Difference between revisions of "Installation instructions"
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+ | ==Electronic structure packages== | ||
+ | The program employs two levels of electronic structure: semiempirical (or Low-Level LL) and ab initio/DFT (or High-Level HL). The LL calculations can be carried out with MOPAC or Entos Qcore, and the HL calculations with Gaussian (G09/G16) or Entos Qcore. | ||
+ | |||
+ | While MOPAC comes with AutoMeKin, if you want to employ xtb method, [https://www.entos.ai/qcore/documentation/ Entos Qcore] must be installed. Additionally, for the HL calculations you may want to use G09/G16, or Entos Qcore. | ||
+ | |||
+ | To install [https://software.entos.ai/qcore/tutorial/ Entos Qcore], we recommend following these steps: | ||
+ | |||
+ | 1. [https://conda.io/projects/conda/en/latest/user-guide/install/linux.html Install miniconda3] | ||
+ | |||
+ | 2. Add the following line to $HOME/.condarc (create the file if not present): | ||
+ | |||
+ | <code>auto_activate_base: false</code> | ||
+ | |||
+ | which avoids activation of base environment. | ||
+ | |||
+ | 3. Install qcore version 0.8.14 in a conda environment (qcore-0.8.14-env): | ||
+ | |||
+ | <code>conda create -n qcore-0.8.14-env -c entos -c conda-forge qcore==0.8.14 'tbb<2021'</code> | ||
+ | |||
+ | 4. Activate the newly created environment: | ||
+ | |||
+ | <code>conda activate qcore-0.8.14-env</code> | ||
+ | |||
+ | 5. After installation, each user will be asked to read the Software License Agreement to generate a unique token: | ||
+ | |||
+ | <code>qcore --academic-license</code> | ||
+ | |||
==Auto installer== | ==Auto installer== | ||
+ | This is the easiest way to install/use AutoMeKin. The auto installer script installs singularity in your computer and downloads the last release container image from sylabs (https://cloud.sylabs.io/library/emartineznunez/default/automekin) as <code>$HOME/automekin_<tag>.sif</code>. Note that this is done only the first time you use it unless a new image is available. Then, the script will detect singularity and the image (that must be located in your <code>$HOME</code>) and will only start an instance of the container. The container includes [https://github.com/dgarayr/amk_tools '''amk-tools'''] | ||
− | 1) Download AutoMeKin's auto installer script | + | 1) Download AutoMeKin's auto installer script Automekin.sh ('''Last update April 4, 2022''') from your terminal: |
− | + | <code>curl -LJO https://github.com/emartineznunez/Singularity_amk/raw/main/installer/Automekin.sh</code> | |
− | + | 2) Make the script executable: | |
− | + | <code>chmod +x Automekin.sh</code> | |
− | + | 3) Run the script: | |
− | + | <code>./Automekin.sh</code> | |
− | + | Note that depending on your Linux configuration, before running the autoinstaller you might need to change some parameters which will require admin or root privilege. If that is the case and once you changed the parameters with your admin or root accounts, no further admin or root privilege will be needed. Return to your user account and run the auto installer again. | |
− | 4) | + | 4) Once the above steps are completed, singularity will be installed under <code>${TMPDIR-/tmp}/amk_installer-${USER}/software</code> in bash shell script syntax and an instance of the container will be started using a sandbox image deployed under <code>/tmp/selfextract.XXXXXX</code> folder (where <code>XXXXXX</code> is a randomly generated character sequence). The container comes with all AutoMeKin's tools installed in <code>$AMK</code> plus vim, gnuplot and molden which can be run from the container. A bash shell session under <code>$HOME</code> 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: | |
− | + | <code>exit</code> | |
− | + | 6) Once your calculations are done, remember to stop the instance: | |
− | + | <code>./Automekin.sh stop</code> | |
− | + | '''Important notes:''' | |
− | + | <ol start="1"> | |
+ | <li>'''To download the file directly from your terminal, curl must be installed'''</li> | ||
+ | <li>'''Make sure your auto installer is up to date (see above)'''</li> | ||
+ | <li>'''The autoinstaller also works on Ubuntu 20.04 LTS on Windows 10. To install Ubuntu 20.04 LTS on Windows 10, follow these instructions: https://docs.microsoft.com/en-us/windows/wsl/install-win10'''</li> | ||
