What is the source for the gfortran binaries?
Are you using the gcc binaries and compiling with the included gfortran and gcc or do you mean the "clean" gfortran binaries and the built in macOS “gcc” (clang)?
Best regards
// Gustaf
> On 2 Apr 2019, at 15:26, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> I personally only use native clang or gcc bundled in gfortran binary for
> macos. Both works well for me. I am not sure if we need macport or brew
> anymore.
>
> Hai
>
> On Tue, Apr 2, 2019 at 9:24 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
>> So after a couple of frustrating runs I have tried to patch the source and
>> compile my own gcc8 version from source, while pushing the error further
>> and further away I can’t compile gcc8 because of the following error:
>>
>> In file included from /usr/include/sys/sysctl.h:83,
>> from ../../gcc/config/darwin-driver.c:30:
>> /usr/include/sys/ucred.h:94:2: error: ‘_Atomic’ does not name a type
>> _Atomic u_long cr_ref; /* reference count */
>> ^~~~~~~
>> make[3]: *** [darwin-driver.o] Error 1
>> make[3]: *** Waiting for unfinished jobs....
>> rm gcc.pod gfortran.pod
>> make[2]: *** [all-stage2-gcc] Error 2
>> make[1]: *** [stage2-bubble] Error 2
>> make: *** [all] Error 2
>>
>> Looks familiar? "error: ‘_Atomic’ does not name a type”. So apparently
>> the supplied patch did not solve this issue as suggested either. Well, at
>> least clang works fairly well with little modification for now. Anyone
>> tried a GNU (gcc/gfortran) installation (no clang) using MacPorts compilers
>> yet? Otherwise I’ll put this on my list of things to try.
>>
>> Best regards
>> // Gustaf
>>
>>> On 2 Apr 2019, at 09:27, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>>
>>>> Do you have a CXX envinroment variable set, and if so, to what?
>>>> ...thx...dac
>>>
>>>
>>> I did not, though setting it does not change anything, unfortunately.
>>>
>>>> This actually appears to be the result of Apple mucking with header
>>>> files and is GNU/C++ specific on Mojave; see
>>>>
>> https://apple.stackexchange.com/questions/355049/compilation-error-with-mojave-error-atomic-does-not-name-a-type
>> .
>>>
>>> So the way that I am reeding this, it stems from an issue with the
>> homebrew gcc installation? I would either need to compile gcc myself from
>> source implementing the patch as indicated or find a way to configure the
>> amber cpptraj compilation without c++11 support? The first option would
>> only be “simple enough” if the patched version of gcc works and I can push
>> it to the homebrew repository fo re-use. The latter might work “out of the
>> box” though it is annoying.
>>>
>>>> This seems like you're using the standalone cpptraj configure from
>>>> inside AmberTools maybe? If so, you should execute it the same way
>>>> $AMBERHOME/AmberTools/src/configure2 does, specifying
>>>> '--with-netcdf=$AMBERHOME' etc so it knows where to get NetCDF etc
>>>> (search for 'Configure CPPTRAJ' in configure2).
>>>>
>>>> -Dan
>>>
>>> I was trying to build the standalone version of cpptraj from GitHub
>> independently from amber to see if it made any difference though I did not
>> manage to get cpptraj to find the system installed NetCDF version that I
>> have. Though maybe now I can specify using
>> --with-netcdf=/location/of/netcdf to completely ignore the amber18 folder
>> and have an isolated compilation of cpptraj?
>>>
>>> Best regards
>>> // Gustaf
>>>
>>>
>>>> On 1 Apr 2019, at 17:18, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>>
>>>> Hi,
>>>>
>>>> On Mon, Apr 1, 2019 at 8:04 AM Gustaf Olsson <gustaf.olsson.lnu.se>
>> wrote:
>>>>> CXX StringRoutines.cpp
>>>>> In file included from
>> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/sysctl.h:83,
>>>>> from StringRoutines.cpp:14:
>>>>>
>> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/ucred.h:94:2:
>> error: '_Atomic' does not name a type
>>>>> _Atomic u_long cr_ref; /* reference count */
>>>>> ^~~~~~~
>>>>> make[4]: *** [StringRoutines.o] Error 1
>>>>> make[3]: *** [install] Error 2
>>>>> make[2]: *** [build_cpptraj] Error 2
>>>>> make[1]: *** [serial] Error 2
>>>>> make: *** [install] Error 2
>>>>>
>>>>> This is seemingly an issue with CPPTRAJ that does not show up when
>> compiling using clang so I am assuming this is somehow related to gcc. Now,
>> I know that macOS does not make it easy compiling though I am curious why
>> something would be sourced from the Xcode CLT when not using the apple
>> compiler.
>>>>
>>>> This actually appears to be the result of Apple mucking with header
>>>> files and is GNU/C++ specific on Mojave; see
>>>>
>> https://apple.stackexchange.com/questions/355049/compilation-error-with-mojave-error-atomic-does-not-name-a-type
>> .
>>>> I'm not sure what the proper workaround is; maybe disabling C++11 for
>>>> cpptraj? Can you try configuring cpptraj standalone (either via
>>>> $AMBERHOME/AmberTools/src/cpptraj or via the GitHub version) with
>>>> -noc++11?
>>>>
>>>>>
>>>>> Trying to build from git, I get a NetCDF test error:
>>>>>
>>>>> Checking NetCDF:
>>>>> Test compile failed: g++ -Wall -O3 -std=gnu++11 -o testp
>> testp.cpp -lnetcdf
>>>>> Error follows:
>>>>> testp.cpp:2:10: fatal error: netcdf.h: No such file or directory
>>>>> #include "netcdf.h"
>>>>
>>>> This seems like you're using the standalone cpptraj configure from
>>>> inside AmberTools maybe? If so, you should execute it the same way
>>>> $AMBERHOME/AmberTools/src/configure2 does, specifying
>>>> '--with-netcdf=$AMBERHOME' etc so it knows where to get NetCDF etc
>>>> (search for 'Configure CPPTRAJ' in configure2).
>>>>
>>>> -Dan
>>>>
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>>>
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Received on Tue Apr 02 2019 - 07:00:02 PDT
