Difference between revisions of "JUSTUS2/Software/Dalton"
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| chem/dalton |
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| − | | Availability |
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| − | | [[BwForCluster_JUSTUS_2]] |
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| License |
| License |
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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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| − | = Availability = |
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| + | = Usage = |
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| − | Dalton is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the [https://www.bwhpc.de/software.html Cluster Information System (CIS)]. |
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| + | == Loading the module == |
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| + | See [[Software Modules]] documentation |
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| + | == Input Files == |
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| − | In order to check which versions of Dalton are installed on the compute cluster, run the following command: |
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| − | <pre> |
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| − | $ module avail chem/dalton |
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| − | </pre> |
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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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| − | = License = |
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| + | == Environment Variables == |
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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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| + | Environment variables understood by Dalton: |
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| − | = Usage = |
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| − | == Loading the module == |
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| − | You can load the default version of ''Dalton'' with the command: |
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| − | <pre> |
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| − | $ module load chem/dalton |
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| − | </pre> |
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| − | |||
| − | The module will try to load modules it needs to function (e.g. compiler, mpi, numlibs). |
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| − | If loading the module fails, check if you have already loaded one of those modules, |
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| − | but not in the version needed for Dalton. |
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| − | If you wish to load a specific (older) version (if available), you can do so using e.g. |
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| − | 'module load chem/dalton/version' to load the version you desires. |
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| − | <pre> |
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| − | $ module avail chem/dalton |
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| − | ------------------------ /opt/bwhpc/common/modulefiles ------------------------- |
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| − | chem/dalton/2013 |
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| − | $ module load chem/dalton/2013 |
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| − | </pre> |
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| − | == Program Binaries == |
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| − | You can find the Dalton binaries in the main folder of the Dalton system. |
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| − | After loading the Dalton module ('module load chem/dalton/version') it's path is |
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| − | also set to the local $PATH- and [[#Dalton-Specific Environments|$DALTON_BIN_DIR environments]]. |
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| − | <br> |
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| − | $DALTON_BIN_DIR=/opt/bwhpc/common/chem/ |
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<pre> |
<pre> |
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| + | DALTON_TMPDIR : scratch directory |
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| − | $ : Example with Dalton 2013 |
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| + | DALTON_USE_GLOBAL_SCRATCH : use global scratch directory, do not copy any files to worker nodes |
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| − | $ echo $DALTON_BIN_DIR |
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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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| − | /opt/bwhpc/common/chem/dalton/2013/bin |
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| + | DALTON_USE_GLOBAL_SCRATCH is defined |
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| − | $ ls -F $DALTON_BIN_DIR |
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| + | DALTON_LAUNCHER : launcher for the dalton.x binary (if defined, -N flag not allowed) |
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| − | basis/ DALTON.STAT GIT_HASH lsdalton.x* tools/ |
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| − | dalton* dalton.x* lsdalton* lslib_tester.x* VERSION |
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</pre> |
</pre> |
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| − | * A '/' at the end of a file name indicates a directory/folder. |
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| − | * '*' is an executable file. |
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== Disk Usage == |
== Disk Usage == |
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| − | Scratch files are written to the current directory by default. |
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| − | <font color=red>Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations.</font> |
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| + | Scratch files are written to <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$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">$DALTON_TMPDIR</span> (e.g., to a dedicated [[workspace]]) before starting your calculations with Dalton. |
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| − | 'dalton_repo' is an example name of a repository you created by using the command 'ws_allocate'. |
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| + | = Examples = |
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| + | |||
