[AMBER] Trouble installing amber tools on new OSX 10.13.1

From: Eiros Zamora, Juan <j.eiros-zamora14.imperial.ac.uk>
Date: Wed, 29 Nov 2017 12:35:00 +0000

Dear Amber developers,

I’m trying to install the ambertools 17 on a new mac computer with 10.13.1 High Sierra OS

Awhile ago, another user in this machine installed the xcode developer tools and macports, and the respective compilers for ambertools.
Unfortunately, ambertools was installed in the user’s home folder and not system wide -- I can’t access that user’s folder.
So I’m not really sure if the problems below are coming from ‘old’ compilers that no longer work after updating the OS to 10.13.

That said, I’m running into an error at the `./configure gnu` step:

First I set the AMBERHOME variable to the folder where it is unpacked (/usr/local/amber16/), and then I run the configure step:

echo $AMBERHOME
$ export AMBERHOME=/usr/local/amber16
$ sudo ./configure gnu
Your AMBERHOME environment variable is not set! Auto set it to:
/usr/local/amber16
I find this odd as I just did it in the above step…
Checking for updates...
Checking for available patches online. This may take a few seconds...

Available AmberTools 17 patches:

No patches available


AMBER_PREFIX=/usr/local/amber16
AMBER_SOURCE=/usr/local/amber16

Using the AmberTools miniconda installation in /usr/local/amber16/miniconda
version 2.7.13

Obtaining the gnu compiler suite versions, e.g.:
     gcc -v
The C version is 4.9.4
The Fortran version is 4.9.4

Testing the gcc compiler:
     gcc -fPIC -DUSE_AMBER_C9XCOMPLEX -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
testp.c:1:19: fatal error: stdio.h: No such file or directory
 #include <stdio.h>
                   ^
compilation terminated.
./configure2: line 2413: ./testp: No such file or directory
Error: Unable to compile a C program using gcc -fPIC -DUSE_AMBER_C9XCOMPLEX -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
       Please check your compiler settings or configure flags.
Configure failed due to the errors above!

It seems there is a problem with the compiler, but it is installed (?):
$ gcc
gcc: fatal error: no input files
compilation terminated.
$ which gcc
/opt/local/bin/gcc
$ gcc --version
gcc (MacPorts gcc49 4.9.4_0) 4.9.4
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

I’ve tried to go the alternative route and install the pre-compiled version from the anaconda package manager:

$ conda create -n amber-install python=3.5 -y
Fetching package metadata ...........
Solving package specifications: .

Package plan for installation in environment /Users/je714/anaconda3/envs/amber-install:

The following NEW packages will be INSTALLED:

    ca-certificates: 2017.08.26-ha1e5d58_0
    certifi: 2017.11.5-py35hd00889a_0
    libcxx: 4.0.1-h579ed51_0
    libcxxabi: 4.0.1-hebd6815_0
    libedit: 3.1-hb4e282d_0
    libffi: 3.2.1-h475c297_4
    ncurses: 6.0-hd04f020_2
    openssl: 1.0.2m-h86d3e6a_1
    pip: 9.0.1-py35h33ce766_4
    python: 3.5.4-he720263_23
    readline: 7.0-hc1231fa_4
    setuptools: 36.5.0-py35h52cde6a_0
    sqlite: 3.20.1-h7e4c145_2
    tk: 8.6.7-h35a86e2_3
    wheel: 0.30.0-py35h5c0b906_1
    xz: 5.2.3-h0278029_2
    zlib: 1.2.11-hf3cbc9b_2

xz-5.2.3-h0278 100% |###################################################################| Time: 0:00:00 11.27 MB/s
python-3.5.4-h 100% |###################################################################| Time: 0:00:00 63.79 MB/s
certifi-2017.1 100% |###################################################################| Time: 0:00:00 63.80 MB/s
setuptools-36. 100% |###################################################################| Time: 0:00:00 50.73 MB/s
wheel-0.30.0-p 100% |###################################################################| Time: 0:00:00 39.84 MB/s
pip-9.0.1-py35 100% |###################################################################| Time: 0:00:00 91.97 MB/s
#
# To activate this environment, use:
# > source activate amber-install
#
# To deactivate an active environment, use:
# > source deactivate
#

$ source activate amber-install
(amber-install) $ conda install -c ambermd ambertools -v -y

Fetching package metadata .............
Solving package specifications: .

