Difference between revisions of "Installation instructions"

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(Singularity container)
(Auto installer)
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This is the easiest way to use AutoMeKin. The auto installer script installs singularity in your computer and downloads the last release container image from sylabs (https://cloud.sylabs.io/library/emartineznunez) as <code>$HOME/automekin2020_<revision number>.sif</code>. Note that this is done only the first time you use it. Then, the script will detect singularity and the image (that must be located in your <code>$HOME</code>) and will only launch the container.
 
This is the easiest way to use AutoMeKin. The auto installer script installs singularity in your computer and downloads the last release container image from sylabs (https://cloud.sylabs.io/library/emartineznunez) as <code>$HOME/automekin2020_<revision number>.sif</code>. Note that this is done only the first time you use it. Then, the script will detect singularity and the image (that must be located in your <code>$HOME</code>) and will only launch the container.
  
1) From your <code>$HOME</code> download AutoMeKin's auto installer script [[Media:automekin.sh| automekin.sh ]]<br />
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1) Download AutoMeKin's auto installer script [[Media:automekin.sh| automekin.sh ]]<br />
  
 
2) Make the script executable:
 
2) Make the script executable:
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<code>chmod +x automekin.sh</code>
 
<code>chmod +x automekin.sh</code>
  
3) Run the script:
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3) From your <code>$HOME</code>, run the script:
  
 
<code>./automekin.sh</code>
 
<code>./automekin.sh</code>
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<code>singularity instance stop automekin</code>
 
<code>singularity instance stop automekin</code>
  
Note, however, that if you want to use <code>g09</code> you must bind it to the container, which should be launched using this script [[Media:singularityg09.sh| singularityg09.sh ]] with the complete path to the sif file as argument:
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Note, however, that if you want to use <code>g09</code> you must bind it to the container. To help you do so, we created this script [[Media:singularityg09.sh| singularityg09.sh ]], which should be run with the complete path to the sif file as argument as in the example:
  
<nowiki>
+
<code>singularityg09.sh $HOME/automekin2020_872.sif</code>
if [ "$#" -eq 0 ]; then
 
  echo ""
 
  echo "Please provide the complete path to your sif file. Example:"
 
  echo ""
 
  echo "$(basename $0) $HOME/automekin2020_872.sif"
 
  echo ""
 
  exit 1
 
fi
 
siffile=$1
 
if [ $(singularity instance list | awk 'END{print NR-1}') -ge 1 ];then
 
  in=$(singularity instance list | awk '{n=$1};END{print n}' | sed 's/automekin//' | awk '{print $1+1}')
 
else
 
  in=1
 
fi
 
if G09DIR=$(dirname $(which g09 2> /dev/null) 2> /dev/null)
 
then
 
  if [ -d $GAUSS_SCRDIR ]
 
  then
 
      SINGULARITYENV_GAUSS_SCRDIR=/scratch SINGULARITYENV_PREPEND_PATH=/opt/g09 singularity instance start --bind $G09DIR:/opt/g09 --bind $GAUSS_SCRDIR:/scratch $siffile automekin$in
 
  else
 
      SINGULARITYENV_PREPEND_PATH=/opt/g09 singularity instance start --bind $G09DIR:/opt/g09 $siffile automekin$in
 
  fi
 
else
 
  echo "Gaussian 09 not available, only low-level calculations available"
 
  singularity instance start $siffile automekin$in
 
fi
 
singularity run instance://automekin$in
 
  
</nowiki>
+
Note that <code>singularityg09.sh</code> will start a new instance of the container every time it is executed. To list the instances use:
 +
 
 +
<code>singularity instance list</code>
 +
 
 +
And stop them as indicated above.
  
 
==Tarball==
 
==Tarball==

Revision as of 07:33, 13 February 2020

Auto installer

This is the easiest way to use AutoMeKin. The auto installer script installs singularity in your computer and downloads the last release container image from sylabs (https://cloud.sylabs.io/library/emartineznunez) as $HOME/automekin2020_<revision number>.sif. Note that this is done only the first time you use it. Then, the script will detect singularity and the image (that must be located in your $HOME) and will only launch the container.

1) Download AutoMeKin's auto installer script automekin.sh

2) Make the script executable:

chmod +x automekin.sh

3) From your $HOME, run the script:

./automekin.sh

Note that depending on your Linux configuration, before running the autoinstaller you might need to change some parameters which will require admin or root privilege. If that is the case and once you changed the parameters with your admin or root accounts, no further admin or root privilege will be needed. Return to your user account and run the auto installer again.

