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

Available AmberTools 19 patches:

update.1 (modifies test, suite)
Released on May 3, 2019 (written by David Case)
Description:
	Comment out some of the pmemd tests that are not intended
	be run with pmemd from Amber18

update.2 (modifies packmol-memgen)
Released on 03 May 2019 (written by Stephan Schott-Verdugo)
Description:
	Avoid using wrong pdb in case of installing over AmberTools18

update.3 (modifies rism3d.snglpnt)
Released on May 15, 2019 (written by Dave Case)
Description:
	Fix command line parsing to recognize "-h" and "--help"
	and to work better with unkown options


There are patches available. Do you want to apply them now? [y/N] (Recommended Y) 
Preparing to apply updates... please wait.
Downloading updates for AmberTools 19
Downloading AmberTools 19/update.1 (4.48 KB)
Applying AmberTools 19/update.1
Downloading AmberTools 19/update.2 (1.24 KB)
Applying AmberTools 19/update.2
Downloading AmberTools 19/update.3 (2.46 KB)
Applying AmberTools 19/update.3

NOTE: update_amber only updates the raw source code! You must recompile if you want 
      any changes to take effect!



AMBER_PREFIX=/opt/amber19/amber18
AMBER_SOURCE=/opt/amber19/amber18




We highly recommend to let AMBER install Python with all prerequisites inside
/opt/amber19/amber18 via a Continuum Miniconda distribution. 
Miniconda is chosen because it comes with great package manager conda, which is 
specially designed for numerical and scientific computing. This makes compiling 
AMBER Python extensions much easier.
This will only need to be done once.
It may take several minutes and will require Internet access.

Should I download and install Miniconda for you? [y/n] Downloading an Amber-compatible Python version 2.7 via Miniconda 
and installing it. This may take several minutes.

================================================================================
This script will download and install a version of Python compatible
with every component of AmberTools and install all required and optional
prerequisites. The Python distribution is downloaded for your operating
system from Miniconda.

Downloading Python 2.7 Miniconda
Detected Linux kernel. Downloading the Linux installer
Downloading the latest Miniconda distribution
    Detected 64-bit Linux
Installing Miniconda Python.
PREFIX=/opt/amber19/amber18/miniconda
installing: python-2.7.15-h9bab390_6 ...
installing: ca-certificates-2018.03.07-0 ...
installing: conda-env-2.6.0-1 ...
installing: libgcc-ng-8.2.0-hdf63c60_1 ...
installing: libstdcxx-ng-8.2.0-hdf63c60_1 ...
installing: libffi-3.2.1-hd88cf55_4 ...
installing: ncurses-6.1-he6710b0_1 ...
installing: openssl-1.1.1a-h7b6447c_0 ...
installing: yaml-0.1.7-had09818_2 ...
installing: zlib-1.2.11-h7b6447c_3 ...
installing: libedit-3.1.20170329-h6b74fdf_2 ...
installing: readline-7.0-h7b6447c_5 ...
installing: tk-8.6.8-hbc83047_0 ...
installing: sqlite-3.26.0-h7b6447c_0 ...
installing: asn1crypto-0.24.0-py27_0 ...
installing: certifi-2018.11.29-py27_0 ...
installing: chardet-3.0.4-py27_1 ...
installing: enum34-1.1.6-py27_1 ...
installing: futures-3.2.0-py27_0 ...
installing: idna-2.8-py27_0 ...
installing: ipaddress-1.0.22-py27_0 ...
installing: pycosat-0.6.3-py27h14c3975_0 ...
installing: pycparser-2.19-py27_0 ...
installing: pysocks-1.6.8-py27_0 ...
installing: ruamel_yaml-0.15.46-py27h14c3975_0 ...
installing: six-1.12.0-py27_0 ...
installing: cffi-1.11.5-py27he75722e_1 ...
installing: setuptools-40.6.3-py27_0 ...
installing: cryptography-2.4.2-py27h1ba5d50_0 ...
installing: wheel-0.32.3-py27_0 ...
installing: pip-18.1-py27_0 ...
installing: pyopenssl-18.0.0-py27_0 ...
installing: urllib3-1.24.1-py27_0 ...
installing: requests-2.21.0-py27_0 ...
installing: conda-4.5.12-py27_0 ...
installation finished.
Updating and installing required and optional packages...
Collecting pip
  Using cached https://files.pythonhosted.org/packages/5c/e0/be401c003291b56efc55aeba6a80ab790d3d4cece2778288d65323009420/pip-19.1.1-py2.py3-none-any.whl
Installing collected packages: pip
  Found existing installation: pip 18.1
    Uninstalling pip-18.1:
      Successfully uninstalled pip-18.1
Successfully installed pip-19.1.1
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/amber19/amber18/miniconda

  added / updated specs: 
    - nomkl


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    nomkl-3.0                  |                0          48 KB
    ca-certificates-2019.1.23  |                0         126 KB
    openssl-1.1.1b             |       h7b6447c_1         4.0 MB
    conda-4.6.14               |           py27_0         2.1 MB
    certifi-2019.3.9           |           py27_0         155 KB
    blas-1.0                   |         openblas          48 KB
    ------------------------------------------------------------
                                           Total:         6.4 MB

The following NEW packages will be INSTALLED:

    blas:            1.0-openblas     
    nomkl:           3.0-0            

The following packages will be UPDATED:

    ca-certificates: 2018.03.07-0      --> 2019.1.23-0      
    certifi:         2018.11.29-py27_0 --> 2019.3.9-py27_0  
    conda:           4.5.12-py27_0     --> 4.6.14-py27_0    
    openssl:         1.1.1a-h7b6447c_0 --> 1.1.1b-h7b6447c_1


Downloading and Extracting Packages
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata: ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/amber19/amber18/miniconda

  added / updated specs:
    - cython=0.29
    - ipython
    - notebook
    - numpy
    - pytest
    - scipy


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    atomicwrites-1.3.0         |           py27_1          13 KB
    attrs-19.1.0               |           py27_1          56 KB
    backports-1.0              |           py27_1           3 KB
    backports.shutil_get_terminal_size-1.0.0|           py27_2           8 KB
    backports_abc-0.5          |             py_0          13 KB
    bleach-3.1.0               |           py27_0         228 KB
    configparser-3.7.4         |           py27_0          41 KB
    cython-0.29.7              |   py27he6710b0_0         2.1 MB
    decorator-4.4.0            |           py27_1          18 KB
    defusedxml-0.6.0           |             py_0          23 KB
    entrypoints-0.3            |           py27_0          12 KB
    funcsigs-1.0.2             |           py27_0          20 KB
    functools32-3.2.3.2        |           py27_1          23 KB
    gmp-6.1.2                  |       h6c8ec71_1         744 KB
    ipykernel-4.10.0           |           py27_0         145 KB
    ipython-5.8.0              |           py27_0         1.0 MB
    ipython_genutils-0.2.0     |           py27_0          38 KB
    jinja2-2.10.1              |           py27_0         181 KB
    jsonschema-3.0.1           |           py27_0          86 KB
    jupyter_client-5.2.4       |           py27_0         125 KB
    jupyter_core-4.4.0         |           py27_0          62 KB
    libgfortran-ng-7.3.0       |       hdf63c60_0         1.3 MB
    libopenblas-0.3.3          |       h5a2b251_3         7.6 MB
    libsodium-1.0.16           |       h1bed415_0         302 KB
    markupsafe-1.1.1           |   py27h7b6447c_0          29 KB
    mistune-0.8.4              |   py27h7b6447c_0          53 KB
    more-itertools-5.0.0       |           py27_0          86 KB
    nbconvert-5.5.0            |             py_0         381 KB
    nbformat-4.4.0             |           py27_0         139 KB
    notebook-5.7.8             |           py27_0         7.2 MB
    numpy-1.16.3               |   py27h99e49ec_0          49 KB
    numpy-base-1.16.3          |   py27h2f8d375_0         4.3 MB
    pandoc-2.2.3.2             |                0        20.8 MB
    pandocfilters-1.4.2        |           py27_1          13 KB
    pathlib2-2.3.3             |           py27_0          31 KB
    pexpect-4.7.0              |           py27_0          80 KB
    pickleshare-0.7.5          |           py27_0          12 KB
    pluggy-0.11.0              |             py_0          20 KB
    prometheus_client-0.6.0    |           py27_0          69 KB
    prompt_toolkit-1.0.15      |   py27h1b593e1_0         333 KB
    ptyprocess-0.6.0           |           py27_0          22 KB
    py-1.8.0                   |           py27_0         137 KB
    pygments-2.4.0             |             py_0         664 KB
    pyrsistent-0.14.11         |   py27h7b6447c_0          88 KB
    pytest-4.5.0               |           py27_0         358 KB
    python-dateutil-2.8.0      |           py27_0         279 KB
    pyzmq-18.0.0               |   py27he6710b0_0         463 KB
    scandir-1.10.0             |   py27h7b6447c_0          32 KB
    scipy-1.2.1                |   py27he2b7bc3_0        17.7 MB
    send2trash-1.5.0           |           py27_0          16 KB
    simplegeneric-0.8.1        |           py27_2           9 KB
    singledispatch-3.4.0.3     |           py27_0          15 KB
    terminado-0.8.2            |           py27_0          22 KB
    testpath-0.4.2             |           py27_0          91 KB
    tornado-5.1.1              |   py27h7b6447c_0         643 KB
    traitlets-4.3.2            |           py27_0         128 KB
    wcwidth-0.1.7              |   py27h9e3e1ab_0          25 KB
    webencodings-0.5.1         |           py27_1          19 KB
    zeromq-4.3.1               |       he6710b0_3         666 KB
    ------------------------------------------------------------
                                           Total:        68.9 MB

