macOS Catalina version 10.15.5
Xcode 11.6 (11E708)
$ cd amber20_src/build
$ CC=/usr/bin/clang && CXX=/usr/bin/clang++ && FC=/usr/local/bin/gfortran-7
$ perl -pi -e -w 's/DCOMPILER=CLANG/DCOMPILER=MANUAL/g;' run_cmake
$ ./run_cmake
-- **************************************************************************
-- Starting configuration of Amber version 20.0.0...
-- CMake Version: 3.18.0
-- For how to use this build system, please read this wiki:
--
http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
-- For a list of important CMake variables, check here:
--
http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
-- **************************************************************************
-- Amber source not found, only building AmberTools
-- The C compiler identification is AppleClang 11.0.3.11030032
-- The CXX compiler identification is AppleClang 11.0.3.11030032
-- The Fortran compiler identification is GNU 7.5.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Checking whether Fortran compiler has -isysroot
-- Checking whether Fortran compiler has -isysroot - yes
-- Checking whether Fortran compiler supports OSX deployment target flag
-- Checking whether Fortran compiler supports OSX deployment target flag - yes
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /usr/local/bin/gfortran - skipped
-- Checking whether /usr/local/bin/gfortran supports Fortran 90
-- Checking whether /usr/local/bin/gfortran supports Fortran 90 - yes
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
-- Miniconda is installed in the build directory!
...
...
...
-- If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
-- /Users/user/Mjukvara/amber20//amber.sh file in your shell. Consider adding the line
-- test -f /Users/user/Mjukvara/amber20//amber.sh && source /Users/user/Mjukvara/amber20//amber.sh
-- to your startup file (e.g., ~/.bashrc)
--
-- If you use a C shell (e.g., csh, tcsh), source the
-- /Users/user/Mjukvara/amber20//amber.csh file in your shell. Consider adding the line
-- test -f /Users/user/Mjukvara/amber20//amber.csh && source /Users/user/Mjukvara/amber20//amber.csh
-- to your startup file (e.g., ~/.cshrc)
--
-- NOTE: MacOS users might need to source it in ~/.bash_profile file
-- Amber will be installed to /Users/user/Mjukvara/amber20/
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/user/Mjukvara/amber20_src/build
As you already have homebrew installed, why not use homebrew to install cmake as well.
Regardless, the configuration works for me. However, the update of xcode that arrived last week obviosly broke the compilation again....!!!...!.!!!
Scanning dependencies of target xblas_build
[ 22%] Creating directories for 'xblas_build'
[ 22%] Performing download step for 'xblas_build'
[ 22%] No update step for 'xblas_build'
[ 22%] No patch step for 'xblas_build'
[ 22%] No configure step for 'xblas_build'
[ 22%] Performing build step for 'xblas_build'
BLAS_error.c:1:10: fatal error: 'stdio.h' file not found
#include <stdio.h>
^~~~~~~~~
1 error generated.
make[4]: *** [BLAS_error.o] Error 1
make[3]: *** [common-lib] Error 2
make[2]: *** [AmberTools/src/xblas/src/xblas_build-stamp/xblas_build-build] Error 2
make[1]: *** [AmberTools/src/xblas/CMakeFiles/xblas_build.dir/all] Error 2
make: *** [all] Error 2
So it looks like another include error and it seems like yet again I am back to square one. Fantastic news as the suggested execution worked last week before the update.
Best regards
// Gustaf
________________________________
Från: Walton Smith <smit7450.mylaurier.ca>
Skickat: den 28 juli 2020 16:03:42
Till: david.case.rutgers.edu; AMBER Mailing List
Ämne: Re: [AMBER] Error building Amber
Hey guys,
I have a libbz2.1.0.tbd file but no libbz2.dylib file in /usr/lib. My version of Xcode is version 11.6, and cmake was downloaded as instructed off of cmake.org. /Applications/Cmake.app/contents/bin was placed in my PATH through the command shown on
https://ambermd.org/InstMacOS.php <
https://ambermd.org/InstMacOS.php>. I installed the gnu gcc compiler you suggested (version 7) and extracted it to a clean build folder and nothing seemed to change.
Thanks for looking into this for me.
Best,
WS
> On Jul 28, 2020, at 9:43 AM, David A Case <david.case.rutgers.edu> wrote:
>
> On Mon, Jul 27, 2020, Walton Smith wrote:
>>
>> I’m using Catalina (10.15.5), and I do have homebrew from when I installed
>> the open source PyMOL. In my /usr/local/lib folder I have cmake, docker,
>> python3.7 and python 3.8 along with an unknown pkgconfig folder and
>> several lib—.dylib and .a files. I have attached the cmake.log file. Let
>> me know if you might have any idea. Thank you so much for getting back to
>> me so fast.
>
> Thanks for the details. Here is the error message from the cmake.log file:
>
> CMake Error at cmake/LibraryUtils.cmake:75 (message):
> Could not determine whether
> "/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/lib/libbz2.tbd"
> is a static or shared library, it does not have a known suffix.
> Call Stack (most recent call first):
> cmake/LibraryTracking.cmake:40 (get_lib_type)
> cmake/LibraryTracking.cmake:196 (using_external_library)
> cmake/3rdPartyTools.cmake:956 (import_libraries)
> CMakeLists.txt:194 (include)
>
> All Mac's have *.tbd files in the indicated directory, but this is the first
> problem report we have seen.
>
> Do you have a libbz2.dylib file in /usr/lib? I would
> think that the external library searching routine should find that one first.
>
> cc-ing to Jaime for his thoughts. Jamie: if the library search finds an
> unknown suffix, why not just ignore it, rather than exiting with an error?
>
> Here is info on .tbd files:
>
> https://stackoverflow.com/questions/31450690/why-xcode-7-shows-tbd-instead-of-dylib
>
> One possible other thing to try: My guess is that you are using the
> homebrew installation of cmake, and that might make your machine different
> from mine. Can you try the suggestion here:
>
> https://ambermd.org/InstMacOS.php
>
> and get (as instructed) /Applications/Cmake.app/Contents/bin first in your
> PATH? That will have you use the version of cmake from cmake.org.
> (This might solve the problem, but it seems to be a bit of a stretch.)
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jul 28 2020 - 15:00:03 PDT