4) Once the above steps are completed, you will be inside the container. The container comes with all AutoMeKin's tools plus vim, gnuplot and molden which can be run from the container. AutoMeKin is installed in $AMK. Note that you can open new sessions and access AutoMeKin's output files from your Linux environment and use your own tools as well.

5) To exit the container just type:

exit

Singularity container

If singularity is already installed in your computer, you can obtain the container from sylabs. First check what the latest revision number is in: (https://cloud.sylabs.io/library/emartineznunez) and replace <revision number> below with its current value. Then, from your $HOME type:

singularity pull library://emartineznunez/default/automekin2020:<revision number>

You can start an instance of the container and run it using:

singularity instance start automekin2020_<revision number>.sif automekin
singularity run instance://automekin

which will allow you to run low-level scripts. You can stop the instance using:

singularity instance stop automekin

Note, however, that if you want to use g09 you must bind it to the container. To help you do so, we created this script singularityg09.sh , which should be run with the complete path to the sif file as argument as in the example:

singularityg09.sh $HOME/automekin2020_872.sif

Note that singularityg09.sh will start a new instance of the container every time it is executed. To list the instances use:

singularity instance list

And stop them as indicated above.

Tarball

If you do not want to use singularity, you can install the code following the steps indicated in this section.

Download the tarball

Untar and unzip the file:

tar xvfz Amk-SOURCE-20XX.tar.gz


Installing dependencies

Before installing amk for the first time, be aware that the following packages are needed:

- GNU Bash

- GNU bc

- environment-modules

- GNU Awk (gawk)

- GNU C Compiler (gcc)

- Gnuplot

- GNU Fortran Compiler (gfortran)

- GNU Parallel

- SQLite (version >= 3)

- Zenity

You can install the missing ones manually, or you can use the scripts located in amk-SOURCE-20XX and called install-required-packages-distro.sh (where distro=ubuntu-16.4lts, centos7 or sl7), which will do the work for you.The ubuntu-16.4lts script installs all dependencies, but for the RHEL derivatives (centos7 and sl7) you have to install parallel separately, and you have two choices:

a) install-gnu-parallel-from-source.sh. This script installs parallel latest version from source thanks to Ole Tange (the author). Also it can fallback to a user private installation into $HOME/bin if you have not administrator permisions to install it globally.

b) install-gnu-parallel-from-epel.sh. Enables the EPEL repository and installs parallel from it.

The program employs python3 and the following python3 libraries are needed (which can be easily installed with pip):

- ASE

- Matplotlib

- NetworkX

- NumPy

- SciPy

The program runs using two levels of theory: semiempirical (or Low-Level LL) and ab initio/DFT (or High-Level HL). So far, the only program interfaced with amk to perform the ab initio/DFT calculations is G09. Therefore, if you want to perform the HL calculations G09 should be installed and should run like in this example:

g09<inputfile>outputfile

These packages might also be useful to analyze the results:

- molden

- sqlitebrowser


Installation

Once the above packages are installed:

go to the amk-SOURCE-20XX folder.

cd amk-SOURCE-20XX

Now type:

./configure

This will install amk in $HOME/amk-20XX by default. If you want to install it in a different directory, type:

./configure --prefix=path_to_program

Finally, complete the installation:

make
make install
make clean

The last command (make clean) is only necessary if you want to remove from the src directory the object files and executables created in the compilation process.

For convenience, and once “Environment Modules” has been installed, you should add the following line to your .bashrc file:

module use path_to_program/modules

where path_to_program is the path where you installed amk (e.g., $HOME/amk-20XX).

Running the test

To run the tests follow these steps:

1) Load the module (only if you do not use singularity):

module load amk/20XX

2) Run the script if amk has been installed in $HOME:

run_test.sh

or

run_test.sh --prefix=path_to_program

otherwise. For instance, if you use singularity, AutoMeKin is installed in $AMK and therefore you should use:

run_test.sh --prefix=$AMK

The results of each test will be gathered in a different directory.

If you want to run a subset of tests use the following:

run_test.sh --tests=FA, FAthermo

which will run FA and FAthermo tests only. These are the tests available in this version: assoc, rdiels_alder, diels_alder, FA_biasH2, FA_biasH2O, FA_bxde, FA_singletraj, FA, FAthermo, FA_programopt and vdW.

The --prefix and --tests options can be used simultaneously.

Note that each each test takes from a few seconds to several minutes.

Older versions

Download the tarball for the 2018 version

And follow the instructions given above (tarball).

Github

AutoMekin is also on GitHub.
2018 version: Github2.png

2020 version: Github2.png


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