Difference between revisions of "JUSTUS2/Software/Dalton"
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+ | | GNU Lesser General Public License (LGPL). |
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'''Dalton''' (named after [https://en.wikipedia.org/wiki/John_Dalton John Dalton]) is an ab initio quantum chemistry computer program designed to to allow convenient, automated determination of a large number of molecular properties based on an HF, HF-srDFT, DFT, MP2, CC, CI, MCSCF, or MC-srDFT reference wave function. For additional information on features please visit the [https://daltonprogram.org/features/ Description of the Dalton suite features] web page. |
'''Dalton''' (named after [https://en.wikipedia.org/wiki/John_Dalton John Dalton]) is an ab initio quantum chemistry computer program designed to to allow convenient, automated determination of a large number of molecular properties based on an HF, HF-srDFT, DFT, MP2, CC, CI, MCSCF, or MC-srDFT reference wave function. For additional information on features please visit the [https://daltonprogram.org/features/ Description of the Dalton suite features] web page. |
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| − | = License = |
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| − | Dalton is free, open-source software released under the GNU Lesser General Public License (LGPL). Anyone interested in using the Dalton program suite must read the conditions described in its [https://gitlab.com/dalton/dalton/-/blob/master/LICENSE license agreement]. |
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= Usage = |
= Usage = |
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| − | == |
+ | == Loading the module == |
| + | See [[Software Modules]] documentation |
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| + | |||
| + | == Input Files == |
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| + | |||
| + | For information about how to construct input files (dalinp{.dal} [molinp{.mol} [potinp{.pot}]]) for Dalton, please consult the [https://daltonprogram.org/manuals/dalton2020manual.pdf vendor documentation]. |
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| + | |||
| + | == Environment Variables == |
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| + | |||
| + | Environment variables understood by Dalton: |
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| + | <pre> |
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| + | DALTON_TMPDIR : scratch directory |
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| + | DALTON_USE_GLOBAL_SCRATCH : use global scratch directory, do not copy any files to worker nodes |
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| + | DALTON_NODELIST : list of nodes, dalton.x will be copied to DALTON_TMPDIR on each node unless |
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| + | DALTON_USE_GLOBAL_SCRATCH is defined |
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| + | DALTON_LAUNCHER : launcher for the dalton.x binary (if defined, -N flag not allowed) |
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| + | </pre> |
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| + | |||
| + | == Disk Usage == |
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Scratch files are written to <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$SCRATCH</span> by default. This configuration option can be changed by setting the environment variable <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$DALTON_TMPDIR</span> (e.g., to a dedicated [[workspace]]) before starting your calculations with Dalton. |
Scratch files are written to <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$SCRATCH</span> by default. This configuration option can be changed by setting the environment variable <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$DALTON_TMPDIR</span> (e.g., to a dedicated [[workspace]]) before starting your calculations with Dalton. |
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| + | |||
| + | = Examples = |
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| + | |||
| + | As with all processes that require more than a few minutes to run, non-trivial compute jobs must be submitted to the cluster queuing system. |
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| + | Example scripts are available in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$DALTON_EXA_DIR</span>: |
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| + | <pre> |
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| + | $ module load chem/dalton # load module |
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| + | $ ls $DALTON_EXA_DIR # show content of directory $DALTON_EXA_DIR |
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| + | $ cat $DALTON_EXA_DIR/README # show examples README |
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| + | </pre> |
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| + | |||
| + | Run a first simple example job on JUSTUS2: |
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| + | <pre> |
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| + | $ module load chem/dalton # load module |
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| + | $ WORKSPACE=`ws_allocate dalton 3` # allocate workspace |
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| + | $ cd $WORKSPACE # change to workspace |
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| + | $ cp -a $DALTON_HOME/bwhpc-examples . # copy example files to workspace |
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| + | $ cd bwhpc-examples # change to test directory |
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| + | $ sbatch dalton-2020.0.slurm # submit job |
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| + | $ squeue # obtain JOBID |
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| + | $ scontrol show job <JOBID> # check state of job |
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| + | $ ls # when job finishes the results will be visible in this directory |
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| + | </pre> |
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= FAQ = |
= FAQ = |
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* [https://en.wikipedia.org/wiki/Dalton_(program) Wikipedia article (english)] |
* [https://en.wikipedia.org/wiki/Dalton_(program) Wikipedia article (english)] |
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* [https://daltonprogram.org/tools/ Plugins for Dalton (english)] |
* [https://daltonprogram.org/tools/ Plugins for Dalton (english)] |
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| − | ---- |
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| − | [[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]] |
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Latest revision as of 11:30, 23 April 2024
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The main documentation is available via |
| Description | Content |
|---|---|
| module load | chem/dalton |
| License | GNU Lesser General Public License (LGPL). |
| Citing | Publications |
| Links | Homepage | Documentation |
| Graphical Interface | No |
Contents
1 Description
Dalton (named after John Dalton) is an ab initio quantum chemistry computer program designed to to allow convenient, automated determination of a large number of molecular properties based on an HF, HF-srDFT, DFT, MP2, CC, CI, MCSCF, or MC-srDFT reference wave function. For additional information on features please visit the Description of the Dalton suite features web page.
2 Usage
2.1 Loading the module
See Software Modules documentation
2.2 Input Files
For information about how to construct input files (dalinp{.dal} [molinp{.mol} [potinp{.pot}]]) for Dalton, please consult the vendor documentation.
2.3 Environment Variables
Environment variables understood by Dalton:
DALTON_TMPDIR : scratch directory
DALTON_USE_GLOBAL_SCRATCH : use global scratch directory, do not copy any files to worker nodes
DALTON_NODELIST : list of nodes, dalton.x will be copied to DALTON_TMPDIR on each node unless
DALTON_USE_GLOBAL_SCRATCH is defined
DALTON_LAUNCHER : launcher for the dalton.x binary (if defined, -N flag not allowed)
2.4 Disk Usage
Scratch files are written to $SCRATCH by default. This configuration option can be changed by setting the environment variable $DALTON_TMPDIR (e.g., to a dedicated workspace) before starting your calculations with Dalton.
3 Examples
As with all processes that require more than a few minutes to run, non-trivial compute jobs must be submitted to the cluster queuing system.
Example scripts are available in the directory $DALTON_EXA_DIR:
$ module load chem/dalton # load module $ ls $DALTON_EXA_DIR # show content of directory $DALTON_EXA_DIR $ cat $DALTON_EXA_DIR/README # show examples README
Run a first simple example job on JUSTUS2:
$ module load chem/dalton # load module $ WORKSPACE=`ws_allocate dalton 3` # allocate workspace $ cd $WORKSPACE # change to workspace $ cp -a $DALTON_HOME/bwhpc-examples . # copy example files to workspace $ cd bwhpc-examples # change to test directory $ sbatch dalton-2020.0.slurm # submit job $ squeue # obtain JOBID $ scontrol show job <JOBID> # check state of job $ ls # when job finishes the results will be visible in this directory
4 FAQ
Q: What to do if my simulations abort with MEMGET ERROR, insufficient work space in memory ?
A: Increase Dalton's usable work memory with either -mb or -gb on the command line.
