The clang version is the following:
Apple LLVM version 8.0.0 (clang-800.0.42.1)
Target: x86_64-apple-darwin16.4.0
Thread model: posix
InstalledDir:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
How do I disable the CC and CXX environments?
On 13 March 2017 at 21:00, Giannis Gl <igaldadas.gmail.com> wrote:
> I can post the whole screen output but really it is too long!! I will post
> a part of it and please find below the content of the config.h.
>
> Compiling basic programs
>
> cd src/leap && /Applications/Xcode.app/Contents/Developer/usr/bin/make
> installteLeap
>
> clang -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
> -DHASBZ2 -D__PLUMED_HAS_DLOPEN \
>
> -o teLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o
> avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o
> vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o
> ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o
> collection.o container.o internal.o list.o loop.o molecule.o oDouble.o
> oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o
> graphUtil.o select.o amber.o build.o elements.o library.o chirality.o
> minimizer.o model.o parmLib.o pdbFile.o mol2File.o mol3File.o tools.o
> variables.o parser.o help.o helptext.o octree.o commands.o mathop.o block.o
> restraint.o hybrid.o tLeap.o -lm /Users/yiannisgaldadas/
> Programs/AmberTools16/amber16/lib/libnetcdf.a
>
> mv teLeap /Users/yiannisgaldadas/Programs/AmberTools16/amber16/bin
>
> Copying shell script
>
> cp tleap /Users/yiannisgaldadas/Programs/AmberTools16/amber16/bin/tleap
>
> chmod +x /Users/yiannisgaldadas/Programs/AmberTools16/amber16/bin/tleap
>
> /Applications/Xcode.app/Contents/Developer/usr/bin/make install_xleap
>
> cd src/Wc && /Applications/Xcode.app/Contents/Developer/usr/bin/make
>
> make[4]: `libWcLeap.a' is up to date.
>
> cd src/Xmu && /Applications/Xcode.app/Contents/Developer/usr/bin/make
>
> make[4]: `libXmu.a' is up to date.
>
> cd src/Xpm && /Applications/Xcode.app/Contents/Developer/usr/bin/make
>
> make[4]: `libXpm.a' is up to date.
>
> cd src/Xraw && /Applications/Xcode.app/Contents/Developer/usr/bin/make
>
> make[4]: `libXaw.a' is up to date.
>
> cd src/leap && /Applications/Xcode.app/Contents/Developer/usr/bin/make
> install
>
> clang -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
> -DHASBZ2 -D__PLUMED_HAS_DLOPEN \
>
> -o teLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o
> avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o
> vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o
> ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o
> collection.o container.o internal.o list.o loop.o molecule.o oDouble.o
> oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o
> graphUtil.o select.o amber.o build.o elements.o library.o chirality.o
> minimizer.o model.o parmLib.o pdbFile.o mol2File.o mol3File.o tools.o
> variables.o parser.o help.o helptext.o octree.o commands.o mathop.o block.o
> restraint.o hybrid.o tLeap.o -lm /Users/yiannisgaldadas/
> Programs/AmberTools16/amber16/lib/libnetcdf.a
>
> clang -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
> -DHASBZ2 -D__PLUMED_HAS_DLOPEN \
>
> -o xaLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o
> avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o
> vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o
> ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o
> collection.o container.o internal.o list.o loop.o molecule.o oDouble.o
> oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o
> graphUtil.o select.o amber.o build.o elements.o library.o chirality.o
