Hi Daniel
No, not as of yet. Configure2 and pytraj setup were the only two files modified to build, although I have not checked any potential warnings or errors logged yet.
I am jumping between lectures and exercises this entire week so “quick and dirty” is the only way I’ve been able to work. Next week will be a lot calmer though and I will look into it and get back to you!
Best regards
// Gustaf
> On 19 Oct 2018, at 01:07, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> So you didn’t need to modify cpptraj configure? Seems like Amber configure2
> may have been forcing cpptraj configure to accept some problematic flags.
> By any chance have you tried the standalone cpptraj configure? I’m curious
> to know if it works.
>
> -Dan
>
> On Thu, Oct 18, 2018 at 3:00 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
>>> The new Xcode doesn't provide much (any?) support for libstdc++,
>>> preferring libc++ instead. So:
>>
>> You are correct, as stated previously, support for libstdc++ has been
>> removed as of the previous Xcode version and seen in the failed compile
>> logs.
>>
>> clang: warning: libstdc++ is deprecated; move to libc++ [-Wdeprecated]
>> warning: include path for stdlibc++ headers not found; pass
>> '-std=libc++' on the
>> command line to use the libc++ standard library instead
>> [-Wstdlibcxx-not-found]
>>
>> All developers have apparently previously been encouraged to move to
>> libc++ instead. I tried restoring libstc++ support by including the
>> appropriate files as had ben suggested as a working solution, though it did
>> not work.
>>
>> I tried the suggested solution for CLANG compilation though I did not
>> succeed.
>>
>> ./configure -macAccelerate clang
>>
>> …
>> …
>> Configuring CPPTRAJ...
>> CPPTRAJ configure failed. Check
>> ‘/amber18/AmberTools/src/cpptraj_config.log' for details.
>>
>> Error: Could not link properly with clang++ on OSX
>>
>> make install
>> make: *** No rule to make target `config.h'. Stop.
>>
>> So, I did a quick sweep of the of the referenced setup.py file an it turns
>> out there were more places needing modification.
>>
>> This is what worked for me using Mac clang to configure and compile:
>>
>> tar xvf AmberTools18.tar.bz2
>> cd amber18
>> export AMBERHOME=/Users/guolaa/SOFTWARE/amber18
>> export PATH=${AMBERHOME}:$PATH
>> export MACOSX_DEPLOYMENT_TARGET='10.14'
>> vi $AMBERHOME/AmberTools/src/configure2
>>
>> # Comment out lines 2237-2241
>> 2237 # if [ "$intelmpi" = 'yes' ]; then
>> 2238 # echo "Intel MPI must be used with the Intel
>> compilers."
>> 2239 # exit 1
>> 2240 # fi
>> 2241 #
>>
>> vi $AMBERHOME/AmberTools/src/pytraj/setup.py
>>
>> 142 extra_compile_args.append('-stdlib=libstdc++’)
>> --->
>> 142 extra_compile_args.append('-stdlib=libc++’)
>>
>>
>> 2289 # mac/clang
>> 2290 if [ "$skippython" = "no" ]; then
>> 2291 cpptrajcxxflags="-stdlib=libstdc++
>> $cpptrajcxxflags"
>> 2292 cpptrajldflags="-stdlib=libstdc++ -L/usr/lib/"
>> 2293 fi
>> --->
>> 2289 # mac/clang
>> 2290 if [ "$skippython" = "no" ]; then
>> 2291 cpptrajcxxflags="-stdlib=libc++ $cpptrajcxxflags"
>> 2292 cpptrajldflags="-stdlib=libc++ -L/usr/lib/"
>> 2293 fi
>>
>> ./configure -macAccelerate clang
>> make install
>> …
>> …
>> Installation of AmberTools18 serial is complete at Thu Oct 18 08:58:37
>> CEST 2018.
>>
>> ==============================================================
>> /Users/guolaa/SOFTWARE/amber18/src/Makefile not found, or -noamber was
>> set.
>> This is expected if you do not have Amber18.
>> ==============================================================
>>
>> So I am still seeing some coloured warnings and potential issues and I
>> have no idea what I might be braking since I have not yet had time to run
>> any tests or evaluate function though this time around it seems to be
>> working.
>>
>> Best regards
>> // Gustaf
>>
>>> On 17 Oct 2018, at 19:25, David A Case <david.case.rutgers.edu> wrote:
>>>
>>> On Mon, Oct 15, 2018, David Case wrote:
>>>
>>> Some more notes on getting AmberTools18/Amber18 built on Mojave:
>>>
>>> The new Xcode doesn't provide much (any?) support for libstdc++,
>>> preferring libc++ instead. So:
>>>
>>> a. Comment out lines 2237-2241 in
>> AMBERHOME/AmberTools/src/configure2:
>>> (these lines refer to libstdc++)
>>> b. In line 142 of setup.py (in the pytraj folder), change
>>> "libstdc++" to "libc++"
>>>
>>> Then a "./configure -macAccelerate clang" seems to be working for me.
>>> (Answer "yes" when asked to download miniconda; might also work with a
>>> different python you already have, but I've not tried that yet.)
>>>
>>> I'm repeating here some notes from an earlier post as well:
>>>
>>>>
>> ---------------------------------------------------------------------------
>>>> 1. As noted before (by Andrew Schaub), you need to get the headers in
>> the
>>>> proper location. Try this:
>>>>
>>>> sudo xcode-select --install (to get the command-line tool installed)
>>>> open
>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>>>>
>>>>
>> ---------------------------------------------------------------------------
>>>> 2. For some reason, you have to tell the miniconda installation what
>>>> version of the OS you have:
>>>>
>>>> export MACOSX_DEPLOYMENT_TARGET='10.14'
>>>>
>>>>
>> ---------------------------------------------------------------------------
>>>> 3. If you get "token not found errors" with -macAccelerate, try this:
>>>>
>>>> sudo port install ld64 +ld64_xcode (this is specific to
>> macports)
>>>>
>>>>
>> ---------------------------------------------------------------------------
>>>
>>> ....dac
>>>
>>> _______________________________________________
>>> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 18 2018 - 23:00:03 PDT
