opaltoolkit-users — Users mailing-list for Opal Toolkit

Re: [Opaltoolkit-users] Opal 2.4 and Tomcat

[Luca C. <luc...@gm...>]

On Thu, Jan 9, 2014 at 1:45 PM, Conrad Huang <co...@cg...> wrote:
> On 1/9/2014 11:35 AM, Luca Clementi wrote:
>>
[...]
> The debug code clears it up a bit.  Here's the end of catalina.out (adding
> debugging code but leaving deploy as "deploy"):
>
>> INFO: Server startup in 2609 ms
>> 2014-01-09 13:28:08,074 INFO
>> edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer.run(OpalDeployService.java:160)
>> - initDeployServlet: axis URL:
>> http://xxx.xxx.ucsf.edu:8080/opal2/servlet/AxisServlet
>> 2014-01-09 13:28:08,075 INFO
>> edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer.run(OpalDeployService.java:161)
>> - initDeployServlet: deploy path: deploy
>> 2014-01-09 13:28:08,075 INFO
>> edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer.run(OpalDeployService.java:162)
>> - initDeployServlet: deploy path: /var/www/deploy
>>
>> Exception in thread "OpalDeployer" java.lang.NullPointerException
>>         at
>> edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer.run(OpalDeployService.java:178)
>
>
> The full deploy path is relative to /var/www, which is the home directory of
> user "apache" which is the account we use for running this instance of
> tomcat.  I guess tomcat6 does not change directory from where it was started
> to $CATALINA_HOME.  Our startup script uses "su - apache -c ..." to start
> tomcat, so it starts in ~apache or /var/www. Specifying the full path in
> etc/opal.properties makes everything work. I have one service deployed!
>

That does not make much sense to me :-(
It should not use the current working directory (that was my first test).
What script do you use to start up tomcat?
You should use the $CATALINA_HOME/bin/startup.sh which sets the proper
working directory:
clem@hermes:~/projects/opaltoolkit$ apache-tomcat-6.0.37/bin/startup.sh
Using CATALINA_BASE:   /home/clem/projects/opaltoolkit/apache-tomcat-6.0.37
Using CATALINA_HOME:   /home/clem/projects/opaltoolkit/apache-tomcat-6.0.37
Using CATALINA_TMPDIR: /home/clem/projects/opaltoolkit/apache-tomcat-6.0.37/temp
Using JRE_HOME:        /usr
Using CLASSPATH:
/home/clem/projects/opaltoolkit/apache-tomcat-6.0.37/bin/bootstrap.jar

No matter where I start it from....
I tried to reproduce your problem but still no luck
cd /tmp
su - clem -c /home/clem/projects/opaltoolkit/apache-tomcat-6.0.37/bin/startup.sh


Luca

Re: [Opaltoolkit-users] Opal 2.4 and Tomcat

[Luca C. <luc...@gm...>]

On Wed, Jan 8, 2014 at 7:39 PM, Conrad Huang <co...@cg...> wrote:
> On 1/8/2014 4:34 PM, Luca Clementi wrote:
>>
>> Hey Conrad,
>> I'm re-adding the list...
>>
>> On Wed, Jan 8, 2014 at 2:10 PM, Conrad Huang <co...@cg...> wrote:
>>>
>>> We're close, but not quite there yet.  I got an instance of Opal 2.5
>>> running
>>> under Tomcat6 by simply following the instructions.  I can reach the
>>> dashboard.  That's the good news.  The bad news are:
>>>
>>> 1. The "Server Info" tab says I'm still running Opal version 2.4.
>>
>>
>> You must have copied you old build.properties from the previous
>> installation.
>> The template in the repo seems correct:
>>
>> https://github.com/nbcrrolls/opaltoolkit/blob/master/opal/opal2-core/build.properties.template
>>
>> Can you try to re-deploy upgrading the version number in it (as in the
>> template)?
>
>
> I removed everything and started over, but the results are still the same:
> "Opal Version:       2.4" in the Server Info tab.  I'm not using any
> configuration files from our production system.  All the .property files
> copied from the .template files and the only changes made are catalina.home
> in build.properties and tomcat.url in opal.properties.
>
> build.properties has "version = 2.5" in it.  In fact, since I've never
> actually installed Opal 2.4, I cannot even imagine where the dashboard is
> finding that version number.  Our current production version is 2.2.
>
> I've been cleaning up the Opal source tree with "ant clean".  Is that the
> proper command?  As for tomcat, I actually delete the directory and recopy
> everything when I start over from scratch.

