Cluster:Gaussian - Revision history

Craigje: Replaced content with "Go here"

2021-08-22T17:40:28Z

Replaced content with "Go here"

← Older revision		Revision as of 17:40, 22 August 2021
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	~~Web interface:~~ [[~~WebMO]]~~		[[Sysadmin:WebMO\|Go here]]

	~~Users for WebMo:~~

	* Create an LDAP user.
	* [http:~~//w0.cluster.earlham.edu/~alice/webmo-cgi-bin/login.cgi Log in] using that user's credentials~~
	* Give the group password. (This is a one-time requirement. Future logins will not ask for it.)
	* Use Gaussian.

	~~== Gaussian Installation ==~~
	~~The current path to Gaussian: /mounts/whedon/software/Gaussian~~

	~~The ISO images for Gaussian installer live in /cluster/gaussian. For whedon, I used the ISO image intended for CPUs that support SSE4.2 instructions.~~
	~~First, mount this image in some directory using mount -o command. After that, follow these instructions: https://gaussian.com/g16/g16bin_install.pdf.~~

	~~You can connect Gaussian to~~ WebMO through WebMO's web interface (log in as admin and go to Interface Manager). The current version of Gaussian that we are using is g16, but our WebMO installation is so old that it only supports Gaussian up to g09. In order to overcome this problem, we have two symlinks /mounts/whedon/software/Gaussian/g09 and /mounts/whedon/software/Gaussian/g16/g09, pointing to the directories /mounts/whedon/software/Gaussian/g16 and /mounts/whedon/software/Gaussian/g16/g16 respectively. After creating these symlinks, use the 'suggest' button in WebMO's Gaussian Manager that provides the paths for different Gaussian directories for you.

	~~To see a particular job's files, go to /mounts/whedon/webmo-users/$user/$job_number/ and examine the relevant files.~~

	~~== An old WebMO configuration example ==~~

	~~[[Cluster:_New_BobSCEd_Install_Log~~\|~~Notes below taken from~~ here~~.]]~~

	~~'''WebMO'''~~
	* yum installed httpd
	* Installed on bs0 with the following params:
	~~<pre>~~
	~~Path to perl: /usr/bin/perl~~
	~~Webserver name: bs0-new.cluster.earlham.edu~~
	~~HTML directory: /var/www/webmo~~
	~~HTML URL: /webmo~~
	~~CGI script directory: /var/www/cgi-bin~~
	~~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>

	~~== Older notes, c. 2005 ==~~
	* [[Cluster:Gaussian environment\|Gaussian environment]]
	* [[Cluster:Running Gaussian in parallel\|Running Gaussian in parallel]]
	* [[Cluster:Gaussian PBS script\|Sample Gaussian PBS script]]

	~~=== Gaussian environment ===~~
	~~I use this in my .bashrc:~~

	~~export GAUSS_EXEDIR=/cluster/bazaar/software/g03~~
	~~export GAUSS_LFLAGS='-nodelist "b0 b1" -opt "Tsnet.Node.lindarsharg: ssh " -mp 2'~~
	~~export GAUSS_SCRDIR=/tmp~~
	~~export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/cluster/bazaar/software/g03~~
	~~export g03root=/cluster/bazaar/software~~
	~~export PATH=$PATH:/cluster/bazaar/software/g03~~

	~~Seems to work, although you might want to tweak the node list.~~

	~~=== Running Gaussian in parallel ===~~
	Understand the distinction between <tt>nprocs</tt> and <tt>nprocl</tt>. <tt>nprocs</tt> is for a shared-memory (single-image) machine, whereas <tt>nprocl</tt> is for a distributed-memory (cluster) system. You want to use <tt>nprocl</tt> on all our computing systems. For example, if you want to run on eight processes (four nodes), add a line like this

	~~%nprocl=8~~

	~~to your input file. You should then specify <tt>qsub -l nodes=4:ppn=2 ''script''</tt> on the command line to submit your PBS script with a requirement of four dual-processor machines.~~

	~~Once you have the number of CPUs specified in the input file, make sure that your nodelist in GAUSS_LFLAGS is set properly. See [[Cluster:Gaussian_environment\|Gaussian environment]] for details.~~

