On Wed, Oct 16, 2019 at 3:49 PM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> So, after making sure that the amber.sh was sourced correctly in zsh,
> compilation still failed with the "locale.h" error.
>
>
> Setting
>
>
>
> CPLUS_INCLUDE_PATH=/amber18/miniconda/pkgs/libcxx-4.0.1-hcfea43d_1/include/c++/v1/
>
>
> Resulted in the same error:
>
> #include <locale.h>
>
> ^~~~~~~~~
>
> 1 warning and 1 error generated.
>
> error: command 'clang' failed with exit status 1
>
> make[2]: *** [parmed] Error 1
> make[1]: *** [serial] Error 2
> make: *** [install] Error 2
>
>
> I will try to verify the suggested edits by Hai for now.
>
>
It’s from Tru Huynh’s email.
Hai
> Best regards
>
> // Gustaf
>
> ________________________________
> Från: Bill Ross <ross.cgl.ucsf.edu>
> Skickat: den 14 oktober 2019 09:34:38
> Till: amber.ambermd.org
> Ämne: Re: [AMBER] Cataline
>
> > The question then is which ones:
>
> The Amber one sounds like a good first try. :-)
>
> > /amber18/miniconda/pkgs/libcxx-4.0.1-hcfea43d_1/include/c++/v1/locale.h
>
> But see what
>
> $ env
>
> tells you about C/C++ bindings. Did you source amber.sh?
>
> Bill
>
> On 10/13/19 11:48 PM, Gustaf Olsson wrote:
> > The question then is which ones:
> >
> > I would assume that for clang, being the preferred mac alternative, it
> would be one of these, likely the first one?
> >
> > /Library/Developer/CommandLineTools/usr/include/c++/v1/locale.h
> > /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> 1/usr/include/locale.h
> >
> /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/locale.h
> >
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/locale.h
> >
> > However, I find multiple instances of the file:
> >
> > /amber18/miniconda/pkgs/libcxx-4.0.1-hcfea43d_1/include/c++/v1/locale.h
> > /usr/local/anaconda3/include/c++/v1/locale.h
> > /usr/local/anaconda3/pkgs/libcxx-4.0.1-hcfea43d_1/include/c++/v1/locale.h
> > /usr/local/miniconda3/include/c++/v1/locale.h
> >
> /usr/local/miniconda3/pkgs/libcxx-4.0.1-hcfea43d_1/include/c++/v1/locale.h
> >
> > According the the release notes for some previous version of Xcode some
> header files would be deprecated with the next (current) version of Xcode,
> files that were previously supplied in a “hidden” installer within Xcode. I
> assume this is related.
> >
> > I am not currently sitting at the computer where I am trying to compile,
> can’t risk breaking my work installation right now. I’ll try to solve/work
> around the issue as soon as I have time. I also need to try compiling using
> GCC (not clang) and see if it works now.
> >
> > Thank you for your feedback and suggestion
> > Best regards
> > // Gustaf
> >
> >> On 13 Oct 2019, at 23:52, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >>
> >>> In file included from src/_rdparm.cpp:17:
> >>> /amber18/AmberTools/src/parmed/src/readparm.h:5:10: fatal error:
> >>> 'locale' file not found
> >>> #include <locale>
> >>> ^~~~~~~~
> >> Brute force for illustration:
> >>
> >> $ sudo find / -name locale.h
> >>
> >> Then add the dir it's in per:
> >>
> >>
> https://stackoverflow.com/questions/558803/how-to-add-a-default-include-path-for-gcc-in-linux
> >>
> >> Bill
> >>
> >> On 10/13/19 1:01 PM, Gustaf Olsson wrote:
> >>> Yes, it is time to upgrade the OS on my Macs and as expected this will
> reap havoc on the install situation for amber. First thing I noticed is
> that we are now expected to use ZSH as default shell instead of "BASH"
> (MacBASH), that aught to cause some issues at some point.
> >>>
> >>>
> >>> Second, it is important to mention that I do not have a "virgin" OS. I
> am updating from older versions. Currently on macOS Catalina 10.15 with
> Xcode 11.1.
