[AMBER] Compilation Instructions for Mac M1?

From: Brandon Orzolek <orzolek.sas.upenn.edu>
Date: Tue, 16 Nov 2021 20:05:03 -0500

Hi all,

I'm wondering if anyone has made a complete installation guide for the new
Mac M1. I'm trying to get everything up and running and keep running into
various compilation errors. I've tried searching the archive but I think
I'm too new to this type of thing to really make anything of the
information already shared.

Thank you in advance!!!
bjo
Here is a copy of the cmake.log:


-- 
**************************************************************************
-- Starting configuration of Amber version 20.0.0...
-- CMake Version: 3.22.0
-- 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 found, building AmberTools and Amber
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!
-- Found perl make: /usr/bin/make
-- Perl modules well be installed to AMBERHOME/lib/perl
-- [1;34mRunning updater... [0m
-- >>> Preparing to apply updates... please wait.
-- >>> No new updates available for AmberTools 21
-- >>> No new updates available for Amber 20
-- [1;34mUpdater done.  If you want to install updates, then set the
APPLY_UPDATES variable to true. [0m
-- Checking whether to use built-in libraries...
-- Unable to locate MKL_HOME for your system.  To use MKL, set MKL_HOME to
point to your MKL installation location.
CMake Warning (dev) at
/Applications/CMake.app/Contents/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:438
(message):
  The package name passed to `find_package_handle_standard_args` (OpenMP_C)
  does not match the name of the calling package (OpenMPFixed).  This can
  lead to problems in calling code that expects `find_package` result
  variables (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408
(find_package_handle_standard_args)
  cmake/hanjianwei/FindMKL.cmake:194 (find_package)
  cmake/3rdPartyTools.cmake:219 (find_package)
  CMakeLists.txt:191 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
(found version "1.0")
CMake Warning (dev) at
/Applications/CMake.app/Contents/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:438
(message):
  The package name passed to `find_package_handle_standard_args`
(OpenMP_CXX)
  does not match the name of the calling package (OpenMPFixed).  This can
  lead to problems in calling code that expects `find_package` result
  variables (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408
(find_package_handle_standard_args)
  cmake/hanjianwei/FindMKL.cmake:194 (find_package)
  cmake/3rdPartyTools.cmake:219 (find_package)
  CMakeLists.txt:191 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS
OpenMP_CXX_LIB_NAMES) (found version "1.0")
CMake Warning (dev) at
/Applications/CMake.app/Contents/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:438
(message):
  The package name passed to `find_package_handle_standard_args`
  (OpenMP_Fortran) does not match the name of the calling package
  (OpenMPFixed).  This can lead to problems in calling code that expects
  `find_package` result variables (e.g., `_FOUND`) to follow a certain
  pattern.
Call Stack (most recent call first):
  cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408
(find_package_handle_standard_args)
  cmake/hanjianwei/FindMKL.cmake:194 (find_package)
  cmake/3rdPartyTools.cmake:219 (find_package)
  CMakeLists.txt:191 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.
-- Found OpenMP_Fortran: -fopenmp
-- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY
MKL_GFORTRAN_INTERFACE_LIBRARY MKL_INTEL_THREADING_LIBRARY MKL_CORE_LIBRARY
OpenMP_C_FOUND MKL_WORKS MKL_FORTRAN_WORKS)
-- Cannot search for FFTW Fortran headers because the serial headers were
not found
-- Could NOT find FFTW (missing: FFTW_LIBRARY_SERIAL FFTW_WORKS
FFTW_INCLUDES_SERIAL FFTW_FORTRAN_WORKS)
-- Failed to find NetCDF interface for F77 (NetCDF_INCLUDES_F77 =
NetCDF_INCLUDES_F77-NOTFOUND, NetCDF_LIBRARIES_F77 =
NetCDF_LIBRARIES_F77-NOTFOUND)
-- Failed to find NetCDF interface for F90 (NetCDF_INCLUDES_F90 =
NetCDF_INCLUDES_F90-NOTFOUND, NetCDF_LIBRARIES_F90 =
NetCDF_LIBRARIES_F90-NOTFOUND)
-- Could NOT find NetCDF (missing: NetCDF_C_WORKS NetCDF_LIBRARIES
NetCDF_INCLUDES)
-- Could NOT find XBLAS (missing: XBLAS_LIBRARY XBLAS_C_WORKS
XBLAS_FORTRAN_WORKS)
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- The ARPACK library was not found.  Please set ARPACK_LIBRARY to point to
