Re: [AMBER] Amber Installation Problem on Mac

From: David A Case <>
Date: Fri, 4 Oct 2019 10:10:13 -0400

On Thu, Oct 03, 2019, Fanglue Ni wrote:
>I'm trying to install Amber19-with-patches on macOS mojave 10.14.6. I
>installed the amber with ./configure gnu and it shows an error message:
>Obtaining the gnu compiler suite versions, e.g.:
> gcc -v
>The C version is 5.5.0
>The Fortran version is 5.5.0
>Testing the gcc compiler:
> gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
>In file included from testp.c:1:0:
>fatal error: _stdio.h: No such file or directory
>compilation terminated.

We are aware of this problem, which seems to have arisen with the recent
release of XCode11. [At least for me, I have no trouble with macports
gcc installations on machines that are still at XCode version 10, but I
see the above problem with XCode 11.]

One part of the problem is that gcc from macports seems to be looking
for an include path that was removed from XCode11. You could try this:

cd /Applications/

If there is not a soft link from MacOSX10.14.sdk -> MacOSX.sdk, you can
create one; (warning: this requires sudo, so decide how much risk you
want to take....) This will fix the configure problem involving
"_stdio.h" listed above, but I still have other compilation problems.
I'll report any other progress I'm able to make.)

>I installed the gcc5 as instruction on the official website.

Can you say what you mean by "the official website"? If it is one of
ours, we may need to fix this. We recommend using clang (and not gcc)
for OSX installations of Amber.


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Received on Fri Oct 04 2019 - 07:30:02 PDT
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