> minimizer.o model.o parmLib.o pdbFile.o mol2File.o mol3File.o tools.o
> variables.o parser.o help.o helptext.o octree.o commands.o mathop.o block.o
> restraint.o hybrid.o xTank.o xAction.o x3d.o xBasics.o xaLeapc.o
> xaUnitEditor.o xaTable.o xaAtomTable.o XrawRegistr.o xaCommand.o
> xaTools.o xaAtomParmTable.o xaBondParmTable.o xaAngleParmTable.o
> xaParmEditor.o xaTorsionParmTable.o xaImproperParmTable.o
> xaHBondParmTable.o ../Xraw/libXaw.a ../Wc/libWcLeap.a ../Xpm/libXpm.a
> ../Xmu/libXmu.a -L/usr/X11R6/lib64 -L/usr/X11R6/lib -lXt -lXext -lSM -lICE
> -lX11 -lXau -lm -lpthread /Users/yiannisgaldadas/
> Programs/AmberTools16/amber16/lib/libnetcdf.a
>
> ld: warning: directory not found for option '-L/usr/X11R6/lib64'
>
> m4 xaLeap.rm4 > XaLeap_wcl
>
> mv teLeap xaLeap /Users/yiannisgaldadas/Programs/AmberTools16/amber16/bin
>
> mv XaLeap_wcl /Users/yiannisgaldadas/Programs/AmberTools16/amber16/dat
>
> Copying shell script
>
> cp xleap /Users/yiannisgaldadas/Programs/AmberTools16/amber16/bin/xleap
>
> chmod +x /Users/yiannisgaldadas/Programs/AmberTools16/amber16/bin/xleap
>
> Copying pixmaps
>
> test -d /Users/yiannisgaldadas/Programs/AmberTools16/amber16/dat/pixmap
> || mkdir /Users/yiannisgaldadas/Programs/AmberTools16/amber16/dat/pixmap
>
> cd pixmap; /bin/cp * /Users/yiannisgaldadas/Programs/AmberTools16/amber16/
> dat/pixmap
>
> Finished with the install of LEaP
>
> (cd lib && /Applications/Xcode.app/Contents/Developer/usr/bin/make
> install)
>
> gfortran -DBINTRAJ -DEMIL -fPIC -I/Users/yiannisgaldadas/
> Programs/AmberTools16/amber16/include -I/Users/yiannisgaldadas/
> Programs/AmberTools16/amber16/include -o new2oldparm new2oldparm.o \
>
> nxtsec.o
>
> mv new2oldparm /Users/yiannisgaldadas/Programs/AmberTools16/amber16/bin
>
> /bin/rm -f
>
> (cd addles && /Applications/Xcode.app/Contents/Developer/usr/bin/make
> install)
>
> cd ../lib && /Applications/Xcode.app/Contents/Developer/usr/bin/make
> mexit.o nxtsec.o
>
> make[3]: `mexit.o' is up to date.
>
> make[3]: `nxtsec.o' is up to date.
>
> gfortran -DBINTRAJ -DEMIL -fPIC -I/Users/yiannisgaldadas/
> Programs/AmberTools16/amber16/include -I/Users/yiannisgaldadas/
> Programs/AmberTools16/amber16/include \
>
> -o /Users/yiannisgaldadas/Programs/AmberTools16/amber16/bin/addles
> lesmain.o addspace.o readprm.o writprm.o readcrd.o writcrd.o pick.o rline.o
> nxt.o intgr.o find.o of.o geti.o unit.o getc.o alert.o
> echo.o get4c.o getd.o wlesprm.o lesprm.o random.o les2prm.o checksz.o
> addspace_atm1st.o \
>
> ../lib/mexit.o ../lib/nxtsec.o
>
> ld: can't write output file: /Users/yiannisgaldadas/
> Programs/AmberTools16/amber16/bin/addles for architecture x86_64
>
> collect2: error: ld returned 1 exit status
>
> make[2]: *** [/Users/yiannisgaldadas/Programs/AmberTools16/amber16/bin/addles]
> Error 1
>
> make[1]: *** [serial] Error 2
>
> make: *** [install] Error 2
>
> -------------------------------------------------------
>
> The content of the config.h is the following:
>
> # Amber configuration file.
> # Created at Mon Mar 13 20:34:15 GMT 2017 via ./configure -macAccelerate
> clang
>
> ############################################################
> ###################
>
> # (1) Location of the installation
>
> BASEDIR=/Users/yiannisgaldadas/Programs/AmberTools16/amber16
> BINDIR=/Users/yiannisgaldadas/Programs/AmberTools16/amber16/bin
> LIBDIR=/Users/yiannisgaldadas/Programs/AmberTools16/amber16/lib
> INCDIR=/Users/yiannisgaldadas/Programs/AmberTools16/amber16/include
