Installing and running executables¶
In this section, we will assume that you have successfully built SIESTA, as well as the utilities you need. If this not the case, yet, you can do it by following the instructions in one of the related sections:
Building SIESTA manually with CMake (all SIESTA versions)
Building SIESTA with the ESL Bundle (SIESTA 5.x and Max-x versions)
Building SIESTA with EasyBuild (SIESTA 5.x and Max-x versions)
As a starting point, we will suppose that you have just built the siesta, gnubands and denchar executables from SIESTA 4.1.5 and that they are still in your build directory, located at $HOME/src/siesta-4.1.5/Obj/.
Preparing an installation directory¶
One thing is to build software, another is to use it reliably. For the latter, we have to decide where we want to store what we have built. Here we will provide an example of good practice that we invite you to tune to best suit your own needs.
In this example, we have chosen to install all files related to SIESTA in a
$HOME/siesta directory. Inside, we first have to create a basic
structure, so that we can build and install several versions of SIESTA at the
same time. Starting with our example, we would type:
mkdir -p $HOME/siesta/4.1.5/bin
As you can see, we are organising files by version (4.1.5) and by type (bin). Feel free to adapt this structure to your preferences. The most important aspect is to make a choice and stay consistent with it over time.
Documenting your choices is a very good practice. A simple way to do it is to create a README file in the siesta/ directory and summarise there how you install files in its subdirectories.
For the moment, even though we are only installing executables, we will store them in a bin/ subdirectory, so that we don’t have to change our directory structure when we install other kinds of files, e.g. libraries or data files.
Copying the files to the installation location¶
In our example, we have built executables from the $HOME/src/siesta-4.1.5/Obj/ build directory. To make them available in a permanent way and free the space for new builds, we just have to copy the executables to our installation directory. In this case, we type:
cp $HOME/src/siesta-4.1.5/Obj/siesta $HOME/siesta/4.1.5/bin cp $HOME/src/siesta-4.1.5/Obj/Util/Bands/gnubands $HOME/siesta/4.1.5/bin cp $HOME/src/siesta-4.1.5/Obj/Util/Denchar/Src/denchar $HOME/siesta/4.1.5/bin
From now on, we can safely run
make clean in the build directory without
loosing the fruit of our efforts.
Saving the arch.make that was used to build teh executables is usually a good idea if we want to keep track of how we have built them. In this case, we can create a conf/ subdirectory where we will store them. In the process, it might also be useful to rename the arch.make to reflect our configuration choices explicitly. If we have built a SIESTA executable with GCC, OpenMPI and the Netlib linear algebra libraries, we can rename the file accordingly:
mkdir -p $HOME/siesta/4.1.5/conf cp $HOME/src/siesta-4.1.5/Obj/arch.make \ $HOME/siesta/4.1.5/conf/gcc-openmpi-netlib.make
Now, if we want to build different flavours of the same SIESTA version using different arch.make files, we could also rename the SIESTA executable following the same conventions:
mv $HOME/siesta/4.1.5/bin/siesta \ $HOME/siesta/4.1.5/bin/siesta-gcc-openmpi-netlib
In this case, it would be advisable to update the $HOME/siesta/README file to keep track of these conventions.
Accessing the executables¶
One important step before being able to run the executables reliably is to update the environment variables. Two of them are of special importance:
LD_LIBRARY_PATH for the libraries.
PATH for the executables.
A good practice is to group these settings in a shell script that will be sourced whenever you want to run a specific version of SIESTA.
The first thing to decide is where to store the script. The most common used options are:
Store the script in the version-specific installation subdirectory, in which case a single name can be used for all the instances of the script. In our example, this would be $HOME/siesta/4.1.5/siesta-vars.sh. If, in the future, we install SIESTA 5.0.0, the corresponding script would be $HOME/siesta/5.0.0/siesta-vars.sh.
Store all the scripts in the same directory, e.g. $HOME/siesta/env/, in which case they would have to be named differently. In the above example, this would be $HOME/siesta/env/siesta-4.1.5-vars.sh and $HOME/siesta/env/siesta-5.0.0-vars.sh.
No solution is better than the other. What is important is that you feel at ease with it.
In the following, we will illustrate option 1. Adapting the instructions to option 2 is relatively easy. For SIESTA 4.1.5, the $HOME/siesta/4.1.5/siesta-vars.sh script will look like the following:
#!/bin/sh PATH="$HOME/siesta/4.1.5/bin:$PATH" export PATH
This is a minimalistic content. If your are familiar with shell scripting, you can of course refine on this.
From SIESTA 5.x on, as well as for the MaX-* releases, you have to install dependencies before compiling SIESTA. In this case, the recommended installation directory for e.g. SIESTA 5.0.0 would be $HOME/siesta/5.0.0/lib/ and the environment script would look like the following:
#!/bin/sh LD_LIBRARY_PATH="$HOME/siesta/5.0.0/lib:$LD_LIBRARY_PATH" export LD_LIBRARY_PATH PATH="$HOME/siesta/5.0.0/bin:$PATH" export PATH
Once the environment is correctly prepared, the SIESTA executables can be run in all kinds of circumstances in a reliable way.
Running the executables¶
Whenever you want to run a SIESTA executable you have installed as recommended here, you will have to source the corresponding script once per terminal session. For instance, if you want to run SIESTA 4.1.5, you will open a new terminal and type the following:
From that moment on, you can run SIESTA and its utilities by typing their
names. If you want to understand better what is happening to the environment,
you can start a terminal session and type
which siesta, then source the
script and type
which siesta again. Your terminal will look like this:
$ which siesta $ source $HOME/siesta/4.1.5/siesta-vars.sh $ which siesta $HOME/siesta/4.1.5/bin/siesta
which command tells you which executable is actually run when you type
the corresponding command. The first time, the SIESTA command is not available
in the environment, hence
which returns nothing. However, after sourcing
the script, the environment has been updated and the command is available.
It is always a good idea to check commands with
which when you install
software, no matter the method you use to install it.
These instructions are also valid when you run SIESTA through a batch scheduler on a HPC cluster. In this case, your batch job would look like the following:
#!/bin/bash #PBS -q dft #PBS -l nodes=1:ppn=12 #PBS -V #PBS -N "Test" # Set environment source $HOME/siesta/4.1.5/siesta-vars.sh which siesta # Run SIESTA cd my_job_dir mpirun -np 12 siesta <my_input.fdf >my_output.log
One last important piece of advice: it is essential to avoid mixing the environments for different versions of SIESTA within the same shell session, as the results are highly impredictable and will likely end up in random crashes or garbled SIESTA output. If you want to run different versions of SIESTA, always prefer running them in different terminal sessions.
You’re now done. Enjoy your shiny new SIESTA installation!