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 start an instance of the container.
1) Download AutoMeKin's auto installer script automekin.sh
2) Make the script executable:
chmod +x automekin.sh
3) Run the script:
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, singularity will be installed under
/tmp/software folder and an instance of the container will be started using a sandbox image deployed under
/tmp/selfextract.XXXXXX folder (where
XXXXXX is a randomly generated character sequence). The container comes with all AutoMeKin's tools installed in
$AMK plus vim, gnuplot and molden which can be run from the container. A bash shell session under
$HOME will start under the deployed instance. 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:
6) Once your calculations are done, you can stop the instance just typing:
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 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.
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
Before installing amk for the first time, be aware that the following packages are needed:
- GNU Bash
- GNU bc
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):
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:
These packages might also be useful to analyze the results:
Once the above packages are installed:
go to the amk-SOURCE-20XX folder.
This will install amk in $HOME/amk-20XX by default. If you want to install it in a different directory, type:
Finally, complete the installation:
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:
otherwise. For instance, if you use singularity, AutoMeKin is installed in
$AMK and therefore you should use:
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:
--tests options can be used simultaneously.
Note that each each test takes from a few seconds to several minutes.
Download the tarball for the 2018 version
And follow the instructions given above (tarball).
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