Re: [AMBER] New compile-issue macOS, CPPTRAJ

From: David A Case <>
Date: Mon, 1 Apr 2019 10:45:28 -0400

On Mon, Apr 01, 2019, Gustaf Olsson 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
>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.

Me too. Do you have a CXX envinroment variable set, and if so, to what?
I suspect that this error, and the one below, are both a result of
having a cpptraj configure script that is separate from Amber's
configure script (since Dan distributes cpptraj as a separate program.)
They are somehow not handshaking with each other like they should.

>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"
> ^~~~~~~~~~
>compilation terminated.

This is a similar problem: somehow, inside the cpptraj configure,
${LIB_INCL[$LNETCDF]} is not being set. It should be looking in
$AMBERHOME/lib, but it's not.

Thanks for the report. We are making a real effort to have AmberTools19
"just work" on OSX, indedepent of Mojave vs. earlier versions, and
independent of whether clang or gcc is used. But we are clearly not
"there" yet. For the git problems, it's probably best to add comments
to issue #45 at gitlab.


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Received on Mon Apr 01 2019 - 08:00:02 PDT
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