BeSTGRID - Recent changes [en]

Software List On BeSTGRID Resources

2012-05-16T03:00:03Z

←Older revision		Revision as of 03:00, 16 May 2012
Line 52:		Line 52:
	\|-		\|-
	\| '''R''' \|\|2.13.1<br>2.9.0 \|\| 2.11.0<br>2.13.1<br>2.14.0<br>2.5.0 \|\| 2.13.0		\| '''R''' \|\|2.13.1<br>2.9.0 \|\| 2.11.0<br>2.13.1<br>2.14.0<br>2.5.0 \|\| 2.13.0
		+	\|-
		+	\| '''RAxML''' \|\| \|\| 7.2.8 \|\|
	\|-		\|-
	\| '''RMPISNOW''' \|\|2.9.0 \|\| 2.11.0<br>2.13.1 \|\| 2.13.0		\| '''RMPISNOW''' \|\|2.9.0 \|\| 2.11.0<br>2.13.1 \|\| 2.13.0

Installing an iRODS slave server

2012-05-11T05:00:08Z

Installing iRODS

←Older revision		Revision as of 05:00, 11 May 2012
Line 509:		Line 509:
	** [http://projects.arcs.org.au/svn/systems/trunk/dataFabricScripts/iRODS/BugFix/patches-2.4/aclpolicy_username.patch aclpolicy_username.patch] (for <tt>server/api/src/rsGenQuery.c</tt>) allowing <tt>$clientUserName</tt> to be used in acAclPolicy (needed for QuickShare). Thanks to Sean Flemming for this patch.		** [http://projects.arcs.org.au/svn/systems/trunk/dataFabricScripts/iRODS/BugFix/patches-2.4/aclpolicy_username.patch aclpolicy_username.patch] (for <tt>server/api/src/rsGenQuery.c</tt>) allowing <tt>$clientUserName</tt> to be used in acAclPolicy (needed for QuickShare). Thanks to Sean Flemming for this patch.
	** [[Media:Irods-2.4.1-initserver-queagentproc.patch.txt\|irods-2.4.1-initserver-queagentproc.patch]], fixing a server crash issue		** [[Media:Irods-2.4.1-initserver-queagentproc.patch.txt\|irods-2.4.1-initserver-queagentproc.patch]], fixing a server crash issue
-	** [[Media:Irods-2.4.1-fileOpr-race.patch.txt\|irods-2.4.1-fileOpr-race.patch], Rob Burrows' fix to a race condition	+	** [[Media:Irods-2.4.1-fileOpr-race.patch.txt\|irods-2.4.1-fileOpr-race.patch]], Rob Burrows' fix to a race condition

	* For iRODS 2.5:		* For iRODS 2.5:

Software List On BeSTGRID Resources

2012-05-11T05:00:03Z

←Older revision		Revision as of 05:00, 11 May 2012
Line 41:		Line 41:
	\| '''MrBayes''' \|\|3.1.2<br>3.2.1 \|\| 3.1.2<br>3.2.1 \|\| 3.1.2		\| '''MrBayes''' \|\|3.1.2<br>3.2.1 \|\| 3.1.2<br>3.2.1 \|\| 3.1.2
	\|-		\|-
-	\| '''NAMD''' \|\| \|\| 2.6 \|\|	+	\| '''NAMD''' \|\| \|\| 2.9 \|\|
	\|-		\|-
	\| '''octave''' \|\|3.0.3 \|\| \|\|		\| '''octave''' \|\|3.0.3 \|\| \|\|

Installing an iRODS slave server

2012-05-11T04:59:53Z

Installing iRODS

←Older revision		Revision as of 04:59, 11 May 2012
Line 508:		Line 508:
	** [https://www.irods.org/index.php/iRODS_2.4.1_Patch_1 iRODS 2.4.1 Patch 1], fixing a problem in FUSE		** [https://www.irods.org/index.php/iRODS_2.4.1_Patch_1 iRODS 2.4.1 Patch 1], fixing a problem in FUSE
	** [http://projects.arcs.org.au/svn/systems/trunk/dataFabricScripts/iRODS/BugFix/patches-2.4/aclpolicy_username.patch aclpolicy_username.patch] (for <tt>server/api/src/rsGenQuery.c</tt>) allowing <tt>$clientUserName</tt> to be used in acAclPolicy (needed for QuickShare). Thanks to Sean Flemming for this patch.		** [http://projects.arcs.org.au/svn/systems/trunk/dataFabricScripts/iRODS/BugFix/patches-2.4/aclpolicy_username.patch aclpolicy_username.patch] (for <tt>server/api/src/rsGenQuery.c</tt>) allowing <tt>$clientUserName</tt> to be used in acAclPolicy (needed for QuickShare). Thanks to Sean Flemming for this patch.
-	** irods-2.4.1-initserver-queagentproc.patch, fixing a server crash issue	+	** [[Media:Irods-2.4.1-initserver-queagentproc.patch.txt\|irods-2.4.1-initserver-queagentproc.patch]], fixing a server crash issue
-	** irods-2.4.1-fileOpr-race.patch, Rob Burrows' fix to a race condition	+	** [[Media:Irods-2.4.1-fileOpr-race.patch.txt\|irods-2.4.1-fileOpr-race.patch], Rob Burrows' fix to a race condition

	* For iRODS 2.5:		* For iRODS 2.5:

Special:Log/upload

2012-05-11T04:57:51Z

uploaded "Image:Irods-2.4.1-fileOpr-race.patch.txt"

Special:Log/upload

2012-05-11T04:57:36Z

uploaded "Image:Irods-2.4.1-initserver-queagentproc.patch.txt"

