Python environment setup

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Qiang Zhu edited this page Aug 22, 2018 · 11 revisions

1. Conda

It is usually good to use the integrated version of python like conda for the beginners. Download and install the version of conda for your operating system from http://conda.pydata.org/miniconda.html.

$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

# If Mac
$ bash Miniconda3-latest-MacOSX-x86_64.sh
# If Linux
$ bash Miniconda3-latest-Linux-x86_64.sh

pymatgen

$ conda install -c matsci pymatgen

ase

$ conda install -c jochym python-ase

or

$ pip install --upgrade --user ase

glibc

This is a very annoying issue if you work with old centOS distribution. Unfortunately, a lot of supercomputing clusters are still using this old centOS version. One cannot update glibc on Centos 6 safely. However you can install 2.14 alongside 2.12 easily, then use it to compile projects etc. Here is how:

mkdir ~/glibc_install; cd ~/glibc_install wget http://ftp.gnu.org/gnu/glibc/glibc-2.14.tar.gz
tar zxvf glibc-2.14.tar.gz
cd glibc-2.14
mkdir build
cd build
../configure --prefix=/opt/glibc-2.14
make -j4
sudo make install
export LD_LIBRARY_PATH=/opt/glibc-2.14/lib

slow installation from China

Conda installation might be very slow in China. In this case, one could use the mirror provided from the following website

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --set show_channel_urls yes

More instructions could be found here

2, Direct compilation from the python source code.

Conda is great, but not optimal. It is not efficient for large scale numerical calculation, and sometimes you will find you local library like glibc is not compatible with conda. Therefore, it is better compile python from the source code, instead of Conda.

$ wget https://www.python.org/ftp/python/3.5.6/Python-3.5.6.tgz
$ tar -xf Python-3.5.6.tgz
$ cd Python-3.5.6
$ ./configure --prefix= /folder address/
$ make
$ make test
$ make install

to install pymatgen and ase

$ pip install pymatgen
$ pip install ase

Computing clusters

Scientific topics

Resources

Clone this wiki locally

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Skip to content
Python environment setup
Jump to bottom

Qiang Zhu edited this page Aug 22, 2018
·
11 revisions
1. Conda
It is usually good to use the integrated version of python like conda for the beginners.
Download and install the version of conda for your operating system from http://conda.pydata.org/miniconda.html.
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

# If Mac
$ bash Miniconda3-latest-MacOSX-x86_64.sh
# If Linux
$ bash Miniconda3-latest-Linux-x86_64.sh

pymatgen
$ conda install -c matsci pymatgen

ase
$ conda install -c jochym python-ase

or
$ pip install --upgrade --user ase

glibc
This is a very annoying issue if you work with old centOS distribution.
Unfortunately, a lot of supercomputing clusters are still using this old centOS version.
One cannot update glibc on Centos 6 safely. However you can install 2.14 alongside 2.12 easily, then use it to compile projects etc. Here is how:
mkdir ~/glibc_install; cd ~/glibc_install wget http://ftp.gnu.org/gnu/glibc/glibc-2.14.tar.gz
tar zxvf glibc-2.14.tar.gz
cd glibc-2.14
mkdir build
cd build
../configure --prefix=/opt/glibc-2.14
make -j4
sudo make install
export LD_LIBRARY_PATH=/opt/glibc-2.14/lib

slow installation from China
Conda installation might be very slow in China. In this case, one could use the mirror provided from the following website
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --set show_channel_urls yes

More instructions could be found here
2, Direct compilation from the python source code.
Conda is great, but not optimal. It is not efficient for large scale numerical calculation, and sometimes you will find you local library like glibc is not compatible with conda. Therefore, it is better compile python from the source code, instead of Conda.
$ wget https://www.python.org/ftp/python/3.5.6/Python-3.5.6.tgz
$ tar -xf Python-3.5.6.tgz
$ cd Python-3.5.6
$ ./configure --prefix= /folder address/
$ make
$ make test
$ make install

to install pymatgen and ase
$ pip install pymatgen
$ pip install ase

Computing clusters
Scientific topics
Resources
Clone this wiki locally

, 'i');
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Skip to content
Python environment setup
Jump to bottom

