So, I am unable to use the "update" script to fetch and install updates, don't know if this is all catalina users with homebrew or just me right now (see "previous" post from today). However, using the latest version of Xcode and macOS (as reported by Tru/Hai) with the suggested modifications:
vi $AMBERHOME/AmberTools/src/parmed/setup.py
37 '18': '10.14', => 37 '18': '10.14',
39 } => 38 '19': '10.15',
=> 39 }
and
vi $AMBERHOME/AmberTools/src/pytraj/setup.py
152 '18': '10.14', => 152 '18': '10.14',
153 } => 153 '19': '10.15',
=> 154 }
with
$ ./configure -macAccelerate clang && make install
Produces a compiled verison.
Installation of AmberTools19 serial is complete at Wed 16 Oct 2019 22:31:16 CEST.
==============================================================
/amber18/src/Makefile not found, or -noamber was set.
This is expected if you do not have Amber18.
==============================================================
I have not run the tests yet, hoepfully I'll have time tomorrow. But at least this is a step in the right direction. I also need to find my license at work for amber, making sure it works and getting the MPI and OMP versions to compile properly.
Thank you all for great feedback and a working solution/workaround!
Best regards
// Gustaf
________________________________
Från: Hai Nguyen <nhai.qn.gmail.com>
Skickat: den 16 oktober 2019 22:00:47
Till: AMBER Mailing List
Ämne: Re: [AMBER] Cataline
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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> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
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> >> AMBER mailing list
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> >
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Received on Wed Oct 16 2019 - 14:00:02 PDT