The following NEW packages will be INSTALLED:

  atomicwrites       pkgs/main/linux-64::atomicwrites-1.3.0-py27_1
  attrs              pkgs/main/linux-64::attrs-19.1.0-py27_1
  backports          pkgs/main/linux-64::backports-1.0-py27_1
  backports.shutil_~ pkgs/main/linux-64::backports.shutil_get_terminal_size-1.0.0-py27_2
  backports_abc      pkgs/main/noarch::backports_abc-0.5-py_0
  bleach             pkgs/main/linux-64::bleach-3.1.0-py27_0
  configparser       pkgs/main/linux-64::configparser-3.7.4-py27_0
  cython             pkgs/main/linux-64::cython-0.29.7-py27he6710b0_0
  decorator          pkgs/main/linux-64::decorator-4.4.0-py27_1
  defusedxml         pkgs/main/noarch::defusedxml-0.6.0-py_0
  entrypoints        pkgs/main/linux-64::entrypoints-0.3-py27_0
  funcsigs           pkgs/main/linux-64::funcsigs-1.0.2-py27_0
  functools32        pkgs/main/linux-64::functools32-3.2.3.2-py27_1
  gmp                pkgs/main/linux-64::gmp-6.1.2-h6c8ec71_1
  ipykernel          pkgs/main/linux-64::ipykernel-4.10.0-py27_0
  ipython            pkgs/main/linux-64::ipython-5.8.0-py27_0
  ipython_genutils   pkgs/main/linux-64::ipython_genutils-0.2.0-py27_0
  jinja2             pkgs/main/linux-64::jinja2-2.10.1-py27_0
  jsonschema         pkgs/main/linux-64::jsonschema-3.0.1-py27_0
  jupyter_client     pkgs/main/linux-64::jupyter_client-5.2.4-py27_0
  jupyter_core       pkgs/main/linux-64::jupyter_core-4.4.0-py27_0
  libgfortran-ng     pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0
  libopenblas        pkgs/main/linux-64::libopenblas-0.3.3-h5a2b251_3
  libsodium          pkgs/main/linux-64::libsodium-1.0.16-h1bed415_0
  markupsafe         pkgs/main/linux-64::markupsafe-1.1.1-py27h7b6447c_0
  mistune            pkgs/main/linux-64::mistune-0.8.4-py27h7b6447c_0
  more-itertools     pkgs/main/linux-64::more-itertools-5.0.0-py27_0
  nbconvert          pkgs/main/noarch::nbconvert-5.5.0-py_0
  nbformat           pkgs/main/linux-64::nbformat-4.4.0-py27_0
  notebook           pkgs/main/linux-64::notebook-5.7.8-py27_0
  numpy              pkgs/main/linux-64::numpy-1.16.3-py27h99e49ec_0
  numpy-base         pkgs/main/linux-64::numpy-base-1.16.3-py27h2f8d375_0
  pandoc             pkgs/main/linux-64::pandoc-2.2.3.2-0
  pandocfilters      pkgs/main/linux-64::pandocfilters-1.4.2-py27_1
  pathlib2           pkgs/main/linux-64::pathlib2-2.3.3-py27_0
  pexpect            pkgs/main/linux-64::pexpect-4.7.0-py27_0
  pickleshare        pkgs/main/linux-64::pickleshare-0.7.5-py27_0
  pluggy             pkgs/main/noarch::pluggy-0.11.0-py_0
  prometheus_client  pkgs/main/linux-64::prometheus_client-0.6.0-py27_0
  prompt_toolkit     pkgs/main/linux-64::prompt_toolkit-1.0.15-py27h1b593e1_0
  ptyprocess         pkgs/main/linux-64::ptyprocess-0.6.0-py27_0
  py                 pkgs/main/linux-64::py-1.8.0-py27_0
  pygments           pkgs/main/noarch::pygments-2.4.0-py_0
  pyrsistent         pkgs/main/linux-64::pyrsistent-0.14.11-py27h7b6447c_0
  pytest             pkgs/main/linux-64::pytest-4.5.0-py27_0
  python-dateutil    pkgs/main/linux-64::python-dateutil-2.8.0-py27_0
  pyzmq              pkgs/main/linux-64::pyzmq-18.0.0-py27he6710b0_0
  scandir            pkgs/main/linux-64::scandir-1.10.0-py27h7b6447c_0
  scipy              pkgs/main/linux-64::scipy-1.2.1-py27he2b7bc3_0
  send2trash         pkgs/main/linux-64::send2trash-1.5.0-py27_0
  simplegeneric      pkgs/main/linux-64::simplegeneric-0.8.1-py27_2
  singledispatch     pkgs/main/linux-64::singledispatch-3.4.0.3-py27_0
  terminado          pkgs/main/linux-64::terminado-0.8.2-py27_0
  testpath           pkgs/main/linux-64::testpath-0.4.2-py27_0
  tornado            pkgs/main/linux-64::tornado-5.1.1-py27h7b6447c_0
  traitlets          pkgs/main/linux-64::traitlets-4.3.2-py27_0
  wcwidth            pkgs/main/linux-64::wcwidth-0.1.7-py27h9e3e1ab_0
  webencodings       pkgs/main/linux-64::webencodings-0.5.1-py27_1
  zeromq             pkgs/main/linux-64::zeromq-4.3.1-he6710b0_3



Downloading and Extracting Packages

pexpect-4.7.0        | 80 KB     |            |   0% 
pexpect-4.7.0        | 80 KB     | ######     |  60% 
pexpect-4.7.0        | 80 KB     | ########## | 100% 

traitlets-4.3.2      | 128 KB    |            |   0% 
traitlets-4.3.2      | 128 KB    | ########## | 100% 

bleach-3.1.0         | 228 KB    |            |   0% 
bleach-3.1.0         | 228 KB    | ########3  |  84% 
bleach-3.1.0         | 228 KB    | ########## | 100% 

decorator-4.4.0      | 18 KB     |            |   0% 
decorator-4.4.0      | 18 KB     | ######6    |  66% 
decorator-4.4.0      | 18 KB     | ########## | 100% 

pickleshare-0.7.5    | 12 KB     |            |   0% 
pickleshare-0.7.5    | 12 KB     | ########## | 100% 

jsonschema-3.0.1     | 86 KB     |            |   0% 
jsonschema-3.0.1     | 86 KB     | ########## | 100% 

libopenblas-0.3.3    | 7.6 MB    |            |   0% 
libopenblas-0.3.3    | 7.6 MB    | 5          |   6% 
libopenblas-0.3.3    | 7.6 MB    | #2         |  13% 
libopenblas-0.3.3    | 7.6 MB    | ##8        |  28% 
libopenblas-0.3.3    | 7.6 MB    | ###5       |  35% 
libopenblas-0.3.3    | 7.6 MB    | ####8      |  49% 
libopenblas-0.3.3    | 7.6 MB    | #####9     |  60% 
libopenblas-0.3.3    | 7.6 MB    | #######    |  71% 
libopenblas-0.3.3    | 7.6 MB    | ########   |  81% 
libopenblas-0.3.3    | 7.6 MB    | ########8  |  88% 
libopenblas-0.3.3    | 7.6 MB    | #########3 |  94% 
libopenblas-0.3.3    | 7.6 MB    | #########8 |  98% 
libopenblas-0.3.3    | 7.6 MB    | ########## | 100% 

