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
>
> _______________________________________________
> 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
Received on Mon Oct 14 2019 - 00:00:02 PDT
