[AMBER] Cataline

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Sun, 13 Oct 2019 20:01:37 +0000

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

Testing the clang++ compiler:
     clang++ -fPIC -o testp testp.cpp

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 ;\
(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
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 - 13:30:01 PDT
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