+ | <li>'''AutoMeKin's third-party packages in the container are updated (see below the minimum required version numbers). Local installations of different versions of these Python packages might interfere in the execution of AutoMeKin'''</li> | ||
+ | </ol> | ||
− | <code> | + | ==Singularity container== |
+ | |||
+ | If singularity is already installed in your computer, you can obtain the container from sylabs. First check what the latest image (Tag) is by typing: | ||
+ | |||
+ | <code>singularity search automekin</code><br /> | ||
+ | |||
+ | and replace <code><Tag></code> below by that number. Then, from your $HOME type:<br /> | ||
+ | |||
+ | <code>singularity pull library://emartineznunez/default/automekin:<Tag></code><br /> | ||
+ | |||
+ | You can start an instance of the container and run it using: | ||
+ | |||
+ | <code>singularity instance start automekin_<Tag>.sif automekin</code><br/> | ||
+ | <code>singularity run instance://automekin</code> | ||
+ | |||
+ | which will allow you to run low-level scripts. You can stop the instance using: | ||
+ | |||
+ | <code>singularity instance stop automekin</code> | ||
+ | |||
+ | Note, however, that if you want to use <code>G09/G16</code> you must bind it to the container. To help you do so, we created the scripts SingularitygXX.sh (XX=09/16), which can be downloaded as: | ||
+ | |||
+ | <code>curl -LJO https://github.com/emartineznunez/Singularity_amk/raw/main/Singularityg09.sh</code> | ||
+ | |||
+ | <code>curl -LJO https://github.com/emartineznunez/Singularity_amk/raw/main/Singularityg16.sh</code> | ||
+ | |||
+ | The script should be run with the complete path to the sif file as argument as in the example: | ||
+ | |||
+ | <code>SingularitygXX.sh $HOME/automekin_<Tag>.sif</code> | ||
+ | |||
+ | Note that <code>SingularitygXX.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. | ||
+ | |||
+ | ==Build from source== | ||
+ | |||
+ | The most recent and up to date version is avaialable at: | ||
+ | |||
+ | <code>https://github.com/emartineznunez/AutoMeKin</code> | ||
+ | |||
+ | You can build (system-wide) from source using this script (on a CentOS): | ||
+ | |||
+ | <code>curl -LJO https://raw.githubusercontent.com/emartineznunez/AutoMeKin/main/Build_Centos.sh</code> | ||
+ | |||
+ | You can also check how to install AutoMeKin using Ubuntu: | ||
+ | |||
+ | <code>https://colab.research.google.com/github/emartineznunez/AutoMeKin/blob/main/AutoMeKin.ipynb</code> | ||
+ | |||
+ | which involves the installation of the following dependencies (before the installation of AutoMeKin): | ||
+ | |||
+ | |||
+ | '''Installing dependencies'''<br /> | ||
− | |||
Before installing amk for the first time, be aware that the following packages are needed: | Before installing amk for the first time, be aware that the following packages are needed: | ||
+ | |||
+ | - [https://www.gnu.org/software/autoconf/ GNU Autoconf] | ||
- [https://www.gnu.org/software/bash/ GNU Bash] | - [https://www.gnu.org/software/bash/ GNU Bash] | ||
Line 54: | Line 140: | ||
- [https://wiki.gnome.org/Projects/Zenity Zenity] | - [https://wiki.gnome.org/Projects/Zenity Zenity] | ||
− | You can install the missing ones manually, or you can use the scripts located in amk-SOURCE- | + | You can install the missing ones manually, or you can use the scripts located in amk-SOURCE-2021 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. | 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. | ||
Line 60: | Line 146: | ||
b) ''install-gnu-parallel-from-epel.sh''. Enables the EPEL repository and installs parallel from it. | 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: | + | The program employs python3 and the following python3 libraries are needed (which can be easily installed with pip): |
− | |||
− | |||
− | |||
− | |||
− | - [https:// | + | - [https://wiki.fysik.dtu.dk/ase/ ASE (version >= 3.21.1)] |
− | - [https:// | + | - [https://matplotlib.org/ Matplotlib (version >= 3.3.4)] |
− | - [https:// | + | - [https://networkx.github.io/ NetworkX (version >= 2.5)] |
− | + | - [https://www.numpy.org/ NumPy (version >= 1.19.5)] | |
− | + | - [https://www.scipy.org/ SciPy (version >= 1.5.4)] | |
