HPC/Applications/atk: Difference between revisions

From CNM Wiki
Jump to navigation Jump to search
 
(55 intermediate revisions by the same user not shown)
Line 1: Line 1:
== Module conflicts ==
== Parallel jobs ==
This package uses MPICH2 (which [[../impi|Intel-MPI]] provides) and hence clashes with [[../vasp|VASP]], which uses [[../openmpi]].
* See [https://docs.quantumwise.com/tutorials/parallelization/parallelization.html QuantumWise's Parallel Guide]
* We use Intel-MPI instead of MPICH2, with the Hydra process manager instead of MPD. See the sample.job file for details:
$ATK_HOME/sample.job
 
<!--
== Module interference ==
The [[HPC/Software/Modules/atk | atk]] module needs MPICH2 libraries (happily provided by [[../impi|Intel-MPI]]), and hence clashes with [[../vasp|VASP]], which uses [[../openmpi | OpenMPI]].
 
=== Intel-MPI vs. OpenMPI ===
The [[HPC/Software/Modules/atk | atk]] module loads [[HPC/Software/Modules/impi | impi]] "behind" [[HPC/Software/Modules/openmpi | openmpi]].
This trick exposes mpiexec.hydra from Intel-MPI, whereas ''all other MPI commands'' continue to refer to OpenMPI.
 
Do not manually load OpenMPI or Intel-MPI unless you have a good reason to do so.


Co-existence is possible as follows:
=== ATK vs. VASP ===
module unload openmpi
Load vasp ''after'' atk.
  module load atk
  module load atk
module load openmpi
  …
  …
  module load vasp5      # … or other versions
  module load vasp5      # … or other versions
-->


== Parallel jobs ==
== Remote access ==
* See [http://quantumwise.com/documents/tutorials/latest/ParallelGuide QuantumWise's Parallel Guide]
To run ATK/VNL directly on your computer (as opposed to running it remotely and sending graphics over the network), follow these steps, ''all on your computer,'' to prepare for and launch the application:
; Local changes:
* We use Intel-MPI instead of MPICH2, with the Hydra process manager instead of MPD. See the sample.job file for details:
$ATK_HOME/sample.job


== Remote access from Windows ==
=== Preparation ===
# [[HPC/Software/Modules/atk/Installation on Windows | Install ATK]] on your machine.
* Log out from all Carbon nodes.
* Log out from Mega.
* Modify your configuration for SSH port forwarding to Mega. On Mac or Linux, make the changes to your file <code>~/.ssh/config</code>. On Windows, apply the changes as shown in the help pages of your SSH application.
<!--
: Add two entries for ''Remote Forwarding'':
Local port: 6200,  Remote Port: 6200@cmgmt3
Local port: '''6201''',  Remote Port: '''6200'''@cmgmt'''4'''.  ---- server died, redundancy lost
: Note that the ''local ports are different'' but the remote ports are the same between the two entries.
-->
: Add an entry for ''Remote Forwarding'':
Local port: 6200,  Remote Port: 6200@cmgmt4
<!--
# [[HPC/Software/Modules/atk/License configuration on Windows | Configure ATK to use forwarded licenses]].
# You will need an ATK license to run VNL or atpkypthon. Choose one of the following to remotely access Carbon's licenses:
# You will need an ATK license to run VNL or atpkypthon. Choose one of the following to remotely access Carbon's licenses:
## Basic: [[HPC/Network Access/PuTTY Configuration/The Carbon login node | Set up license forwarding using PuTTY]].
## Basic: [[HPC/Network Access/PuTTY Configuration/Accessing Carbon licenses remotely | Set up license forwarding using PuTTY]].
## Advanced: [[HPC/Software/Modules/atk/Remote Access using Cygwin | Set up license forwarding using Cygwin]].
## Advanced: [[HPC/Software/Modules/atk/Remote Access using Cygwin | Set up license forwarding using Cygwin]].
# [[HPC/Software/Modules/atk/License configuration on Windows | Configure ATK to use forwarded licenses]].
-->
* Log back in to Mega. This will activate the tunnel configuration that you added previously, to be used later by the ATK License Configuration wizard.
 
=== Configure ===
<!--
=== Download, Install, and Configure ===
* [http://quantumwise.com/products/download Download ATK from QuantumWise]
* Follow the [http://docs.quantumwise.com/guides/InstallationGuides/installation.html installation instructions] until you reach the license configuration step.
-->
* In the License Configuration helper, choose <code>Configure license settings</code>, <code>Advanced setup</code>. In the field for QUANTUM_LICENSE_PATH+= add:
localhost:6200@localhost
<!--
* Finish the helper.
-->
 
=== Launching ATK/VNL ===
* Log in to Mega if you are not alreay logged in.
*: You need to have ''exactly one'' Mega session active to access any kind of service on Carbon, be it for a single use or several ones concurrently.
* Start VNL or atkpython normally for your platform.
 