	~~If you have a bunch of input files you want to modify, use the add_nproc.pl script in /cluster/generic/bin. First cd to the directory with your input files, and then do:~~

	~~perl /cluster/generic/bin/add_nproc.pl ''n''~~

	~~where ''n'' is the number proecssors you want to run on.~~

	~~After that, fire it up with <tt>$g03root/bsd/g03l</tt>.~~

	~~=== Sample Gaussian PBS script ===~~

	~~This is a sample PBS script for Gaussian:~~

	~~#!/bin/sh~~
	~~#PBS -N gaussian_test061.com_nodes=2:ppn=2~~
	~~#PBS -o /cluster/home/skylar/bazaar/gaussian_nodes2/test061.com.out~~
	~~#PBS -e /cluster/home/skylar/bazaar/gaussian_nodes2/test061.com.err~~
	~~#PBS -q batch~~
	~~#PBS -m abe~~
	~~#PBS -l nodes=2:ppn=2~~

	~~cd $PBS_O_WORKDIR~~
	~~/cluster/bazaar/software/g03/bsd/g03l < /cluster/bazaar/software/g03/tests/com_smp4/test061.com > /cluster/home/skylar/bazaar/gaussian_nodes2/test061.com.log~~

	~~exit $!~~

Craigje: /* Gaussian Installation */

2020-10-26T13:41:21Z

Gaussian Installation

← Older revision		Revision as of 13:41, 26 October 2020
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	You can connect Gaussian to WebMO through WebMO's web interface (log in as admin and go to Interface Manager). The current version of Gaussian that we are using is g16, but our WebMO installation is so old that it only supports Gaussian up to g09. In order to overcome this problem, we have two symlinks /mounts/whedon/software/Gaussian/g09 and /mounts/whedon/software/Gaussian/g16/g09, pointing to the directories /mounts/whedon/software/Gaussian/g16 and /mounts/whedon/software/Gaussian/g16/g16 respectively. After creating these symlinks, use the 'suggest' button in WebMO's Gaussian Manager that provides the paths for different Gaussian directories for you.		You can connect Gaussian to WebMO through WebMO's web interface (log in as admin and go to Interface Manager). The current version of Gaussian that we are using is g16, but our WebMO installation is so old that it only supports Gaussian up to g09. In order to overcome this problem, we have two symlinks /mounts/whedon/software/Gaussian/g09 and /mounts/whedon/software/Gaussian/g16/g09, pointing to the directories /mounts/whedon/software/Gaussian/g16 and /mounts/whedon/software/Gaussian/g16/g16 respectively. After creating these symlinks, use the 'suggest' button in WebMO's Gaussian Manager that provides the paths for different Gaussian directories for you.

			To see a particular job's files, go to /mounts/whedon/webmo-users/$user/$job_number/ and examine the relevant files.

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

Dkvart17 at 00:48, 17 September 2020

2020-09-17T00:48:36Z

← Older revision		Revision as of 00:48, 17 September 2020
Line 14:		Line 14:
	First, mount this image in some directory using mount -o command. After that, follow these instructions: https://gaussian.com/g16/g16bin_install.pdf.		First, mount this image in some directory using mount -o command. After that, follow these instructions: https://gaussian.com/g16/g16bin_install.pdf.

	You can connect Gaussian to WebMO through WebMO's web interface(log in as admin and go to Interface Manager). The current version of Gaussian that we are using is g16, but our WebMO installation is so old that it only supports up to g09. In order to overcome this problem, we have two symlinks /mounts/whedon/software/Gaussian/g09 and /mounts/whedon/software/Gaussian/g16/g09, pointing to the directories /mounts/whedon/software/Gaussian/g16 and /mounts/whedon/software/Gaussian/g16/g16 respectively. After creating these symlinks, use the 'suggest' button in WebMO's Gaussian Manager ~~to provide~~ the paths for different Gaussian directories.		You can connect Gaussian to WebMO through WebMO's web interface (log in as admin and go to Interface Manager). The current version of Gaussian that we are using is g16, but our WebMO installation is so old that it only supports Gaussian up to g09. In order to overcome this problem, we have two symlinks /mounts/whedon/software/Gaussian/g09 and /mounts/whedon/software/Gaussian/g16/g09, pointing to the directories /mounts/whedon/software/Gaussian/g16 and /mounts/whedon/software/Gaussian/g16/g16 respectively. After creating these symlinks, use the 'suggest' button in WebMO's Gaussian Manager that provides the paths for different Gaussian directories for you.


