Speech:Spring 2017 Miniconda Install Documentation

Miniconda Install Documentation

Author: Jeffrey Gancarz

This is the documentation for the installation of Miniconda on Asterix on 3/29/17.

Steps 1: Sign into Caesar as root login as: root root@caesar.unh.edu's password: Last login: Wed Mar 29 15:11:42 2017 from jeffrey.ra.unh.edu / __ \ \____/\__,_|\___||___/\__,_|_|                  Welcomes you!
 * / \/ __ _  ___  ___  __ _ _ __
 * |   / _` |/ _ \/ __|/ _` | '__|
 * \__/\ (_| | __/\__ \ (_| | |

[root@caesar ~]#

Step 2: ssh into Asterix ssh asterix

Step 3: change into the /mnt/main/ directory cd /mnt/main

Step 4: unmount /mnt/main/ umount -a

Step 5: change into the /usr/bin/ directory cd /usr/bin/

Step 6: create miniconda directory and change into that directory mkdir miniconda cd miniconda

Step 7: perform first step in installing miniconda wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86.sh

--2017-03-28 16:23:41-- https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86.sh Resolving repo.continuum.io... 104.16.19.10, 104.16.18.10, 2400:cb00:2048:1::6810:130a, ... Connecting to repo.continuum.io|104.16.19.10|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 24351995 (23M) [application/x-sh] Saving to: “Miniconda2-latest-Linux-x86.sh”

100%[======================================>] 24,351,995 10.7M/s   in 2.2s

2017-03-28 16:23:43 (10.7 MB/s) - “Miniconda2-latest-Linux-x86.sh” saved [24351995/24351995]

Step 8: change the miniconda file into an executable file [root@asterix miniconda]# chmod +x Miniconda2-latest-Linux-x86.sh

Step 9: run the miniconda executable file [root@asterix miniconda]# ./Miniconda2-latest-Linux-x86.sh

Welcome to Miniconda2 4.3.11 (by Continuum Analytics, Inc.)

In order to continue the installation process, please review the license agreement. Please, press ENTER to continue >>>

=
==== Miniconda License

=
====

Copyright 2016, Continuum Analytics, Inc.

All rights reserved under the 3-clause BSD License:

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

this list of conditions and the following disclaimer.
 * Redistributions of source code must retain the above copyright notice,

this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
 * Redistributions in binary form must reproduce the above copyright notice,

contributors may be used to endorse or promote products derived from this software without specific prior written permission.
 * Neither the name of Continuum Analytics, Inc. nor the names of its

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL CONTINUUM ANALYTICS, INC. BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Notice of Third Party Software Licenses

=
==========================

Anaconda contains open source software packages from third parties. These are available on an "as is" basis and subject to their individual license agreements. These licenses are available in Anaconda or at http://docs.continuum.io/anaconda/pkg-docs. Any binary packages of these third party tools you obtain via Anaconda are subject to their individual licenses as well as the Anaconda license. Continuum reserves the right to change which third party tools are provided in Anaconda.

Cryptography Notice

=
====== This distribution includes cryptographic software. The country in which you currently reside may have restrictions on the import, possession, use, and/or re-export to another country, of encryption software. BEFORE using any encryption software, please check your country's laws, regulations and policies concerning the import, possession, or use, and re-export of encryption software, to see if this is permitted. See the Wassenaar Arrangement  for more information.

Continuum Analytics has self-classified this software as Export Commodity Control Number (ECCN) 5D002.C.1, which includes information security software using or performing cryptographic functions with asymmetric algorithms. The form and manner of this distribution makes it eligible for export under the License Exception ENC Technology Software Unrestricted (TSU) exception (see the BIS Export Administration Regulations, Section 740.13) for both object code and source code.

The following packages are included in this distribution that relate to cryptography:

openssl The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolkit implementing the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols as well as a full-strength general purpose cryptography library.

pycrypto A collection of both secure hash functions (such as SHA256 and RIPEMD160), and various encryption algorithms (AES, DES, RSA, ElGamal, etc.).

Do you approve the license terms? [yes|no] >>> yes

Miniconda2 will now be installed into this location: /root/miniconda2

- Press ENTER to confirm the location - Press CTRL-C to abort the installation - Or specify a different location below

[/root/miniconda2] >>> /usr/local mkdir: cannot create directory `/usr/local': File exists ERROR: Could not create directory: /usr/local [root@asterix miniconda]# ./Miniconda2-latest-Linux-x86.sh

Welcome to Miniconda2 4.3.11 (by Continuum Analytics, Inc.)