=== Troubleshooting licensing ===
 
==== Check license configuration ====
To check the basic license configuration for ATK,
without requiring X11 or VNC graphics,
run the ATK Python script interpreter <code>atkpython</code>.
It requires a license regardless of whether the script actually uses NanoLang constructs.
<source lang="bash">
atkpython -c 'print("Hello", 1+3/2)'
</source>
 
* The ''expected'' output will look like:
<source>
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 2017.2 [Build 997d195]                                     |
|                                                                              |
+------------------------------------------------------------------------------+
('Hello', 1)
 
Timing:                          Total    Per Step        %
…
Total                  :      2.24 s
</source>
 
* ''Failure'' to obtain a license, such as from an incorrect configuration or a server being down, looks like:
<source>
License Error: (Internal: 511 Feature: ATKPython)
 
[NETWORK] 6200@localhost - (Err: 15) Unable to connect to license server
 
License configuration (environment variables):
---------------------------------------------------------------------------
QUANTUM_LICENSE_PATH = …
---------------------------------------------------------------------------
*** Make sure to include the information above when contacting support ***
…
</source>


To connect:
==== References ====
# Follow [[HPC/Network Access/PuTTY Configuration#Connecting | section Connecting]] to reach clogin.
* http://docs.quantumwise.com/guides/InstallationGuides/licensing.html
# Start VNL or atkpython normally on your machine.
* On Mac and Linux, the configuration file is stored on the client computer at <code>~/.quantumwise/licenses.licconf</code>.
# [[HPC/Software/Modules/atk/License troubleshooting on Windows | Troubleshoot ATK licensing]].
* [[HPC/Software/Modules/atk/License troubleshooting on Windows]] (older page, written for ATK-12).

Latest revision as of 15:39, December 11, 2021

Parallel jobs

  • See QuantumWise's Parallel Guide
  • We use Intel-MPI instead of MPICH2, with the Hydra process manager instead of MPD. See the sample.job file for details:
$ATK_HOME/sample.job


Remote access

To run ATK/VNL directly on your computer (as opposed to running it remotely and sending graphics over the network), follow these steps, all on your computer, to prepare for and launch the application:

Preparation

  • Log out from all Carbon nodes.
  • Log out from Mega.
  • Modify your configuration for SSH port forwarding to Mega. On Mac or Linux, make the changes to your file ~/.ssh/config. On Windows, apply the changes as shown in the help pages of your SSH application.
Add an entry for Remote Forwarding:
Local port: 6200,   Remote Port: 6200@cmgmt4
  • Log back in to Mega. This will activate the tunnel configuration that you added previously, to be used later by the ATK License Configuration wizard.

Configure

  • In the License Configuration helper, choose Configure license settings, Advanced setup. In the field for QUANTUM_LICENSE_PATH+= add:
localhost:6200@localhost

Launching ATK/VNL

  • Log in to Mega if you are not alreay logged in.
    You need to have exactly one Mega session active to access any kind of service on Carbon, be it for a single use or several ones concurrently.
  • Start VNL or atkpython normally for your platform.

Troubleshooting licensing

Check license configuration

To check the basic license configuration for ATK, without requiring X11 or VNC graphics, run the ATK Python script interpreter atkpython. It requires a license regardless of whether the script actually uses NanoLang constructs. 

atkpython -c 'print("Hello", 1+3/2)'
  • The expected output will look like:
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 2017.2 [Build 997d195]                                     |
|                                                                              |
+------------------------------------------------------------------------------+
('Hello', 1)

Timing:                          Total     Per Step        %
…
Total                   :       2.24 s
  • Failure to obtain a license, such as from an incorrect configuration or a server being down, looks like:
License Error: (Internal: 511 Feature: ATKPython)

[NETWORK] 6200@localhost - (Err: 15) Unable to connect to license server

License configuration (environment variables):
---------------------------------------------------------------------------
QUANTUM_LICENSE_PATH = …
---------------------------------------------------------------------------
*** Make sure to include the information above when contacting support ***
…

References

Retrieved from "https://wiki.anl.gov/wiki_cnm/index.php?title=HPC/Applications/atk&oldid=7074"