it. (missing: ARPACK_LIBRARY ARPACK_WORKS)
-- Could not find some or all of the five main APBS libraries. Please set
APBS_GENERIC_LIB, APBS_ROUTINES_LIB,
APBS_PMGC_LIB, APBS_MG_LIB, and APBS_MALOC_LIB to point to the correct
libraries (missing: APBS_API_LIB APBS_ROUTINES_LIB APBS_MG_LIB
APBS_PMGC_LIB APBS_GENERIC_LIB APBS_MALOC_LIB APBS_WORKS APBS_INCLUDES)
The operation couldn’t be completed. Unable to locate a Java Runtime.
Please visit http://www.java.com for information on installing Java.
-- Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2
JAVA_AWT_INCLUDE_PATH)
-- Could NOT find PUPIL (missing: PUPIL_MAIN_LIB PUPIL_BLIND_LIB
PUPIL_TIME_LIB JNI_FOUND PUPIL_WORKS)
-- Could NOT find LIO (missing: LIO_G2G_LIBRARY LIO_AMBER_LIBRARY
LIO_WORKS)
-- Could NOT find PLUMED (missing: PLUMED_LIBRARY PLUMED_KERNEL_LIBRARY
PLUMED_INCLUDES PLUMED_WORKS) (Required is at least version "2.5")
-- Checking for perl module Chemistry::Mol
-- Checking for perl module Chemistry::Mol - failed
-- Failed to find Perl modules: Chemistry::Mol (missing:
PERLMODULES_CHEMISTRY_MOL_MODULE)
-- Could NOT find Boost (missing: Boost_INCLUDE_DIR thread system
program_options iostreams regex timer chrono filesystem graph)
-- Could NOT find MBX (missing: MBX_DIR)
-- Could not find MBX.  To locate it, add its install dir to the prefix
path.
-- Could NOT find tng_io (missing: tng_io_DIR)
-- Could not find tng_io.  To locate it, add its install dir to the prefix
path.
-- Cannot find PLUMED.  You will still be able to load it at runtime.  If
you want to link it at build time, set PLUMED_ROOT to where you installed
it.
-- Generating amber source scripts
-- Configuring subdirs...
-- FFTW: compiler supports stack alignment: FALSE
CMake Error at
/Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface.cmake:391
(message):
  The Fortran compiler:
    /usr/local/bin/gfortran
  and the C compiler:
    /usr/bin/clang
  failed to compile a simple test project using both languages.  The output
  was:
    Change Dir:
/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC
    Run Build Command(s):/usr/bin/make -f Makefile VerifyFortranC &&
/Applications/CMake.app/Contents/bin/cmake
-S/Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify
-B/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC
--check-build-system CMakeFiles/Makefile.cmake 0
    /Library/Developer/CommandLineTools/usr/bin/make  -f
CMakeFiles/Makefile2 VerifyFortranC
    /Applications/CMake.app/Contents/bin/cmake
-S/Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify
-B/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC
--check-build-system CMakeFiles/Makefile.cmake 0
    /Applications/CMake.app/Contents/bin/cmake -E cmake_progress_start
/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC/CMakeFiles
5
    /Library/Developer/CommandLineTools/usr/bin/make  -f
CMakeFiles/Makefile2 CMakeFiles/VerifyFortranC.dir/all
    /Library/Developer/CommandLineTools/usr/bin/make  -f
CMakeFiles/VerifyFortran.dir/build.make CMakeFiles/VerifyFortran.dir/depend
    cd
/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC
&& /Applications/CMake.app/Contents/bin/cmake -E cmake_depends "Unix
Makefiles"
/Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify
/Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify
/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC
/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC
/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC/CMakeFiles/VerifyFortran.dir/DependInfo.cmake
    Scanning dependencies of target VerifyFortran
    /Library/Developer/CommandLineTools/usr/bin/make  -f
CMakeFiles/VerifyFortran.dir/build.make CMakeFiles/VerifyFortran.dir/build
    [ 20%] Building Fortran object
CMakeFiles/VerifyFortran.dir/VerifyFortran.f.o
    /usr/local/bin/gfortran
 -I/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC
-Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none
-Wno-unused-dummy-argument -Wno-unused-variable -isysroot
/Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk -c
/Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify/VerifyFortran.f
-o CMakeFiles/VerifyFortran.dir/VerifyFortran.f.o
    [ 40%] Linking Fortran static library libVerifyFortran.a
    /Applications/CMake.app/Contents/bin/cmake -P
CMakeFiles/VerifyFortran.dir/cmake_clean_target.cmake
    /Applications/CMake.app/Contents/bin/cmake -E cmake_link_script
