On Mon, Mar 13, 2017 at 5:01 PM, Giannis Gl <igaldadas.gmail.com> wrote:
> 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?
>
unset CC CXX
But looking at your config.h, I think you don't need to do above step.
I myself run-out of solution now. So I let others to chime in. :D
cheers.
Hai
>
> 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
> >> > > > > AMBER.ambermd.org
> >> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > > >
> >> > > > _______________________________________________
> >> > > > 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
> >> > >
> >> > _______________________________________________
> >> > 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
> >>
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Mar 13 2017 - 14:30:05 PDT
