Hey guys, I thought I should add what the ./configure -macAccelerate clang gave as a result:
waltonsmith.Waltons-Air amber20_src % ./configure -macAccelerate clang
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 20 patches:
No patches available
AMBER_PREFIX=/applications/amber20_src
AMBER_SOURCE=/applications/amber20_src
Using the AmberTools miniconda installation in /applications/amber20_src/miniconda
version 2.7.18
Obtaining the clang compiler suite versions, e.g.:
clang -v
The C version is 11.0.3
The Fortran version is ../gcc-6.3.0/configure
6.3.0
Testing the clang compiler:
clang -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK
Testing the clang++ compiler:
clang++ -fPIC -o testp testp.cpp
OK
Testing the gfortran compiler:
gfortran -fPIC -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
clang -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c
gfortran -fPIC -O0 -c -o testp.f.o testp.f
clang -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0/../../../ -lgfortran -w -framework Accelerate
OK
Testing pointer size:
clang -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size test_pointer_size.c
Detected 64 bit operating system.
Testing flex: OK
Testing bison: OK
Checking NetCDF...
Using bundled NetCDF library.
Starting NetCDF build.
Configuring NetCDF C interface (may be time-consuming)...
Compiling the NetCDF C interface (may be time-consuming)...
Configuring NetCDF Fortran interface (may be time-consuming)...
Compiling the NetCDF Fortran interface (may be time-consuming)...
NetCDF build succeeded.
Checking for zlib: OK
Checking for libbz2: OK
Configuring fftw-3.3 (may be time-consuming)...OK
Compiling the FFTW3 interface (may be time-consuming)...OK
Configuring boost (may be time-consuming)...OK
Compiling boost (may be time-consuming)...
Error: Boost compile failed.
Check /applications/amber20_src/AmberTools/src/boost_config.log
memembed and moft will not be built
Configuring XBLAS (may be time-consuming)...OK
Compiling XBLAS (may be time-consuming)...OK
Configuring CPPTRAJ...OK
The configuration file, config.h, was successfully created.
--------------------------------------------------------------------------------
Environment resource files are provided to set the proper environment
variables to use AMBER and AmberTools. This is required to run any Python
programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj)
If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
/applications/amber20_src/amber.sh file in your shell. Consider adding the line
test -f /applications/amber20_src/amber.sh && source /applications/amber20_src/amber.sh
to your startup file (e.g., ~/.bashrc)
If you use a C shell (e.g., csh, tcsh), source the
/applications/amber20_src/amber.csh file in your shell. Consider adding the line
test -f /applications/amber20_src/amber.csh && source /applications/amber20_src/amber.csh
to your startup file (e.g., ~/.cshrc)
NOTE: MacOS users might need to add the content to ~/.bash_profile file
(You need to do the above before running 'make install')
--------------------------------------------------------------------------------
The next step is to source the amber.sh or amber.csh file
(if needed, see above), and then to type 'make install'
Cleaning the src directories. This may take a few moments.
Configure complete.
Best,
WS
> On Jul 29, 2020, at 3:50 PM, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> So, just make sure you have the right compilers:
>
>
> ~ which gcc
>
> /usr/bin/gcc
>
> ~ gcc --version
>
> ...
>
> Apple clang version 11.0.3 (clang-1103.0.32.62)
>
> ...
>
> ~ clang --version
>
> ...
>
> Apple clang version 11.0.3 (clang-1103.0.32.62)
>
> ...
>
> Meaning that /usr/bin/gcc is a symlink to /usr/bin/clang (they are the same)
>
> ~ which gfortran
> /usr/local/bin/gfortran
> ~ gfortran --version
> GNU Fortran (Homebrew GCC 10.1.0) 10.1.0
>
> I have not managed to compile amber using any version of gcc higher then 7, this is why I switch to gcc7 or lower. So for you I hope that the output is 7.X.X or lower.
>
> If these things are correct, you should go to "/path/to/amber20_src/" and try to do a "./configure -macAccelerate clang" and see what happens.
>
> Best regards
> // Gustaf
>
> ________________________________
> Från: Walton Smith <smit7450.mylaurier.ca>
> Skickat: den 29 juli 2020 16:26:19
> Till: AMBER Mailing List
> Ämne: Re: [AMBER] Error building Amber
>
> When I try and run the legacy build it gives me this error: ERROR:
>
> Wrong compiler. You specify compiler=gnu but actually using clang
> Please change compiler option to clang, or set correct PATH (or CC, CXX) to GNU compiler
>
> I thought that I fixed the compiler issue and set the correct path. Again, I’m a huge noob when it comes to using terminal. Maybe this will give you more insight into the issue?
>
> WS
>
>
>> On Jul 29, 2020, at 7:58 AM, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>
>> I had conflicting headers as I had not restarted my computer after the Xcode update, this resolved the stdio.h issue.
>>
>>
>> However, when I try to use the cmake configure script now I also fail with an error:
>>
>>
>> ld: unknown option: --no-as-needed
>> clang: error: linker command failed with exit code 1 (use -v to see invocation)
>> make[1]: *** [cmTC_99500] Error 1
>> make: *** [cmTC_99500/fast] Error 2
>>
>>
>> I am not sure that the OSX linker supports the "no-as-needed" option.
>>
>>
>> This fails with both gcc7 and 10. The "legacy" configure script finishes though I have not yet had time to see if the build succeeds.
>>
>>
>> // Gustaf
>>
>> ________________________________
>> Från: David A Case <david.case.rutgers.edu>
>> Skickat: den 29 juli 2020 05:17:05
>> Till: AMBER Mailing List
>> Ämne: Re: [AMBER] Error building Amber
>>
>>> On Tue, Jul 28, 2020, Walton Smith wrote:
>>>>
>>>> I have a libbz2.1.0.tbd file but no libbz2.dylib file in /usr/lib. My
>>>> version of Xcode is version 11.6.
>>
>> Quick update: I've upgraded to XCode 11.6, and OSX 10.15.6. I don't see any
>> .tbd files in /usr/lib, just .dylib files.
>>
>> Amber installation using cmake runs fine for me.
>>
>> So, one needs to figure out how it is you don't have libbz2.dylib (and, I'm
>> assuming, other *.dylib files) in /usr/lib. I use a mac, but am no OSX guru
>> by any means. I don't see any obvious hits on Google. We'll see if any other
>> OSX user on the list reports a configuration like yours.
>>
>> ....dac
>>
>>
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>
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Received on Wed Jul 29 2020 - 18:00:02 PDT
