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
> > > >> _______________________________________________
> > > >> 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 - 14:00:04 PDT