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

Dkvart17 at 00:47, 17 September 2020

2020-09-17T00:47:08Z

← Older revision		Revision as of 00:47, 17 September 2020
Line 8:		Line 8:
	* Use Gaussian.		* Use Gaussian.

			== Gaussian Installation ==
			The current path to Gaussian: /mounts/whedon/software/Gaussian

			The ISO images for Gaussian installer live in /cluster/gaussian. For whedon, I used the ISO image intended for CPUs that support SSE4.2 instructions.
			First, mount this image in some directory using mount -o command. After that, follow these instructions: https://gaussian.com/g16/g16bin_install.pdf.

			You can connect Gaussian to WebMO through WebMO's web interface(log in as admin and go to Interface Manager). The current version of Gaussian that we are using is g16, but our WebMO installation is so old that it only supports up to g09. In order to overcome this problem, we have two symlinks /mounts/whedon/software/Gaussian/g09 and /mounts/whedon/software/Gaussian/g16/g09, pointing to the directories /mounts/whedon/software/Gaussian/g16 and /mounts/whedon/software/Gaussian/g16/g16 respectively. After creating these symlinks, use the 'suggest' button in WebMO's Gaussian Manager to provide the paths for different Gaussian directories.

Craigje at 17:46, 8 June 2020

2020-06-08T17:46:27Z

@@ Line 7: / Line 7: @@
 * Give the group password. (This is a one-time requirement. Future logins will not ask for it.)
 * Use Gaussian.
 == Older notes, c. 2005 ==

Craigje at 19:31, 26 September 2019

2019-09-26T19:31:55Z

← Older revision		Revision as of 19:31, 26 September 2019
Line 1:		Line 1:
	Web interface: [[WebMO]]		Web interface: [[WebMO]]

	Users for WebMo		Users for WebMo:

			* Create an LDAP user.
			* [http://w0.cluster.earlham.edu/~alice/webmo-cgi-bin/login.cgi Log in] using that user's credentials
			* Give the group password. (This is a one-time requirement. Future logins will not ask for it.)
			* Use Gaussian.

	== Older notes, c. 2005 ==		== Older notes, c. 2005 ==

Craigje at 15:08, 26 September 2019

2019-09-26T15:08:14Z

@@ Line 1: / Line 1: @@
 * [[Cluster:Gaussian environment|Gaussian environment]]
 * [[Cluster:Running Gaussian in parallel|Running Gaussian in parallel]]
 * [[Cluster:Gaussian PBS script|Sample Gaussian PBS script]]

Skylar at 15:01, 2 July 2005

2005-07-02T15:01:22Z

← Older revision		Revision as of 15:01, 2 July 2005
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	* [[Cluster:Gaussian environment\|Gaussian environment]]		* [[Cluster:Gaussian environment\|Gaussian environment]]
	* [[Cluster:Running Gaussian in parallel\|Running Gaussian in parallel]]		* [[Cluster:Running Gaussian in parallel\|Running Gaussian in parallel]]
			* [[Cluster:Gaussian PBS script\|Sample Gaussian PBS script]]

Skylar at 15:57, 1 July 2005

2005-07-01T15:57:53Z

← Older revision		Revision as of 15:57, 1 July 2005
Line 1:		Line 1:
			* [[Cluster:Gaussian environment\|Gaussian environment]]
	* [[Cluster:Running Gaussian in parallel\|Running Gaussian in parallel]]		* [[Cluster:Running Gaussian in parallel\|Running Gaussian in parallel]]

Skylar at 15:57, 1 July 2005

2005-07-01T15:57:13Z

New page

* [[Cluster:Running Gaussian in parallel|Running Gaussian in parallel]]