> DATDIR=/Users/yiannisgaldadas/Programs/AmberTools16/amber16/dat
> LOGDIR=/Users/yiannisgaldadas/Programs/AmberTools16/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
> -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0/../../../
> -lgfortran -w -framework Accelerate
> FLIBS_PTRAJ= -larpack -L/usr/local/gfortran/lib/gcc/
> x86_64-apple-darwin16/6.3.0/../../../ -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=clang
> CFLAGS=-fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
> -DHASBZ2 -D__PLUMED_HAS_DLOPEN $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
> CNOOPTFLAGS=
> COPTFLAGS=-O3
> AMBERCFLAGS= $(AMBERBUILDFLAGS)
> WARNFLAGS=-Wall -Wno-unused-function
>
> CXX=clang++
> CPLUSPLUS=clang++
> 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=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0/../../../
> -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 -lc++
>
> ZLIB=-lz
> BZLIB=-lbz2
>
> HASFC=yes
> MTKPP=install_mtkpp
> XBLAS=$(LIBDIR)/libxblas-amb.a
> FFTW3=$(LIBDIR)/libfftw3.a
> MDGX=yes
>
> COMPILER=clang
> 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=clang
> PMEMD_COPTFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ
> $(AMBERBUILDFLAGS)
> PMEMD_FLIBSF= $(LIBDIR)/libemil.a -lc++
> PMEMD_LD=gfortran $(AMBERBUILDFLAGS)
> LDOUT= -o
> PMEMD_GNU_BUG303=
>
> #for NAB:
> MPI=
>
> #1D-RISM
> RISM=yes
>
> #3D-RISM NAB
> RISMSFF=-DRISMSFF
> SFF_RISM_INTERFACE=../rism/amber_rism_interface.NAB.o
> TESTRISMSFF=testrism
>
> #3D-RISM SANDER
> RISMSANDER=-DRISMSANDER
> SANDER_RISM_INTERFACE=../rism/amber_rism_interface.SANDER.o
> FLIBS_RISMSANDER=-lrism
>
> #for EMIL:
> EMIL_MPIFLAGS=
>
> #PUPIL
> PUPILLIBS=-lm -lc -L${PUPIL_PATH}/lib -lPUPIL -lPUPILBlind
>
> #Python interpreter we are using and install options
> PYTHON=/Users/yiannisgaldadas/miniconda3/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 13 March 2017 at 20:51, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>> > 3. The context of the make file that ./configure -macAccelerate clang
>> generated:
>>
>>
>> Hi, poor my English. I mean: the screen output (and may be the content of
>> config.h file too).
>>
>> Hai
>>
>> On Mon, Mar 13, 2017 at 4:46 PM, Giannis Gl <igaldadas.gmail.com> wrote:
>>
>> > Hi :)
>> >
>> > 1. Yes, I did a fresh installation.
>> >
>> > 2. gcc-6.3.0_1 , cmake version 3.7.2
>> >
>> > Configured with: --prefix=/Applications/Xcode.a
>> pp/Contents/Developer/usr
>> > --with-gxx-include-dir=/usr/include/c++/4.2.1
>> >
>> > Apple LLVM version 8.0.0 (clang-800.0.42.1)
>> >
>> > Target: x86_64-apple-darwin16.4.0
>> >
>> >
>> > 3. The context of the make file that ./configure -macAccelerate clang
>> > generated:
>> >
>> >
>> > # Simple top-level Makefile to point users to those hidden below:
>> >
>> >
>> > CONFIG_FILE=config.h
>> >
>> > include $(CONFIG_FILE)
>> >
>> >
>> > install:
>> >
>> > cd AmberTools/src && $(MAKE) install
>> >
>> > .(if [ -n "$(BUILDAMBER)" ] ; then \
>> >
>> > cd src && $(MAKE) install; \
>> >
>> > else \
>> >
>> > echo "=============================================================="
>> ;\
>> >
>> > echo "$(AMBERHOME)/src/Makefile not found, or -noamber was set." ;\
>> >
>> > echo "This is expected if you do not have Amber16." ;\
>> >
>> > echo "=============================================================="
>> ;\
>> >
>> > fi ;\
>> >
>> > )
>> >
>> >
>> > python:
>> >
>> > cd AmberTools/src && $(MAKE) parmed mmpbsa_py pymsmt $(PYTRAJ)
>> >
>> > cd AmberTools/src/etc && $(MAKE) python
>> >
>> > # If it needs to be done, fix conda's libgfortran issue... sigh.