Installing an iRODS slave server

2012-05-11T04:46:53Z

Installing iRODS

←Older revision		Revision as of 04:46, 11 May 2012
Line 504:		Line 504:
	** [https://www.irods.org/index.php/irods_2.4_patch_1 irods_2.4_patch_1] [http://groups.google.com/group/irod-chat/browse_thread/thread/6ced0321d5ff1c27 fixing a seg fault problem in the irodsServer]		** [https://www.irods.org/index.php/irods_2.4_patch_1 irods_2.4_patch_1] [http://groups.google.com/group/irod-chat/browse_thread/thread/6ced0321d5ff1c27 fixing a seg fault problem in the irodsServer]
	** [http://projects.arcs.org.au/svn/systems/trunk/dataFabricScripts/iRODS/BugFix/patches-2.4/aclpolicy_username.patch aclpolicy_username.patch] (for <tt>server/api/src/rsGenQuery.c</tt>) allowing <tt>$clientUserName</tt> to be used in acAclPolicy (needed for QuickShare). Thanks to Sean Flemming for this patch.		** [http://projects.arcs.org.au/svn/systems/trunk/dataFabricScripts/iRODS/BugFix/patches-2.4/aclpolicy_username.patch aclpolicy_username.patch] (for <tt>server/api/src/rsGenQuery.c</tt>) allowing <tt>$clientUserName</tt> to be used in acAclPolicy (needed for QuickShare). Thanks to Sean Flemming for this patch.
		+
		+	* For iRODS 2.4.1, apply the following patches:
		+	** [https://www.irods.org/index.php/iRODS_2.4.1_Patch_1 iRODS 2.4.1 Patch 1], fixing a problem in FUSE
		+	** [http://projects.arcs.org.au/svn/systems/trunk/dataFabricScripts/iRODS/BugFix/patches-2.4/aclpolicy_username.patch aclpolicy_username.patch] (for <tt>server/api/src/rsGenQuery.c</tt>) allowing <tt>$clientUserName</tt> to be used in acAclPolicy (needed for QuickShare). Thanks to Sean Flemming for this patch.
		+	** irods-2.4.1-initserver-queagentproc.patch, fixing a server crash issue
		+	** irods-2.4.1-fileOpr-race.patch, Rob Burrows' fix to a race condition

	* For iRODS 2.5:		* For iRODS 2.5:

Installing an iRODS slave server

2012-05-10T22:16:04Z

Installing iRODS FUSE Client

←Older revision		Revision as of 22:16, 10 May 2012
Line 455:		Line 455:
	</pre>		</pre>

-	*Even easier for users, is this script which finds and unmounts their iRODS Fuse mounts.	+	*Even easier for users, is this script which finds and unmounts their iRODS Fuse mounts. (Nb. /bin/mount on different systems have slightly different formats, so this may need modifying)
	<pre>		<pre>
	#!/usr/bin/ruby		#!/usr/bin/ruby

Computational Grid Resources

2012-05-08T23:48:36Z

←Older revision		Revision as of 23:48, 8 May 2012
Line 11:		Line 11:
	\| BeSTGRID Prototype Cluster \|\| University of Canterbury \|\| x86 Xeon \|\| Linux \|\| 4 \|\| 3.0GHz \|\| Prototype cluster, serving the community since June 2007.		\| BeSTGRID Prototype Cluster \|\| University of Canterbury \|\| x86 Xeon \|\| Linux \|\| 4 \|\| 3.0GHz \|\| Prototype cluster, serving the community since June 2007.
	\|-		\|-
-	\| [http://www.bluefern.canterbury.ac.nz/ BlueFern ~~p575~~] \|\| University of Canterbury \|\| ~~Power5+~~ \|\| AIX/Linux \|\| ~~128~~ \|\| 1.~~9GHz~~ \|\| 8 nodes, 16 CPU cores each.	+	\| [http://www.bluefern.canterbury.ac.nz/ BlueFern p755] \|\| University of Canterbury \|\| Power7 \|\| AIX/Linux \|\| 416 \|\| 3.3GHz \|\| 13 nodes, 32 CPU cores each.
	\|-		\|-
-	\| [http://www.bluefern.canterbury.ac.nz/ BlueFern BlueGene] \|\| University of Canterbury \|\| PowerPC \|\| Linux \|\| ~~4096~~ \|\| ~~770MHz~~ \|\| Available only together with a [http://www.bluefern.canterbury.ac.nz/access/ local account].	+	\| [http://www.bluefern.canterbury.ac.nz/ BlueFern BlueGene] \|\| University of Canterbury \|\| PowerPC \|\| Linux \|\| up to 8192 \|\| 850MHz \|\| Available only together with a [http://www.bluefern.canterbury.ac.nz/access/ local account].
	\|-		\|-
	\| Maggie \|\| University of Otago \|\| x86 Pentium 4 \|\| Linux \|\| 10 \|\| 3.0GHz \|\| No MPI available		\| Maggie \|\| University of Otago \|\| x86 Pentium 4 \|\| Linux \|\| 10 \|\| 3.0GHz \|\| No MPI available

Installing an iRODS slave server

2012-05-07T22:16:49Z

Installing Globus from RPMs for building iRODS with Globus

←Older revision		Revision as of 22:16, 7 May 2012
(2 intermediate revisions not shown.)
Line 120:		Line 120:
	* Can now yum install (without VDT). Note though, that RH6 has different hash, and the keys need renaming to match. Could probably cull a lot of the globus installs to just get the libraries.		* Can now yum install (without VDT). Note though, that RH6 has different hash, and the keys need renaming to match. Could probably cull a lot of the globus installs to just get the libraries.
	<pre>		<pre>
-	~~mkdir~~ /~~opt~~/globus	+	#installed the repository RPM from http://www.globus.org/toolkit/downloads/latest-stable/
		+	rpm -i Globus-5.2.stable-config.redhat-5Server-1.noarch.rpm
		+	yum groupinstall globus-resource-management-sdk

	#For our 64bit systems with /usr/lib64		#For our 64bit systems with /usr/lib64
		+	#Setting config/irods.config $GLOBUS_LOCATION = '/opt/globus'
		+	mkdir /opt/globus
	ln -s /usr/lib64 /opt/globus/lib		ln -s /usr/lib64 /opt/globus/lib