Package plan for installation in environment /Users/je714/anaconda3/envs/amber-install:

The following NEW packages will be INSTALLED:

    ambertools: 16.21.1-py35_1 ambermd
    asn1crypto: 0.23.0-py35ha0e154b_0
    bzip2: 1.0.6-h649919c_2
    cffi: 1.11.2-py35h5806a83_0
    chardet: 3.0.4-py35h16a84c2_1
    cryptography: 2.1.3-py35h95e8285_0
    idna: 2.6-py35h01aacb0_1
    intel-openmp: 2018.0.0-h8158457_8
    libgfortran: 3.0.1-h93005f0_2
    mkl: 2018.0.1-hfbd8650_4
    numpy: 1.13.3-py35hfd7066c_0
    pycparser: 2.18-py35hab820b0_1
    pyopenssl: 17.2.0-py35h4737193_0
    pysocks: 1.6.7-py35h3cfcbe1_1
    requests: 2.18.4-py35h0d65e6b_1
    six: 1.11.0-py35h39a4c60_1
    urllib3: 1.22-py35he002d57_0

()

===> LINKING PACKAGE: defaults::bzip2-1.0.6-h649919c_2 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/bzip2-1.0.6-h649919c_2


===> LINKING PACKAGE: defaults::intel-openmp-2018.0.0-h8158457_8 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/intel-openmp-2018.0.0-h8158457_8


===> LINKING PACKAGE: defaults::libgfortran-3.0.1-h93005f0_2 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/libgfortran-3.0.1-h93005f0_2


===> LINKING PACKAGE: defaults::mkl-2018.0.1-hfbd8650_4 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/mkl-2018.0.1-hfbd8650_4


===> LINKING PACKAGE: defaults::asn1crypto-0.23.0-py35ha0e154b_0 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/asn1crypto-0.23.0-py35ha0e154b_0


===> LINKING PACKAGE: defaults::chardet-3.0.4-py35h16a84c2_1 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/chardet-3.0.4-py35h16a84c2_1


===> LINKING PACKAGE: defaults::idna-2.6-py35h01aacb0_1 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/idna-2.6-py35h01aacb0_1


===> LINKING PACKAGE: defaults::numpy-1.13.3-py35hfd7066c_0 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/numpy-1.13.3-py35hfd7066c_0


===> LINKING PACKAGE: defaults::pycparser-2.18-py35hab820b0_1 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/pycparser-2.18-py35hab820b0_1


===> LINKING PACKAGE: defaults::pysocks-1.6.7-py35h3cfcbe1_1 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/pysocks-1.6.7-py35h3cfcbe1_1


===> LINKING PACKAGE: defaults::six-1.11.0-py35h39a4c60_1 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/six-1.11.0-py35h39a4c60_1


===> LINKING PACKAGE: defaults::cffi-1.11.2-py35h5806a83_0 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/cffi-1.11.2-py35h5806a83_0


===> LINKING PACKAGE: defaults::cryptography-2.1.3-py35h95e8285_0 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/cryptography-2.1.3-py35h95e8285_0


===> LINKING PACKAGE: defaults::pyopenssl-17.2.0-py35h4737193_0 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/pyopenssl-17.2.0-py35h4737193_0


===> LINKING PACKAGE: defaults::urllib3-1.22-py35he002d57_0 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/urllib3-1.22-py35he002d57_0


===> LINKING PACKAGE: defaults::requests-2.18.4-py35h0d65e6b_1 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/requests-2.18.4-py35h0d65e6b_1


===> LINKING PACKAGE: ambermd::ambertools-16.21.1-py35_1 <===
  prefix=/Users/je714/anaconda3/envs/amber-install
  source=/Users/je714/anaconda3/pkgs/ambertools-16.21.1-py35_1


