> 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
> > > > >> _______________________________________________
> > > > >> 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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>
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Received on Mon Mar 13 2017 - 14:00:05 PDT