>> >
>> > $(PYTHON) AmberTools/src/fix_conda_fortran.py
>> >
>> >
>> > clean:
>> >
>> > -(cd AmberTools/src && $(MAKE) clean)
>> >
>> > -(cd src && $(MAKE) clean)
>> >
>> >
>> > uninstall:
>> >
>> > -(cd src && $(MAKE) uninstall)
>> >
>> > -(cd AmberTools/src && $(MAKE) uninstall)
>> >
>> >
>> > clean.test:
>> >
>> > -(cd AmberTools/test && $(MAKE) clean)
>> >
>> > -(cd test && $(MAKE) clean)
>> >
>> >
>> > test.clean: clean.test
>> >
>> >
>> > # This target cleans all generated files including all executables;
>> >
>> > # the intention is that distclean returns the distribution to a
>> >
>> > # pristine state as though the user just untarred a fresh copy of the
>> code
>> > and
>> >
>> > # applied their updates
>> >
>> > distclean: clean clean.test uninstall
>> >
>> > /bin/rm -rf miniconda include/* lib/*
>> >
>> > /bin/rm -rf updateutils/__pycache__ ./updateutils/*.pyc
>> >
>> > /bin/rm -rf AmberTools/src/pytraj/scripts/*.pyc
>> >
>> > /bin/rm -f ./$(CONFIG_FILE) ./AmberTools/src/$(CONFIG_FILE)
>> >
>> >
>> > test:: test.$(INSTALLTYPE)
>> >
>> >
>> > test.serial:
>> >
>> > (cd AmberTools/test && $(MAKE) test)
>> >
>> > .(if [ -n "$(BUILDAMBER)" ] ; then \
>> >
>> > cd test && $(MAKE) test; \
>> >
>> > echo ""; \
>> >
>> > echo "Summary of AmberTools serial tests:"; \
>> >
>> > echo ""; cat ../logs/test_at_serial/at_summary; \
>> >
>> > else \
>> >
>> > echo "=============================================================="
>> ;\
>> >
>> > echo "$(AMBERHOME)/src/Makefile not found." ;\
>> >
>> > echo "This is expected if you have not installed Amber16." ;\
>> >
>> > echo "=============================================================="
>> ;\
>> >
>> > fi ;\
>> >
>> > )
>> >
>> >
>> > test.openmp:
>> >
>> > (cd AmberTools/test && $(MAKE) test.openmp)
>> >
>> >
>> > test.parallel:
>> >
>> > (cd AmberTools/test && $(MAKE) test.parallel)
>> >
>> > .(if [ -n "$(BUILDAMBER)" ] ; then \
>> >
>> > cd test && $(MAKE) test.parallel; \
>> >
>> > echo ""; \
>> >
>> > echo "Summary of AmberTools parallel tests:"; \
>> >
>> > echo ""; cat ../logs/test_at_parallel/at_summary; \
>> >
>> > else \
>> >
>> > echo "=============================================================="
>> ;\
>> >
>> > echo "$(AMBERHOME)/src/Makefile not found." ;\
>> >
>> > echo "This is expected if you have not installed Amber16." ;\
>> >
>> > echo "=============================================================="
>> ;\
>> >
>> > fi ;\
>> >
>> > )
>> >
>> >
>> > test.cuda_serial:
>> >
>> > -(cd test && $(MAKE) test.cuda.serial)
>> >
>> >
>> > test.cuda_parallel:
>> >
>> > -(cd test && $(MAKE) test.cuda.parallel)
>> >
>> >
>> > test.mic_offload:
>> >
>> > -(cd test && $(MAKE) test.mic_offload)
>> >
>> >
>> > test.mic2:
>> >
>> > -(cd test && $(MAKE) test.parallel.pmemd.mic2)
>> >
>> >
>> > nabonly:
>> >
>> > -(cd AmberTools/src && $(MAKE) nabonly)
>> >
>> >
>> > openmp:
>> >
>> > -(cd AmberTools/src && $(MAKE) openmp)
>> >
>> >
>> > help:
>> >
>> > .echo "configure is the first step in the installation. Execute this: "
>> >
>> > .echo "./configure --help"
>> >
>> > On 13 March 2017 at 20:37, Hai Nguyen <nhai.qn.gmail.com> wrote:
>> >
>> > > hi,
>> > >
>> > > 1. Did you make a fresh (no previous compiled files) install?
>> > > 2. What's your CC CXX env?
>> > > 3. Output of "./configure -macAccelerate clang"
>> > >
>> > > Hai
>> > >
>> > > On Mon, Mar 13, 2017 at 4:32 PM, Giannis Gl <igaldadas.gmail.com>
>> wrote:
>> > >
>> > > > Hello!
>> > > >
>> > > > The exact sequence of commands that I used is:
>> > > >
>> > > >
>> > > > ./configure -macAccelerate clang
>> > > >
>> > > > make install
>> > > >
>> > > >
>> > > > And the last lines before the error appears are the followings:
>> > > >
>> > > >
>> > > >
>> > > > mv new2oldparm /Users/yiannisgaldadas/Program
>> s/AmberTools16/amber16/
>> > bin
>> > > >
>> > > > override rwxr-xr-x root/staff for
>> > > > /Users/yiannisgaldadas/Programs/AmberTools16/amber16/bin/
>> new2oldparm?
>> > > (y/n
>> > > > [n]) y
>> > > >
>> > > > /bin/rm -f
>> > > >
>> > > > (cd addles && /Applications/Xcode.app/Conten
>> ts/Developer/usr/bin/make
>> > > > install)
>> > > >
>> > > > cd ../lib && /Applications/Xcode.app/Conten
>> ts/Developer/usr/bin/make
>> > > > mexit.o nxtsec.o
>> > > >
>> > > > make[3]: `mexit.o' is up to date.
