WebMO - Revision history

Pelibby16: add another link

2025-02-04T16:46:24Z

add another link

← Older revision		Revision as of 16:46, 4 February 2025
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	WebMO is a web interface to the Gaussian chemistry tool maintained in the cluster world.		WebMO is a web interface to the Gaussian chemistry tool maintained in the cluster world.

			Login to our instance here: [https://webmo.cluster.earlham.edu/ webmo.cluster.earlham.edu]

	== Overview ==		== Overview ==

Pelibby16: fix link

2025-02-04T16:45:26Z

fix link

← Older revision		Revision as of 16:45, 4 February 2025
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	== Overview ==		== Overview ==

	WebMO is a scientific web application providing a user interface for domain scientists to perform chemistry simulations. It provides a mechanism for domain scientists to perform chemistry simulations on high-performance computing systems through a web browser. Currently it and Gaussian live on the ~~Wachowski~~ cluster. The official project website is [https://www.webmo.net/ here] and you can access our instance (if you have a WebMO-specific user account) [~~http~~://w0.cluster.earlham.edu/~~~alice/webmo-cgi-bin/login.cgi~~ here].		WebMO is a scientific web application providing a user interface for domain scientists to perform chemistry simulations. It provides a mechanism for domain scientists to perform chemistry simulations on high-performance computing systems through a web browser. Currently it and Gaussian live on the Whedon cluster. The official project website is [https://www.webmo.net/ here] and you can access our instance (if you have a WebMO-specific user account) [https://webmo.cluster.earlham.edu/ here].

	Strictly "WebMO" is the web interface and associated configurations, but here we will use it as shorthand for "the computational chemistry stack". This accords with local usage.		Strictly "WebMO" is the web interface and associated configurations, but here we will use it as shorthand for "the computational chemistry stack". This accords with local usage.

Craigje at 17:35, 22 August 2021

2021-08-22T17:35:43Z

← Older revision		Revision as of 17:35, 22 August 2021
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	WebMO is a web interface to the Gaussian chemistry tool maintained in the cluster world. Currently it and Gaussian live on ~~Whedon~~. The official project website is [https://www.webmo.net/ here] and you can access our instance (if you have a WebMO-specific user account) [http://w0.cluster.earlham.edu/~alice/webmo-cgi-bin/login.cgi here].		WebMO is a web interface to the Gaussian chemistry tool maintained in the cluster world.

			== Overview ==

			WebMO is a scientific web application providing a user interface for domain scientists to perform chemistry simulations. It provides a mechanism for domain scientists to perform chemistry simulations on high-performance computing systems through a web browser. Currently it and Gaussian live on the Wachowski cluster. The official project website is [https://www.webmo.net/ here] and you can access our instance (if you have a WebMO-specific user account) [http://w0.cluster.earlham.edu/~alice/webmo-cgi-bin/login.cgi here].

			Strictly "WebMO" is the web interface and associated configurations, but here we will use it as shorthand for "the computational chemistry stack". This accords with local usage.

	This is a guide for students and others who want to use WebMO.		This is a guide for students and others who want to use WebMO.

	== ~~First time logging in~~ ==		=== Sysadmins ===



	~~Use the `wu*` password (ask a chemistry professor) to join the webmo group~~.		Sysadmins should view [[Sysadmin:WebMO\|this page]].

	== ~~Disclaimer~~ ==		== Running a job ==

	~~Sometimes we have had issues with people submitting WebMO/Gaussian jobs from off-campus - specifically~~, ~~that~~ the ~~web interface would display an error after submitting some jobs (pattern not clear from logs etc.). If this occurs~~, ~~remain calm because your job is still being run.~~		Process:
			# Log in using your credentials
			# Submit job
			# Allow to run
			# Check job status as desired
			# On completion:
			## If the job was successful, view output
			## If the job failed, try again or change parameters

	~~To retrieve the job afterward, you can look at your job history in WebMO.~~		== Issues ==

	== ~~Fixing WebMO off-campus jobs~~ ==		=== First time logging in ===

	~~[[Sysadmin:~~WebMO ~~from off-campus\|See this page~~.]]		Some user accounts have been used to log in to WebMO to use Gaussian but others have not.

	~~== Admin note on resolving down nodes ==~~		Use the `wu*` password (ask a chemistry professor) to join the webmo group.

