biolocal:BioinfogroupMng - Revision history

Mauro at 13:44, 12 March 2010

Mauro — Fri, 12 Mar 2010 13:44:45 GMT

←Older revision		Revision as of 13:44, 12 March 2010
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	\| 561		\| 561
	\| 561		\| 561
		+	\|-
		+	\|-
		+	\| nunzia
		+	\| 564
		+	\| 564
	\|-		\|-
	\|}		\|}

Gianluca at 16:13, 10 March 2008

Gianluca — Mon, 10 Mar 2008 16:13:04 GMT

←Older revision		Revision as of 16:13, 10 March 2008
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	\| 560		\| 560
	\| 560		\| 560
		+	\|-
		+	\|-
		+	\| pippi
		+	\| 561
		+	\| 561
	\|-		\|-
	\|}		\|}

Gianluca: Bioinfolocal:bioinfogroupMng moved to biolocal:BioinfogroupMng: moving to the right namespace

Gianluca — Mon, 18 Feb 2008 10:54:29 GMT

Bioinfolocal:bioinfogroupMng moved to biolocal:BioinfogroupMng: moving to the right namespace

←Older revision

Revision as of 10:54, 18 February 2008

Gianluca at 10:25, 5 February 2008

Gianluca — Tue, 05 Feb 2008 10:25:17 GMT

←Older revision		Revision as of 10:25, 5 February 2008
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	\| 559		\| 559
	\| 559		\| 559
		+	\|-
		+	\|-
		+	\| paolo
		+	\| 560
		+	\| 560
	\|-		\|-
	\|}		\|}

Gianluca at 16:35, 13 November 2007

Gianluca — Tue, 13 Nov 2007 16:35:24 GMT

←Older revision		Revision as of 16:35, 13 November 2007
Line 76:		Line 76:

	Coming soon...		Coming soon...
-
-	'''Setup the access to the grid'''
-
-	The bioinfoaccess server can also be used to access the SCOPE grid, using the personal certificate, properly installed and initialized.
-	If you have your personal certificate already installed in your browser, export it as file and save it in your home directory, under the .globus directory.
-
-	[[Image:Cert_download.jpg]]
-
-	In the image, a certificate file will be generated and should be uploaded on the bioinfoaccess server:
-
-	scp myCertificate.p12 gianluca@bioinfoaccess.ceinge.unina.it:
-
-	On the bioinfo access server, some commands should still be used to have the personal certificate installed correctly:
-
-	<pre>
-	mkdir .globus
-	cd .globus
-	openssl pkcs12 -nocerts -in ../myCertificate.p12 -out userkey.pem
-	openssl pkcs12 -clcerts -nokeys -in ../myCertificate.p12 -out usercert.pem
-	chmod 400 userkey.pem
-	chmod 600 usercert.pem
-	</pre>
-
-	The two openssl command are needed to extract the private and public key from the pk12 certificate file. Don't forget to change the access mode of the files!
-
-	The account is now configured to provide the correct credentials when the access to the grid is requested.
-
-	'''Access and use the grid'''
-
-	Before start submitting jobs to the grid, a new proxy certificate should be created in the scope VO:
-
-	<pre>
-	voms-proxy-init -voms scope
-	</pre>
-
-	To get information about the proxy certificate, use the voms-proxy-info command. Particularly useful to know the remaining time of validity.
-
-	To execute a job a jdl file should be compiled as follows:
-	<pre>
-	Executable = "/bin/echo";
-	Arguments = "Hello World";
-	StdOutput = "message.txt";
-	StdError = "stderror";
-	OutputSandbox = {"message.txt","stderror"};
-	</pre>
-	To submit and view the state of the job use the command:
-	<pre>
-	edg-job-submit test1.jdl
-	edg-job-status https://scoperb01.dsf.unina.it:9000/DXWtFSVPAjfLeAIBlRcfdw
-	</pre>
-
-	In the above example, after the submission a url is returned to refer to the submitted job. It is used to get the status.
-
-	When the state becomes "done", the result can be retreived with the command:
-	<pre>
-	edg-job-get-output https://scoperb01.dsf.unina.it:9000/DXWtFSVPAjfLeAIBlRcfdw
-	</pre>

Gianluca at 16:16, 13 November 2007

Gianluca — Tue, 13 Nov 2007 16:16:07 GMT

←Older revision		Revision as of 16:16, 13 November 2007
Line 103:		Line 103:
	The account is now configured to provide the correct credentials when the access to the grid is requested.		The account is now configured to provide the correct credentials when the access to the grid is requested.

-	'''Access the grid'''	+	'''Access and use the grid'''

	Before start submitting jobs to the grid, a new proxy certificate should be created in the scope VO:		Before start submitting jobs to the grid, a new proxy certificate should be created in the scope VO:

Gianluca at 16:11, 13 November 2007

Gianluca — Tue, 13 Nov 2007 16:11:50 GMT

←Older revision		Revision as of 16:11, 13 November 2007
Line 77:		Line 77:
	Coming soon...		Coming soon...