backports_abc-0.5    | 13 KB     |            |   0% 
backports_abc-0.5    | 13 KB     | ########## | 100% 

numpy-base-1.16.3    | 4.3 MB    |            |   0% 
numpy-base-1.16.3    | 4.3 MB    | #2         |  12% 
numpy-base-1.16.3    | 4.3 MB    | ###1       |  32% 
numpy-base-1.16.3    | 4.3 MB    | #####1     |  52% 
numpy-base-1.16.3    | 4.3 MB    | #######1   |  71% 
numpy-base-1.16.3    | 4.3 MB    | ########5  |  86% 
numpy-base-1.16.3    | 4.3 MB    | #########6 |  96% 
numpy-base-1.16.3    | 4.3 MB    | ########## | 100% 

pluggy-0.11.0        | 20 KB     |            |   0% 
pluggy-0.11.0        | 20 KB     | ########## | 100% 

pygments-2.4.0       | 664 KB    |            |   0% 
pygments-2.4.0       | 664 KB    | #######8   |  78% 
pygments-2.4.0       | 664 KB    | ########## | 100% 

scandir-1.10.0       | 32 KB     |            |   0% 
scandir-1.10.0       | 32 KB     | ###7       |  38% 
scandir-1.10.0       | 32 KB     | ########## | 100% 

webencodings-0.5.1   | 19 KB     |            |   0% 
webencodings-0.5.1   | 19 KB     | ########## | 100% 

ipython-5.8.0        | 1.0 MB    |            |   0% 
ipython-5.8.0        | 1.0 MB    | #####5     |  56% 
ipython-5.8.0        | 1.0 MB    | #######9   |  80% 
ipython-5.8.0        | 1.0 MB    | #########3 |  94% 
ipython-5.8.0        | 1.0 MB    | ########## | 100% 

defusedxml-0.6.0     | 23 KB     |            |   0% 
defusedxml-0.6.0     | 23 KB     | ########## | 100% 

zeromq-4.3.1         | 666 KB    |            |   0% 
zeromq-4.3.1         | 666 KB    | #######7   |  77% 
zeromq-4.3.1         | 666 KB    | #########9 | 100% 
zeromq-4.3.1         | 666 KB    | ########## | 100% 

libsodium-1.0.16     | 302 KB    |            |   0% 
libsodium-1.0.16     | 302 KB    | ########   |  80% 
libsodium-1.0.16     | 302 KB    | ########## | 100% 

ipykernel-4.10.0     | 145 KB    |            |   0% 
ipykernel-4.10.0     | 145 KB    | ########## | 100% 

functools32-3.2.3.2  | 23 KB     |            |   0% 
functools32-3.2.3.2  | 23 KB     | ########## | 100% 

py-1.8.0             | 137 KB    |            |   0% 
py-1.8.0             | 137 KB    | ########## | 100% 

backports.shutil_get | 8 KB      |            |   0% 
backports.shutil_get | 8 KB      | ########## | 100% 

pyzmq-18.0.0         | 463 KB    |            |   0% 
pyzmq-18.0.0         | 463 KB    | ########1  |  81% 
pyzmq-18.0.0         | 463 KB    | ########## | 100% 

atomicwrites-1.3.0   | 13 KB     |            |   0% 
atomicwrites-1.3.0   | 13 KB     | ########## | 100% 

entrypoints-0.3      | 12 KB     |            |   0% 
entrypoints-0.3      | 12 KB     | ########## | 100% 

attrs-19.1.0         | 56 KB     |            |   0% 
attrs-19.1.0         | 56 KB     | ########## | 100% 

markupsafe-1.1.1     | 29 KB     |            |   0% 
markupsafe-1.1.1     | 29 KB     | ########## | 100% 

pandoc-2.2.3.2       | 20.8 MB   |            |   0% 
pandoc-2.2.3.2       | 20.8 MB   | 1          |   1% 
pandoc-2.2.3.2       | 20.8 MB   | 5          |   5% 
pandoc-2.2.3.2       | 20.8 MB   | 9          |  10% 
pandoc-2.2.3.2       | 20.8 MB   | #3         |  14% 
pandoc-2.2.3.2       | 20.8 MB   | #7         |  18% 
pandoc-2.2.3.2       | 20.8 MB   | ##1        |  22% 
pandoc-2.2.3.2       | 20.8 MB   | ##5        |  26% 
pandoc-2.2.3.2       | 20.8 MB   | ###        |  30% 
pandoc-2.2.3.2       | 20.8 MB   | ###4       |  34% 
pandoc-2.2.3.2       | 20.8 MB   | ###8       |  38% 
pandoc-2.2.3.2       | 20.8 MB   | ####2      |  42% 
pandoc-2.2.3.2       | 20.8 MB   | ####6      |  46% 
pandoc-2.2.3.2       | 20.8 MB   | #####      |  51% 
pandoc-2.2.3.2       | 20.8 MB   | #####4     |  55% 
pandoc-2.2.3.2       | 20.8 MB   | #####9     |  59% 
pandoc-2.2.3.2       | 20.8 MB   | ######3    |  63% 
pandoc-2.2.3.2       | 20.8 MB   | ######7    |  67% 
pandoc-2.2.3.2       | 20.8 MB   | #######1   |  71% 
pandoc-2.2.3.2       | 20.8 MB   | #######5   |  75% 
pandoc-2.2.3.2       | 20.8 MB   | #######8   |  79% 
pandoc-2.2.3.2       | 20.8 MB   | ########1  |  81% 
pandoc-2.2.3.2       | 20.8 MB   | ########3  |  83% 
pandoc-2.2.3.2       | 20.8 MB   | ########4  |  85% 
pandoc-2.2.3.2       | 20.8 MB   | ########5  |  86% 
pandoc-2.2.3.2       | 20.8 MB   | ########6  |  87% 
pandoc-2.2.3.2       | 20.8 MB   | ########7  |  88% 
pandoc-2.2.3.2       | 20.8 MB   | ########8  |  88% 
pandoc-2.2.3.2       | 20.8 MB   | ########8  |  89% 
pandoc-2.2.3.2       | 20.8 MB   | ########9  |  89% 
pandoc-2.2.3.2       | 20.8 MB   | ########9  |  90% 
pandoc-2.2.3.2       | 20.8 MB   | #########  |  90% 
pandoc-2.2.3.2       | 20.8 MB   | #########  |  91% 
pandoc-2.2.3.2       | 20.8 MB   | #########1 |  91% 
pandoc-2.2.3.2       | 20.8 MB   | #########1 |  92% 
pandoc-2.2.3.2       | 20.8 MB   | #########2 |  92% 
pandoc-2.2.3.2       | 20.8 MB   | #########2 |  93% 
pandoc-2.2.3.2       | 20.8 MB   | #########3 |  93% 
pandoc-2.2.3.2       | 20.8 MB   | #########3 |  94% 
pandoc-2.2.3.2       | 20.8 MB   | #########3 |  94% 
pandoc-2.2.3.2       | 20.8 MB   | #########4 |  94% 
pandoc-2.2.3.2       | 20.8 MB   | #########4 |  95% 
pandoc-2.2.3.2       | 20.8 MB   | #########5 |  95% 
pandoc-2.2.3.2       | 20.8 MB   | #########5 |  96% 
pandoc-2.2.3.2       | 20.8 MB   | #########5 |  96% 
pandoc-2.2.3.2       | 20.8 MB   | #########6 |  96% 
pandoc-2.2.3.2       | 20.8 MB   | #########6 |  97% 
pandoc-2.2.3.2       | 20.8 MB   | #########7 |  97% 
pandoc-2.2.3.2       | 20.8 MB   | #########7 |  98% 
pandoc-2.2.3.2       | 20.8 MB   | #########8 |  98% 
pandoc-2.2.3.2       | 20.8 MB   | #########8 |  99% 
pandoc-2.2.3.2       | 20.8 MB   | #########8 |  99% 
pandoc-2.2.3.2       | 20.8 MB   | #########9 |  99% 
pandoc-2.2.3.2       | 20.8 MB   | #########9 | 100% 
pandoc-2.2.3.2       | 20.8 MB   | ########## | 100% 

cython-0.29.7        | 2.1 MB    |            |   0% 
cython-0.29.7        | 2.1 MB    | ##6        |  26% 
cython-0.29.7        | 2.1 MB    | ######3    |  64% 
cython-0.29.7        | 2.1 MB    | ########   |  80% 
cython-0.29.7        | 2.1 MB    | #########4 |  94% 
cython-0.29.7        | 2.1 MB    | ########## | 100% 