-	#~~for the irods compilation~~, ~~so you can specify globus GLOBUS_LOCATION as~~ /~~opt~~/~~globus~~	+	#For 32bit system, or one just using /usr/lib
-	~~ln -s~~ /usr~~/include /opt/globus/include~~	+	#Setting config/irods.config $GLOBUS_LOCATION = '/usr'

-	yum --assumeyes install dcap-tunnel-gsi.i686
-	yum --assumeyes install globus-gsi-callback.i686
-	yum --assumeyes install globus-gsi-callback-devel.i686
-	yum --assumeyes install globus-gsi-cert-utils.i686
-	yum --assumeyes install globus-gsi-cert-utils-devel.i686
-	yum --assumeyes install globus-gsi-cert-utils-progs.i686
-	yum --assumeyes install globus-gsi-credential.i686
-	yum --assumeyes install globus-gsi-credential-devel.i686
-	yum --assumeyes install globus-gsi-openssl-error.i686
-	yum --assumeyes install globus-gsi-openssl-error-devel.i686
-	yum --assumeyes install globus-gsi-proxy-core.i686
-	yum --assumeyes install globus-gsi-proxy-core-devel.i686
-	yum --assumeyes install globus-gsi-proxy-ssl.i686
-	yum --assumeyes install globus-gsi-proxy-ssl-devel.i686
-	yum --assumeyes install globus-gsi-sysconfig.i686
-	yum --assumeyes install globus-gsi-sysconfig-devel.i686
-	yum --assumeyes install globus-gssapi-gsi.i686
-	yum --assumeyes install globus-gssapi-gsi-devel.i686
-	yum --assumeyes install globus-xio-gsi-driver.i686
-	yum --assumeyes install globus-xio-gsi-driver-devel.i686
-	yum --assumeyes install gsi-openssh.i686
-	#Commented out gsi-openssh-clients, as on one system, it killed our sshd and we don't need it for irods anyway.
-	#yum --assumeyes install gsi-openssh-clients.i686
-	#yum --assumeyes install gsi-openssh-server.i686
-	yum --assumeyes install gsim85.i686

-	#These ln commands are a HACK so that irods config can have $GSI_INSTALL_TYPE = 'gcc';	+	#These ln commands are a HACK so that irods config/irods.config can have $GSI_INSTALL_TYPE = 'gcc';
	#not setting GSI_INSTALL_TYPE results in trying to link libraries with an '_' added!		#not setting GSI_INSTALL_TYPE results in trying to link libraries with an '_' added!
	#There is probably a better way to do this.		#There is probably a better way to do this.
-	ln -s /usr/~~lib~~/~~libglobus_gsi_callback~~.so /usr/~~lib~~/~~libglobus_gsi_callback_gcc~~.so	+	ln -s /usr/lib64/libglobus_gss_assist.so /usr/lib64/libglobus_gss_assist_gcc.so
-	ln -s /usr/~~lib~~/~~libglobus_gsi_cert_utils~~.so /usr/~~lib~~/~~libglobus_gsi_cert_utils_gcc~~.so	+	ln -s /usr/lib64/libglobus_gssapi_gsi.so /usr/lib64/libglobus_gssapi_gsi_gcc.so
-	ln -s /usr/~~lib~~/libglobus_gsi_credential.so /usr/~~lib~~/libglobus_gsi_credential_gcc.so	+	ln -s /usr/lib64/libglobus_gsi_credential.so /usr/lib64/libglobus_gsi_credential_gcc.so
-	ln -s /usr/~~lib~~/libglobus_gsi_proxy_core.so /usr/~~lib~~/libglobus_gsi_proxy_core_gcc.so	+	ln -s /usr/lib64/libglobus_gsi_proxy_core.so /usr/lib64/libglobus_gsi_proxy_core_gcc.so
-	ln -s /usr/~~lib~~/~~libglobus_gsi_sysconfig~~.so /usr/~~lib~~/~~libglobus_gsi_sysconfig_gcc~~.so	+	ln -s /usr/lib64/libglobus_gsi_callback.so /usr/lib64/libglobus_gsi_callback_gcc.so
-	ln -s /usr/~~lib~~/~~libglobus_gssapi_gsi~~.so /usr/~~lib~~/~~libglobus_gssapi_gsi_gcc~~.so	+	ln -s /usr/lib64/libglobus_oldgaa.so /usr/lib64/libglobus_oldgaa_gcc.so
-	ln -s /usr/~~lib~~/~~libglobus_xio_gsi_driver.la /usr/lib/libglobus_xio_gsi_driver_gcc.la~~	+	ln -s /usr/lib64/libglobus_gsi_sysconfig.so /usr/lib64/libglobus_gsi_sysconfig_gcc.so
-	~~ln -s /usr/lib/libglobus_xio_gsi_driver~~.so /usr/~~lib~~/~~libglobus_xio_gsi_driver_gcc~~.so	+	ln -s /usr/lib64/libglobus_gsi_cert_utils.so /usr/lib64/libglobus_gsi_cert_utils_gcc.so
-	ln -s /usr/~~lib~~/~~libltdl~~.so /usr/~~lib~~/~~libltdl_gcc~~.so	+	ln -s /usr/lib64/libglobus_openssl_error.so /usr/lib64/libglobus_openssl_error_gcc.so
-	ln -s /usr/~~lib~~/~~libglobus_gss_assist~~.so /usr/~~lib~~/~~libglobus_gss_assist_gcc~~.so	+	ln -s /usr/lib64/libglobus_openssl.so /usr/lib64/libglobus_openssl_gcc.so
-	ln -s /usr/~~lib~~/~~libglobus_oldgaa~~.so~~.0.4.1~~ /usr/~~lib~~/~~libglobus_oldgaa_gcc~~.so	+	ln -s /usr/lib64/libglobus_proxy_ssl.so /usr/lib64/libglobus_proxy_ssl_gcc.so
-	ln -s /usr/~~lib~~/~~libglobus_openssl_error~~.so~~.0.2.1~~ /usr/~~lib~~/~~libglobus_openssl_error_gcc~~.so	+	ln -s /usr/lib64/libglobus_common.so /usr/lib64/libglobus_common_gcc.so
-	ln -s /usr/~~lib~~/~~libglobus_openssl~~.so /usr/~~lib~~/~~libglobus_openssl_gcc~~.so	+	ln -s /usr/lib64/libglobus_callout.so /usr/lib64/libglobus_callout_gcc.so
-	ln -s /usr/~~lib~~/~~libglobus_proxy_ssl~~.so /usr/~~lib~~/~~libglobus_proxy_ssl_gcc~~.so	+	ln -s /usr/lib64/libltdl.so /usr/lib64/libltdl_gcc.so
-	ln -s /usr/~~lib~~/~~libglobus_common~~.so /usr/~~lib~~/~~libglobus_common_gcc~~.so	+
-	~~ln -s /usr/lib/libglobus_callout.so /usr/lib/libglobus_callout_gcc.so~~	+	#Also needed
-	ln -s /usr/~~lib~~/libltdl.so.~~7.2.1~~ /usr/~~lib~~/libltdl.so	+	ln -s /usr/lib64/libltdl.so.3 /usr/lib64/libltdl.so
	</pre>		</pre>