-	'''~~Access~~ the grid'''	+	'''Setup the access to the grid'''

	The bioinfoaccess server can also be used to access the SCOPE grid, using the personal certificate, properly installed and initialized.		The bioinfoaccess server can also be used to access the SCOPE grid, using the personal certificate, properly installed and initialized.
Line 84:		Line 84:
	[[Image:Cert_download.jpg]]		[[Image:Cert_download.jpg]]

-	In the image a certificate file will be generated and should be uploaded on the bioinfoaccess server:	+	In the image, a certificate file will be generated and should be uploaded on the bioinfoaccess server:

	scp myCertificate.p12 gianluca@bioinfoaccess.ceinge.unina.it:		scp myCertificate.p12 gianluca@bioinfoaccess.ceinge.unina.it:
Line 100:		Line 100:

	The two openssl command are needed to extract the private and public key from the pk12 certificate file. Don't forget to change the access mode of the files!		The two openssl command are needed to extract the private and public key from the pk12 certificate file. Don't forget to change the access mode of the files!
		+
		+	The account is now configured to provide the correct credentials when the access to the grid is requested.
		+
		+	'''Access the grid'''
		+
		+	Before start submitting jobs to the grid, a new proxy certificate should be created in the scope VO:
		+
		+	<pre>
		+	voms-proxy-init -voms scope
		+	</pre>
		+
		+	To get information about the proxy certificate, use the voms-proxy-info command. Particularly useful to know the remaining time of validity.
		+
		+	To execute a job a jdl file should be compiled as follows:
		+	<pre>
		+	Executable = "/bin/echo";
		+	Arguments = "Hello World";
		+	StdOutput = "message.txt";
		+	StdError = "stderror";
		+	OutputSandbox = {"message.txt","stderror"};
		+	</pre>
		+	To submit and view the state of the job use the command:
		+	<pre>
		+	edg-job-submit test1.jdl
		+	edg-job-status https://scoperb01.dsf.unina.it:9000/DXWtFSVPAjfLeAIBlRcfdw
		+	</pre>
		+
		+	In the above example, after the submission a url is returned to refer to the submitted job. It is used to get the status.
		+
		+	When the state becomes "done", the result can be retreived with the command:
		+	<pre>
		+	edg-job-get-output https://scoperb01.dsf.unina.it:9000/DXWtFSVPAjfLeAIBlRcfdw
		+	</pre>

Gianluca at 15:35, 13 November 2007

Gianluca — Tue, 13 Nov 2007 15:35:49 GMT

←Older revision		Revision as of 15:35, 13 November 2007
Line 76:		Line 76:

	Coming soon...		Coming soon...
		+
		+	'''Access the grid'''
		+
		+	The bioinfoaccess server can also be used to access the SCOPE grid, using the personal certificate, properly installed and initialized.
		+	If you have your personal certificate already installed in your browser, export it as file and save it in your home directory, under the .globus directory.
		+
		+	[[Image:Cert_download.jpg]]
		+
		+	In the image a certificate file will be generated and should be uploaded on the bioinfoaccess server:
		+
		+	scp myCertificate.p12 gianluca@bioinfoaccess.ceinge.unina.it:
		+
		+	On the bioinfo access server, some commands should still be used to have the personal certificate installed correctly:
		+
		+	<pre>
		+	mkdir .globus
		+	cd .globus
		+	openssl pkcs12 -nocerts -in ../myCertificate.p12 -out userkey.pem
		+	openssl pkcs12 -clcerts -nokeys -in ../myCertificate.p12 -out usercert.pem
		+	chmod 400 userkey.pem
		+	chmod 600 usercert.pem
		+	</pre>
		+
		+	The two openssl command are needed to extract the private and public key from the pk12 certificate file. Don't forget to change the access mode of the files!

Gianluca: New page: {| border="1" cellspacing="0" cellpadding="5" align="right" ! ! Uid ! Gid |- | giovanni | 550 | 550 |- |- | gianluca | 551 | 551 |- |- | mauro | 552 | 552 |- |- | angelo | 553 | 553 |-...

Gianluca — Tue, 13 Nov 2007 14:34:39 GMT

New page: {| border="1" cellspacing="0" cellpadding="5" align="right" ! ! Uid ! Gid |- | giovanni | 550 | 550 |- |- | gianluca | 551 | 551 |- |- | mauro | 552 | 552 |- |- | angelo | 553 | 553 |-...

New page

{| border="1" cellspacing="0" cellpadding="5" align="right"
!
! Uid
! Gid
|-
| giovanni
| 550
| 550
|-
|-
| gianluca
| 551
| 551
|-
|-
| mauro
| 552
| 552
|-
|-
| angelo
| 553
| 553
|-
|-
| vittorio
| 554
| 554
|-
|-
| luca
| 555
| 555
|-
|-
| concita
| 556
| 556
|-
|-
| leandra
| 557
| 557
|-
|-
| angela
| 558
| 558
|-
|-
| marisa
| 559
| 559
|-
|}

'''UIDs and GIDs assignement'''

Each username is associated with a numeric id to manage the ownership of the files. The user lists on the servers are configured following a predefined schema, as shown in the table.

'''Server access'''

Each registered user can access by ssh the server:

bioinfoaccess.ceinge.unina.it

This server is accessible from any internet address and can be used to reach servers closed to the external network.

'''Access to the cluster network'''

The bioinfoAccess.ceinge.unina.it server can also be used to access to the cluster network, by using a dedicated interface configured on the 192.168.151.x network; the IP interface is:

192.168.151.184

'''Working on the cluster network'''

Coming soon...