ah, how's about skipping install "addles" (comment the addles line in
AmberTools/src/Makefile) and try to "make install" again'?
Hai
On Mon, Mar 13, 2017 at 5:11 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>
> 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/XcodeD
>> efault.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/Program
>> s/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/Program
>> s/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-dar
>> win16/6.3.0/../../../
>> > -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 - 14:30:06 PDT