Software List On BeSTGRID Resources

2012-05-06T23:00:04Z

←Older revision		Revision as of 23:00, 6 May 2012
Line 39:		Line 39:
	\| '''mpiBLAST''' \|\|1.5.0 \|\| 1.6.0 \|\|		\| '''mpiBLAST''' \|\|1.5.0 \|\| 1.6.0 \|\|
	\|-		\|-
-	\| '''MrBayes''' \|\|3.1.2 \|\| 3.1.2<br>3.2.1 \|\| 3.1.2	+	\| '''MrBayes''' \|\|3.1.2<br>3.2.1 \|\| 3.1.2<br>3.2.1 \|\| 3.1.2
	\|-		\|-
	\| '''NAMD''' \|\| \|\| 2.6 \|\|		\| '''NAMD''' \|\| \|\| 2.6 \|\|

Using the DataFabric

2012-05-03T21:54:32Z

Creating a MyProxy login

←Older revision		Revision as of 21:54, 3 May 2012
(7 intermediate revisions not shown.)
Line 93:		Line 93:
	=== Windows - alternative solutions ===		=== Windows - alternative solutions ===

-	On Windows Vista ~~and Windows 7~~, it is necessary to use external tools for mounting a webDAV URL - and Windows XP users may also get additional performance.	+	On Windows Vista, it is necessary to use external tools for mounting a webDAV URL - and Windows XP users may also get additional performance.

	The tools available are [http://www.netdrive.net/ NetDrive], [http://www.webdrive.com/products/webdrive/ WebDrive], and [http://www.bitkinex.com/ BitKinex]. Read a brief comparison and review of these clients [[Review of Windows webDAV clients\|here]], note that only BitKinex has shown to reliably transfer files greater than 2GB in size.		The tools available are [http://www.netdrive.net/ NetDrive], [http://www.webdrive.com/products/webdrive/ WebDrive], and [http://www.bitkinex.com/ BitKinex]. Read a brief comparison and review of these clients [[Review of Windows webDAV clients\|here]], note that only BitKinex has shown to reliably transfer files greater than 2GB in size.
Line 101:		Line 101:
	'''NOTE:''' Some of the alternative clients do not work with files or directories with special characters. Use only letters, numbers, spaces, dashes, underscores, and periods in file and directory names.		'''NOTE:''' Some of the alternative clients do not work with files or directories with special characters. Use only letters, numbers, spaces, dashes, underscores, and periods in file and directory names.

-	'''NOTE:''' ~~There~~ is Microsoft patch available to make WebDAV native support working: [http://help.wildapricot.com/display/DOC/Setting+Up+WebDAV+in+Windows+7]	+	'''NOTE:''' For Windows 7, there is Microsoft patch available to make WebDAV native support working: [http://help.wildapricot.com/display/DOC/Setting+Up+WebDAV+in+Windows+7]
-		+

	=== Mac - using Finder ===		=== Mac - using Finder ===
Line 186:		Line 185:
	* Enter your institutional username and password		* Enter your institutional username and password
	* Click the '''Authenticate''' button, this will create a local proxy certificate.		* Click the '''Authenticate''' button, this will create a local proxy certificate.
-	* Click the '''Upload''' button and ~~pick~~ a username and password. ~~This will upload the certificate~~ to ~~MyProxy~~.	+
		+	[[Image:grix-main-page.png]]
		+	* This will fill in the Identity, Authenticated, Time remaining and Group fields in the bottom half of the window.
		+
		+	* Click the '''Upload''' button and you will get this window.
		+
		+	[[Image:Grix-upload-identy.png]]
		+	* Enter a username and a password in this window, and click Upload (these can be any username and a made up password just for using with Webdav).
		+
		+
		+	* You can now use Webdav to login to the DF with the username and password you entered in the last window.
		+	[[Using_the_DataFabric#Windows_XP_with_default_webDAV_client]]
		+
		+	A Better Windows client, which works with files bigger than 2G [[WebDAV_using_BitKinex]]
		+
		+	[[Using_the_DataFabric#Mac_-_using_Finder]]
		+

	This process will not work through a HTTP proxy.		This process will not work through a HTTP proxy.