In order to continue the installation process, please review the license agreement. Please, press ENTER to continue >>>

=
==== Miniconda License

=
====

Copyright 2016, Continuum Analytics, Inc.

All rights reserved under the 3-clause BSD License:

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

this list of conditions and the following disclaimer.
 * Redistributions of source code must retain the above copyright notice,

this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
 * Redistributions in binary form must reproduce the above copyright notice,

contributors may be used to endorse or promote products derived from this software without specific prior written permission.
 * Neither the name of Continuum Analytics, Inc. nor the names of its

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL CONTINUUM ANALYTICS, INC. BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Notice of Third Party Software Licenses

=
==========================

Anaconda contains open source software packages from third parties. These are available on an "as is" basis and subject to their individual license agreements. These licenses are available in Anaconda or at http://docs.continuum.io/anaconda/pkg-docs. Any binary packages of these third party tools you obtain via Anaconda are subject to their individual licenses as well as the Anaconda license. Continuum reserves the right to change which third party tools are provided in Anaconda.

Cryptography Notice

=
====== This distribution includes cryptographic software. The country in which you currently reside may have restrictions on the import, possession, use, and/or re-export to another country, of encryption software. BEFORE using any encryption software, please check your country's laws, regulations and policies concerning the import, possession, or use, and re-export of encryption software, to see if this is permitted. See the Wassenaar Arrangement  for more information.

Continuum Analytics has self-classified this software as Export Commodity Control Number (ECCN) 5D002.C.1, which includes information security software using or performing cryptographic functions with asymmetric algorithms. The form and manner of this distribution makes it eligible for export under the License Exception ENC Technology Software Unrestricted (TSU) exception (see the BIS Export Administration Regulations, Section 740.13) for both object code and source code.

The following packages are included in this distribution that relate to cryptography:

openssl The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolkit implementing the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols as well as a full-strength general purpose cryptography library.

pycrypto A collection of both secure hash functions (such as SHA256 and RIPEMD160), and various encryption algorithms (AES, DES, RSA, ElGamal, etc.).

Do you approve the license terms? [yes|no] Please answer 'yes' or 'no': >>> yes

Step 10: confirm a location for miniconda to be located Miniconda2 will now be installed into this location: /root/miniconda2

- Press ENTER to confirm the location - Press CTRL-C to abort the installation - Or specify a different location below

[/root/miniconda2] >>> /root/usr/bin PREFIX=/root/usr/bin installing: python-2.7.13-0 ... installing: cffi-1.9.1-py27_0 ... installing: conda-env-2.6.0-0 ... installing: cryptography-1.7.1-py27_0 ... installing: enum34-1.1.6-py27_0 ... installing: idna-2.2-py27_0 ... installing: ipaddress-1.0.18-py27_0 ... installing: libffi-3.2.1-1 ... installing: openssl-1.0.2k-0 ... installing: pyasn1-0.1.9-py27_0 ... installing: pycosat-0.6.1-py27_1 ... installing: pycparser-2.17-py27_0 ... installing: pyopenssl-16.2.0-py27_0 ... installing: readline-6.2-2 ... installing: requests-2.12.4-py27_0 ... installing: ruamel_yaml-0.11.14-py27_1 ... installing: setuptools-27.2.0-py27_0 ... installing: six-1.10.0-py27_0 ... installing: sqlite-3.13.0-0 ... installing: tk-8.5.18-0 ... installing: yaml-0.1.6-0 ... installing: zlib-1.2.8-3 ... installing: conda-4.3.11-py27_0 ... installing: pip-9.0.1-py27_1 ... installing: wheel-0.29.0-py27_0 ... Python 2.7.13 :: Continuum Analytics, Inc. creating default environment... installation finished.

Step 11: wish the installer to prepend Miniconda file location Do you wish the installer to prepend the Miniconda2 install location to PATH in your /root/.bashrc ? [yes|no] [no] >>> yes

Prepending PATH=/root/usr/bin/bin to PATH in /root/.bashrc A backup will be made to: /root/.bashrc-miniconda2.bak

For this change to become active, you have to open a new terminal.

Thank you for installing Miniconda2!

Step 12: Install numpy and scipy This is where we are currently running into our problems. We cannot seem to run miniconda on Asterix and have the software find python 2.7. When we use miniconda it goes back and uses the older python version of 2.6. We need to figure this step out so we can continue with the installation of numpy and scipy. After that we will update this page.