Jason,
Your Solution #1 appears to work just fine. AmberTools16 installed and
the tests are OK. Thanks!
Originally, my configuration command was
./configure -macAccelerate gnu
which yielded the following config.h:
# (1) Location of the installation
BASEDIR=/Users/JEAdams/amber16
BINDIR=/Users/JEAdams/amber16/bin
LIBDIR=/Users/JEAdams/amber16/lib
INCDIR=/Users/JEAdams/amber16/include
DATDIR=/Users/JEAdams/amber16/dat
LOGDIR=/Users/JEAdams/amber16/logs
###########################################################################
####
# (2) If you want NAB 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 -lnetcdf -lgfortran -w
-framework Accelerate
FLIBS_PTRAJ= -larpack -lgfortran -w -framework Accelerate
FLIBSF= -larpack -lxblas-amb -framework Accelerate
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=
# 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=-fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
-DHASBZ2 -D__PLUMED_HAS_DLOPEN $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
CNOOPTFLAGS=
COPTFLAGS=-O3 -mtune=native
AMBERCFLAGS= $(AMBERBUILDFLAGS)
WARNFLAGS=-Wall -Wno-unused-function
CXX=g++
CPLUSPLUS=g++
CXXFLAGS=-fPIC $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
CXXNOOPTFLAGS=
CXXOPTFLAGS=-fPIC -O3
AMBERCXXFLAGS= $(AMBERBUILDFLAGS)
NABFLAGS= $(AMBERBUILDFLAGS)
PBSAFLAG=-DFFTW $(AMBERBUILDFLAGS)
FP_FLAGS=
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=skip
BLAS=skip
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
WINE=
# Information about Fortran compilation:
FC=gfortran
FFLAGS= -fPIC $(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 -DEMIL $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
AMBERFPPFLAGS=$(AMBERBUILDFLAGS)
FCREAL8=-fdefault-real-8
NOFORTRANMAIN=-lgfortran -w -framework Accelerate
FWARNFLAGS=-Wall -Wno-unused-function
XHOME= /usr/X11R6
XLIBS= -L/usr/X11R6/lib64 -L/usr/X11R6/lib
MAKE_XLEAP=install_xleap
NETCDF=$(INCDIR)/netcdf.mod
NETCDFLIB=$(LIBDIR)/libnetcdf.a
NETCDFLIBF=$(LIBDIR)/libnetcdff.a $(LIBDIR)/libnetcdf.a
NETCDFINC=-I$(INCDIR)
PNETCDFLIB=
PNETCDFINC=
PNETCDFDEF=
FFTWLIB=-lfftw3
SANDERAPI_LIB=-L$(LIBDIR) -lsander
SANDERAPI_DEF=-DUSE_SANDERLIB
SANDERAPI_DEP=$(LIBDIR)/libsander$(SHARED_SUFFIX)
BUILD_SANDERAPI=build_sanderapi
EMIL=EMIL
EMILLIB=$(LIBDIR)/libemil.a -lstdc++
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=
READLINE=readline/libreadline.a
#CUDA Specific build flags
NVCC=
PMEMD_CU_INCLUDES=
PMEMD_CU_LIBS=
PMEMD_CU_DEFINES=
#PMEMD Specific build flags
PMEMD_F90=gfortran -DBINTRAJ -DEMIL -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= $(LIBDIR)/libemil.a -lstdc++
PMEMD_LD=gfortran $(AMBERBUILDFLAGS)
LDOUT= -o
PMEMD_GNU_BUG303=-fno-tree-vectorize
#for NAB:
MPI=
#1D-RISM
RISM=yes
#3D-RISM NAB
RISMSFF=-DRISMSFF
SFF_RISM_INTERFACE=../rism/amber_rism_interface.NAB.o
TESTRISMSFF=testrism
#3D-RISM SANDER
RISMSANDER=-DRISMSANDER
SANDER_RISM_INTERFACE=../rism/amber_rism_interface.SANDER.o
FLIBS_RISMSANDER=-lrism
#for EMIL:
EMIL_MPIFLAGS=
#PUPIL
PUPILLIBS=-lm -lc -L${PUPIL_PATH}/lib -lPUPIL -lPUPILBlind
#Python interpreter we are using and install options
PYTHON=/usr/bin/python
PYTHON_INSTALL=--prefix=$(AMBERHOME)
SKIP_PYTHON=no
PYSANDER=install
PYTRAJ=pytraj
MAKE_SAXS=install
#For LIO QM GPU Library
LIOLIBS=
# OS-specific rules for making shared objects
SHARED_SUFFIX=.dylib
MAKE_SHARED=-dynamiclib
# PLUMED related variables:
PLUMED_INCLUDE_FILE=
PLUMED_LOAD=Plumed.o -ldl
PLUMED_DEPENDENCIES=Plumed.o
--
On 5/10/16, 10:57 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
>On Tue, May 10, 2016 at 10:48 AM, Adams, John E. <AdamsJE.missouri.edu>
>wrote:
>
>> Although the configure process associated with installing AmberTools16
>>on
>> my Mac (OS X 10.11) appears to proceed normally, “make install”
>>eventually
>> terminates with the following message.
>>
>> running build_ext
>> building 'pytraj.c_dict' extension
>> creating build/temp.macosx-10.11-intel-2.7
>> creating build/temp.macosx-10.11-intel-2.7/pytraj
>> gcc -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g
>> -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE
>>-DMACOSX
>> -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g
>>-fwrapv
>> -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64
>>-pipe
>> -I/Users/JEAdams/amber16/AmberTools/src/cpptraj/src
>> -I/Users/JEAdams/amber16/AmberTools/src/pytraj/pytraj/
>>
>>-I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python
>>2.7
>> -c pytraj/c_dict.cpp -o
>>build/temp.macosx-10.11-intel-2.7/pytraj/c_dict.o
>> -O0 -ggdb
>> gcc: error: unrecognized command line option '-Wshorten-64-to-32'
>> error: command 'gcc' failed with exit status 1
>> make[2]: *** [pytraj] Error 1
>> make[1]: *** [serial] Error 2
>> make: *** [install] Error 2
>>
>> My compiler is gcc4.9, and I have python2.7. (The output from the
>> configuration step indicated no issues.) A quick search of the internet
>> indicates that ‘-Wshorten-64-to-32’ is not recognized by gcc. Any
>> suggestions for working around the above error?
>>
>
>There are a couple simple solutions:
>
>1
>. Re-run configure specifying the "clang" compiler instead of "gnu".
>2. Run the $AMBERHOME/AmberTools/src/configure_python script to install a
>compatible Python inside $AMBERHOME
>3. Comment-out the pytraj installation in
>$AMBERHOME/AmberTools/src/Makefile (obviously if you want pytraj or need
>to
>use it, this option won't work).
>
>As an aside, to help us figure out how to fix this, can you give us the
>configure command you used in addition to the config.h file that was
>generated? If you are using the standard system Python, step 1 is
>probably
>the easiest.
>
>HTH,
>Jason
>
>--
>Jason M. Swails
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue May 10 2016 - 11:00:03 PDT