CMakeFiles/VerifyFortran.dir/link.txt --verbose=1
    /usr/bin/ar qc libVerifyFortran.a
CMakeFiles/VerifyFortran.dir/VerifyFortran.f.o
    /usr/bin/ranlib libVerifyFortran.a
    [ 40%] Built target VerifyFortran
    /Library/Developer/CommandLineTools/usr/bin/make  -f
CMakeFiles/VerifyFortranC.dir/build.make
CMakeFiles/VerifyFortranC.dir/depend
    cd
/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC
&& /Applications/CMake.app/Contents/bin/cmake -E cmake_depends "Unix
Makefiles"
/Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify
/Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify
/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC
/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC
/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC/CMakeFiles/VerifyFortranC.dir/DependInfo.cmake
    /Library/Developer/CommandLineTools/usr/bin/make  -f
CMakeFiles/VerifyFortranC.dir/build.make CMakeFiles/VerifyFortranC.dir/build
    [ 60%] Building C object CMakeFiles/VerifyFortranC.dir/main.c.o
    /usr/bin/clang
 -I/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC
-Wall -Wno-unused-function -arch arm64 -isysroot
/Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk -MD -MT
CMakeFiles/VerifyFortranC.dir/main.c.o -MF
CMakeFiles/VerifyFortranC.dir/main.c.o.d -o
CMakeFiles/VerifyFortranC.dir/main.c.o -c
/Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify/main.c
    [ 80%] Building C object CMakeFiles/VerifyFortranC.dir/VerifyC.c.o
    /usr/bin/clang
 -I/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/FortranCInterface/VerifyC
-Wall -Wno-unused-function -arch arm64 -isysroot
/Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk -MD -MT
CMakeFiles/VerifyFortranC.dir/VerifyC.c.o -MF
CMakeFiles/VerifyFortranC.dir/VerifyC.c.o.d -o
CMakeFiles/VerifyFortranC.dir/VerifyC.c.o -c
/Applications/CMake.app/Contents/share/cmake-3.22/Modules/FortranCInterface/Verify/VerifyC.c
    [100%] Linking C executable VerifyFortranC
    /Applications/CMake.app/Contents/bin/cmake -E cmake_link_script
CMakeFiles/VerifyFortranC.dir/link.txt --verbose=1
    /usr/bin/clang  -Wall -Wno-unused-function -arch arm64 -isysroot
/Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk
-Wl,-search_paths_first -Wl,-headerpad_max_install_names
CMakeFiles/VerifyFortranC.dir/main.c.o
CMakeFiles/VerifyFortranC.dir/VerifyC.c.o -o VerifyFortranC
-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0
 -L/usr/local/gfortran/lib  libVerifyFortran.a -lgfortran -lgcc_ext.10.5
-lgcc -lquadmath -lm -lgcc_ext.10.5 -lgcc
    ld: warning: ignoring file
/usr/local/gfortran/lib/libgcc_ext.10.5.dylib, missing required
architecture arm64 in file /usr/local/gfortran/lib/libgcc_ext.10.5.dylib (1
slices)
    ld: warning: ignoring file libVerifyFortran.a, building for macOS-arm64
but attempting to link with file built for macOS-x86_64
    ld: warning: ignoring file
/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0/libgcc.a, building
for macOS-arm64 but attempting to link with file built for macOS-x86_64
    ld: warning: ignoring file /usr/local/gfortran/lib/libgfortran.dylib,
building for macOS-arm64 but attempting to link with file built for
macOS-x86_64
    ld: warning: ignoring file /usr/local/gfortran/lib/libquadmath.dylib,
building for macOS-arm64 but attempting to link with file built for
macOS-x86_64
    Undefined symbols for architecture arm64:
      "_VerifyFortran", referenced from:
          _main in main.c.o
    ld: symbol(s) not found for architecture arm64
    clang: error: linker command failed with exit code 1 (use -v to see
invocation)
    make[3]: *** [VerifyFortranC] Error 1
    make[2]: *** [CMakeFiles/VerifyFortranC.dir/all] Error 2
    make[1]: *** [CMakeFiles/VerifyFortranC.dir/rule] Error 2
    make: *** [VerifyFortranC] Error 2
Call Stack (most recent call first):
  AmberTools/src/fftw-3.3/CMakeLists.txt:420 (FortranCInterface_VERIFY)
-- Configuring incomplete, errors occurred!
See also
"/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/CMakeOutput.log".
See also
"/Users/orz/Applications/apps/amber20_src/build/CMakeFiles/CMakeError.log".
-- 
Brandon J. Orzolek
*Pronouns: *he/him, they/them
Ph.D. Candidate, University of Pennsylvania
Department of Chemistry
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Received on Tue Nov 16 2021 - 17:30:02 PST
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