pytest-4.5.0         | 358 KB    |            |   0% 
pytest-4.5.0         | 358 KB    | #########  |  91% 
pytest-4.5.0         | 358 KB    | ########## | 100% 

mistune-0.8.4        | 53 KB     |            |   0% 
mistune-0.8.4        | 53 KB     | ########## | 100% 

tornado-5.1.1        | 643 KB    |            |   0% 
tornado-5.1.1        | 643 KB    | #######9   |  79% 
tornado-5.1.1        | 643 KB    | ########## | 100% 

ptyprocess-0.6.0     | 22 KB     |            |   0% 
ptyprocess-0.6.0     | 22 KB     | ########## | 100% 

jinja2-2.10.1        | 181 KB    |            |   0% 
jinja2-2.10.1        | 181 KB    | ########## | 100% 

pyrsistent-0.14.11   | 88 KB     |            |   0% 
pyrsistent-0.14.11   | 88 KB     | ########## | 100% 

send2trash-1.5.0     | 16 KB     |            |   0% 
send2trash-1.5.0     | 16 KB     | ########## | 100% 

python-dateutil-2.8. | 279 KB    |            |   0% 
python-dateutil-2.8. | 279 KB    | ########## | 100% 

backports-1.0        | 3 KB      |            |   0% 
backports-1.0        | 3 KB      | ########## | 100% 

funcsigs-1.0.2       | 20 KB     |            |   0% 
funcsigs-1.0.2       | 20 KB     | ########## | 100% 

jupyter_client-5.2.4 | 125 KB    |            |   0% 
jupyter_client-5.2.4 | 125 KB    | ########## | 100% 

simplegeneric-0.8.1  | 9 KB      |            |   0% 
simplegeneric-0.8.1  | 9 KB      | #######5   |  75% 
simplegeneric-0.8.1  | 9 KB      | ########## | 100% 

libgfortran-ng-7.3.0 | 1.3 MB    |            |   0% 
libgfortran-ng-7.3.0 | 1.3 MB    | ####3      |  43% 
libgfortran-ng-7.3.0 | 1.3 MB    | #######9   |  80% 
libgfortran-ng-7.3.0 | 1.3 MB    | #########6 |  97% 
libgfortran-ng-7.3.0 | 1.3 MB    | ########## | 100% 

numpy-1.16.3         | 49 KB     |            |   0% 
numpy-1.16.3         | 49 KB     | ########## | 100% 

terminado-0.8.2      | 22 KB     |            |   0% 
terminado-0.8.2      | 22 KB     | ########## | 100% 

nbformat-4.4.0       | 139 KB    |            |   0% 
nbformat-4.4.0       | 139 KB    | ########## | 100% 

ipython_genutils-0.2 | 38 KB     |            |   0% 
ipython_genutils-0.2 | 38 KB     | ########## | 100% 

pandocfilters-1.4.2  | 13 KB     |            |   0% 
pandocfilters-1.4.2  | 13 KB     | ########## | 100% 

prompt_toolkit-1.0.1 | 333 KB    |            |   0% 
prompt_toolkit-1.0.1 | 333 KB    | ########9  |  89% 
prompt_toolkit-1.0.1 | 333 KB    | ########## | 100% 

more-itertools-5.0.0 | 86 KB     |            |   0% 
more-itertools-5.0.0 | 86 KB     | ########## | 100% 

configparser-3.7.4   | 41 KB     |            |   0% 
configparser-3.7.4   | 41 KB     | ########## | 100% 

pathlib2-2.3.3       | 31 KB     |            |   0% 
pathlib2-2.3.3       | 31 KB     | ########## | 100% 

jupyter_core-4.4.0   | 62 KB     |            |   0% 
jupyter_core-4.4.0   | 62 KB     | ########## | 100% 

singledispatch-3.4.0 | 15 KB     |            |   0% 
singledispatch-3.4.0 | 15 KB     | ########## | 100% 

testpath-0.4.2       | 91 KB     |            |   0% 
testpath-0.4.2       | 91 KB     | ########## | 100% 

wcwidth-0.1.7        | 25 KB     |            |   0% 
wcwidth-0.1.7        | 25 KB     | ########## | 100% 

gmp-6.1.2            | 744 KB    |            |   0% 
gmp-6.1.2            | 744 KB    | #######7   |  77% 
gmp-6.1.2            | 744 KB    | ########## | 100% 

notebook-5.7.8       | 7.2 MB    |            |   0% 
notebook-5.7.8       | 7.2 MB    | 8          |   8% 
notebook-5.7.8       | 7.2 MB    | ##         |  20% 
notebook-5.7.8       | 7.2 MB    | ###1       |  32% 
notebook-5.7.8       | 7.2 MB    | ####3      |  44% 
notebook-5.7.8       | 7.2 MB    | #####5     |  56% 
notebook-5.7.8       | 7.2 MB    | ######7    |  67% 
notebook-5.7.8       | 7.2 MB    | #######7   |  77% 
notebook-5.7.8       | 7.2 MB    | ########5  |  86% 
notebook-5.7.8       | 7.2 MB    | #########1 |  92% 
notebook-5.7.8       | 7.2 MB    | #########6 |  96% 
notebook-5.7.8       | 7.2 MB    | #########9 | 100% 
notebook-5.7.8       | 7.2 MB    | ########## | 100% 

nbconvert-5.5.0      | 381 KB    |            |   0% 
nbconvert-5.5.0      | 381 KB    | ########4  |  84% 
nbconvert-5.5.0      | 381 KB    | ########## | 100% 

scipy-1.2.1          | 17.7 MB   |            |   0% 
scipy-1.2.1          | 17.7 MB   | 3          |   3% 
scipy-1.2.1          | 17.7 MB   | 8          |   8% 
scipy-1.2.1          | 17.7 MB   | #3         |  13% 
scipy-1.2.1          | 17.7 MB   | #7         |  18% 
scipy-1.2.1          | 17.7 MB   | ##2        |  23% 
scipy-1.2.1          | 17.7 MB   | ##7        |  27% 
scipy-1.2.1          | 17.7 MB   | ###2       |  32% 
scipy-1.2.1          | 17.7 MB   | ###7       |  37% 
scipy-1.2.1          | 17.7 MB   | ####2      |  42% 
scipy-1.2.1          | 17.7 MB   | ####6      |  47% 
scipy-1.2.1          | 17.7 MB   | #####1     |  52% 
scipy-1.2.1          | 17.7 MB   | #####6     |  57% 
scipy-1.2.1          | 17.7 MB   | ######1    |  61% 
scipy-1.2.1          | 17.7 MB   | ######6    |  66% 
scipy-1.2.1          | 17.7 MB   | #######1   |  71% 
scipy-1.2.1          | 17.7 MB   | #######5   |  76% 
scipy-1.2.1          | 17.7 MB   | #######9   |  80% 
scipy-1.2.1          | 17.7 MB   | ########2  |  83% 
scipy-1.2.1          | 17.7 MB   | ########5  |  85% 
scipy-1.2.1          | 17.7 MB   | ########6  |  87% 
scipy-1.2.1          | 17.7 MB   | ########8  |  88% 
scipy-1.2.1          | 17.7 MB   | ########9  |  90% 
scipy-1.2.1          | 17.7 MB   | #########  |  91% 
scipy-1.2.1          | 17.7 MB   | #########1 |  92% 
scipy-1.2.1          | 17.7 MB   | #########2 |  93% 
scipy-1.2.1          | 17.7 MB   | #########3 |  93% 
scipy-1.2.1          | 17.7 MB   | #########3 |  94% 
scipy-1.2.1          | 17.7 MB   | #########4 |  94% 
scipy-1.2.1          | 17.7 MB   | #########4 |  95% 
scipy-1.2.1          | 17.7 MB   | #########5 |  95% 
scipy-1.2.1          | 17.7 MB   | #########5 |  96% 
scipy-1.2.1          | 17.7 MB   | #########6 |  96% 
scipy-1.2.1          | 17.7 MB   | #########6 |  97% 
scipy-1.2.1          | 17.7 MB   | #########6 |  97% 
scipy-1.2.1          | 17.7 MB   | #########7 |  97% 
scipy-1.2.1          | 17.7 MB   | #########7 |  98% 
scipy-1.2.1          | 17.7 MB   | #########8 |  98% 
scipy-1.2.1          | 17.7 MB   | #########8 |  99% 
scipy-1.2.1          | 17.7 MB   | #########9 |  99% 
scipy-1.2.1          | 17.7 MB   | #########9 | 100% 
scipy-1.2.1          | 17.7 MB   | ########## | 100% 

