Setting up Yambo - Revision history

Davide: Reorganization of sections

2024-10-03T12:01:15Z

Reorganization of sections

← Older revision		Revision as of 12:01, 3 October 2024
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	To able to follow the tutorials you need a running version of the yambo, yambopy (and QE or abinit codes).		To able to follow the tutorials you need a running version of the yambo, yambopy (and QE or abinit codes).

	~~== Setting up Yambo (and eventually QE or abinit) ==~~
	There are several different ways to prepare a working environment.		There are several different ways to prepare a working environment.

	=== Virtual Machine(s) ===		== Virtual Machine(s) ==
	The easiest way is to access to a virtual machine which contains both (i) yambo/QE and (ii) the tutorials.		The easiest way is to access to a virtual machine which contains both (i) yambo/QE and (ii) the tutorials.

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	-->		-->

	=== User installation ===		== User installation ==
	You can also setup the yambo code on your on laptop / desktop using different methods.		You can also setup the yambo code on your on laptop / desktop using different methods.

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	* Install yambo on your laptop/desktop/cluster [https://github.com/nicspalla/my-repo via Spack].		* Install yambo on your laptop/desktop/cluster [https://github.com/nicspalla/my-repo via Spack].
	* Install using Anaconda.		* Install using Anaconda.

			== Setting up an environment ==

			=== python env ===

			You can create a python environment and activate it:
			python -m venv MYPATH/yamboenv/
			source MYPATH/yamboenv/bin/activate

			=== conda env ===
			As an alternative we suggest to consider conda environments.
			To setup Anaconda, please start from installing [https://www.anaconda.com/products/distribution#Downloads Anaconda] or [https://docs.conda.io/en/latest/miniconda.html Miniconda].
			Then to create a conda environment and activate it:
			conda create --name yambo-env -c conda-forge
			conda activate yambo-env

	=== Yambo User Installation with Anaconda ===		=== Yambo User Installation with Anaconda ===
	It is possible to install Yambo (up to v5.0.4) and Quantum-ESPRESSO via conda-forge (a conda channel/repository):		It is possible to install Yambo (up to v5.0.4) and Quantum-ESPRESSO via conda-forge (a conda channel/repository):
	~~To setup Anaconda, please start from installing [https://www.anaconda.com/products/distribution#Downloads Anaconda] or [https://docs.conda.io/en/latest/miniconda.html Miniconda].~~

	~~Then we suggest to create a conda environment and activate it:~~
	~~conda create --name yambo-env -c conda-forge~~
	~~conda activate yambo-env~~
	Then you can install the prerequisites and the two codes:		Then you can install the prerequisites and the two codes:
	conda install numpy scipy netcdf4 matplotlib pyyaml lxml pandas		conda install numpy scipy netcdf4 matplotlib pyyaml lxml pandas
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	conda install qe		conda install qe

	==Setting up Yambopy==		== Setting up Yambopy inside an enviroment ==

	You can simply type in a suitable python environment.		You can simply type in a suitable python environment.

	~~python -m venv MYPATH/yamboenv/~~
	~~source MYPATH/yamboenv/bin/activate~~
	pip install yambopy		pip install yambopy

	For more information, go to the [[First steps in Yambopy\| Yambopy setup page]].		For more information, go to the [[First steps in Yambopy\| Yambopy setup page]].

Davide: /* Setting up Yambopy */

2024-10-03T10:02:17Z

Setting up Yambopy

← Older revision		Revision as of 10:02, 3 October 2024
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	pip install yambopy		pip install yambopy

	For more information, go to the [[First steps in Yambopy\| Yambopy setup page]].		For more information, go to the [[First steps in Yambopy\| Yambopy setup page]].

Davide: /* Setting up Yambopy */

2024-10-03T10:02:08Z

Setting up Yambopy

← Older revision		Revision as of 10:02, 3 October 2024
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	==Setting up Yambopy==		==Setting up Yambopy==

	You can simply type		You can simply type in a suitable python environment.

			python -m venv MYPATH/yamboenv/
			source MYPATH/yamboenv/bin/activate
	pip install yambopy		pip install yambopy

	~~In a suitable python environment.~~ For more information, go to the [[First steps in Yambopy\| Yambopy setup page]].		For more information, go to the [[First steps in Yambopy\| Yambopy setup page]].

Fulvio: /* Setting up Yambopy */

2024-02-01T18:11:53Z

Setting up Yambopy

@@ Line 41: / Line 41: @@
 ==Setting up Yambopy==
-===Quick installation===
+You can simply type
-A quick way to start using Yambopy is described here.
+ pip install yambopy
-* Make sure that you are using Python 3 and that you have the following python packages: <code>numpy</code>, <code>scipy</code>, <code>matplotlib</code>, <code>netCDF4</code>, <code>lxml</code>, <code>pyyaml</code>. Optionally, you may want to have abipy [[https://abinit.github.io/abipy/index.html]] installed for band structure interpolations.
+In a suitable python environment. For more information, go to the [[First steps in Yambopy| Yambopy setup page]].

