Dear Hai and David:
Thanks so much for your response! I think the clang compiler was the issue. I did “make distclean” to uninstall AmberTools17 and removed the entire directory and then did what Hai suggested. After reinstallation, tLeap seems to be exporting the files successfully now!
Thanks again!
Best,
Andy Liu
> On Jun 21, 2017, at 4:37 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> hi, you can try either
>
> - install binary distribution
> - If you already installed suggested gfortran (amber website), you can
> switch to GNU compiler
> export CC=/usr/local/gfortran/bin/gcc
> export CXX=/usr/local/gfortran/bin/g++
>
> ./configure gnu
>
> (or set CC and CXX to your installed GNU compiler)
>
> .Dave: I got similar issue with tleap, macos+clang on my mac for amber-dev
> too (reported).
>
> Hai
>
>
> On Wed, Jun 21, 2017 at 9:53 AM, Xichong Liu <xichongl.princeton.edu> wrote:
>
>> Hi David:
>>
>> I used ./configure clang -macAccelerate for the configure script during
>> the installation. “Which gcc” gives “/usr/bin/gcc” and “gcc -v” gives:
>>
>> Configured with: --prefix=/Library/Developer/CommandLineTools/usr
>> --with-gxx-include-dir=/usr/include/c++/4.2.1
>> Apple LLVM version 8.1.0 (clang-802.0.42)
>> Target: x86_64-apple-darwin16.6.0
>> Thread model: posix
>> InstalledDir: /Library/Developer/CommandLineTools/usr/bin
>>
>> After running configure with -debug option, the same error messages
>> remained and no new information was generated. I’m not sure if this is
>> specific for AmberTools17 because it’s the only one I have installed. I
>> could try using a different version later. The MacOS I’m using is Sierra
>> 10.12.5.
>>
>> Thanks for the help!
>>
>> Andy Liu
>>
>>
>>> On Jun 21, 2017, at 2:45 PM, David A Case <david.case.rutgers.edu>
>> wrote:
>>>
>>> On Wed, Jun 21, 2017, Xichong Liu wrote:
>>>>
>>>> I have recently installed AmberTools17 on my personal MacBook and ran
>>>> into some issues with Leap.
>>>
>>> Thanks for the report. What options did you give to the configure
>> script?
>>> What is the result of the commands "which gcc" and "gcc -v"? Finally,
>>> what version of MacOS are you using?
>>>
>>> This sounds like a tough thing to debug until someone else has a machine
>>> on which the tleap tests fail in this manner. You can try this:
>>>
>>> Re-run configure with the "-debug" option; recompile; then see what
>> happens
>>> on one of the tleap test cases. It may work then; or you may get more
>>> information; or you may not learn anything useful.
>>>
>>> (Aside: do you know if this is specific to AmberTools17? That is, have
>>> you run an earlier version of AmberTools using this machine and
>> compilers?)
>>>
>>> ...dac
>>>
>>>
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>>
>>
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Received on Wed Jun 21 2017 - 14:00:02 PDT