| + | As with all processes that require more than a few minutes to run, non-trivial compute jobs must be submitted to the cluster queuing system. |
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| + | |||
| + | Example scripts are available in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$DALTON_EXA_DIR</span>: |
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<pre> |
<pre> |
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| + | $ module load chem/dalton # load module |
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| − | $ cd $(ws_find dalton_repo) |
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| + | $ ls $DALTON_EXA_DIR # show content of directory $DALTON_EXA_DIR |
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| − | ['your-id'-dalton_repo-0]$ pwd |
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| + | $ cat $DALTON_EXA_DIR/README # show examples README |
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| − | /work/workspace/scratch/'your-id'-dalton_repo-0 |
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| − | ['your-id'-dalton_repo-0]$ |
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</pre> |
</pre> |
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| + | |||
| − | <br> |
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| + | Run a first simple example job on JUSTUS2: |
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| − | = Examples = |
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| − | == bwHPC examples == |
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| − | You can copy a simple interactive example to your '''workspace''' and run it, using 'msub' |
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<pre> |
<pre> |
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| + | $ module load chem/dalton # load module |
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| − | $ cd $(ws_find dalton_repo) |
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| + | $ WORKSPACE=`ws_allocate dalton 3` # allocate workspace |
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| − | $ cp $DALTON_EXA_DIR/bwunicluster-dalton-example.moab . |
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| + | $ cd $WORKSPACE # change to workspace |
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| − | $ cp bwunicluster-dalton-example.moab mydaltonjob.moab |
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| + | $ cp -a $DALTON_HOME/bwhpc-examples . # copy example files to workspace |
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| − | § vi mydaltonjob.moab # do your own modifications |
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| + | $ cd bwhpc-examples # change to test directory |
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| − | $ msub mydaltonjob.moab # start job submission |
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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> |
</pre> |
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| − | It is strongly recommended to use [[#Dalton-Specific Environments|$DALTON_EXA_DIR]] to find the bwHPC examples. |
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| − | <br> |
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| − | === bwHPC Moab submit script === |
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| − | Here is an excerpt from the supplied bwunicluster-dalton-example.moab script as found in $DALTON_EXA_DIR. |
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| − | {{bwFrameA| |
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| − | <source lang="bash"> |
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| − | [...] |
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| − | echo " " |
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| − | echo "### Copying input test files for job (if required):" |
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| − | echo " " |
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| − | cp -vr ${DALTON_EXA_DIR}/ethane-blyp-benchmark.{dal,mol} . |
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| + | = FAQ = |
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| − | echo " " |
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| + | |||
| − | echo "### Redefine TMPDIR for storing temporary Dalton files ..." |
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| + | '''Q:''' What to do if my simulations abort with <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080"> MEMGET ERROR, insufficient work space in memory </span>? |
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| − | echo " " |
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| − | export TMPDIR="${TMP_WORK_DIR}/dalton_tmp" |
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| − | export DALTON_TMPDIR="${TMP_WORK_DIR}/dalton_tmp" |
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| − | echo "TMPDIR = ${TMPDIR}" |
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| − | echo "DALTON_TMPDIR = ${TMPDIR}" |
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| − | echo " " |
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| − | echo "### Calling dalton command ..." |
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| − | echo " " |
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| + | '''A:''' Increase Dalton's usable work memory with either -mb or -gb on the command line. |
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| − | # Here is the main Dalton command showing how to run a regular |
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| − | # Dalton job (mpirun is invoked within the 'dalton' script automatically). |
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| − | # For details on the Dalton job see 'ethane-blyp-benchmark.info'. |
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| − | # Example job input: ethane-blyp-benchmark.{dal,mol} |
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| − | # Example job output: bwhpc-example.out ethane-blyp-benchmark.tar.gz. |
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| − | export workdir=${TMP_WORK_DIR} |
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| − | cd ${TMP_WORK_DIR} |
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| − | time $DALTON_BIN_DIR/dalton -N ${MOAB_PROCCOUNT} -o bwhpc-example.out ethane-blyp-benchmark.dal ethane-blyp-benchmark.mol |
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| − | [...] |
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| − | </source> |
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| − | }} |
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| − | <br> |
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= Useful links = |
= Useful links = |
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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.