> >>>
> >>>
> >>> Trying to just run the configuration script produced this error:
> >>>
> >>>
> >>> Could not find the X11 libraries; you may need to edit config.h
> >>> to set the XHOME and XLIBS variables.
> >>> Error: The X11 libraries are not in the usual location !
> >>> To search for them try the command: locate libXt
> >>> On new Fedora OS's install the libXt-devel libXext-devel
> >>> libX11-devel libICE-devel libSM-devel packages.
> >>> On old Fedora OS's install the xorg-x11-devel package.
> >>> On RedHat OS's install the XFree86-devel package.
> >>> On Ubuntu OS's install the xorg-dev and xserver-xorg packages.
> >>>
> >>> ...more info for various linuxes at ambermd.org/ubuntu.html
> >>>
> >>> To build Amber without XLEaP, re-run configure with '-noX11:
> >>> ./configure -noX11 -macAccelerate clang
> >>> Configure failed due to the errors above!
> >>>
> >>> XQuartz was installed and working, however I also noticed a folder on
> my desktop containing "Moved Files" in which my X11 folder was dumped from
> /usr/, now present in /opt/.
> >>>
> >>> Re-installing xquarts from using "brew" solved this issue:
> >>>
> >>> Done installing Miniconda!
> >>>
> >>> Obtaining the clang compiler suite versions, e.g.:
> >>> clang -v
> >>> The C version is 11.0.0
> >>> The Fortran version is 9.2.0
> >>>
> >>> Testing the clang compiler:
> >>> clang -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
> testp.c
> >>> OK
> >>>
> >>> Testing the clang++ compiler:
> >>> clang++ -fPIC -o testp testp.cpp
> >>> OK
> >>>
> >>> Testing the gfortran compiler:
> >>> gfortran -fPIC -O0 -o testp testp.f
> >>> ld: library not found for -lSystem
> >>> collect2: error: ld returned 1 exit status
> >>> ./configure2: line 2485: ./testp: No such file or directory
> >>> Error: Unable to compile a Fortran program using gfortran -fPIC -O0
> >>> Please check your compiler settings and configure flags.
> >>> Configure failed due to the errors above!
> >>>
> >>> Sigh... So even if Xcode was installed and working, you need to
> re-install CLT:
> >>>
> >>> xcode-select --install
> >>>
> >>> Now, configuration completed without complaints. However, make install
> now bailed with the previously discussed "locale" issue (libc++/libstdc++).
> >>>
> >>> [NFE] CXX nfe-umbrella-slice
> >>> (if [ "no" = "no" ]; then \
> >>> /Applications/Xcode.app/Contents/Developer/usr/bin/make python_serial
> ;\
> >>> fi;\
> >>> )
> >>> (cd parmed &&
> PYTHONPATH=/Users/gustafO/Mjukvara/amber18/lib/python2.7/site-packages
> /amber18/bin/amber.python setup.py install -f --prefix=/amber18 > build.log)
> >>> warning: no files found matching 'versioneer.py'
> >>> warning: include path for stdlibc++ headers not found; pass
> '-stdlib=libc++' on
> >>> the command line to use the libc++ standard library instead
> >>> [-Wstdlibcxx-not-found]
> >>> In file included from src/_rdparm.cpp:17:
> >>> /amber18/AmberTools/src/parmed/src/readparm.h:5:10: fatal error:
> >>> 'locale' file not found
> >>> #include <locale>
> >>> ^~~~~~~~
> >>> 1 warning and 1 error generated.
> >>> error: command 'clang' failed with exit status 1
> >>> make[2]: *** [parmed] Error 1
> >>> make[1]: *** [serial] Error 2
> >>> make: *** [install] Error 2
> >>>
> >>> And this is where I have to leave it for now. I know I have the notes
> regarding how to produce a workaround for this issue though any more
> permanent solutions are of course welcome.
> >>>
> >>> Best regards
> >>> // Gustaf
> >>> _______________________________________________
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Received on Wed Oct 16 2019 - 13:30:02 PDT