Qiang Zhu edited this page Aug 22, 2018
·
11 revisions
1. Conda
It is usually good to use the integrated version of python like conda for the beginners.
Download and install the version of conda for your operating system from http://conda.pydata.org/miniconda.html.
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

# If Mac
$ bash Miniconda3-latest-MacOSX-x86_64.sh
# If Linux
$ bash Miniconda3-latest-Linux-x86_64.sh

pymatgen
$ conda install -c matsci pymatgen

ase
$ conda install -c jochym python-ase

or
$ pip install --upgrade --user ase

glibc
This is a very annoying issue if you work with old centOS distribution.
Unfortunately, a lot of supercomputing clusters are still using this old centOS version.
One cannot update glibc on Centos 6 safely. However you can install 2.14 alongside 2.12 easily, then use it to compile projects etc. Here is how:
mkdir ~/glibc_install; cd ~/glibc_install wget http://ftp.gnu.org/gnu/glibc/glibc-2.14.tar.gz
tar zxvf glibc-2.14.tar.gz
cd glibc-2.14
mkdir build
cd build
../configure --prefix=/opt/glibc-2.14
make -j4
sudo make install
export LD_LIBRARY_PATH=/opt/glibc-2.14/lib

slow installation from China
Conda installation might be very slow in China. In this case, one could use the mirror provided from the following website
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --set show_channel_urls yes

More instructions could be found here
2, Direct compilation from the python source code.
Conda is great, but not optimal. It is not efficient for large scale numerical calculation, and sometimes you will find you local library like glibc is not compatible with conda. Therefore, it is better compile python from the source code, instead of Conda.
$ wget https://www.python.org/ftp/python/3.5.6/Python-3.5.6.tgz
$ tar -xf Python-3.5.6.tgz
$ cd Python-3.5.6
$ ./configure --prefix= /folder address/
$ make
$ make test
$ make install

to install pymatgen and ase
$ pip install pymatgen
$ pip install ase

Computing clusters
Scientific topics
Resources
Clone this wiki locally

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var __m = "*";
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Skip to content
Python environment setup
Jump to bottom

Qiang Zhu edited this page Aug 22, 2018
·
11 revisions
1. Conda
It is usually good to use the integrated version of python like conda for the beginners.
Download and install the version of conda for your operating system from http://conda.pydata.org/miniconda.html.
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

# If Mac
$ bash Miniconda3-latest-MacOSX-x86_64.sh
# If Linux
$ bash Miniconda3-latest-Linux-x86_64.sh

pymatgen
$ conda install -c matsci pymatgen

ase
$ conda install -c jochym python-ase

or
$ pip install --upgrade --user ase

glibc
This is a very annoying issue if you work with old centOS distribution.
Unfortunately, a lot of supercomputing clusters are still using this old centOS version.
One cannot update glibc on Centos 6 safely. However you can install 2.14 alongside 2.12 easily, then use it to compile projects etc. Here is how:
mkdir ~/glibc_install; cd ~/glibc_install wget http://ftp.gnu.org/gnu/glibc/glibc-2.14.tar.gz
tar zxvf glibc-2.14.tar.gz
cd glibc-2.14
mkdir build
cd build
../configure --prefix=/opt/glibc-2.14
make -j4
sudo make install
export LD_LIBRARY_PATH=/opt/glibc-2.14/lib

slow installation from China
Conda installation might be very slow in China. In this case, one could use the mirror provided from the following website
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --set show_channel_urls yes

More instructions could be found here
2, Direct compilation from the python source code.
Conda is great, but not optimal. It is not efficient for large scale numerical calculation, and sometimes you will find you local library like glibc is not compatible with conda. Therefore, it is better compile python from the source code, instead of Conda.
$ wget https://www.python.org/ftp/python/3.5.6/Python-3.5.6.tgz
$ tar -xf Python-3.5.6.tgz
$ cd Python-3.5.6
$ ./configure --prefix= /folder address/
$ make
$ make test
$ make install

to install pymatgen and ase
$ pip install pymatgen
$ pip install ase

Computing clusters
Scientific topics
Resources
Clone this wiki locally

, 'i');
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(function(){
try {
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var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Python environment setup
Jump to bottom