>> > > >
>> > > > make[3]: `nxtsec.o' is up to date.
>> > > >
>> > > > gfortran -DBINTRAJ -DEMIL -fPIC
>> > > > -I/Users/yiannisgaldadas/Programs/AmberTools16/amber16/include
>> > > > -I/Users/yiannisgaldadas/Programs/AmberTools16/amber16/include \
>> > > >
>> > > > -o /Users/yiannisgaldadas/Programs/AmberTools16/amber16/bin/addles
>> > > > lesmain.o addspace.o readprm.o writprm.o readcrd.o writcrd.o pick.o
>> > > > rline.o
>> > > > nxt.o intgr.o find.o of.o geti.o unit.o getc.o alert.o
>> > > > echo.o get4c.o getd.o wlesprm.o lesprm.o random.o les2prm.o
>> > > checksz.o
>> > > > addspace_atm1st.o \
>> > > >
>> > > > ../lib/mexit.o ../lib/nxtsec.o
>> > > >
>> > > > ld: can't write output file:
>> > > > /Users/yiannisgaldadas/Programs/AmberTools16/amber16/bin/addles for
>> > > > architecture x86_64
>> > > >
>> > > > collect2: error: ld returned 1 exit status
>> > > >
>> > > > make[2]: ***
>> > > > [/Users/yiannisgaldadas/Programs/AmberTools16/amber16/bin/addles]
>> > Error
>> > > 1
>> > > >
>> > > > make[1]: *** [serial] Error 2
>> > > >
>> > > > make: *** [install] Error 2
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > > On 13 March 2017 at 20:27, Hai Nguyen <nhai.qn.gmail.com> wrote:
>> > > >
>> > > > > Did you use clang + gfortran?
>> > > > >
>> > > > > Hai
>> > > > >
>> > > > > On Mon, Mar 13, 2017 at 4:27 PM, Hai Nguyen <nhai.qn.gmail.com>
>> > wrote:
>> > > > >
>> > > > > > hi,
>> > > > > >
>> > > > > > can you post exact command and output? thanks.
>> > > > > >
>> > > > > > Hai
>> > > > > >
>> > > > > >
>> > > > > > On Mon, Mar 13, 2017 at 3:10 PM, Giannis Gl <
>> igaldadas.gmail.com>
>> > > > wrote:
>> > > > > >
>> > > > > >> Dear Amber users,
>> > > > > >>
>> > > > > >> I try to install AmberTools16 on my MacBood (macOS Sierra,
>> > 10.12.3),
>> > > > > >> but the make install command terminates with the following
>> error:
>> > > > > >>
>> > > > > >>
>> > > > > >> ld: can't write output file: /Users/yiannisgaldadas/
>> > > > > >> Programs/AmberTools16/amber16/bin/addles for architecture
>> x86_64
>> > > > > >>
>> > > > > >> collect2: error: ld returned 1 exit status
>> > > > > >>
>> > > > > >> make[2]: *** [/Users/yiannisgaldadas/
>> > Programs/AmberTools16/amber16/
>> > > > bin/
>> > > > > >> addles]
>> > > > > >> Error 1
>> > > > > >>
>> > > > > >> make[1]: *** [serial] Error 2
>> > > > > >>
>> > > > > >> make: *** [install] Error 2
>> > > > > >>
>> > > > > >>
>> > > > > >> I have already installed gfortrant compiler and patched the
>> file
>> > > that
>> > > > is
>> > > > > >> recommended in the following archive to solve another error
>> that
>> > > > > >>
>> > > > > >> occurred
>> > > > > >>
>> > > > > >>
>> > > > > >> http://archive.ambermd.org/201702/0042.html
>> > > > > >>
>> > > > > >>
>> > > > > >> but I can not find any solution to the error that I get now.
>> > > > > >>
>> > > > > >> Any idea what might cause this error?
>> > > > > >>
>> > > > > >>
>> > > > > >> Thanks,
>> > > > > >>
>> > > > > >> Yiannis
>> > > > > >> _______________________________________________
>> > > > > >> AMBER mailing list
>> > > > > >> AMBER.ambermd.org
>> > > > > >> http://lists.ambermd.org/mailman/listinfo/amber
>> > > > > >>
>> > > > > >
>> > > > > >
>> > > > > _______________________________________________
>> > > > > AMBER mailing list
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>> > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > >
>> > > > _______________________________________________
>> > > > AMBER mailing list
>> > > > AMBER.ambermd.org
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>> > > >
>> > > _______________________________________________
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>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
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>> >
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Received on Mon Mar 13 2017 - 14:30:03 PDT
