler? (e.g. before
> you
> installed the new OS)? You might try typing "make uninstall" (in
> $AMBERHOME),
> then configuring and compiling again. Use "gnu" as the compiler suite if
> you
> are not already doing that (or even if you are!)
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Oct 31 2013 - 04:30:02 PDT
