Well I think I am the one who needs to say tank you, its not like I would work this out in any reasonable time on my own.
I’m pretty much tied up for the rest of Friday and the weekend though I’ll continue the efforts, focusing on only the cpptraj compilation, as soon as I can and get back to you.
Best regards and have a fantastic weekend.
// Gustaf
> On 12 Oct 2018, at 14:41, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> On Fri, Oct 12, 2018 at 2:28 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>
>> clang++ -O3 -o testp testprogram.cpp
>>
>> No messages, no errors.
>
> This is strange, because this is the first thing that CPPTRAJ
> configure tries (line 1296 of configure). The 'libstdc++' flag test
> only occurs if this one fails. The only thing I can think of to try
> now is to make CPPTRAJ configure
> ($AMBERHOME/AmberTools/src/cpptraj/configure) more verbose during the
> OSX tests. You can do this by removing the 'quiet' argument from the
> 'TestProgram' lines (1296, 1299, 1329, and 1337). So they go from:
>
> TestProgram quiet "Without stdlib flag" "$CXX" "$CXXFLAGS" testp.cpp
>
> to
>
> TestProgram "Without stdlib flag" "$CXX" "$CXXFLAGS" testp.cpp
>
> Also, you may want to try just running cpptraj's configure directly so
> you can skip over the rest of what configure is doing.
>
> cd $AMBERHOME/AmberTools/src/cpptraj
> ./configure -amberlib [-macAccelerate] clang
>
> I can try to get my hands on a copy of Mojave, but for now this is
> unfortunately the best I can do. Thanks for working with me on this.
>
> -Dan
>
>>
>> ./testp
>> $ Testing
>>
>> So far so good
>>
>> clang++ -O3 -std=c++11 -o testp testprogram.cpp
>>
>> No messages, no errors.
>>
>> ./testp
>> $ Testing
>>
>> Onwards and upwards
>>
>> clang++ -O3 -stdlib=libstdc++ -o testp testprogram.cpp
>>
>> And bom goes the dynamite:
>>
>> 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]
>> testprogram.cpp:1:10: fatal error: 'cstdio' file not found
>> #include <cstdio>
>> ^~~~~~~~
>> 1 warning and 1 error generated.
>>
>> I saw Andrew Schaubs response as well stating the following:
>>
>> StackExchange referenced twitter about libstdc++ and it's removal from
>> Xcode 10.0. The suggested work around was to install Xcode 9.4, and simply
>> copy the folders over:
>>
>> cp
>> /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk/usr/lib/libstdc++.*
>> /Applications/Xcode-beta.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk/usr/lib/
>> cp
>> /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk/usr/lib/libstdc++.*
>> /Applications/Xcode-beta.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk/usr/lib/
>>
>> "PSA: libstdc++ is gone from the iOS 12.0 SDK (it is present in the runtime
>> for binary compatibility). It's days are numbered on macOS as well. Migrate
>> over to libc++ if you haven't already. #WWDC2018 #cplusplus" @jeremyhu
>> https://stackoverflow.com/questions/50694822/xcode-10-ios-12-does-not-contain-libstdc6-0-9
>>
>> https://twitter.com/jeremyhu/status/1003882060556062720
>>
>> So obviously the libstdc++ is the issue. It should be replaced using libc++ instead, which I assume is a bunch of work. The workaround that Andrew provided might actually work, I do have my backups from where I could just pull the lib file/files i need. I will most likely try this since I have a hard time not leaving things undone though this is not a solution for the mac-related issues obviously.
>>
>> Thank you everyone for you help and input, I really enjoy posting to the AMBER forum since there is always good people providing excellent support here!
>>
>> Best regards
>> // Gustaf
>>
>> On 10 Oct 2018, at 15:52, Daniel Roe <daniel.r.roe.gmail.com<mailto:daniel.r.roe.gmail.com>> wrote:
>>
>> clang++ -O3 -o testp testprogram.cpp
>>
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Received on Fri Oct 12 2018 - 06:00:05 PDT
