Install SIESTA & TranSIESTA#

ASAP workflows guide the user in all necessary steps involved in a computer simulation with SIESTA and TranSIESTA. ASAP supports SIESTA (TranSIESTA) versions 4.1 and 5.0.

We have decoupled ASAP into different subproducts to satisfy user-specific needs: ASAP HTEP, ASAP Pro and ASAP Pro Transport, see ASAP Subproducts.

ASAP trial users can take advantage of all available calculators implemented in ASAP Pro Transport, the most advanced version of ASAP.

If you are a beginner and want to run your first SIESTA (TranSIESTA) simulations through ASAP, we recommend doing so on your local computer. The only external requirement is to have the appropriate version of SIESTA (TranSIESTA) installed. In section SIESTA version 4.0, 4.1 - serial, we explain how to use our embedded installer, which simplifies the process by fetching a pre-compiled SIESTA serial executable (version 4.0 and 4.1) and automatically configuring ASAP to use it.

For non-expert users, this chapter also provides instructions for installing different SIESTA (TranSIESTA) versions (serial and parallel) on your local computer. We detail various installation options, depending on your operating system and the required SIESTA (TranSIESTA) version; see section SIESTA (TranSIESTA) version 4.1 - parallel to have access to parallel binaries for different operating systems and section SIESTA version 5.2 to install SIESTA (TranSIESTA) through Anaconda and Miniconda.

SIESTA parallel version, allows you to run SIESTA using several processors. Please note that in order to fully benefit from this feature, in addition to installing SIESTA, you may need to install the parallel library for your operating system.

If you are a SIESTA expert, you can build it from source and configure ASAP to use it. Visit the public GitLab repository siesta-project/siesta for installation details.

Once SIESTA (TranSIESTA) are installed, you must specify the executable path in the Program widget in ASAP (Managing local and remote runners).

SIESTA version 4.0, 4.1 - serial#

We recommend you to use our embedded installer, which simplifies the process by fetching a pre-compiled SIESTA serial executable and automatically configuring ASAP to use it, as described below.

You can download the binary through the “Help / Download Siesta…” menu in ASAP.

Once the download widget appears, you can select the SIESTA serial version to install (SIESTA 4.0 by default).

Please note that only a limited number of operating systems are supported: Windows, Debian, Linux Mint, Ubuntu and MacOS/Darwin.

Click the Install and configure button to start the process of downloading, installing and automatically configuring ASAP runner. The process may take a few seconds. Runners can be seen as pre-set configurations that can be saved and used to run simulations either on your local machine or on a remote server. See section Managing local and remote runners for further information on runner configuration. If the operation takes too much time or gets stalled, you can cancel it by clicking the Cancel button and try the process again.

You can download more than one version of SIESTA. They will be stored on your hard disk with different and explicit names.

Should you encounter any problem with the downloaded binary, please contact us at team@simuneatomistics.com.

SIESTA (TranSIESTA) version 4.1 - parallel#

Although ASAP does not currently support the automatic download of the parallel SIESTA 4.1 (TranSIESTA 4.1) version.

Please visit our webpage at https://www.simuneatomistics.com/siesta-toolkit/siesta-binaries to download the binary for your operating system.

Once SIESTA (TranSIESTA) are installed you must specify the executable path in the Program widget in ASAP (Managing local and remote runners).

Remember that you might need to install the parallel library for your operating system, check how to do so in Windows in section Windows: Installing Microsoft MPI v10.1.3 and in Debian/Ubuntu/Mint in section Debian/Ubuntu/Mint: Installing Scalapack Openmpi library.

If your operating system is not in the binary list at https://www.simuneatomistics.com/siesta-toolkit/siesta-binaries and you run Linux or MacOS, we suggest you install SIESTA 5.2.

Please consult the section SIESTA version 5.2 for guidance.

Windows: Installing Microsoft MPI v10.1.3#

Microsoft MPI v10.1.3 is a Windows mpi library necessary to run SIESTA using several processors. It is a microsoft software and can be downloaded from https://www.microsoft.com/en-us/download/details.aspx?id=105289. When you click on download please choose the item msmpisetup.exe.

Once downloaded just double-click on it and follow the instructions to install the tool.

Debian/Ubuntu/Mint: Installing Scalapack Openmpi library#

To install Scalapack Openmpi library use the apt install command (you need to be superuser),

sudo apt install libscalapack-openmpi2.1

Version 2.1 must to be used to be compatible with the SIESTA binary that we provide.

If your operating system is not in the above list and you run Linux or MacOS operating system you can check section SIESTA version 5.2.

SIESTA version 5.2#

If your operative system is Linux or MacOS, we recommend installing SIESTA version 5.2 using Anaconda or Miniconda. With this method you can easily install both serial and parallel SIESTA versions.

Notice that from SIESTA 5.0 onwards, TranSIESTA is integrated within the SIESTA package and does not require separate installation.

Step 1. Download and install Miniconda#

If you already have Anaconda or Miniconda installed you can skip this step.

Follow the instructions at https://docs.anaconda.com/miniconda/install/#quick-command-line-install to install Miniconda for your operating system.

Step 2. Create and activate a Conda Python environment for SIESTA#

Once Miniconda is installed, create a new environment for SIESTA by running the following command in your terminal,

conda create -n py312 python=3.12

Activate the newly created environment by running,

conda activate py312

Step 3: Install SIESTA & TranSIESTA 5.2#

To install the serial version of SIESTA 5.2, use the following command,

conda install -c conda-forge siesta

If you require the parallel version of SIESTA (recommended when you need to perform computationally intensive simulations that can benefit from running on multiple processors simultaneously), you need to install before the scalapack package (high-performance linear algebra library for parallel distributed memory machines),

conda install conda-forge::scalapack

Afterwards, to install parallel version of SIESTA, type the following command,

conda install -c conda-forge "siesta=*=*openmpi*"

Alternatively, you can use the MPICH library for the same purpose,

conda install -c conda-forge "siesta=*=*mpich*"

Once the parallel version of SIESTA is installed, keep open your terminal and verify your installation following instructions given in the next section, Step 4. Verify your installation.

Step 4. Verify your installation#

To confirm that SIESTA has been successfully installed, on the same terminal window type from which you installed SIESTA 5.2 as described in section Step 3: Install SIESTA & TranSIESTA 5.2,type the following command,

siesta --version

You should see the SIESTA version information displayed in the terminal as shown in the example below,

Executable      : siesta
Version         : 5.2.0
Architecture    : x86_64
Compiler version: GNU-13.3.0
Compiler flags  : -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem <prefix>/include -I<prefix>/_build_env/include -fdebug-prefix-map=<prefix>/work=/usr/local/src/conda/siesta-5.2.0 -fdebug-prefix-map=<prefix>=/usr/local/src/conda-prefix -I<prefix>/lib -fallow-argument-mismatch -O3
Parallelisations: MPI
...