Qiang Zhu edited this page Aug 22, 2018
·
11 revisions
1. Conda
It is usually good to use the integrated version of python like conda for the beginners.
Download and install the version of conda for your operating system from http://conda.pydata.org/miniconda.html.
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

# If Mac
$ bash Miniconda3-latest-MacOSX-x86_64.sh
# If Linux
$ bash Miniconda3-latest-Linux-x86_64.sh

pymatgen
$ conda install -c matsci pymatgen

ase
$ conda install -c jochym python-ase

or
$ pip install --upgrade --user ase

glibc
This is a very annoying issue if you work with old centOS distribution.
Unfortunately, a lot of supercomputing clusters are still using this old centOS version.
One cannot update glibc on Centos 6 safely. However you can install 2.14 alongside 2.12 easily, then use it to compile projects etc. Here is how:
mkdir ~/glibc_install; cd ~/glibc_install wget http://ftp.gnu.org/gnu/glibc/glibc-2.14.tar.gz
tar zxvf glibc-2.14.tar.gz
cd glibc-2.14
mkdir build
cd build
../configure --prefix=/opt/glibc-2.14
make -j4
sudo make install
export LD_LIBRARY_PATH=/opt/glibc-2.14/lib

slow installation from China
Conda installation might be very slow in China. In this case, one could use the mirror provided from the following website
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --set show_channel_urls yes

More instructions could be found here
2, Direct compilation from the python source code.
Conda is great, but not optimal. It is not efficient for large scale numerical calculation, and sometimes you will find you local library like glibc is not compatible with conda. Therefore, it is better compile python from the source code, instead of Conda.
$ wget https://www.python.org/ftp/python/3.5.6/Python-3.5.6.tgz
$ tar -xf Python-3.5.6.tgz
$ cd Python-3.5.6
$ ./configure --prefix= /folder address/
$ make
$ make test
$ make install

to install pymatgen and ase
$ pip install pymatgen
$ pip install ase

Computing clusters
Scientific topics
Resources
Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
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(function(){
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var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Python environment setup
Jump to bottom

Qiang Zhu edited this page Aug 22, 2018
·
11 revisions
1. Conda
It is usually good to use the integrated version of python like conda for the beginners.
Download and install the version of conda for your operating system from http://conda.pydata.org/miniconda.html.
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

# If Mac
$ bash Miniconda3-latest-MacOSX-x86_64.sh
# If Linux
$ bash Miniconda3-latest-Linux-x86_64.sh

pymatgen
$ conda install -c matsci pymatgen

ase
$ conda install -c jochym python-ase

or
$ pip install --upgrade --user ase

glibc
This is a very annoying issue if you work with old centOS distribution.
Unfortunately, a lot of supercomputing clusters are still using this old centOS version.
One cannot update glibc on Centos 6 safely. However you can install 2.14 alongside 2.12 easily, then use it to compile projects etc. Here is how:
mkdir ~/glibc_install; cd ~/glibc_install wget http://ftp.gnu.org/gnu/glibc/glibc-2.14.tar.gz
tar zxvf glibc-2.14.tar.gz
cd glibc-2.14
mkdir build
cd build
../configure --prefix=/opt/glibc-2.14
make -j4
sudo make install
export LD_LIBRARY_PATH=/opt/glibc-2.14/lib

slow installation from China
Conda installation might be very slow in China. In this case, one could use the mirror provided from the following website
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --set show_channel_urls yes

More instructions could be found here
2, Direct compilation from the python source code.
Conda is great, but not optimal. It is not efficient for large scale numerical calculation, and sometimes you will find you local library like glibc is not compatible with conda. Therefore, it is better compile python from the source code, instead of Conda.
$ wget https://www.python.org/ftp/python/3.5.6/Python-3.5.6.tgz
$ tar -xf Python-3.5.6.tgz
$ cd Python-3.5.6
$ ./configure --prefix= /folder address/
$ make
$ make test
$ make install

to install pymatgen and ase
$ pip install pymatgen
$ pip install ase

Computing clusters
Scientific topics
Resources
Clone this wiki locally

, 'i');
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Skip to content
Python environment setup
Jump to bottom