	~~If Slurm,~~ WebMO~~, etc. are running but no~~ jobs are running (or there's a queue that's longer than it should be), run <code>sinfo</code> to see the status. Likely the nodes are marked down and you need to make the daemons go to work. To bring them back, run this or equivalent for the right machine:		=== Fixing WebMO off-campus jobs ===

	~~<pre>~~		Sometimes we have had issues with people submitting WebMO/Gaussian jobs from off-campus - specifically, that the web interface would display an error after submitting some jobs (pattern not clear from logs etc.). If this occurs, remain calm because your job is still being run.
	~~scontrol update NodeName=lo[0~~-~~4] State=RESUME~~
	~~</pre>~~

	~~The important part is "<code>State=RESUME</code>"~~.		To retrieve the job afterward, you can look at your job history in WebMO.

	~~You can also use the command bellow to display information about a particular node~~.		[[Sysadmin:WebMO from off-campus\|Admins, see this page.]]
	~~<pre>~~
	~~scontrol show node <node-name>~~
	~~</pre>~~

Craigje: /* If the services are running but no jobs are running */

2021-03-30T16:34:51Z

If the services are running but no jobs are running

← Older revision		Revision as of 16:34, 30 March 2021
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	== Admin note on resolving down nodes ==		== Admin note on resolving down nodes ==

	~~= If the services are running but no jobs are running =~~

	If Slurm, WebMO, etc. are running but no jobs are running (or there's a queue that's longer than it should be), run <code>sinfo</code> to see the status. Likely the nodes are marked down and you need to make the daemons go to work. To bring them back, run this or equivalent for the right machine:		If Slurm, WebMO, etc. are running but no jobs are running (or there's a queue that's longer than it should be), run <code>sinfo</code> to see the status. Likely the nodes are marked down and you need to make the daemons go to work. To bring them back, run this or equivalent for the right machine:

Craigje at 16:34, 30 March 2021

2021-03-30T16:34:37Z

← Older revision		Revision as of 16:34, 30 March 2021
Line 18:		Line 18:

	[[Sysadmin:WebMO from off-campus\|See this page.]]		[[Sysadmin:WebMO from off-campus\|See this page.]]

			== Admin note on resolving down nodes ==

			= If the services are running but no jobs are running =

			If Slurm, WebMO, etc. are running but no jobs are running (or there's a queue that's longer than it should be), run <code>sinfo</code> to see the status. Likely the nodes are marked down and you need to make the daemons go to work. To bring them back, run this or equivalent for the right machine:

			<pre>
			scontrol update NodeName=lo[0-4] State=RESUME
			</pre>

			The important part is "<code>State=RESUME</code>".

			You can also use the command bellow to display information about a particular node.
			<pre>
			scontrol show node <node-name>
			</pre>

Craigje at 15:17, 16 December 2020

2020-12-16T15:17:56Z

← Older revision		Revision as of 15:17, 16 December 2020
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	To retrieve the job afterward, you can look at your job history in WebMO.		To retrieve the job afterward, you can look at your job history in WebMO.

			== Fixing WebMO off-campus jobs ==

			[[Sysadmin:WebMO from off-campus\|See this page.]]

Craigje at 17:46, 8 June 2020

2020-06-08T17:46:29Z

← Older revision		Revision as of 17:46, 8 June 2020
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	WebMO is a web interface to the Gaussian chemistry tool maintained in the cluster world. Currently it and Gaussian live on Whedon. The official project website is [https://www.webmo.net/ here] and you can access our instance (if you have a WebMO-specific user account) [http://w0.cluster.earlham.edu/~alice/webmo-cgi-bin/login.cgi here].		WebMO is a web interface to the Gaussian chemistry tool maintained in the cluster world. Currently it and Gaussian live on Whedon. The official project website is [https://www.webmo.net/ here] and you can access our instance (if you have a WebMO-specific user account) [http://w0.cluster.earlham.edu/~alice/webmo-cgi-bin/login.cgi here].

	~~== An old configuration example ==~~		This is a guide for students and others who want to use WebMO.