prometheus_client-0. | 69 KB     |            |   0% 
prometheus_client-0. | 69 KB     | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting matplotlib
  Downloading https://files.pythonhosted.org/packages/32/6b/0368cfa5e1d1ae169ab7dc78addda3fd5e6262e48d7373a9114bac7caff7/matplotlib-2.2.4-cp27-cp27mu-manylinux1_x86_64.whl (12.8MB)
Requirement already satisfied: python-dateutil>=2.1 in /opt/amber19/amber18/miniconda/lib/python2.7/site-packages (from matplotlib) (2.8.0)
Collecting subprocess32 (from matplotlib)
  Downloading https://files.pythonhosted.org/packages/32/c8/564be4d12629b912ea431f1a50eb8b3b9d00f1a0b1ceff17f266be190007/subprocess32-3.5.4.tar.gz (97kB)
Collecting cycler>=0.10 (from matplotlib)
  Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Requirement already satisfied: six>=1.10 in /opt/amber19/amber18/miniconda/lib/python2.7/site-packages (from matplotlib) (1.12.0)
Collecting backports.functools-lru-cache (from matplotlib)
  Downloading https://files.pythonhosted.org/packages/03/8e/2424c0e65c4a066e28f539364deee49b6451f8fcd4f718fefa50cc3dcf48/backports.functools_lru_cache-1.5-py2.py3-none-any.whl
Collecting pytz (from matplotlib)
  Downloading https://files.pythonhosted.org/packages/3d/73/fe30c2daaaa0713420d0382b16fbb761409f532c56bdcc514bf7b6262bb6/pytz-2019.1-py2.py3-none-any.whl (510kB)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib)
  Downloading https://files.pythonhosted.org/packages/dd/d9/3ec19e966301a6e25769976999bd7bbe552016f0d32b577dc9d63d2e0c49/pyparsing-2.4.0-py2.py3-none-any.whl (62kB)
Requirement already satisfied: numpy>=1.7.1 in /opt/amber19/amber18/miniconda/lib/python2.7/site-packages (from matplotlib) (1.16.3)
Collecting kiwisolver>=1.0.1 (from matplotlib)
  Downloading https://files.pythonhosted.org/packages/3d/78/cb9248b2289ec31e301137cedbe4ca503a74ca87f88cdbfd2f8be52323bf/kiwisolver-1.1.0-cp27-cp27mu-manylinux1_x86_64.whl (93kB)
Requirement already satisfied: setuptools in /opt/amber19/amber18/miniconda/lib/python2.7/site-packages (from kiwisolver>=1.0.1->matplotlib) (40.6.3)
Building wheels for collected packages: subprocess32
  Building wheel for subprocess32 (setup.py): started
  Building wheel for subprocess32 (setup.py): finished with status 'error'
  Running setup.py clean for subprocess32
Failed to build subprocess32
Installing collected packages: subprocess32, cycler, backports.functools-lru-cache, pytz, pyparsing, kiwisolver, matplotlib
  Running setup.py install for subprocess32: started
    Running setup.py install for subprocess32: finished with status 'error'
Collecting package metadata: ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/amber19/amber18/miniconda

  added / updated specs:
    - matplotlib


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    backports.functools_lru_cache-1.5|           py27_1           9 KB
    cycler-0.10.0              |           py27_0          13 KB
    dbus-1.13.6                |       h746ee38_0         587 KB
    expat-2.2.6                |       he6710b0_0         187 KB
    fontconfig-2.13.0          |       h9420a91_0         291 KB
    freetype-2.9.1             |       h8a8886c_1         822 KB
    glib-2.56.2                |       hd408876_0         5.0 MB
    gst-plugins-base-1.14.0    |       hbbd80ab_1         6.3 MB
    gstreamer-1.14.0           |       hb453b48_1         3.8 MB
    icu-58.2                   |       h9c2bf20_1        22.5 MB
    jpeg-9b                    |       h024ee3a_2         248 KB
    kiwisolver-1.1.0           |   py27he6710b0_0          91 KB
    libpng-1.6.37              |       hbc83047_0         364 KB
    libuuid-1.0.3              |       h1bed415_2          16 KB
    libxcb-1.13                |       h1bed415_1         502 KB
    libxml2-2.9.9              |       he19cac6_0         2.0 MB
    matplotlib-2.2.3           |   py27hb69df0a_0         6.5 MB
    pcre-8.43                  |       he6710b0_0         260 KB
    pyparsing-2.4.0            |             py_0          58 KB
    pyqt-5.9.2                 |   py27h05f1152_2         5.4 MB
    pytz-2019.1                |             py_0         236 KB
    qt-5.9.7                   |       h5867ecd_1        85.9 MB
    sip-4.19.8                 |   py27hf484d3e_0         291 KB
    subprocess32-3.5.3         |   py27h7b6447c_0          44 KB
    xz-5.2.4                   |       h14c3975_4         366 KB
    ------------------------------------------------------------
                                           Total:       141.7 MB

The following NEW packages will be INSTALLED:

  backports.functoo~ pkgs/main/linux-64::backports.functools_lru_cache-1.5-py27_1
  cycler             pkgs/main/linux-64::cycler-0.10.0-py27_0
  dbus               pkgs/main/linux-64::dbus-1.13.6-h746ee38_0
  expat              pkgs/main/linux-64::expat-2.2.6-he6710b0_0
  fontconfig         pkgs/main/linux-64::fontconfig-2.13.0-h9420a91_0
  freetype           pkgs/main/linux-64::freetype-2.9.1-h8a8886c_1
  glib               pkgs/main/linux-64::glib-2.56.2-hd408876_0
  gst-plugins-base   pkgs/main/linux-64::gst-plugins-base-1.14.0-hbbd80ab_1
  gstreamer          pkgs/main/linux-64::gstreamer-1.14.0-hb453b48_1
  icu                pkgs/main/linux-64::icu-58.2-h9c2bf20_1
  jpeg               pkgs/main/linux-64::jpeg-9b-h024ee3a_2
  kiwisolver         pkgs/main/linux-64::kiwisolver-1.1.0-py27he6710b0_0
  libpng             pkgs/main/linux-64::libpng-1.6.37-hbc83047_0
  libuuid            pkgs/main/linux-64::libuuid-1.0.3-h1bed415_2
  libxcb             pkgs/main/linux-64::libxcb-1.13-h1bed415_1
  libxml2            pkgs/main/linux-64::libxml2-2.9.9-he19cac6_0
  matplotlib         pkgs/main/linux-64::matplotlib-2.2.3-py27hb69df0a_0
  pcre               pkgs/main/linux-64::pcre-8.43-he6710b0_0
  pyparsing          pkgs/main/noarch::pyparsing-2.4.0-py_0
  pyqt               pkgs/main/linux-64::pyqt-5.9.2-py27h05f1152_2
  pytz               pkgs/main/noarch::pytz-2019.1-py_0
  qt                 pkgs/main/linux-64::qt-5.9.7-h5867ecd_1
  sip                pkgs/main/linux-64::sip-4.19.8-py27hf484d3e_0
  subprocess32       pkgs/main/linux-64::subprocess32-3.5.3-py27h7b6447c_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4



Downloading and Extracting Packages

matplotlib-2.2.3     | 6.5 MB    |            |   0% 
matplotlib-2.2.3     | 6.5 MB    | 6          |   6% 
matplotlib-2.2.3     | 6.5 MB    | #4         |  15% 
matplotlib-2.2.3     | 6.5 MB    | ###        |  30% 
matplotlib-2.2.3     | 6.5 MB    | ####3      |  44% 
matplotlib-2.2.3     | 6.5 MB    | #####6     |  57% 
matplotlib-2.2.3     | 6.5 MB    | ######9    |  70% 
matplotlib-2.2.3     | 6.5 MB    | ########   |  81% 
matplotlib-2.2.3     | 6.5 MB    | ########9  |  89% 
matplotlib-2.2.3     | 6.5 MB    | #########5 |  95% 
matplotlib-2.2.3     | 6.5 MB    | ########## | 100% 

dbus-1.13.6          | 587 KB    |            |   0% 
dbus-1.13.6          | 587 KB    | ########2  |  82% 
dbus-1.13.6          | 587 KB    | ########## | 100% 

libuuid-1.0.3        | 16 KB     |            |   0% 
libuuid-1.0.3        | 16 KB     | ########## | 100% 

sip-4.19.8           | 291 KB    |            |   0% 
sip-4.19.8           | 291 KB    | #########  |  90% 
sip-4.19.8           | 291 KB    | ########## | 100% 

