JUSTUS2/Software/Dalton: Difference between revisions
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= Examples = |
= Examples = |
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== bwHPC 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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You can copy a simple interactive example to your '''workspace''' and run it, using 'msub' |
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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 show chem/dalton # show environment variables, which will be available after 'module load' |
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$ cd $(ws_find dalton_repo) |
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$ module load chem/dalton # load module |
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$ cp $DALTON_EXA_DIR/bwunicluster-dalton-example.moab . |
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$ ls $DALTON_EXA_DIR # show content of directory $DALTON_EXA_DIR |
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$ cp bwunicluster-dalton-example.moab mydaltonjob.moab |
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$ cat $DALTON_EXA_DIR/README # show examples README |
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$ msub mydaltonjob.moab # start job submission |
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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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=== 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 ${DALTON_EXA_DIR}/ethane-blyp-benchmark.{dal,mol} . |
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Run several example jobs on '''JUSTUS 2''': |
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echo " " |
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<pre> |
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echo "### Redefine TMPDIR for storing temporary Dalton files ..." |
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$ module load chem/dalton # load module |
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echo " " |
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$ WORKSPACE=`ws_allocate dalton 3` # allocate workspace |
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export TMPDIR="${TMP_WORK_DIR}/dalton_tmp" |
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$ cd $WORKSPACE # change to workspace |
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export DALTON_TMPDIR="${TMP_WORK_DIR}/dalton_tmp" |
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$ cp -a $DALTON_HOME/bwhpc-examples . # copy example files to workspace |
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echo "TMPDIR = ${TMPDIR}" |
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$ cd bwhpc-examples # change to test directory |
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echo "DALTON_TMPDIR = ${TMPDIR}" |
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$ sbatch dalton-2020.0.slurm # submit job |
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echo " " |
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$ squeue # obtain JOBID |
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echo "### Calling dalton command ..." |
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$ scontrol show job <JOBID> # check state of job |
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echo " " |
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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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# 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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= Useful links = |
= Useful links = |
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Revision as of 16:32, 18 March 2021
| Description | Content |
|---|---|
| module load | chem/dalton |
| Availability | BwForCluster_JUSTUS_2 |
| License | Open-source software, distributed under the GNU Lesser General Public License (LGPL). More... |
| Citing | Publications |
| Links | Homepage | Documentation |
| Graphical Interface | No |
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.
Availability
Dalton is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the Cluster Information System (CIS).
In order to check which versions of Dalton are installed on the compute cluster, run the following command:
$ module avail chem/dalton
License
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 license agreement.
Usage
Loading the module
You can load the default version of Dalton with the command:
$ module load chem/dalton
The module will try to load modules it needs to function (e.g. compiler, mpi, numlibs). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Dalton. If you wish to load a specific (older) version (if available), you can do so using e.g. 'module load chem/dalton/version' to load the version you desires.
$ module avail chem/dalton ------------------------ /opt/bwhpc/common/modulefiles ------------------------- chem/dalton/2013 $ module load chem/dalton/2013
Program Binaries
You can find the Dalton binaries in the main folder of the Dalton system.
After loading the Dalton module ('module load chem/dalton/version') it's path is
also set to the local $PATH- and $DALTON_BIN_DIR environments.
$DALTON_BIN_DIR=/opt/bwhpc/common/chem/
$ : Example with Dalton 2013 $ echo $DALTON_BIN_DIR /opt/bwhpc/common/chem/dalton/2013/bin $ ls -F $DALTON_BIN_DIR basis/ DALTON.STAT GIT_HASH lsdalton.x* tools/ dalton* dalton.x* lsdalton* lslib_tester.x* VERSION
- A '/' at the end of a file name indicates a directory/folder.
- '*' is an executable file.
Disk Usage
Scratch files are written to the current directory by default. Please change to a local directory or to your local workspace (preferred) before starting your calculations.
'dalton_repo' is an example name of a repository you created by using the command 'ws_allocate'.
$ cd $(ws_find dalton_repo) ['your-id'-dalton_repo-0]$ pwd /work/workspace/scratch/'your-id'-dalton_repo-0 ['your-id'-dalton_repo-0]$
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 show chem/dalton # show environment variables, which will be available after 'module load' $ 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 several example jobs on JUSTUS 2:
$ 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