Could you try compiling it now?
On Tuesday 6 August 2024, Vishwaa Kannan <vishwaakannan.icloud.com> wrote:
> Is gfortran not gcc?
>
> vishwaa.vishwaa build % gfortran -v
>
> Using built-in specs.
>
> COLLECT_GCC=gfortran
>
> COLLECT_LTO_WRAPPER=/opt/homebrew/Cellar/gcc/14.1.0_2/
> bin/../libexec/gcc/aarch64-apple-darwin23/14/lto-wrapper
>
> Target: aarch64-apple-darwin23
>
> Configured with: ../configure --prefix=/opt/homebrew/opt/gcc
> --libdir=/opt/homebrew/opt/gcc/lib/gcc/current --disable-nls
> --enable-checking=release --with-gcc-major-version-only
> --enable-languages=c,c++,objc,obj-c++,fortran,m2 --program-suffix=-14
> --with-gmp=/opt/homebrew/opt/gmp --with-mpfr=/opt/homebrew/opt/mpfr
> --with-mpc=/opt/homebrew/opt/libmpc --with-isl=/opt/homebrew/opt/isl
> --with-zstd=/opt/homebrew/opt/zstd --with-pkgversion='Homebrew GCC
> 14.1.0_2' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues
> --with-system-zlib --build=aarch64-apple-darwin23 --with-sysroot=/Library/
> Developer/CommandLineTools/SDKs/MacOSX14.sdk
>
> Thread model: posix
>
> Supported LTO compression algorithms: zlib zstd
>
> gcc version 14.1.0 (Homebrew GCC 14.1.0_2)
>
> vishwaa.vishwaa build %
>
> On Aug 6, 2024, at 10:43, Elvis Martis <elvis.afmartis.gmail.com> wrote:
>
> Have you installed gfortran?
>
> What is the output for
>
> gfortran -v
> ??
> On Tuesday 6 August 2024, Vishwaa Kannan <vishwaakannan.icloud.com> wrote:
>
>> vishwaa.vishwaa build % mpirun --version
>>
>> mpirun (Open MPI) 5.0.3
>>
>> Report bugs to https://www.open-mpi.org/community/help/
>> vishwaa.vishwaa build % clang --version
>> Apple clang version 15.0.0 (clang-1500.3.9.4)
>> Target: arm64-apple-darwin23.6.0
>> Thread model: posix
>> InstalledDir: /Applications/Xcode.app/Conten
>> ts/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>> vishwaa.vishwaa build % xcode-select --version
>> xcode-select version 2408.
>> vishwaa.vishwaa build % cmake --version
>> cmake version 3.30.1
>>
>> CMake suite maintained and supported by Kitware (kitware.com/cmake).
>> vishwaa.vishwaa build % gcc --version
>> Apple clang version 15.0.0 (clang-1500.3.9.4)
>> Target: arm64-apple-darwin23.6.0
>> Thread model: posix
>> InstalledDir: /Applications/Xcode.app/Conten
>> ts/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>> vishwaa.vishwaa build %
>>
>> Any other ones needed?
>>
>> On Aug 6, 2024, at 10:23, Elvis Martis via AMBER <amber.ambermd.org>
>> wrote:
>>
>> Can you confirm your compiler versions ?
>>
>> On Tuesday 6 August 2024, Vishwaa Kannan <vishwaakannan.icloud.com>
>> wrote:
>>
>> Same error
>>
>> I tried this:
>> export LD_LIBRARY_PATH=/opt/homebrew/Cellar/open-mpi/5.0.3_1/lib:$
>> LD_LIBRARY_PATH
>> Source ~/.zshrc
>>
>> On Aug 6, 2024, at 08:38, Elvis Martis <elvis.afmartis.gmail.com> wrote:
>>
>> Could try to explicitly define the paths for all libraries using
>> LD_LIBRARY_PATH in your bashrc.
>>
>> On Tuesday 6 August 2024, Vishwaa Kannan <vishwaakannan.icloud.com>
>> wrote:
>>
>> When I disable the two, and have -DMPI = TRUE, I get an error at 34% mark:
>>
>> [ 34%] Linking CXX shared library libquick_mpi.dylib ld: warning:
>>
>> -undefined error is deprecated ld: warning: -commons use_dylibs is no
>> longer supported, using error treatment instead ld: common symbol
>> '_mpi_fortran_argv_null_' from '/Users/vishwaa/amber/amber24_
>> src/build/AmberTools/src/quick/src/CMakeFiles/libquick_mpi.
>> dir/modules/quick_mpi_module.f90.o' conflicts with definition from dylib
>> '_mpi_fortran_argv_null_' from '/opt/homebrew/Cellar/open-mpi
>> /5.0.3_1/lib/libmpi_usempi_ignore_tkr.40.dylib' clang: error: linker
>> command failed with exit code 1 (use -v to see invocation) make[2]: ***
>> [AmberTools/src/quick/src/libquick_mpi.dylib] Error 1 make[1]: ***
>> [AmberTools/src/quick/src/CMakeFiles/libquick_mpi.dir/all] Error 2 make:
>> *** [all] Error 2 vishwaa.vishwaa build %
>>
>> If I don’t install open-mpi via home-brew, then I get an error in the
>> build portion. Please help.
>>
>> On Aug 6, 2024, at 05:49, Elvis Martis via AMBER <amber.ambermd.org>
>>
>> wrote:
>>
>>
>> Hi Xavier
>>
>> For some reason it is known problem with M2.
>> You need to disable moft also.
>>
>> To disable both
>> -DDISABLE_TOOLS=“packmol_memgen;moft”
>>
>> I hope this helps
>>
>>
>> On Tuesday 6 August 2024, Xavier Brazzolotto via AMBER <
>>
>> amber.ambermd.org>
>>
>> wrote:
>>
>> I have issues installing Amber/AmberTools24 on my MacBookPro M2
>>
>> Make install ends with an error with packmol_memgen.
>>
>> If I remove this tool using -DDISABLE_TOOLS=« packmol_memgen » the
>> compilation stops then at the « moft » tool
>>
>> I didn’t find a way to remove both tools together. Any idea of the
>>
>> right
>>
>> synthax to use ?
>>
>> Xavier
>>
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>>
>>
>>
>> --
>> Best Regards
>> Elvis
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>
>> --
>> Best Regards
>> Elvis
>>
>>
>>
>>
>> --
>> Best Regards
>> Elvis
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>
> --
> Best Regards
> Elvis
>
>
>
--
Best Regards
Elvis
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Received on Tue Aug 06 2024 - 09:00:01 PDT