qt-5.9.7             | 85.9 MB   |            |   0% 
qt-5.9.7             | 85.9 MB   |            |   1% 
qt-5.9.7             | 85.9 MB   | 1          |   2% 
qt-5.9.7             | 85.9 MB   | 2          |   3% 
qt-5.9.7             | 85.9 MB   | 3          |   4% 
qt-5.9.7             | 85.9 MB   | 4          |   5% 
qt-5.9.7             | 85.9 MB   | 5          |   6% 
qt-5.9.7             | 85.9 MB   | 6          |   7% 
qt-5.9.7             | 85.9 MB   | 7          |   8% 
qt-5.9.7             | 85.9 MB   | 8          |   9% 
qt-5.9.7             | 85.9 MB   | 9          |  10% 
qt-5.9.7             | 85.9 MB   | #          |  11% 
qt-5.9.7             | 85.9 MB   | #1         |  12% 
qt-5.9.7             | 85.9 MB   | #2         |  13% 
qt-5.9.7             | 85.9 MB   | #3         |  14% 
qt-5.9.7             | 85.9 MB   | #4         |  15% 
qt-5.9.7             | 85.9 MB   | #5         |  16% 
qt-5.9.7             | 85.9 MB   | #6         |  17% 
qt-5.9.7             | 85.9 MB   | #7         |  17% 
qt-5.9.7             | 85.9 MB   | #8         |  18% 
qt-5.9.7             | 85.9 MB   | #9         |  19% 
qt-5.9.7             | 85.9 MB   | ##         |  20% 
qt-5.9.7             | 85.9 MB   | ##1        |  21% 
qt-5.9.7             | 85.9 MB   | ##2        |  22% 
qt-5.9.7             | 85.9 MB   | ##3        |  23% 
qt-5.9.7             | 85.9 MB   | ##4        |  24% 
qt-5.9.7             | 85.9 MB   | ##5        |  25% 
qt-5.9.7             | 85.9 MB   | ##6        |  26% 
qt-5.9.7             | 85.9 MB   | ##7        |  27% 
qt-5.9.7             | 85.9 MB   | ##8        |  28% 
qt-5.9.7             | 85.9 MB   | ##9        |  29% 
qt-5.9.7             | 85.9 MB   | ###        |  30% 
qt-5.9.7             | 85.9 MB   | ###1       |  31% 
qt-5.9.7             | 85.9 MB   | ###2       |  32% 
qt-5.9.7             | 85.9 MB   | ###3       |  33% 
qt-5.9.7             | 85.9 MB   | ###4       |  34% 
qt-5.9.7             | 85.9 MB   | ###5       |  35% 
qt-5.9.7             | 85.9 MB   | ###6       |  36% 
qt-5.9.7             | 85.9 MB   | ###7       |  37% 
qt-5.9.7             | 85.9 MB   | ###8       |  38% 
qt-5.9.7             | 85.9 MB   | ###9       |  39% 
qt-5.9.7             | 85.9 MB   | ####       |  40% 
qt-5.9.7             | 85.9 MB   | ####1      |  41% 
qt-5.9.7             | 85.9 MB   | ####2      |  42% 
qt-5.9.7             | 85.9 MB   | ####3      |  43% 
qt-5.9.7             | 85.9 MB   | ####4      |  44% 
qt-5.9.7             | 85.9 MB   | ####5      |  45% 
qt-5.9.7             | 85.9 MB   | ####6      |  46% 
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Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Creating symlinks to /opt/amber19/amber18/bin and /opt/amber19/amber18/lib

Done. Miniconda installed in /opt/amber19/amber18/miniconda
Cache location: /opt/amber19/amber18/miniconda/pkgs
Will remove the following tarballs:

/opt/amber19/amber18/miniconda/pkgs
-----------------------------------
numpy-1.16.3-py27h99e49ec_0.tar.bz2           49 KB
pytest-4.5.0-py27_0.tar.bz2                  358 KB
singledispatch-3.4.0.3-py27_0.tar.bz2         15 KB
wheel-0.32.3-py27_0.tar.bz2                   34 KB
tk-8.6.8-hbc83047_0.tar.bz2                  3.1 MB
futures-3.2.0-py27_0.tar.bz2                  24 KB
nomkl-3.0-0.tar.bz2                           48 KB
simplegeneric-0.8.1-py27_2.tar.bz2             9 KB
ipykernel-4.10.0-py27_0.tar.bz2              145 KB
sip-4.19.8-py27hf484d3e_0.tar.bz2            291 KB
libopenblas-0.3.3-h5a2b251_3.tar.bz2         7.6 MB
markupsafe-1.1.1-py27h7b6447c_0.tar.bz2       29 KB
asn1crypto-0.24.0-py27_0.tar.bz2             155 KB
subprocess32-3.5.3-py27h7b6447c_0.tar.bz2      44 KB
zeromq-4.3.1-he6710b0_3.tar.bz2              666 KB
notebook-5.7.8-py27_0.tar.bz2                7.2 MB
libgfortran-ng-7.3.0-hdf63c60_0.tar.bz2      1.3 MB
libffi-3.2.1-hd88cf55_4.tar.bz2               43 KB
ncurses-6.1-he6710b0_1.tar.bz2               958 KB
pluggy-0.11.0-py_0.tar.bz2                    20 KB
zlib-1.2.11-h7b6447c_3.tar.bz2               120 KB
py-1.8.0-py27_0.tar.bz2                      137 KB
jupyter_core-4.4.0-py27_0.tar.bz2             62 KB
pyopenssl-18.0.0-py27_0.tar.bz2               80 KB
xz-5.2.4-h14c3975_4.tar.bz2                  366 KB
ptyprocess-0.6.0-py27_0.tar.bz2               22 KB
jinja2-2.10.1-py27_0.tar.bz2                 181 KB
openssl-1.1.1b-h7b6447c_1.tar.bz2            4.0 MB
pycparser-2.19-py27_0.tar.bz2                173 KB
pyrsistent-0.14.11-py27h7b6447c_0.tar.bz2      88 KB
libpng-1.6.37-hbc83047_0.tar.bz2             364 KB
kiwisolver-1.1.0-py27he6710b0_0.tar.bz2       91 KB
jpeg-9b-h024ee3a_2.tar.bz2                   248 KB
jsonschema-3.0.1-py27_0.tar.bz2               86 KB
