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