$ /bin/bash -x /Users/je714/anaconda3/envs/amber-install/bin/.ambertools-post-link.sh
==> cwd: /Users/je714/anaconda3/envs/amber-install/bin <==
==> exit code: 1 <==
==> stdout <==
b'----------------------------------------------------------------------------------------------------\nLooking for $HOME/.amberrc or .amberrc registration file\n\nWe are asking users to fill out the simple form below, \nso that we can justify our existence by having a record of who is using the code\n----------------------------------------------------------------------------------------------------\nPlease enter your info\nPlease put your name here: '
==> stderr <==
b'+ amber_registration\nTraceback (most recent call last):\n File "/Users/je714/anaconda3/envs/amber-install/bin/amber_registration", line 91, in <module>\n main()\n File "/Users/je714/anaconda3/envs/amber-install/bin/amber_registration", line 53, in main\n value = input("Please put your name here: ")\nEOFError: EOF when reading a line\n+ exit 1\n'


An error occurred while installing package 'ambermd::ambertools-16.21.1-py35_1'.
LinkError: post-link script failed for package ambermd::ambertools-16.21.1-py35_1
running your command again with `-v` will provide additional information
location of failed script: /Users/je714/anaconda3/envs/amber-install/bin/.ambertools-post-link.sh
==> script messages <==
<None>

Attempting to roll back.


===> REVERSING PACKAGE LINK: ambermd::ambertools-16.21.1-py35_1 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::requests-2.18.4-py35h0d65e6b_1 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::urllib3-1.22-py35he002d57_0 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::pyopenssl-17.2.0-py35h4737193_0 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::cryptography-2.1.3-py35h95e8285_0 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::cffi-1.11.2-py35h5806a83_0 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::six-1.11.0-py35h39a4c60_1 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::pysocks-1.6.7-py35h3cfcbe1_1 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::pycparser-2.18-py35hab820b0_1 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::numpy-1.13.3-py35hfd7066c_0 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::idna-2.6-py35h01aacb0_1 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::chardet-3.0.4-py35h16a84c2_1 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::asn1crypto-0.23.0-py35ha0e154b_0 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::mkl-2018.0.1-hfbd8650_4 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::libgfortran-3.0.1-h93005f0_2 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::intel-openmp-2018.0.0-h8158457_8 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


===> REVERSING PACKAGE LINK: defaults::bzip2-1.0.6-h649919c_2 <===
  prefix=/Users/je714/anaconda3/envs/amber-install


An unexpected error has occurred.
Please consider posting the following information to the
conda GitHub issue tracker at:

    https://github.com/conda/conda/issues



Current conda install:

               platform : osx-64
          conda version : 4.3.30
       conda is private : False
      conda-env version : 4.3.30
    conda-build version : 2.0.2
         python version : 3.5.2.final.0
       requests version : 2.14.2
       root environment : /Users/je714/anaconda3 (writable)
    default environment : /Users/je714/anaconda3/envs/amber-install
       envs directories : /Users/je714/anaconda3/envs
                          /Users/je714/.conda/envs
          package cache : /Users/je714/anaconda3/pkgs
                          /Users/je714/.conda/pkgs
           channel URLs : https://conda.anaconda.org/ambermd/osx-64
                          https://conda.anaconda.org/ambermd/noarch
                          https://repo.continuum.io/pkgs/main/osx-64
                          https://repo.continuum.io/pkgs/main/noarch
                          https://repo.continuum.io/pkgs/free/osx-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/osx-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/osx-64
                          https://repo.continuum.io/pkgs/pro/noarch
            config file : None
             netrc file : None
           offline mode : False
             user-agent : conda/4.3.30 requests/2.14.2 CPython/3.5.2 Darwin/17.2.0 OSX/10.13.1
                UID:GID : 505:20

`$ /Users/je714/anaconda3/envs/amber-install/bin/conda install -c ambermd ambertools -v -y`




