> 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 Sun Oct 13 2019 - 15:00:01 PDT