Special:Log/upload

2012-05-02T23:30:11Z

uploaded "Image:Grix-upload-identy.png": grix upload user credentials

Special:Log/upload

2012-05-02T23:29:20Z

uploaded "Image:Grix-main-page.png": Grix MyProxy Main Page

Installing an iRODS slave server

2012-05-02T22:13:10Z

Installing Globus from RPMs for building iRODS with Globus

(Difference between revisions)

Software List On BeSTGRID Resources

2012-05-01T05:00:03Z

←Older revision		Revision as of 05:00, 1 May 2012
(4 intermediate revisions not shown.)
Line 3:		Line 3:
	This page documents the software available via BeSTGRID at each of the sites. For each site, it either lists the version installed (if the package is installed at the site with the particular version), or blank (if it's not installed or not advertised via the grid interface).		This page documents the software available via BeSTGRID at each of the sites. For each site, it either lists the version installed (if the package is installed at the site with the particular version), or blank (if it's not installed or not advertised via the grid interface).
	{\| border="1" cellpadding="5" cellspacing="0"		{\| border="1" cellpadding="5" cellspacing="0"
-	! Software Package !!Auckland!!Canterbury~~!!Otago~~!!SCENZ-Cluster	+	! Software Package !!Auckland!!Canterbury!!SCENZ-Cluster
	\|-		\|-
-	\| '''Abaqus''' \|\|6.8-EF2 \|\| \|\| \|\|	+	\| '''Abaqus''' \|\|6.8-EF2 \|\| \|\|
	\|-		\|-
-	\| '''BayesPhylogenies''' \|\| \|\| 1.0 \|\| \|\|	+	\| '''BayesPhylogenies''' \|\| \|\| 1.0 \|\|
	\|-		\|-
-	\| '''BEAST''' \|\|1.6.1 \|\| 1.6.1 ~~\|\| 1.5.4~~ \|\|	+	\| '''BEAST''' \|\|1.6.1 \|\| 1.6.1 \|\|
	\|-		\|-
-	\| '''BEST''' \|\| \|\| 2.3.1 \|\| \|\|	+	\| '''BEST''' \|\| \|\| 2.3.1 \|\|
	\|-		\|-
-	\| '''BLAST''' \|\| \|\| 2.2.21 \|\| \|\|	+	\| '''BLAST''' \|\| \|\| 2.2.21 \|\|
	\|-		\|-
-	\| '''Blender''' \|\| ~~\|\| 2.49a~~ \|\| 2.49a \|\|	+	\| '''Blender''' \|\| \|\| 2.49a \|\|
	\|-		\|-
-	\| '''ClustalW''' \|\| \|\| 1.83 \|\| \|\| 2.0.11	+	\| '''ClustalW''' \|\| \|\| 1.83 \|\| 2.0.11
	\|-		\|-
-	\| '''ClustalW Parallel''' \|\| \|\| 0.13 \|\| \|\|	+	\| '''ClustalW Parallel''' \|\| \|\| 0.13 \|\|
	\|-		\|-
-	\| '''Gold''' \|\|5.0 \|\| \|\| \|\|	+	\| '''Gold''' \|\|5.0 \|\| \|\|
	\|-		\|-
-	\| '''ilog''' \|\|12.2 \|\| \|\| \|\|	+	\| '''ilog''' \|\|12.2 \|\| \|\|
	\|-		\|-
-	\| '''infernal''' \|\| \|\| 1.0 \|\| \|\|	+	\| '''infernal''' \|\| \|\| 1.0 \|\|
	\|-		\|-
-	\| '''Java''' \|\|1.6 \|\| 1.6.0<br>java-1.6.0-openjdk-1.6.0.0-1.22.1.9.8.el5_6 \|\| \|\| openjdk-1.6.0.0-0.30.b09.el5	+	\| '''Java''' \|\|1.6 \|\| 1.6.0<br>java-1.6.0-openjdk-1.6.0.0-1.22.1.9.8.el5_6 \|\| openjdk-1.6.0.0-0.30.b09.el5
	\|-		\|-
-	\| '''LAMARC''' \|\| ~~\|\| 2.1~~ \|\| 2.1 \|\|	+	\| '''LAMARC''' \|\| \|\| 2.1 \|\|
	\|-		\|-
-	\| '''MEME''' \|\| ~~\|\| 4.1.0~~ \|\| 4.1.0 \|\|	+	\| '''MEME''' \|\| \|\| 4.1.0 \|\|
	\|-		\|-
-	\| '''ModelTest''' \|\| \|\| 3.7 \|\| \|\|	+	\| '''ModelTest''' \|\| \|\| 3.7 \|\|
	\|-		\|-
-	\| '''Mono''' \|\| \|\| \|\| \|\| 2.6.7	+	\| '''Mono''' \|\| \|\| \|\| 2.6.7
	\|-		\|-
-	\| '''mpiBLAST''' \|\|1.5.0 \|\| 1.6.0 \|\| \|\|	+	\| '''mpiBLAST''' \|\|1.5.0 \|\| 1.6.0 \|\|
	\|-		\|-
-	\| '''MrBayes''' \|\|3.1.2 \|\| 3.1.2<br>~~3.2.1 \|\|~~ 3.2.1 \|\| 3.1.2	+	\| '''MrBayes''' \|\|3.1.2 \|\| 3.1.2<br>3.2.1 \|\| 3.1.2
	\|-		\|-
-	\| '''NAMD''' \|\| \|\| 2.6 \|\| \|\|	+	\| '''NAMD''' \|\| \|\| 2.6 \|\|
	\|-		\|-
-	\| '''octave''' \|\|3.0.3 \|\| \|\| \|\|	+	\| '''octave''' \|\|3.0.3 \|\| \|\|
	\|-		\|-
-	\| '''PARSWMS''' \|\| \|\| Aug06 \|\| \|\|	+	\| '''PARSWMS''' \|\| \|\| Aug06 \|\|
	\|-		\|-
-	\| '''PAUP*''' \|\| \|\| 4.0 beta \|\| \|\|	+	\| '''PAUP*''' \|\| \|\| 4.0 beta \|\|
	\|-		\|-
-	\| '''python''' \|\|2.4<br>2.6 \|\| 2.4<br>2.6<br>2.6.2 \|\| \|\| 2.4	+	\| '''python''' \|\|2.4<br>2.6 \|\| 2.4<br>2.6<br>2.6.2 \|\| 2.4
	\|-		\|-
-	\| '''R''' \|\|2.13.1<br>2.9.0 \|\| 2.11.0<br>2.13.1<br>2.14.0<br>2.5.0 \|\| \|\| 2.13.0	+	\| '''R''' \|\|2.13.1<br>2.9.0 \|\| 2.11.0<br>2.13.1<br>2.14.0<br>2.5.0 \|\| 2.13.0
	\|-		\|-
-	\| '''RMPISNOW''' \|\|2.9.0 \|\| 2.11.0<br>2.13.1 \|\| \|\| 2.13.0	+	\| '''RMPISNOW''' \|\|2.9.0 \|\| 2.11.0<br>2.13.1 \|\| 2.13.0
	\|-		\|-
-	\| '''SAS''' \|\| \|\| 9.2 \|\| \|\|	+	\| '''SAS''' \|\| \|\| 9.2 \|\|
	\|-		\|-
-	\| '''szybki''' \|\|1.3.4 \|\| \|\| \|\|	+	\| '''szybki''' \|\|1.3.4 \|\| \|\|
	\|-		\|-
-	\| '''teiresias''' \|\| ~~\|\| 18AUG2004~~ \|\| 18AUG2004 \|\|	+	\| '''teiresias''' \|\| \|\| 18AUG2004 \|\|
	\|-		\|-
-	\| '''UnixCommands''' \|\|coreutils-5.2.1-31.7 \|\| coreutils-5.2.1-23.8-HPC<br>coreutils-5.2.1-31.7<br>coreutils-5.97-19.el5 ~~\|\| coreutils-5.2.1-31.2~~ \|\| coreutils-5.2.1-31.7	+	\| '''UnixCommands''' \|\|coreutils-5.2.1-31.7 \|\| coreutils-5.2.1-23.8-HPC<br>coreutils-5.2.1-31.7<br>coreutils-5.97-19.el5 \|\| coreutils-5.2.1-31.7
	\|-		\|-
-	\| '''WRF-main''' \|\| \|\| 1.0 \|\| \|\|	+	\| '''WRF-main''' \|\| \|\| 1.0 \|\|
	\|-		\|-
-	\| '''WRF-post''' \|\| \|\| 1.0 \|\| \|\|	+	\| '''WRF-post''' \|\| \|\| 1.0 \|\|
	\|-		\|-
-	\| '''WRF-prep''' \|\| \|\| 1.0 \|\| \|\|	+	\| '''WRF-prep''' \|\| \|\| 1.0 \|\|
	\|-		\|-
	\|}		\|}

