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.app/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/Programs/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/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
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > 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
> > > > > >> _______________________________________________
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> > > > > >> AMBER.ambermd.org
> > > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >>
> > > > > >
> > > > > >
> > > > > _______________________________________________
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> > > > >
> > > > _______________________________________________
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> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
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> > > 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 - 14:30:03 PDT