These packages might also be useful to analyze the results: | These packages might also be useful to analyze the results: | ||
Line 82: | Line 164: | ||
- [https://github.com/sqlitebrowser/sqlitebrowser sqlitebrowser] | - [https://github.com/sqlitebrowser/sqlitebrowser sqlitebrowser] | ||
− | |||
− | |||
− | + | '''Installation''' | |
− | + | Once the above packages are installed, you can now install AutoMeKin following these steps:.<br /> | |
− | + | Clone AutoMeKin from GitHub: | |
− | <code> | + | <code>git clone https://github.com/emartineznunez/AutoMeKin.git</code> |
− | + | Go to the AutoMeKin folder. | |
− | <code> | + | <code>cd AutoMeKin</code> |
− | + | Now type: | |
+ | |||
+ | <code>autoreconf -i</code> | ||
<code>./configure --prefix=path_to_program</code> | <code>./configure --prefix=path_to_program</code> | ||
+ | |||
+ | Where you can specify where you want to install it, e.g., <code>/opt/AutoMeKin</code> | ||
Finally, complete the installation: | Finally, complete the installation: | ||
Line 109: | Line 193: | ||
The last command (<code>make clean</code>) is only necessary if you want to remove from the src directory the object files and executables created in the compilation process. | The last command (<code>make clean</code>) 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 | + | For convenience, and once “Environment Modules” has been installed, you should add the following line to your <code>.bashrc</code> file: |
− | + | <code>module use path_to_program/modules</code> | |
− | where | + | where <code>path_to_program</code> is the path where you installed amk (e.g., <code>$HOME/amk-2021</code>). |
− | ==Running the | + | ==Running the tests== |
− | To run the | + | To run the tests follow these steps: |
− | 1) Load the module: | + | 1) Load the module (unless you use singularity): |
− | <code>module load amk/ | + | <code>module load amk/2021</code> |
− | 2) Run the script | + | 2) Run the following script to run all tests: |
<code>run_test.sh</code> | <code>run_test.sh</code> | ||
− | + | '''Note that each test takes from a few seconds to several minutes.''' | |
− | |||
− | |||
− | |||
− | |||
− | |||
The results of each test will be gathered in a different directory. | The results of each test will be gathered in a different directory. | ||
Line 139: | Line 218: | ||
<code>run_test.sh --tests=FA, FAthermo</code> | <code>run_test.sh --tests=FA, FAthermo</code> | ||
− | which will run FA and FAthermo tests only. These are the tests available in this version: <code>assoc</code>, | + | which will run FA and FAthermo tests only. These are the tests available in this version: <code>assoc</code>, <code>assoc_qcore</code> |
− | <code> | + | <code>rdiels_bias</code>, <code>diels_bias</code>, <code>FA_biasH2</code>, <code>FA_biasH2O</code>, <code>FA_bxde</code>, <code>FA_singletraj</code>, <code>FA</code>, <code>FAthermo</code>, |
− | <code>FA_programopt</code> | + | <code>FA_programopt</code>, <code>vdW</code>, <code>FA_ck</code>, <code>FA_qcore</code>, <code>FA_bxde_qcore</code> and <code>ttors</code> |
− | |||
− | |||
− | |||
− | |||
==Older versions== | ==Older versions== | ||
− | Download the | + | Download the [[Media:Amk-SOURCE-2020.tar.gz| tarball ]] for the 2020 version (revision 993)<br /> |
And follow the instructions given above (tarball). | And follow the instructions given above (tarball). | ||
− | + | Download [[Media:Tutorial2020.pdf| tutorial2020 ]]<br /> | |
− | |||
− | |||
− | |||
− | |||
− | |||
Return to [[AutoMeKin]] | Return to [[AutoMeKin]] |
Latest revision as of 07:25, 2 February 2024
Contents
Electronic structure packages
The program employs two levels of electronic structure: semiempirical (or Low-Level LL) and ab initio/DFT (or High-Level HL). The LL calculations can be carried out with MOPAC or Entos Qcore, and the HL calculations with Gaussian (G09/G16) or Entos Qcore.
While MOPAC comes with AutoMeKin, if you want to employ xtb method, Entos Qcore must be installed. Additionally, for the HL calculations you may want to use G09/G16, or Entos Qcore.
To install Entos Qcore, we recommend following these steps:
2. Add the following line to $HOME/.condarc (create the file if not present):
auto_activate_base: false
which avoids activation of base environment.
