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[[Category:Software]] | [[Category:Software]] | ||
==Introduction== <!--T: | ==Introduction== <!--T:2--> | ||
The [https://www.scm.com/ ADF (Amsterdam Density Functional) Modeling Suite] offers powerful computational chemistry tools for many research areas such as homogeneous and heterogeneous catalysis, inorganic chemistry, heavy element chemistry, various types of spectroscopy, and biochemistry. | The [https://www.scm.com/ ADF (Amsterdam Density Functional) Modeling Suite] offers powerful computational chemistry tools for many research areas such as homogeneous and heterogeneous catalysis, inorganic chemistry, heavy element chemistry, various types of spectroscopy, and biochemistry. | ||
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Compute Canada users have access to the following products: | Compute Canada users have access to the following products: | ||
*ADF | *ADF | ||
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*NBO6 | *NBO6 | ||
==Running ADF on Graham== <!--T: | ==Running ADF on Graham== <!--T:6--> | ||
ADF is installed only on [[Graham]] due to license restrictions. To check what versions are available on Graham, use the <code>module spider adf</code> command, for example | ADF is installed only on [[Graham]] due to license restrictions. To check what versions are available on Graham, use the <code>module spider adf</code> command, for example | ||
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[name@server $] module spider adf | [name@server $] module spider adf | ||
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For module commands, please see [[Utiliser des modules/en|Using modules]]. | For module commands, please see [[Utiliser des modules/en|Using modules]]. | ||
===Job submission=== <!--T: | ===Job submission=== <!--T:12--> | ||
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Graham uses the Slurm scheduler; for details about submitting jobs, see [[Running jobs]]. | Graham uses the Slurm scheduler; for details about submitting jobs, see [[Running jobs]]. | ||
====Single ADF or BAND run==== <!--T: | ====Single ADF or BAND run==== <!--T:16--> | ||
This mysub.sh script is for a whole-node job. The last two lines load version 2017.207 and call ADF directly. | This mysub.sh script is for a whole-node job. The last two lines load version 2017.207 and call ADF directly. | ||
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ADF adf_test.inp | ADF adf_test.inp | ||
}} | }} | ||
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This is the input file used in the script: | This is the input file used in the script: | ||
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====Multiple ADF or BAND runs within one input file==== <!--T: | ====Multiple ADF or BAND runs within one input file==== <!--T:20--> | ||
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Multiple calculations can be combined into a single job by creating a script such as this: | Multiple calculations can be combined into a single job by creating a script such as this: | ||
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mv TAPE21 H2O.t21 | mv TAPE21 H2O.t21 | ||
}} | }} | ||
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The following script is identical to the one used for a single run (mysub.sh), except that the last line calls the GO_H2O.run script, instead of ADF. | The following script is identical to the one used for a single run (mysub.sh), except that the last line calls the GO_H2O.run script, instead of ADF. | ||
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===Examples=== <!--T: | ===Examples=== <!--T:26--> | ||
Example input/output for ADF can be found on Graham under | Example input/output for ADF can be found on Graham under | ||
/home/jemmyhu/tests/test_ADF/2017.207/test_adf/ | /home/jemmyhu/tests/test_ADF/2017.207/test_adf/ | ||
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The same procedure applies to BAND jobs, see band_test.inp and band_test.sh examples under | The same procedure applies to BAND jobs, see band_test.inp and band_test.sh examples under | ||
/home/jemmyhu/tests/test_ADF/2017.207/test_band | /home/jemmyhu/tests/test_ADF/2017.207/test_band | ||
==Running ADF-GUI | ==Running ADF-GUI== <!--T:30--> | ||
Rendering over an SSH connection with X11 forwarding is very slow for GUI applications such as ADF-GUI. We recommend you use [[VNC]] to connect if you will be running ADF-GUI. | Rendering over an SSH connection with X11 forwarding is very slow for GUI applications such as ADF-GUI. We recommend you use [[VNC]] to connect if you will be running ADF-GUI. | ||
===Graham=== <!--T: | ===Graham=== <!--T:32--> | ||
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Adf can be run interactively in graphical mode on a graham compute node (3hr time limit) over TigerVNC with these steps: | Adf can be run interactively in graphical mode on a graham compute node (3hr time limit) over TigerVNC with these steps: | ||
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# [https://docs.computecanada.ca/wiki/VNC#Setup Install] TigerVNC client on your desktop | # [https://docs.computecanada.ca/wiki/VNC#Setup Install] TigerVNC client on your desktop | ||
# [https://docs.computecanada.ca/wiki/VNC#Compute_Nodes Connect] to a cluster compute node with vncviewer | # [https://docs.computecanada.ca/wiki/VNC#Compute_Nodes Connect] to a cluster compute node with vncviewer | ||
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# <code>adfinput</code> | # <code>adfinput</code> | ||
===Gra-vdi=== <!--T: | ===Gra-vdi=== <!--T:36--> | ||
NOTE: gra-vdi is currently OFFLINE for upgrading with a return to use date sometime in june | NOTE: gra-vdi is currently OFFLINE for upgrading with a return to use date sometime in june | ||
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Adf can be run interactively in graphical mode on gra-vdi (no connection time limit) over TigerVNC with these steps: | Adf can be run interactively in graphical mode on gra-vdi (no connection time limit) over TigerVNC with these steps: | ||
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# [https://docs.computecanada.ca/wiki/VNC#Setup Install] TigerVNC client on your desktop | # [https://docs.computecanada.ca/wiki/VNC#Setup Install] TigerVNC client on your desktop | ||
# [https://docs.computecanada.ca/wiki/VNC#VDI_Nodes Connect] to gra-vdi.computecanada.ca with vncviewer | # [https://docs.computecanada.ca/wiki/VNC#VDI_Nodes Connect] to gra-vdi.computecanada.ca with vncviewer | ||
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# <code>adfinput</code> | # <code>adfinput</code> | ||
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A tutorial pdf showing how to install, connect and run ADF-GUI using TigerVNC on gra-vdi can be found | A tutorial pdf showing how to install, connect and run ADF-GUI using TigerVNC on gra-vdi can be found | ||
[https://www.sharcnet.ca/~jemmyhu/TigerVNC-for-ADF-GUI.pdf here]. | [https://www.sharcnet.ca/~jemmyhu/TigerVNC-for-ADF-GUI.pdf here]. | ||
===Locally=== <!--T: | ===Locally=== <!--T:44--> | ||
SCM has a separate license to run ADF-GUI on a local desktop machine. If you are interested contact [mailto:license@scm.com license@scm.com] to purchase your own license. | SCM has a separate license to run ADF-GUI on a local desktop machine. If you are interested contact [mailto:license@scm.com license@scm.com] to purchase your own license. | ||
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