    Traceback (most recent call last):
      File "/Users/je714/anaconda3/lib/python3.5/site-packages/conda/core/link.py", line 497, in run_script
        subprocess_call(command_args, env=env, path=dirname(path))
      File "/Users/je714/anaconda3/lib/python3.5/site-packages/conda/gateways/subprocess.py", line 56, in subprocess_call
        output=_format_output(command_str, path, rc, stdout, stderr))
    subprocess.CalledProcessError: Command '['/bin/bash', '-x', '/Users/je714/anaconda3/envs/amber-install/bin/.ambertools-post-link.sh']' returned non-zero exit status 1

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/Users/je714/anaconda3/lib/python3.5/site-packages/conda/core/link.py", line 327, in _execute_actions
        run_script(target_prefix, Dist(pkg_data), 'post-unlink' if is_unlink else 'post-link')
      File "/Users/je714/anaconda3/lib/python3.5/site-packages/conda/core/link.py", line 513, in run_script
        raise LinkError(message)
    conda.exceptions.LinkError: post-link script failed for package ambermd::ambertools-16.21.1-py35_1
    running your command again with `-v` will provide additional information
    location of failed script: /Users/je714/anaconda3/envs/amber-install/bin/.ambertools-post-link.sh
    ==> script messages <==
    <None>


    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/Users/je714/anaconda3/lib/python3.5/site-packages/conda/core/link.py", line 281, in execute
        pkg_data, actions)
      File "/Users/je714/anaconda3/lib/python3.5/site-packages/conda/core/link.py", line 344, in _execute_actions
        reverse_excs,
    conda.CondaMultiError: post-link script failed for package ambermd::ambertools-16.21.1-py35_1
    running your command again with `-v` will provide additional information
    location of failed script: /Users/je714/anaconda3/envs/amber-install/bin/.ambertools-post-link.sh
    ==> script messages <==
    <None>



    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/Users/je714/anaconda3/lib/python3.5/site-packages/conda/exceptions.py", line 640, in conda_exception_handler
        return_value = func(*args, **kwargs)
      File "/Users/je714/anaconda3/lib/python3.5/site-packages/conda/cli/main.py", line 140, in _main
        exit_code = args.func(args, p)
      File "/Users/je714/anaconda3/lib/python3.5/site-packages/conda/cli/main_install.py", line 80, in execute
        install(args, parser, 'install')
      File "/Users/je714/anaconda3/lib/python3.5/site-packages/conda/cli/install.py", line 326, in install
        execute_actions(actions, index, verbose=not context.quiet)
      File "/Users/je714/anaconda3/lib/python3.5/site-packages/conda/plan.py", line 828, in execute_actions
        execute_instructions(plan, index, verbose)
      File "/Users/je714/anaconda3/lib/python3.5/site-packages/conda/instructions.py", line 247, in execute_instructions
        cmd(state, arg)
      File "/Users/je714/anaconda3/lib/python3.5/site-packages/conda/instructions.py", line 108, in UNLINKLINKTRANSACTION_CMD
        txn.execute()
      File "/Users/je714/anaconda3/lib/python3.5/site-packages/conda/core/link.py", line 297, in execute
        rollback_excs,
    conda.CondaMultiError: post-link script failed for package ambermd::ambertools-16.21.1-py35_1
    running your command again with `-v` will provide additional information
    location of failed script: /Users/je714/anaconda3/envs/amber-install/bin/.ambertools-post-link.sh
    ==> script messages <==
    <None>

And there’s a problem now with gfortran if I try to run any of the ambertools programs:
$ cpptraj
dyld: Library not loaded: /usr/local/gfortran/lib/libgfortran.3.dylib
  Referenced from: /Users/je714/anaconda3/bin/cpptraj
  Reason: image not found
Abort trap: 6
$ sander
dyld: Library not loaded: /usr/local/gfortran/lib/libgfortran.3.dylib
  Referenced from: /Users/je714/anaconda3/bin/sander
  Reason: image not found
Abort trap: 6
Any suggestions on how to fix this?

Best regards,

Juan

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Received on Wed Nov 29 2017 - 05:00:02 PST
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