pexpect-4.7.0-py27_0.tar.bz2                  80 KB
cryptography-2.4.2-py27h1ba5d50_0.tar.bz2     605 KB
pytz-2019.1-py_0.tar.bz2                     236 KB
nbconvert-5.5.0-py_0.tar.bz2                 381 KB
python-dateutil-2.8.0-py27_0.tar.bz2         279 KB
ipython-5.8.0-py27_0.tar.bz2                 1.0 MB
libedit-3.1.20170329-h6b74fdf_2.tar.bz2      172 KB
freetype-2.9.1-h8a8886c_1.tar.bz2            822 KB
cffi-1.11.5-py27he75722e_1.tar.bz2           209 KB
qt-5.9.7-h5867ecd_1.tar.bz2                 85.9 MB
gstreamer-1.14.0-hb453b48_1.tar.bz2          3.8 MB
pickleshare-0.7.5-py27_0.tar.bz2              12 KB
ipython_genutils-0.2.0-py27_0.tar.bz2         38 KB
gst-plugins-base-1.14.0-hbbd80ab_1.tar.bz2     6.3 MB
mistune-0.8.4-py27h7b6447c_0.tar.bz2          53 KB
terminado-0.8.2-py27_0.tar.bz2                22 KB
libxml2-2.9.9-he19cac6_0.tar.bz2             2.0 MB
cycler-0.10.0-py27_0.tar.bz2                  13 KB
pandocfilters-1.4.2-py27_1.tar.bz2            13 KB
pycosat-0.6.3-py27h14c3975_0.tar.bz2         103 KB
readline-7.0-h7b6447c_5.tar.bz2              392 KB
ruamel_yaml-0.15.46-py27h14c3975_0.tar.bz2     241 KB
numpy-base-1.16.3-py27h2f8d375_0.tar.bz2     4.3 MB
configparser-3.7.4-py27_0.tar.bz2             41 KB
python-2.7.15-h9bab390_6.tar.bz2            12.8 MB
funcsigs-1.0.2-py27_0.tar.bz2                 20 KB
libstdcxx-ng-8.2.0-hdf63c60_1.tar.bz2        2.9 MB
sqlite-3.26.0-h7b6447c_0.tar.bz2             1.9 MB
ipaddress-1.0.22-py27_0.tar.bz2               32 KB
atomicwrites-1.3.0-py27_1.tar.bz2             13 KB
icu-58.2-h9c2bf20_1.tar.bz2                 22.5 MB
blas-1.0-openblas.tar.bz2                     48 KB
matplotlib-2.2.3-py27hb69df0a_0.tar.bz2      6.5 MB
conda-env-2.6.0-1.tar.bz2                      3 KB
setuptools-40.6.3-py27_0.tar.bz2             627 KB
expat-2.2.6-he6710b0_0.tar.bz2               187 KB
certifi-2019.3.9-py27_0.tar.bz2              155 KB
scipy-1.2.1-py27he2b7bc3_0.tar.bz2          17.7 MB
requests-2.21.0-py27_0.tar.bz2                84 KB
scandir-1.10.0-py27h7b6447c_0.tar.bz2         32 KB
cython-0.29.7-py27he6710b0_0.tar.bz2         2.1 MB
traitlets-4.3.2-py27_0.tar.bz2               128 KB
pcre-8.43-he6710b0_0.tar.bz2                 260 KB
prometheus_client-0.6.0-py27_0.tar.bz2        69 KB
tornado-5.1.1-py27h7b6447c_0.tar.bz2         643 KB
libuuid-1.0.3-h1bed415_2.tar.bz2              16 KB
pip-18.1-py27_0.tar.bz2                      1.8 MB
conda-4.6.14-py27_0.tar.bz2                  2.1 MB
libxcb-1.13-h1bed415_1.tar.bz2               502 KB
certifi-2018.11.29-py27_0.tar.bz2            146 KB
testpath-0.4.2-py27_0.tar.bz2                 91 KB
pandoc-2.2.3.2-0.tar.bz2                    20.8 MB
dbus-1.13.6-h746ee38_0.tar.bz2               587 KB
libsodium-1.0.16-h1bed415_0.tar.bz2          302 KB
decorator-4.4.0-py27_1.tar.bz2                18 KB
defusedxml-0.6.0-py_0.tar.bz2                 23 KB
send2trash-1.5.0-py27_0.tar.bz2               16 KB
pathlib2-2.3.3-py27_0.tar.bz2                 31 KB
attrs-19.1.0-py27_1.tar.bz2                   56 KB
ca-certificates-2019.1.23-0.tar.bz2          126 KB
conda-4.5.12-py27_0.tar.bz2                  1.0 MB
gmp-6.1.2-h6c8ec71_1.tar.bz2                 744 KB
entrypoints-0.3-py27_0.tar.bz2                12 KB
yaml-0.1.7-had09818_2.tar.bz2                 85 KB
urllib3-1.24.1-py27_0.tar.bz2                147 KB
functools32-3.2.3.2-py27_1.tar.bz2            23 KB
pyzmq-18.0.0-py27he6710b0_0.tar.bz2          463 KB
fontconfig-2.13.0-h9420a91_0.tar.bz2         291 KB
six-1.12.0-py27_0.tar.bz2                     22 KB
prompt_toolkit-1.0.15-py27h1b593e1_0.tar.bz2     333 KB
backports-1.0-py27_1.tar.bz2                   3 KB
webencodings-0.5.1-py27_1.tar.bz2             19 KB
pyparsing-2.4.0-py_0.tar.bz2                  58 KB
backports.shutil_get_terminal_size-1.0.0-py27_2.tar.bz2       8 KB
glib-2.56.2-hd408876_0.tar.bz2               5.0 MB
jupyter_client-5.2.4-py27_0.tar.bz2          125 KB
wcwidth-0.1.7-py27h9e3e1ab_0.tar.bz2          25 KB
pyqt-5.9.2-py27h05f1152_2.tar.bz2            5.4 MB
bleach-3.1.0-py27_0.tar.bz2                  228 KB
backports_abc-0.5-py_0.tar.bz2                13 KB
more-itertools-5.0.0-py27_0.tar.bz2           86 KB
pygments-2.4.0-py_0.tar.bz2                  664 KB
openssl-1.1.1a-h7b6447c_0.tar.bz2            5.0 MB
backports.functools_lru_cache-1.5-py27_1.tar.bz2       9 KB
ca-certificates-2018.03.07-0.tar.bz2         124 KB
chardet-3.0.4-py27_1.tar.bz2                 180 KB
libgcc-ng-8.2.0-hdf63c60_1.tar.bz2           7.6 MB
pysocks-1.6.8-py27_0.tar.bz2                  22 KB
idna-2.8-py27_0.tar.bz2                      133 KB
nbformat-4.4.0-py27_0.tar.bz2                139 KB
enum34-1.1.6-py27_1.tar.bz2                   57 KB

