Difference between revisions of "JUSTUS2/Software/Turbomole"

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== Description ==
+
= Description =
 
'''Turbomole''' is a general purpose ''quantum chemistry'' software package for ''ab initio'' electronic structure calculations and provides:
 
'''Turbomole''' is a general purpose ''quantum chemistry'' software package for ''ab initio'' electronic structure calculations and provides:
 
* ground state calculations for methods such as Hartree-Fock, DFT, MP2, and CCSD(T);
 
* ground state calculations for methods such as Hartree-Fock, DFT, MP2, and CCSD(T);
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<br>
 
<br>
   
== Versions and Availability ==
+
= Versions and Availability =
 
A current list of the versions available on the bwUniCluster and bwForClusters can be obtained from the Cluster Information System: [http://cis-hpc.uni-konstanz.de/prod.cis/turbomole CIS Information on Turbomole]
 
A current list of the versions available on the bwUniCluster and bwForClusters can be obtained from the Cluster Information System: [http://cis-hpc.uni-konstanz.de/prod.cis/turbomole CIS Information on Turbomole]
   
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<br>
 
<br>
   
=== Parallel computing ===
+
== Parallel computing ==
 
The Turbomole ''Module'' subsumes all available parallel computing variants of Turbomole's binaries. Turbomole defines the following parallel computing variants:
 
The Turbomole ''Module'' subsumes all available parallel computing variants of Turbomole's binaries. Turbomole defines the following parallel computing variants:
 
* SMP = Shared-memory parallel computing based on OpenMP and Fork() with the latter using separated address spaces.
 
* SMP = Shared-memory parallel computing based on OpenMP and Fork() with the latter using separated address spaces.
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<br>
 
<br>
   
== Usage ==
+
= Usage =
=== Loading the module ===
+
== Before loading the Module ==
  +
Before loading the Turbomole ''Module'' the parallel computing variant has to be defined via the environment variable $PARA_ARCH using the abbreviations SMP, MPI or GA, e.g.:
You can load the default version of ''Turbomole'' with the command
 
  +
<pre>
  +
$ export PARA_ARCH=MPI
  +
</pre>
  +
will [[#Loading the Module|later load]] the MPI binary variants. If the variable $PARA_ARCH is not defined or empty, the sequential binary variants will be active once the Turbomole Module is loaded.
  +
<br>
  +
  +
== Loading the Module ==
  +
You can load the default version of ''Turbomole'' with the command:
 
<pre>
 
<pre>
 
$ module load chem/turbomole
 
$ module load chem/turbomole
 
</pre>
 
</pre>
   
The ''Module'' Turbomole does not depend on any other ''Module''. Moreover, Turbomole provides its own libraries regarding ''OpenMP'', ''Fork()'', ''MPI'', and ''Global Array'' based parallelization.
+
The Turbomole ''Module'' does not depend on any other ''Module''. Moreover, Turbomole provides its own libraries regarding ''OpenMP'', ''Fork()'', ''MPI'', and ''Global Array'' based parallelization.
 
If you wish to load a specific (older) version you can do so using e.g.:
 
If you wish to load a specific (older) version you can do so using e.g.:
 
<pre>
 
<pre>
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<br>
 
<br>
   
=== Program Binaries and Scripts ===
+
== Program Binaries ==
 
 
The '''Turbomole''' software package consists of a set of stand-alone program binaries providing different features and parallelization support:
 
The '''Turbomole''' software package consists of a set of stand-alone program binaries providing different features and parallelization support:
   
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! style="background-color:#AAA;padding:3px"| Features
 
! style="background-color:#AAA;padding:3px"| Features
 
! style="background-color:#AAA;padding:3px"| OpenMP
 
! style="background-color:#AAA;padding:3px"| OpenMP
! style="background-color:#AAA;padding:3px"| MPI
 
 
! style="background-color:#AAA;padding:3px"| Fork
 
! style="background-color:#AAA;padding:3px"| Fork
! style="background-color:#AAA;padding:3px"| Global Arrays
+
! style="background-color:#AAA;padding:3px"| MPI
  +
! style="background-color:#AAA;padding:3px"| GA
 
|- style="vertical-align:top;"
 
|- style="vertical-align:top;"
 
| style="background-color:#d3ddd8;height=20px; text-align:left;padding:3px"| define
 
| style="background-color:#d3ddd8;height=20px; text-align:left;padding:3px"| define
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| style="height=20px; text-align:left;padding:3px"| Electronic excitation energies, transition moments and properties of excited states
 
| style="height=20px; text-align:left;padding:3px"| Electronic excitation energies, transition moments and properties of excited states
 
