Please don’t run configure with sudo - it’s not intended to be run that
way, has not been tested, and may cause big headaches for you. If you need
Amber to go system-wide your best bet may be to create a folder with
writable permissions and install there with the —prefix configure argument.
Others with more OSX experience may have better advice.
-Dan
On Wed, Nov 29, 2017 at 7:35 AM Eiros Zamora, Juan <
j.eiros-zamora14.imperial.ac.uk> wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 29 2017 - 05:30:05 PST