IRODS deployment plan

2012-04-26T12:14:58Z

Post-configuration: DONE

←Older revision		Revision as of 12:14, 26 April 2012
(2 intermediate revisions not shown.)
Line 172:		Line 172:
	=== Post-configuration: DONE ===		=== Post-configuration: DONE ===

-	* Increase Postgres connection limit: edit <tt>/opt/iRODS/Postgres/pgsql/data/postgresql.conf</tt> (and restart Postgres):<pre>max_connections = ~~500~~</pre>	+	* Increase Postgres connection limit: edit <tt>/opt/iRODS/Postgres/pgsql/data/postgresql.conf</tt> (and restart Postgres):<pre>max_connections = 1500</pre>
		+	** Postgres connection settings are documented at http://www.postgresql.org/docs/8.2/static/runtime-config-connection.html
		+	** The connection settings must match the SysV IPC limits: http://www.postgresql.org/docs/8.2/static/kernel-resources.html#SYSVIPC
		+	** SEMMNS is the second parameter in output of <tt>cat /proc/sys/kernel/sem</tt> (default value 32000)
		+	** SEMMNI is the last parameter there, default value 128 - this is the limiting factor - SEMMNI must be at least <b><tt>at least ceil(max_connections / 16)</tt></b>
		+	** More at http://www.puschitz.com/TuningLinuxForOracle.shtml#TheSEMMNSParameter
		+	** Note: any further increase of <tt>max_connections</tt> would require increasing SEMMNI: override <tt>kernel.sem</tt> in <tt>/etc/sysctl.conf</tt>: <pre>kernel.sem='250 32000 32 256'</pre>
		+

	* Setup directory permissions		* Setup directory permissions

Setup GRAM5 on CentOS 5

2012-04-25T23:08:42Z

Using Globus

←Older revision		Revision as of 23:08, 25 April 2012
(One intermediate revision not shown.)
Line 359:		Line 359:
	Globus job manager verifies all elements received in the job RSL against the specification in <tt>$GLOBUS_LOCATION/share/globus_gram_job_manager/pbs.rvf</tt>.		Globus job manager verifies all elements received in the job RSL against the specification in <tt>$GLOBUS_LOCATION/share/globus_gram_job_manager/pbs.rvf</tt>.