Qiang Zhu edited this page Aug 22, 2018
·
11 revisions
1. Conda
It is usually good to use the integrated version of python like conda for the beginners.
Download and install the version of conda for your operating system from http://conda.pydata.org/miniconda.html.
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

# If Mac
$ bash Miniconda3-latest-MacOSX-x86_64.sh
# If Linux
$ bash Miniconda3-latest-Linux-x86_64.sh

pymatgen
$ conda install -c matsci pymatgen

ase
$ conda install -c jochym python-ase

or
$ pip install --upgrade --user ase

glibc
This is a very annoying issue if you work with old centOS distribution.
Unfortunately, a lot of supercomputing clusters are still using this old centOS version.
One cannot update glibc on Centos 6 safely. However you can install 2.14 alongside 2.12 easily, then use it to compile projects etc. Here is how:
mkdir ~/glibc_install; cd ~/glibc_install wget http://ftp.gnu.org/gnu/glibc/glibc-2.14.tar.gz
tar zxvf glibc-2.14.tar.gz
cd glibc-2.14
mkdir build
cd build
../configure --prefix=/opt/glibc-2.14
make -j4
sudo make install
export LD_LIBRARY_PATH=/opt/glibc-2.14/lib

slow installation from China
Conda installation might be very slow in China. In this case, one could use the mirror provided from the following website
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --set show_channel_urls yes

More instructions could be found here
2, Direct compilation from the python source code.
Conda is great, but not optimal. It is not efficient for large scale numerical calculation, and sometimes you will find you local library like glibc is not compatible with conda. Therefore, it is better compile python from the source code, instead of Conda.
$ wget https://www.python.org/ftp/python/3.5.6/Python-3.5.6.tgz
$ tar -xf Python-3.5.6.tgz
$ cd Python-3.5.6
$ ./configure --prefix= /folder address/
$ make
$ make test
$ make install

to install pymatgen and ase
$ pip install pymatgen
$ pip install ase

Computing clusters
Scientific topics
Resources
Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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Python environment setup
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Qiang Zhu edited this page Aug 22, 2018
·
11 revisions
1. Conda
It is usually good to use the integrated version of python like conda for the beginners.
Download and install the version of conda for your operating system from http://conda.pydata.org/miniconda.html.
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

# If Mac
$ bash Miniconda3-latest-MacOSX-x86_64.sh
# If Linux
$ bash Miniconda3-latest-Linux-x86_64.sh

pymatgen
$ conda install -c matsci pymatgen

ase
$ conda install -c jochym python-ase

or
$ pip install --upgrade --user ase

glibc
This is a very annoying issue if you work with old centOS distribution.
Unfortunately, a lot of supercomputing clusters are still using this old centOS version.
One cannot update glibc on Centos 6 safely. However you can install 2.14 alongside 2.12 easily, then use it to compile projects etc. Here is how:
mkdir ~/glibc_install; cd ~/glibc_install wget http://ftp.gnu.org/gnu/glibc/glibc-2.14.tar.gz
tar zxvf glibc-2.14.tar.gz
cd glibc-2.14
mkdir build
cd build
../configure --prefix=/opt/glibc-2.14
make -j4
sudo make install
export LD_LIBRARY_PATH=/opt/glibc-2.14/lib

slow installation from China
Conda installation might be very slow in China. In this case, one could use the mirror provided from the following website
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --set show_channel_urls yes

More instructions could be found here
2, Direct compilation from the python source code.
Conda is great, but not optimal. It is not efficient for large scale numerical calculation, and sometimes you will find you local library like glibc is not compatible with conda. Therefore, it is better compile python from the source code, instead of Conda.
$ wget https://www.python.org/ftp/python/3.5.6/Python-3.5.6.tgz
$ tar -xf Python-3.5.6.tgz
$ cd Python-3.5.6
$ ./configure --prefix= /folder address/
$ make
$ make test
$ make install

to install pymatgen and ase
$ pip install pymatgen
$ pip install ase

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