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
>>
>> _______________________________________________
>> 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 Tue Apr 02 2019 - 06:30:03 PDT