-	~~Apply~~ the following ~~modifications to~~ this file to enable the RSL extensions commonly used in ARCS grid / BeSTGRID:	+	Add the following entries at the end of this file to enable the RSL extensions commonly used in ARCS grid / BeSTGRID:

		+	* Note: in GRAM 5.2, the file to modify is /usr/share/globus/globus_gram_job_manager/globus-gram-job-manager.rvf
	<pre>		<pre>
-	~~--- pbs.rvf.orig 2011-09-14 12:00:19.000000000 +1200~~	+	# NeSI extensions
-	~~+++ pbs.rvf 2011-09-14 12:10:02.000000000 +1200~~	+	Attribute: jobname
-	~~@@ -22,6 +22,22 @@~~	+	Description: "job name, up to 6 characters"
-	~~Values: yes no~~	+	ValidWhen: GLOBUS_GRAM_JOB_SUBMIT
-	~~ValidWhen: GLOBUS_GRAM_JOB_SUBMIT~~	+
-		+	Attribute: module
-	+Attribute: jobname	+	Description: "module string"
-	+Description: "job name, up to 6 characters"	+	ValidWhen: GLOBUS_GRAM_JOB_SUBMIT
-	+ValidWhen: GLOBUS_GRAM_JOB_SUBMIT	+
-	+	+	Attribute: emaildebug
-	+Attribute: module	+	Description: "send script"
-	+Description: "module string"	+	ValidWhen: GLOBUS_GRAM_JOB_SUBMIT
-	+ValidWhen: GLOBUS_GRAM_JOB_SUBMIT	+
-	+	+	Attribute: vo
-	+Attribute: emaildebug	+	Description: "voname for accounting"
-	+Description: "send script"	+	ValidWhen: GLOBUS_GRAM_JOB_SUBMIT
-	+ValidWhen: GLOBUS_GRAM_JOB_SUBMIT	+
-	+	+	Attribute: email_address
-	+Attribute: vo	+	Description: "Email address for notifications"
-	+Description: "voname for accounting"	+	ValidWhen: GLOBUS_GRAM_JOB_SUBMIT
-	+ValidWhen: GLOBUS_GRAM_JOB_SUBMIT	+
-	+	+	Attribute: email_on_abort
-	Attribute: ~~name~~	+	Description: "Send email notifications when job aborts"
-	Description: "~~The name of~~ job ~~to submit to the PBS batch scheduler~~"	+	ValidWhen: GLOBUS_GRAM_JOB_SUBMIT
-	ValidWhen: GLOBUS_GRAM_JOB_SUBMIT	+
		+	Attribute: email_on_execution
		+	Description: "Send email notifications when job starts"
		+	ValidWhen: GLOBUS_GRAM_JOB_SUBMIT
		+
		+	Attribute: email_on_termination
		+	Description: "Send email notifications when job terminates"
		+	ValidWhen: GLOBUS_GRAM_JOB_SUBMIT
	</pre>		</pre>

Line 685:		Line 693:
	* Run a simple job and watch streaming output:<pre>globusrun -o -r ng1 '&(executable=/bin/hostname)'</pre>		* Run a simple job and watch streaming output:<pre>globusrun -o -r ng1 '&(executable=/bin/hostname)'</pre>
	* Run a 2-CPU MPI job<pre> globusrun -o -r ng1 '&(executable=mb)(count=2)(job_type=mpi)'</pre>		* Run a 2-CPU MPI job<pre> globusrun -o -r ng1 '&(executable=mb)(count=2)(job_type=mpi)'</pre>
		+	* Run a BGP job specifying email notification options, multiple environment variables with custom BG/P options (mode & connect) and multiple arguments:<pre>globusrun -o -r gram5bgpdev.canterbury.ac.nz/jobmanager-loadleveler '&(executable=/bin/echo)(arguments=Hello World)(queue=bgp)(email_address=vladimir.mencl@canterbury.ac.nz)( email_on_abort = "yes" )( email_on_execution = "yes" )( email_on_termination = "yes" )(jobname="my BGP test job")(count=256)(jobtype=mpi)(environment=(BG_MODE DUAL) (BG_CONNECT MESH))'</pre>
	* Run a job in batch mode (detach from the job)<pre>globusrun -r ng1 -batch '&(executable=/bin/sleep)(arguments=60)'</pre>		* Run a job in batch mode (detach from the job)<pre>globusrun -r ng1 -batch '&(executable=/bin/sleep)(arguments=60)'</pre>
	** Produces:		** Produces:

Software List On BeSTGRID Resources

2012-04-23T06:00:02Z

←Older revision		Revision as of 06:00, 23 April 2012
(One intermediate revision not shown.)
Line 3:		Line 3:
	This page documents the software available via BeSTGRID at each of the sites. For each site, it either lists the version installed (if the package is installed at the site with the particular version), or blank (if it's not installed or not advertised via the grid interface).		This page documents the software available via BeSTGRID at each of the sites. For each site, it either lists the version installed (if the package is installed at the site with the particular version), or blank (if it's not installed or not advertised via the grid interface).
	{\| border="1" cellpadding="5" cellspacing="0"		{\| border="1" cellpadding="5" cellspacing="0"
-	! Software Package !!Auckland!!Canterbury	+	! Software Package !!Auckland!!Canterbury!!Otago!!SCENZ-Cluster
	\|-		\|-
-	\| '''Abaqus''' \|\|6.8-EF2 \|\|	+	\| '''Abaqus''' \|\|6.8-EF2 \|\| \|\| \|\|
	\|-		\|-
-	\| '''BayesPhylogenies''' \|\| \|\| 1.0	+	\| '''BayesPhylogenies''' \|\| \|\| 1.0 \|\| \|\|
	\|-		\|-
-	\| '''BEAST''' \|\|1.6.1 \|\| 1.6.1	+	\| '''BEAST''' \|\|1.6.1 \|\| 1.6.1 \|\| 1.5.4 \|\|
	\|-		\|-
-	\| '''BEST''' \|\| \|\| 2.3.1	+	\| '''BEST''' \|\| \|\| 2.3.1 \|\| \|\|
	\|-		\|-
-	\| '''BLAST''' \|\| \|\| 2.2.21	+	\| '''BLAST''' \|\| \|\| 2.2.21 \|\| \|\|
	\|-		\|-
-	\| '''Blender''' \|\| \|\| 2.49a	+	\| '''Blender''' \|\| \|\| 2.49a \|\| 2.49a \|\|
	\|-		\|-
-	\| '''ClustalW''' \|\| \|\| 1.83	+	\| '''ClustalW''' \|\| \|\| 1.83 \|\| \|\| 2.0.11
	\|-		\|-
-	\| '''ClustalW Parallel''' \|\| \|\| 0.13	+	\| '''ClustalW Parallel''' \|\| \|\| 0.13 \|\| \|\|
	\|-		\|-
-	\| '''Gold''' \|\|5.0 \|\|	+	\| '''Gold''' \|\|5.0 \|\| \|\| \|\|
	\|-		\|-
-	\| '''ilog''' \|\|12.2 \|\|	+	\| '''ilog''' \|\|12.2 \|\| \|\| \|\|
	\|-		\|-
-	\| '''infernal''' \|\| \|\| 1.0	+	\| '''infernal''' \|\| \|\| 1.0 \|\| \|\|
	\|-		\|-
-	\| '''Java''' \|\|1.6 \|\| 1.6.0<br>java-1.6.0-openjdk-1.6.0.0-1.22.1.9.8.el5_6	+	\| '''Java''' \|\|1.6 \|\| 1.6.0<br>java-1.6.0-openjdk-1.6.0.0-1.22.1.9.8.el5_6 \|\| \|\| openjdk-1.6.0.0-0.30.b09.el5
	\|-		\|-
-	\| '''LAMARC''' \|\| \|\| 2.1	+	\| '''LAMARC''' \|\| \|\| 2.1 \|\| 2.1 \|\|
	\|-		\|-
-	\| '''MEME''' \|\| \|\| 4.1.0	+	\| '''MEME''' \|\| \|\| 4.1.0 \|\| 4.1.0 \|\|
	\|-		\|-
-	\| '''ModelTest''' \|\| \|\| 3.7	+	\| '''ModelTest''' \|\| \|\| 3.7 \|\| \|\|
	\|-		\|-
-	\| '''~~mpiBLAST~~''' \|\|~~1.5.0~~ \|\| 1.6.0	+	\| '''Mono''' \|\| \|\| \|\| \|\| 2.6.7
	\|-		\|-
-	\| '''~~MrBayes~~''' \|\|3.1.2 \|\| 3.1.~~2<br>3~~.~~2.1~~	+	\| '''mpiBLAST''' \|\|1.5.0 \|\| 1.6.0 \|\| \|\|
	\|-		\|-
-	\| '''~~NAMD~~''' \|\| \|\| 2.6	+	\| '''MrBayes''' \|\|3.1.2 \|\| 3.1.2<br>3.2.1 \|\| 3.2.1 \|\| 3.1.2
	\|-		\|-
-	\| '''~~octave~~''' \|\|3.~~0.3~~ \|\|	+	\| '''NAMD''' \|\| \|\| 2.6 \|\| \|\|
	\|-		\|-
-	\| '''~~PARSWMS~~''' \|\| \|\| ~~Aug06~~	+	\| '''octave''' \|\|3.0.3 \|\| \|\| \|\|
	\|-		\|-
-	\| '''PAUP*''' \|\| \|\| ~~4.0 beta~~	+	\| '''PARSWMS''' \|\| \|\| Aug06 \|\| \|\|
	\|-		\|-
-	\| '''~~python~~''' \|\|2.4~~<br>2~~.6 \|\| ~~2.4<br>2.6<br>2.6.2~~	+	\| '''PAUP*''' \|\| \|\| 4.0 beta \|\| \|\|
	\|-		\|-
-	\| '''R''' \|\|2.~~13.1~~<br>2.~~9.0~~ \|\| 2.~~11.0~~<br>2.~~13.1~~<br>2.14.~~0<br>~~2.~~5.0~~	+	\| '''python''' \|\|2.4<br>2.6 \|\| 2.4<br>2.6<br>2.6.2 \|\| \|\| 2.4
	\|-		\|-
-	\| '''~~RMPISNOW~~''' \|\|2.9.0 \|\| 2.11.0<br>2.13.1	+	\| '''R''' \|\|2.13.1<br>2.9.0 \|\| 2.11.0<br>2.13.1<br>2.14.0<br>2.5.0 \|\| \|\| 2.13.0
	\|-		\|-
-	\| '''~~SAS~~''' \|\| \|\| 9.2	+	\| '''RMPISNOW''' \|\|2.9.0 \|\| 2.11.0<br>2.13.1 \|\| \|\| 2.13.0
	\|-		\|-
-	\| '''~~szybki~~''' \|\|1.~~3.4~~ \|\|	+	\| '''SAS''' \|\| \|\| 9.2 \|\| \|\|
	\|-		\|-
-	\| '''~~teiresias~~''' \|\| \|\| ~~18AUG2004~~	+	\| '''szybki''' \|\|1.3.4 \|\| \|\| \|\|
	\|-		\|-
-	\| '''~~UnixCommands~~''' \|\|~~coreutils-5.2.1-31.7~~ \|\| ~~coreutils-5.2.1-23.8-HPC<br>coreutils-5.2.1-31.7<br>coreutils-5.97-19.el5~~	+	\| '''teiresias''' \|\| \|\| 18AUG2004 \|\| 18AUG2004 \|\|
	\|-		\|-
-	\| '''~~WRF-main~~''' \|\| \|\| 1.0	+	\| '''UnixCommands''' \|\|coreutils-5.2.1-31.7 \|\| coreutils-5.2.1-23.8-HPC<br>coreutils-5.2.1-31.7<br>coreutils-5.97-19.el5 \|\| coreutils-5.2.1-31.2 \|\| coreutils-5.2.1-31.7
	\|-		\|-
-	\| '''WRF-~~post~~''' \|\| \|\| 1.0	+	\| '''WRF-main''' \|\| \|\| 1.0 \|\| \|\|
	\|-		\|-
-	\| '''WRF-prep''' \|\| \|\| 1.0	+	\| '''WRF-post''' \|\| \|\| 1.0 \|\| \|\|
		+	\|-
		+	\| '''WRF-prep''' \|\| \|\| 1.0 \|\| \|\|
	\|-		\|-
	\|}		\|}