Fulvio: /* Yambo User Installation with Anaconda */

2024-02-01T17:40:28Z

Yambo User Installation with Anaconda

← Older revision		Revision as of 17:40, 1 February 2024
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	Then we suggest to create a conda environment and activate it:		Then we suggest to create a conda environment and activate it:
	conda create --name ~~yambopy~~ -c conda-forge		conda create --name yambo-env -c conda-forge
	conda activate ~~yambopy~~		conda activate yambo-env
	Then you can install the prerequisites and the two codes:		Then you can install the prerequisites and the two codes:
	conda install numpy scipy netcdf4 matplotlib pyyaml lxml pandas		conda install numpy scipy netcdf4 matplotlib pyyaml lxml pandas

Davide at 09:42, 14 September 2023

2023-09-14T09:42:51Z

← Older revision		Revision as of 09:42, 14 September 2023
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	~~== Setting up Yambo, yambopy (and eventually QE or abinit) ==~~		To able to follow the tutorials you need a running version of the yambo, yambopy (and QE or abinit codes).
	To be able to follow the ~~school~~ you need a running version of the yambo, yambopy (and QE or abinit codes).

			== Setting up Yambo (and eventually QE or abinit) ==
	There are several different ways to prepare a working environment.		There are several different ways to prepare a working environment.

Davide: Created page with details about the installation of yambo

2023-09-14T09:41:58Z

Created page with details about the installation of yambo

New page

== Setting up Yambo, yambopy (and eventually QE or abinit) ==
To be able to follow the school you need a running version of the yambo, yambopy (and QE or abinit codes).

There are several different ways to prepare a working environment.

=== Virtual Machine(s) ===
The easiest way is to access to a virtual machine which contains both (i) yambo/QE and (ii) the tutorials.

You can do it in one of two ways:
* Virtual machine via [[ICTP cloud|ICTP cloud]] If the schools you are attending provided an ICTP virtual machine this is the preferred option. It works through internet connection inside a browser.
* Install the [[Yambo_Virtual_Machine|yambo virtual machine]] on your laptop / desktop. This requires Oracle virtual box. Pre-download of the Virtual machine. No internet connection needed.


=== User installation ===
You can also setup the yambo code on your on laptop / desktop using different methods.

As far as the Yambo source is concerned you can:
* Install [[Yambo via Docker|Yambo via Docker]]
* [[download|Download]] and [[Installation|install]] yambo on your laptop / desktop (requires a linux machine).
* Install yambo on your laptop/desktop/cluster [https://github.com/nicspalla/my-repo via Spack].
* Install using Anaconda.

=== Yambo User Installation with Anaconda ===
It is possible to install Yambo (up to v5.0.4) and Quantum-ESPRESSO via conda-forge (a conda channel/repository):
To setup Anaconda, please start from installing [https://www.anaconda.com/products/distribution#Downloads Anaconda] or [https://docs.conda.io/en/latest/miniconda.html Miniconda].

Then we suggest to create a conda environment and activate it:
conda create --name yambopy -c conda-forge
conda activate yambopy
Then you can install the prerequisites and the two codes:
conda install numpy scipy netcdf4 matplotlib pyyaml lxml pandas
conda install yambo
conda install qe

==Setting up Yambopy==

===Quick installation===

A quick way to start using Yambopy is described here.

* Make sure that you are using Python 3 and that you have the following python packages: <code>numpy</code>, <code>scipy</code>, <code>matplotlib</code>, <code>netCDF4</code>, <code>lxml</code>, <code>pyyaml</code>. Optionally, you may want to have abipy [[https://abinit.github.io/abipy/index.html]] installed for band structure interpolations.

* Go to a directory of your choice and clone yambopy from the git repository

git clone https://github.com/yambo-code/yambopy.git

If you don't want to use git, you may download a tarball from the git repository instead.

* Enter into the yambopy folder and install

cd yambopy
sudo python setup.py install

If you don't have administrative privileges (for example on a computing cluster), type instead

cd yambopy
python setup.py install --user

===Installing dependencies with Anaconda===
We suggest installing yambopy using Anaconda [[https://www.anaconda.com/products/distribution]] to manage the various python packages.

In this case, you can follow these steps.

First, install the required dependencies:
conda install numpy scipy netcdf4 lxml pyyaml

Then we create a conda environment based on python 3.6 (this is to ensure compatibility with abipy if we want to install it later on):
conda create --name NAME_ENV python=3.6
Here choose <code>NAME_ENV</code> as you want, e.g. <code>yenv</code>.

Now, we install abipy and its dependency pymatgen using <code>pip</code>. Here make sure that you are using the <code>pip</code> version provided by Anaconda and not your system version.

pip install pymatgen
pip install abipy

Finally, we are ready to install yambopy:

git clone https://github.com/yambo-code/yambopy.git

(or download and extract tarball) and follow the steps outlined in the quick installation section.

Now enter into the yambopy folder and install

cd yambopy
sudo python setup.py install

If you don't have administrative privileges (for example on a computing cluster), type instead

cd yambopy
python setup.py install --user

===Frequent issues===
When running the installation you may get a <code>SyntaxError</code> related to utf-8 encoding or it may complain that module <code>setuptools</code> is not installed even though it is. In this case, it means that the <code>sudo</code> command is not preserving the correct <code>PATH</code> for your python executable.

Solve the problem by running the installation step as

sudo /your/path/to/python setup.py install
or
sudo env PATH=$PATH python setup.py install

This applies only to the installation step and not to subsequent yambopy use.