| style="height=20px; text-align:left;padding:3px"| yes
 
| style="height=20px; text-align:left;padding:3px"| yes
  +
| style="height=20px; text-align:left;padding:3px"| no
 
| style="height=20px; text-align:left;padding:3px"| yes
 
| style="height=20px; text-align:left;padding:3px"| yes
| style="height=20px; text-align:left;padding:3px"| no
 
 
| style="height=20px; text-align:left;padding:3px"| no
 
| style="height=20px; text-align:left;padding:3px"| no
 
|- style="vertical-align:top;"
 
|- style="vertical-align:top;"
 
| style="background-color:#d3ddd8;height=20px; text-align:left;padding:3px"| aoforce
 
| style="background-color:#d3ddd8;height=20px; text-align:left;padding:3px"| aoforce
 
| style="height=20px; text-align:left;padding:3px"| Analytic calculation of force constants, vibrational frequencies and IR intensities
 
| style="height=20px; text-align:left;padding:3px"| Analytic calculation of force constants, vibrational frequencies and IR intensities
| style="height=20px; text-align:left;padding:3px"| no
 
 
| style="height=20px; text-align:left;padding:3px"| no
 
| style="height=20px; text-align:left;padding:3px"| no
 
| style="height=20px; text-align:left;padding:3px"| yes
 
| style="height=20px; text-align:left;padding:3px"| yes
  +
| style="height=20px; text-align:left;padding:3px"| no
 
| style="height=20px; text-align:left;padding:3px"| no
 
| style="height=20px; text-align:left;padding:3px"| no
 
|- style="vertical-align:top;"
 
|- style="vertical-align:top;"
 
| style="background-color:#d3ddd8;height=20px; text-align:left;padding:3px"| escf
 
| style="background-color:#d3ddd8;height=20px; text-align:left;padding:3px"| escf
 
| style="height=20px; text-align:left;padding:3px"| Calc. of time dependent and dielectric properties
 
| style="height=20px; text-align:left;padding:3px"| Calc. of time dependent and dielectric properties
| style="height=20px; text-align:left;padding:3px"| no
 
 
| style="height=20px; text-align:left;padding:3px"| no
 
| style="height=20px; text-align:left;padding:3px"| no
 
| style="height=20px; text-align:left;padding:3px"| yes
 
| style="height=20px; text-align:left;padding:3px"| yes
  +
| style="height=20px; text-align:left;padding:3px"| no
 
| style="height=20px; text-align:left;padding:3px"| no
 
| style="height=20px; text-align:left;padding:3px"| no
 
|- style="vertical-align:top;"
 
|- style="vertical-align:top;"
 
| style="background-color:#d3ddd8;height=20px; text-align:left;padding:3px"| egrad
 
| style="background-color:#d3ddd8;height=20px; text-align:left;padding:3px"| egrad
 
| style="height=20px; text-align:left;padding:3px"| gradients and first-order properties of excited states
 
| style="height=20px; text-align:left;padding:3px"| gradients and first-order properties of excited states
| style="height=20px; text-align:left;padding:3px"| no
 
 
| style="height=20px; text-align:left;padding:3px"| no
 
| style="height=20px; text-align:left;padding:3px"| no
 
| style="height=20px; text-align:left;padding:3px"| yes
 
| style="height=20px; text-align:left;padding:3px"| yes
  +
| style="height=20px; text-align:left;padding:3px"| no
 
| style="height=20px; text-align:left;padding:3px"| no
 
| style="height=20px; text-align:left;padding:3px"| no
 
|- style="vertical-align:top;"
 
|- style="vertical-align:top;"
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|}
 
|}
 
For the complete set of binaries and more detailed description of their features read [http://www.turbomole-gmbh.com/manuals/version_6_5/Documentation_html/node8.html here].
 
For the complete set of binaries and more detailed description of their features read [http://www.turbomole-gmbh.com/manuals/version_6_5/Documentation_html/node8.html here].
  +
<br>
  +
   
=== Disk Usage ===
+
== Disk Usage ==
 
By default, scratch files of Turbomole binaries are placed in the directory of Turbmole binary execution. Please do not run your Turbomole calculations in your $HOME or $WORK directory.
 
By default, scratch files of Turbomole binaries are placed in the directory of Turbmole binary execution. Please do not run your Turbomole calculations in your $HOME or $WORK directory.
 