3. Install qcore version 0.8.14 in a conda environment (qcore-0.8.14-env):
conda create -n qcore-0.8.14-env -c entos -c conda-forge qcore==0.8.14 'tbb<2021'
4. Activate the newly created environment:
conda activate qcore-0.8.14-env
5. After installation, each user will be asked to read the Software License Agreement to generate a unique token:
qcore --academic-license
Auto installer
This is the easiest way to install/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/default/automekin) as $HOME/automekin_<tag>.sif
. Note that this is done only the first time you use it unless a new image is available. 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. The container includes amk-tools
1) Download AutoMeKin's auto installer script Automekin.sh (Last update April 4, 2022) from your terminal:
curl -LJO https://github.com/emartineznunez/Singularity_amk/raw/main/installer/Automekin.sh
2) Make the script executable:
chmod +x Automekin.sh
3) 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, singularity will be installed under ${TMPDIR-/tmp}/amk_installer-${USER}/software
in bash shell script syntax 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:
exit
6) Once your calculations are done, remember to stop the instance:
./Automekin.sh stop
Important notes:
- To download the file directly from your terminal, curl must be installed
- Make sure your auto installer is up to date (see above)
- The autoinstaller also works on Ubuntu 20.04 LTS on Windows 10. To install Ubuntu 20.04 LTS on Windows 10, follow these instructions: https://docs.microsoft.com/en-us/windows/wsl/install-win10
- AutoMeKin's third-party packages in the container are updated (see below the minimum required version numbers). Local installations of different versions of these Python packages might interfere in the execution of AutoMeKin
Singularity container
If singularity is already installed in your computer, you can obtain the container from sylabs. First check what the latest image (Tag) is by typing:
singularity search automekin
and replace <Tag>
below by that number. Then, from your $HOME type:
singularity pull library://emartineznunez/default/automekin:<Tag>
You can start an instance of the container and run it using:
singularity instance start automekin_<Tag>.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/G16
you must bind it to the container. To help you do so, we created the scripts SingularitygXX.sh (XX=09/16), which can be downloaded as:
curl -LJO https://github.com/emartineznunez/Singularity_amk/raw/main/Singularityg09.sh
curl -LJO https://github.com/emartineznunez/Singularity_amk/raw/main/Singularityg16.sh
The script should be run with the complete path to the sif file as argument as in the example:
SingularitygXX.sh $HOME/automekin_<Tag>.sif
Note that SingularitygXX.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.
Build from source
The most recent and up to date version is avaialable at:
https://github.com/emartineznunez/AutoMeKin
You can build (system-wide) from source using this script (on a CentOS):
curl -LJO https://raw.githubusercontent.com/emartineznunez/AutoMeKin/main/Build_Centos.sh
You can also check how to install AutoMeKin using Ubuntu:
https://colab.research.google.com/github/emartineznunez/AutoMeKin/blob/main/AutoMeKin.ipynb
which involves the installation of the following dependencies (before the installation of AutoMeKin):
Installing dependencies
Before installing amk for the first time, be aware that the following packages are needed:
- GNU Bash
- GNU bc
- Gnuplot
- GNU Fortran Compiler (gfortran)
- Zenity
You can install the missing ones manually, or you can use the scripts located in amk-SOURCE-2021 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):
- Matplotlib (version >= 3.3.4)
These packages might also be useful to analyze the results:
- molden
Installation
Once the above packages are installed, you can now install AutoMeKin following these steps:.
Clone AutoMeKin from GitHub:
git clone https://github.com/emartineznunez/AutoMeKin.git
Go to the AutoMeKin folder.
cd AutoMeKin
Now type:
autoreconf -i
./configure --prefix=path_to_program
Where you can specify where you want to install it, e.g., /opt/AutoMeKin
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-2021
).
Running the tests
To run the tests follow these steps:
1) Load the module (unless you use singularity):
module load amk/2021
2) Run the following script to run all tests:
run_test.sh
Note that each test takes from a few seconds to several minutes. 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
, assoc_qcore
rdiels_bias
, diels_bias
, FA_biasH2
, FA_biasH2O
, FA_bxde
, FA_singletraj
, FA
, FAthermo
,
FA_programopt
, vdW
, FA_ck
, FA_qcore
, FA_bxde_qcore
and ttors
Older versions
Download the tarball for the 2020 version (revision 993)
And follow the instructions given above (tarball).
Download tutorial2020
Return to AutoMeKin