---------------------------------------------------
Total:                                     258.0 MB

Removed numpy-1.16.3-py27h99e49ec_0.tar.bz2
Removed pytest-4.5.0-py27_0.tar.bz2
Removed singledispatch-3.4.0.3-py27_0.tar.bz2
Removed wheel-0.32.3-py27_0.tar.bz2
Removed tk-8.6.8-hbc83047_0.tar.bz2
Removed futures-3.2.0-py27_0.tar.bz2
Removed nomkl-3.0-0.tar.bz2
Removed simplegeneric-0.8.1-py27_2.tar.bz2
Removed ipykernel-4.10.0-py27_0.tar.bz2
Removed sip-4.19.8-py27hf484d3e_0.tar.bz2
Removed libopenblas-0.3.3-h5a2b251_3.tar.bz2
Removed markupsafe-1.1.1-py27h7b6447c_0.tar.bz2
Removed asn1crypto-0.24.0-py27_0.tar.bz2
Removed subprocess32-3.5.3-py27h7b6447c_0.tar.bz2
Removed zeromq-4.3.1-he6710b0_3.tar.bz2
Removed notebook-5.7.8-py27_0.tar.bz2
Removed libgfortran-ng-7.3.0-hdf63c60_0.tar.bz2
Removed libffi-3.2.1-hd88cf55_4.tar.bz2
Removed ncurses-6.1-he6710b0_1.tar.bz2
Removed pluggy-0.11.0-py_0.tar.bz2
Removed zlib-1.2.11-h7b6447c_3.tar.bz2
Removed py-1.8.0-py27_0.tar.bz2
Removed jupyter_core-4.4.0-py27_0.tar.bz2
Removed pyopenssl-18.0.0-py27_0.tar.bz2
Removed xz-5.2.4-h14c3975_4.tar.bz2
Removed ptyprocess-0.6.0-py27_0.tar.bz2
Removed jinja2-2.10.1-py27_0.tar.bz2
Removed openssl-1.1.1b-h7b6447c_1.tar.bz2
Removed pycparser-2.19-py27_0.tar.bz2
Removed pyrsistent-0.14.11-py27h7b6447c_0.tar.bz2
Removed libpng-1.6.37-hbc83047_0.tar.bz2
Removed kiwisolver-1.1.0-py27he6710b0_0.tar.bz2
Removed jpeg-9b-h024ee3a_2.tar.bz2
Removed jsonschema-3.0.1-py27_0.tar.bz2
Removed pexpect-4.7.0-py27_0.tar.bz2
Removed cryptography-2.4.2-py27h1ba5d50_0.tar.bz2
Removed pytz-2019.1-py_0.tar.bz2
Removed nbconvert-5.5.0-py_0.tar.bz2
Removed python-dateutil-2.8.0-py27_0.tar.bz2
Removed ipython-5.8.0-py27_0.tar.bz2
Removed libedit-3.1.20170329-h6b74fdf_2.tar.bz2
Removed freetype-2.9.1-h8a8886c_1.tar.bz2
Removed cffi-1.11.5-py27he75722e_1.tar.bz2
Removed qt-5.9.7-h5867ecd_1.tar.bz2
Removed gstreamer-1.14.0-hb453b48_1.tar.bz2
Removed pickleshare-0.7.5-py27_0.tar.bz2
Removed ipython_genutils-0.2.0-py27_0.tar.bz2
Removed gst-plugins-base-1.14.0-hbbd80ab_1.tar.bz2
Removed mistune-0.8.4-py27h7b6447c_0.tar.bz2
Removed terminado-0.8.2-py27_0.tar.bz2
Removed libxml2-2.9.9-he19cac6_0.tar.bz2
Removed cycler-0.10.0-py27_0.tar.bz2
Removed pandocfilters-1.4.2-py27_1.tar.bz2
Removed pycosat-0.6.3-py27h14c3975_0.tar.bz2
Removed readline-7.0-h7b6447c_5.tar.bz2
Removed ruamel_yaml-0.15.46-py27h14c3975_0.tar.bz2
Removed numpy-base-1.16.3-py27h2f8d375_0.tar.bz2
Removed configparser-3.7.4-py27_0.tar.bz2
Removed python-2.7.15-h9bab390_6.tar.bz2
Removed funcsigs-1.0.2-py27_0.tar.bz2
Removed libstdcxx-ng-8.2.0-hdf63c60_1.tar.bz2
Removed sqlite-3.26.0-h7b6447c_0.tar.bz2
Removed ipaddress-1.0.22-py27_0.tar.bz2
Removed atomicwrites-1.3.0-py27_1.tar.bz2
Removed icu-58.2-h9c2bf20_1.tar.bz2
Removed blas-1.0-openblas.tar.bz2
Removed matplotlib-2.2.3-py27hb69df0a_0.tar.bz2
Removed conda-env-2.6.0-1.tar.bz2
Removed setuptools-40.6.3-py27_0.tar.bz2
Removed expat-2.2.6-he6710b0_0.tar.bz2
Removed certifi-2019.3.9-py27_0.tar.bz2
Removed scipy-1.2.1-py27he2b7bc3_0.tar.bz2
Removed requests-2.21.0-py27_0.tar.bz2
Removed scandir-1.10.0-py27h7b6447c_0.tar.bz2
Removed cython-0.29.7-py27he6710b0_0.tar.bz2
Removed traitlets-4.3.2-py27_0.tar.bz2
Removed pcre-8.43-he6710b0_0.tar.bz2
Removed prometheus_client-0.6.0-py27_0.tar.bz2
Removed tornado-5.1.1-py27h7b6447c_0.tar.bz2
Removed libuuid-1.0.3-h1bed415_2.tar.bz2
Removed pip-18.1-py27_0.tar.bz2
Removed conda-4.6.14-py27_0.tar.bz2
Removed libxcb-1.13-h1bed415_1.tar.bz2
Removed certifi-2018.11.29-py27_0.tar.bz2
Removed testpath-0.4.2-py27_0.tar.bz2
Removed pandoc-2.2.3.2-0.tar.bz2
Removed dbus-1.13.6-h746ee38_0.tar.bz2
Removed libsodium-1.0.16-h1bed415_0.tar.bz2
Removed decorator-4.4.0-py27_1.tar.bz2
Removed defusedxml-0.6.0-py_0.tar.bz2
Removed send2trash-1.5.0-py27_0.tar.bz2
Removed pathlib2-2.3.3-py27_0.tar.bz2
Removed attrs-19.1.0-py27_1.tar.bz2
Removed ca-certificates-2019.1.23-0.tar.bz2
Removed conda-4.5.12-py27_0.tar.bz2
Removed gmp-6.1.2-h6c8ec71_1.tar.bz2
Removed entrypoints-0.3-py27_0.tar.bz2
Removed yaml-0.1.7-had09818_2.tar.bz2
Removed urllib3-1.24.1-py27_0.tar.bz2
Removed functools32-3.2.3.2-py27_1.tar.bz2
Removed pyzmq-18.0.0-py27he6710b0_0.tar.bz2
Removed fontconfig-2.13.0-h9420a91_0.tar.bz2
Removed six-1.12.0-py27_0.tar.bz2
Removed prompt_toolkit-1.0.15-py27h1b593e1_0.tar.bz2
Removed backports-1.0-py27_1.tar.bz2
Removed webencodings-0.5.1-py27_1.tar.bz2
Removed pyparsing-2.4.0-py_0.tar.bz2
Removed backports.shutil_get_terminal_size-1.0.0-py27_2.tar.bz2
Removed glib-2.56.2-hd408876_0.tar.bz2
Removed jupyter_client-5.2.4-py27_0.tar.bz2
Removed wcwidth-0.1.7-py27h9e3e1ab_0.tar.bz2
Removed pyqt-5.9.2-py27h05f1152_2.tar.bz2
Removed bleach-3.1.0-py27_0.tar.bz2
Removed backports_abc-0.5-py_0.tar.bz2
Removed more-itertools-5.0.0-py27_0.tar.bz2
Removed pygments-2.4.0-py_0.tar.bz2
Removed openssl-1.1.1a-h7b6447c_0.tar.bz2
Removed backports.functools_lru_cache-1.5-py27_1.tar.bz2
Removed ca-certificates-2018.03.07-0.tar.bz2
Removed chardet-3.0.4-py27_1.tar.bz2
Removed libgcc-ng-8.2.0-hdf63c60_1.tar.bz2
Removed pysocks-1.6.8-py27_0.tar.bz2
Removed idna-2.8-py27_0.tar.bz2
Removed nbformat-4.4.0-py27_0.tar.bz2
Removed enum34-1.1.6-py27_1.tar.bz2
Cache location: /opt/amber19/amber18/miniconda/pkgs
Will remove the following packages:
/opt/amber19/amber18/miniconda/pkgs
-----------------------------------

pip-18.1-py27_0                              7.6 MB
numpy-1.16.3-py27h99e49ec_0                  256 KB
conda-env-2.6.0-1                              6 KB
conda-4.5.12-py27_0                          6.3 MB
blas-1.0-openblas                            281 KB
certifi-2018.11.29-py27_0                    285 KB
openssl-1.1.1a-h7b6447c_0                   22.6 MB
ca-certificates-2018.03.07-0                 231 KB
nomkl-3.0-0                                  281 KB

---------------------------------------------------
Total:                                      37.9 MB

removing pip-18.1-py27_0
removing numpy-1.16.3-py27h99e49ec_0
removing conda-env-2.6.0-1
removing conda-4.5.12-py27_0
removing blas-1.0-openblas
removing certifi-2018.11.29-py27_0
removing openssl-1.1.1a-h7b6447c_0
removing ca-certificates-2018.03.07-0
removing nomkl-3.0-0
================================================================================
Done installing Miniconda!

Obtaining the gnu compiler suite versions, e.g.:
     gcc -v
The C version is 8.3.0
The Fortran version is 8.3.0

Testing the gcc compiler:
     gcc -fPIC  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -o testp testp.c
OK

Testing the g++ compiler:
     g++ -fPIC  -o testp testp.cpp
OK

Testing the gfortran compiler:
     gfortran -fPIC  -O0 -o testp testp.f 
OK

Testing mixed C/Fortran compilation:
     gcc -fPIC  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -c -o testp.c.o testp.c
     gfortran -fPIC  -O0 -c -o testp.f.o testp.f
     gcc -fPIC  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lgfortran -w 
OK

Testing pointer size:
     gcc -fPIC  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -o test_pointer_size test_pointer_size.c
Detected 64 bit operating system.

Testing flex:OK

Testing bison:
OK

Checking NetCDF...
	Using bundled NetCDF library.
	Starting NetCDF build.
	Configuring NetCDF C interface (may be time-consuming)...
	Compiling the NetCDF C interface (may be time-consuming)...
	Configuring NetCDF Fortran interface (may be time-consuming)...
	Compiling the NetCDF Fortran interface (may be time-consuming)...
NetCDF build succeeded.

Checking for zlib: OK

Checking for libbz2: OK

Configuring fftw-3.3 (may be time-consuming)...

    fftw-3.3 configure succeeded.

Configuring boost (may be time-consuming)...OK
Compiling boost (may be time-consuming)...OK

Configuring XBLAS (may be time-consuming)...

    XBLAS configure succeeded.

Configuring CPPTRAJ...complete.
 
The configuration file, config.h, was successfully created.
 
--------------------------------------------------------------------------------
Environment resource files are provided to set the proper environment
variables to use AMBER and AmberTools. This is required to run any Python
programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj)

If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
/opt/amber19/amber18/amber.sh file in your shell. Consider adding the line
  test -f /opt/amber19/amber18/amber.sh && source /opt/amber19/amber18/amber.sh
to your startup file (e.g., ~/.bashrc)

If you use a C shell (e.g., csh, tcsh), source the
/opt/amber19/amber18/amber.csh file in your shell. Consider adding the line
  test -f /opt/amber19/amber18/amber.csh && source /opt/amber19/amber18/amber.csh
to your startup file (e.g., ~/.cshrc)

NOTE: MacOS users might need to add the content to ~/.bash_profile file
(You need to do the above before running 'make install')
--------------------------------------------------------------------------------

The next step is to source the amber.sh or amber.csh file
  (if needed, see above), and then to type 'make install'

Cleaning the src directories. This may take a few moments.
Configure complete.
