semvec/pypi-packages huggingface dataset:
acellera-atm 0.1.1
A molecule reading/writing and manipulation package.
Requires Python: >=3.8

# Acellera-ATM

Acellera-ATM is an [Alchemical Transfer Method (ATM)](https://pubs.acs.org/doi/10.1021/acs.jcim.1c01129)
package for the Acellera platform.
The implementation is based on the AToM-OpenMM codebase https://github.com/Gallicchio-Lab/AToM-OpenMM
by Emilio Gallicchio's lab.

## Installation and usage

You can install the Acellera-ATM package via `conda` or `pip`. To use `conda` you need a working conda installation, we recommend using the
[Miniforge package](https://github.com/conda-forge/miniforge) for this.

Once conda is installed, you can install the Acellera-ATM package with the following command:

```bash
conda create -n atm -y # Create a new conda environment
conda activate atm     # Activate the environment
conda install acellera-atm python=3.10 -c acellera -c conda-forge # Install the package
```

## Usage

To use the Acellera-ATM package, you can either use it from command line or from python.
You can follow the tutorial [here](https://github.com/Acellera/quantumbind_rbfe) to get started.

### Citations

- [Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method](https://pubs.acs.org/doi/10.1021/acs.jcim.1c01129)

- [Alchemical Transfer Approach to Absolute Binding Free Energy Estimation](https://pubs.acs.org/doi/10.1021/acs.jctc.1c00266)

- [Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing](http://www.compmolbiophysbc.org/publications#asyncre_software_2015)
slurm-sbalance 0.2.4
Slurm utility for checking account balance
Requires Python: !=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,<4
Keywords: slurm

# slurm-sbalance
`sbalance` is a Slurm utility for checking account balance. The utility calculates the remaining *service units* or *SU* left in the account. 

# Prerequisites
*  Slurm with Accounting enabled 

Currently `sbalance` has been tested with: 
* Python 2.7.5 and Python 3.6.6
* Slurm 18.08.5

# Usage
```
usage: sbalance [-h] [-V] [-k] [-m] [-v]

Query slurm account balance.

optional arguments:
  -h, --help     show this help message and exit
  -V, --version  show program's version number and exit
  -k             show output in kSU (1,000 SU)
  -m             show output in MSU (1,000,000 SU)
  -v, --verbose  verbose mode (multiple -v's increase verbosity)

```

# Setting up Slurm
`sbalance` currently support following setup. 
* Balance is limited per account
* Account limit is set through QoS with `GrpTRESMins` and `NoDecay` flag.

Following is an example setup

Creating account `tutorial` and QoS `test` with billing balance of 1000000
```
sacctmgr add qos test set GrpTRESMins=billing=1000000 Flags=NoDecay 
sacctmgr add account tutorial set QoS=test DefaultQoS=test
```

Add `test` user to account `tutorial`
```
sacctmgr add user test set Account=tutorial
```

Checking balance for `test` user
```
[test@localhost ~]$ sbalance 
Account balances for user: test
tutorial:
	Allocation:               1000000.00 SU
	Remaining Balance:         991896.00 SU ( 99.19%)
	Used:                        8104.00 SU
```