	~~[[Cluster:_New_BobSCEd_Install_Log\|Notes below taken from here.]]~~		== First time logging in ==

	~~'''~~WebMO~~'''~~		Some user accounts have been used to log in to WebMO on the first login, so that the software knows what group to associate each user with. After that, user accounts work as expected.)
	* yum installed httpd
	* Installed on ~~bs0 with~~ the ~~following params:~~		Use the `wu*` password (ask a chemistry professor) to join the webmo group.
	~~<pre>~~
	~~Path~~ to ~~perl: /usr/bin/perl~~		== Disclaimer ==
	~~Webserver name: bs0-new~~.~~cluster~~.~~earlham.edu~~
	~~HTML directory: /var/www/webmo~~		Sometimes we have had issues with people submitting WebMO/Gaussian jobs from off-campus - specifically, that the web interface would display an error after submitting some jobs (pattern not clear from logs etc.). If this occurs, remain calm because your job is still being run.
	~~HTML URL: /~~webmo
	~~CGI script directory: /var/www/cgi-bin~~		To retrieve the job afterward, you can look at your job history in WebMO.
	~~CGI script URL: /cgi-bin~~
	~~User files directory: /mounts/bobsced/WebMO</pre>~~
	* Get this error when authing with ~~LDAP: <code>Can't locate Authen~~/~~Simple/LDAP.pm</code>~~
	* yum installed perl-~~LDAP.noarch, didn't work, so used CPAN to install Authen::Simple::LDAP~~
	* edited /var/www/cgi-~~bin/interfaces/authen.conf for our LDAP settings~~
	* Before externally authenticated users can use it, ~~you have to go in as administrator and check~~ the ~~box to allow them in the Webmo group~~ (~~or whatever other group)~~
	* Gamess:
	** yum install compat-gcc-34-g77.x86_64 and gfortran
	** Followed directions from ~~[http://www~~.~~webmo~~.~~net/support/gamess_linux~~.~~html Webmo site]~~
	* Added the ~~following line to httpd.conf:~~
	~~:<code>SuexecUserGroup bob users </code>~~
	* Gaussian 09 not supported, ~~though it's installed~~ in ~~/mounts/bobsced/usr/local/g09~~
	* Installed g03, except get errors:
	~~<pre>Erroneous write during file extend. write 160 instead of 4096~~
	~~Probably out of disk space~~.
	~~Write error in NtrExt1: No such file or directory~~
	~~</pre>~~
	or
	~~<pre>Write error in NtrExt1: Bad address</pre>~~
	** To fix this, do <code>echo 0 > /proc/sys/kernel/randomize_va_space</code>
	** <font color="green">This needs to be set to happen all the time on boot</font>

Craigje at 14:56, 26 September 2019

2019-09-26T14:56:14Z

← Older revision		Revision as of 14:56, 26 September 2019
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	WebMO is a ~~computational~~ chemistry tool maintained in the cluster world. Currently it ~~lives~~ on Whedon. The official project website is [https://www.webmo.net/ here] and you can access our instance (if you have a WebMO-specific user account) [http://w0.cluster.earlham.edu/~alice/webmo-cgi-bin/login.cgi here].		WebMO is a web interface to the Gaussian chemistry tool maintained in the cluster world. Currently it and Gaussian live on Whedon. The official project website is [https://www.webmo.net/ here] and you can access our instance (if you have a WebMO-specific user account) [http://w0.cluster.earlham.edu/~alice/webmo-cgi-bin/login.cgi here].

	== An old configuration example ==		== An old configuration example ==

Craigje at 12:40, 21 August 2019

2019-08-21T12:40:49Z

← Older revision		Revision as of 12:40, 21 August 2019
Line 1:		Line 1:
	WebMO is a computational chemistry tool maintained in the cluster world.		WebMO is a computational chemistry tool maintained in the cluster world. Currently it lives on Whedon. The official project website is [https://www.webmo.net/ here] and you can access our instance (if you have a WebMO-specific user account) [http://w0.cluster.earlham.edu/~alice/webmo-cgi-bin/login.cgi here].

	== An old configuration example ==		== An old configuration example ==

Craigje at 12:33, 21 August 2019

2019-08-21T12:33:40Z

@@ Line 1: / Line 1: @@
 WebMO is a computational chemistry tool maintained in the cluster world.
-Some possibly useful pages:
+== An old configuration example ==
-* [[Cluster:_New_BobSCEd_Install_Log|an early WebMO configuration example]]