> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Oct 14 2019 - 01:00:02 PDT
