[AMBER] help for the installation of Ambertools 17 on Mac

From: huangwc8 <drhuangwc8.gmail.com>
Date: Fri, 13 Oct 2017 06:40:50 +0100

Dear all

I am trying to install Ambertools 17 onto Macbook Sierra 10.12

and I followed "all" available instructions, including installation of
Xquartz, Xcode and Gfortran.

However, I used './configure -macAccelerate clang' and kept getting the
following error messages... HELP, please!!


Checking for updates...

Checking for available patches online. This may take a few seconds...

Available AmberTools 17 patches:

No patches available



Using the AmberTools miniconda installation in

version 2.7.13

Obtaining the clang compiler suite versions, e.g.:

     clang -v

The C version is 9.0.0

The Fortran version is 配置為:../gcc-6.3.0/configure


Testing the clang compiler:

     clang -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp


Testing the clang++ compiler:

     clang++ -fPIC -o testp testp.cpp


Testing the gfortran compiler:

     gfortran -fPIC -O0 -o testp testp.f


Testing mixed C/Fortran compilation:

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 -lgfortran -w -framework Accelerate

Undefined symbols for architecture x86_64:

  "__gfortran_st_write", referenced from:

      _hello_ in testp.f.o

  "__gfortran_st_write_done", referenced from:

      _hello_ in testp.f.o

  "__gfortran_transfer_character_write", referenced from:

      _hello_ in testp.f.o

ld: symbol(s) not found for architecture x86_64

clang: *error: *linker command failed with exit code 1 (use -v to see

./configure2: line 2495: ./testp: No such file or directory

Error: Unable to compile mixed C/Fortran code.

       Please check your compiler settings and configure flags.

Configure failed due to the errors above!


And the 'clang -v' output is ::


Apple LLVM version 9.0.0 (clang-900.0.37)

Target: x86_64-apple-darwin16.7.0

Thread model: posix



In addition, the 'port installed' output is ::


The following ports are currently installed:

  bzip2 .1.0.6_0 (active)

  cctools .895_4+llvm40 (active)

  cloog .0.18.4_1 (active)

  cmake .3.9.3_0

  cmake .3.9.4_0 (active)

  curl .7.55.1_0+ssl

  curl @7.56.0_0+ssl (active)

  curl-ca-bundle .7.55.1_0

  curl-ca-bundle @7.56.0_0 (active)

  db48 .4.8.30_4 (active)

  expat .2.2.4_0 (active)

  gcc6 .6.4.0_0

  gcc7 .7.2.0_0

  gcc48 .4.8.5_2

  gcc49 .4.9.4_2 (active)

  gcc_select @0.1_8 (active)

  gettext . (active)

  gmake .4.2.1_0 (active)

  gmp .6.1.2_1 (active)

  hdf5 @1.10.1_1+cxx+gcc48+hl (active)

  isl .0.18_0 (active)

  isl14 .0.14.1_0 (active)

  ld64 .3_0 (active)

  ld64-latest @274.2_1+llvm40 (active)

  libarchive .3.3.2_1 (active)

  libcxx .3.9.1_0+universal (active)

  libedit @20170329-3.1_1

  libedit .20170329-3.1_2 (active)

  libffi @3.2.1_0 (active)

  libgcc .7.2.0_0

  libgcc .7.2.0_1 (active)

  libgcc6 .6.4.0_1 (active)

  libiconv .1.15_0 (active)

  libmpc .1.0.3_0 (active)

  libuv .1.14.1_0

  libuv .1.15.0_0 (active)

  libxml2 .2.9.5_0

  libxml2 @2.9.6_0 (active)

  llvm-4.0 .4.0.1_0

  llvm-4.0 @4.0.1_1 (active)

  llvm_select .2_0 (active)

  lz4 .1.8.0_0 (active)

  lzo2 .2.10_0 (active)

  molden .5.7-20170920124800_0+gcc6

  molden .5.7-20170920124800_0+gcc7 (active)

  mpfr .3.1.6_0 (active)

  mpi-doc .3.2_0 (active)

  mpi_select .0.0_3 (active)

  mpich-gcc49 .3.2_4+fortran (active)

  ncurses .6.0-20170916_0 (active)

  netcdf @ (active)

  netcdf-fortran @4.4.4_0+gcc7

  netcdf-fortran .4.4.4_0+gcc48 (active)

  openssl .1.0.2l_0 (active)

  python2_select .0.0_2 (active)

  python27 .2.7.14_0 (active)

  python_select @0.3_7 (active)

  sqlite3 .3.20.1_0 (active)

  xar .1.6.1_0 (active)

  xorg-kbproto .1.0.7_0 (active)

  xorg-libpthread-stubs @0.3_0 (active)

  xorg-libX11 .1.6.5_0 (active)

  xorg-libXau .1.0.8_0 (active)

  xorg-libxcb @1.12_2+python27 (active)

  xorg-libXdmcp .1.1.2_0 (active)

  xorg-xcb-proto .1.12_1+python27 (active)

  xorg-xproto @7.0.31_0 (active)

  xz .5.2.3_0 (active)

  zlib @1.2.11_0 (active)


Any advice or suggestions will be greatly appreciated.
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Received on Thu Oct 12 2017 - 23:00:02 PDT
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