<br>
 
<br>
   
== Examples ==
+
= Examples =
 
You can copy a simple MOAB example to your home directory and run it, by doing the following steps:
 
You can copy a simple MOAB example to your home directory and run it, by doing the following steps:
 
<pre>
 
<pre>
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<br>
 
<br>
   
== Version-Specific Information ==
+
= Version-Specific Information =
 
For specific information about version ''X'', see the information available via the module system with the command
 
For specific information about version ''X'', see the information available via the module system with the command
 
<pre>
 
<pre>

Revision as of 23:17, 30 April 2014

Name
module load chem/turbomole
Availability bwUniCluster
License commerical
Citing See Turbomole manual
Links Homepage; Documentation
Graphical Interface No (Yes, for generating input)
User Forum external

1 Description

Turbomole is a general purpose quantum chemistry software package for ab initio electronic structure calculations and provides:

  • ground state calculations for methods such as Hartree-Fock, DFT, MP2, and CCSD(T);
  • excited state calculations at different levels such as full RPA, TDDFT, CIS(D), CC2, an ADC(2);
  • geometry optimizations, transition state searches, molecular dynamics calculations;
  • property and spectra calculations such as IR, UV/VIS, Raman, and CD;
  • approximations like resolution-of-the-identity (RI) to speed-up the calculations without introducing uncontrollable or unknown errors; as well as
  • parallel versions (OpenMP, Fork, MPI and Global Arrays) for almost all kind of jobs.

For more information on Turbmole's features please visit http://www.turbomole-gmbh.com/program-overview.html.

2 Versions and Availability

A current list of the versions available on the bwUniCluster and bwForClusters can be obtained from the Cluster Information System: CIS Information on Turbomole

On the command line interface (CLI) of a particular bwHPC cluster a list of all available Turbomole versions can be inquired as followed

$ module avail chem/turbomole


2.1 Parallel computing

The Turbomole Module subsumes all available parallel computing variants of Turbomole's binaries. Turbomole defines the following parallel computing variants:

  • SMP = Shared-memory parallel computing based on OpenMP and Fork() with the latter using separated address spaces.
  • MPI = Message passing interface protocol based parallel computing
  • GA = Global arrays, API for "shared-memory" programming for distributed-memory computers which can be used e.g. to complement MPI.

However only one of the 3 parallel variants or the sequential variant can be loaded at once. Like for Turbomole installations without a Module system, the variants are triggered by the environment variable $PARA_ARCH.

3 Usage

3.1 Before loading the Module

Before loading the Turbomole Module the parallel computing variant has to be defined via the environment variable $PARA_ARCH using the abbreviations SMP, MPI or GA, e.g.:

$ export PARA_ARCH=MPI

will later load the MPI binary variants. If the variable $PARA_ARCH is not defined or empty, the sequential binary variants will be active once the Turbomole Module is loaded.

3.2 Loading the Module

You can load the default version of Turbomole with the command:

$ module load chem/turbomole

The Turbomole Module does not depend on any other Module. Moreover, Turbomole provides its own libraries regarding OpenMP, Fork(), MPI, and Global Array based parallelization. If you wish to load a specific (older) version you can do so using e.g.:

$ module load chem/turbomole/6.5

to load the version 6.5

3.3 Program Binaries

The Turbomole software package consists of a set of stand-alone program binaries providing different features and parallelization support:

Binary Features OpenMP Fork MPI GA
define Interactive input generator no no no no
dscf Energy calculations yes yes yes no
grad Gradient calculations no yes yes no
ridft Energy calc. with fast Coulomb approximation no yes yes yes
rdgrad Gradient calc. with fast Coulomb approximation no yes yes yes
ricc2 Electronic excitation energies, transition moments and properties of excited states yes no yes no
aoforce Analytic calculation of force constants, vibrational frequencies and IR intensities no yes no no
escf Calc. of time dependent and dielectric properties no yes no no
egrad gradients and first-order properties of excited states no yes no no
odft Orbital-dependent energy calc. yes no no no

For the complete set of binaries and more detailed description of their features read here.


3.4 Disk Usage

By default, scratch files of Turbomole binaries are placed in the directory of Turbmole binary execution. Please do not run your Turbomole calculations in your $HOME or $WORK directory.

4 Examples

You can copy a simple MOAB example to your home directory and run it, by doing the following steps:

$ mkdir -vp ~/Turbomole-example/
$ cd ~/Turbomole-examples/
$ cp -r $TURBOMOLE_EXA_DIR/* ~/Turbmole-example/
$ msub bwUniCluster_turbomole_single-node_example.sh

The last step submits the job example script bwUniCluster_turbomole_single-node_example.sh to the queueing system. Once started on a compute node, all calculations will be done under an unique directory on the local file system of that particular compute node.

5 Version-Specific Information

For specific information about version X, see the information available via the module system with the command

$ module help chem/turbomole/X