My bad. Sorry for not checking the code before answering.
The version was not updated in web.xml.
It's fixed now in the code (I just pushed it).

>>> 2. When I first tried to deploy an application (I copied the
>>> clustalw_config.xml file and changed the binary path), I got:
>>>
>>
>> No, the new opal has a new deployment method.
>> No need to run any command, just drop the file inside
>> $CATALINA_HOME/deploy.
>> To undeply rm the file from the folder.
>> This is one of the new feature of opal 2.5.
>>
>> See the docs in dockboot (I know it is not very readable :-():
>>
>> https://github.com/nbcrrolls/opaltoolkit/blob/master/opal/opal2-core/docbook/serversetup.sgml#L314
>>
>> In particular:
>> <para>Deploy the services inside Tomcat, by copying the
>> <emphasis>date.xml</emphasis> file inside the
>> directory specified in
>> <emphasis>$OPAL_HOME/etc/opal.properties</emphasis> with the keyword
>> <emphasis>opal.deploy.path</emphasis>.
>> If you have not changed this property the default directory is
>> <emphasis>$CATALINA_HOME/deploy</emphasis>.
>> <screen>
>>      cp configs/date.xml $CATALINA_HOME/deploy
>> </screen>
>> </para>
>
>
> I missed that one.  Now, in opal.properties, I have:
>         opal.deploy.path=deploy
> My CATALINA_HOME is /usr/local/opal-tomcat6 and I copied clustalw_config.xml
> to /usr/local/opal-tomcat6/deploy.  Going to the dashboard, I do not see the
> service.  However, I did see in $CATALINA_HOME/logs/catalina.out the
> following:
>
>> Jan 8, 2014 7:19:34 PM org.apache.catalina.startup.Catalina start
>> INFO: Server startup in 2500 ms
>> 2014-01-08 19:19:36,967 INFO
>> edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer
>> .run(OpalDeployService.java:160) - initDeployServlet: axis URL:
>> http://crick.cgl
>> .ucsf.edu:8080/opal2/servlet/AxisServlet
>> 2014-01-08 19:19:36,968 INFO
>> edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer
>> .run(OpalDeployService.java:161) - initDeployServlet: deploy path: deploy
>> Exception in thread "OpalDeployer" java.lang.NullPointerException
>>         at
>> edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer.run(OpalDeployServ
>> ice.java:177)

This is really weird.
It seems that the user the tomcat container is running under does not
have listing permission on the deploy directory.
Can you verify that?

The code looks ok to me:
            logger.info("initDeployServlet: deploy path: " + deployPathFile );
            [...]
            File [] deployFileList = deployPathFile.listFiles();
            for (File configFile : deployFileList){

listFile() returns null only if the deployPathFile is non existent.

Sincerely,
Luca

Re: [Opaltoolkit-users] Opal 2.4 and Tomcat

[Conrad H. <co...@cg...>]

On 1/8/2014 4:34 PM, Luca Clementi wrote:
> Hey Conrad,
> I'm re-adding the list...
>
> On Wed, Jan 8, 2014 at 2:10 PM, Conrad Huang <co...@cg...> wrote:
>> We're close, but not quite there yet.  I got an instance of Opal 2.5 running
>> under Tomcat6 by simply following the instructions.  I can reach the
>> dashboard.  That's the good news.  The bad news are:
>>
>> 1. The "Server Info" tab says I'm still running Opal version 2.4.
>
> You must have copied you old build.properties from the previous installation.
> The template in the repo seems correct:
> https://github.com/nbcrrolls/opaltoolkit/blob/master/opal/opal2-core/build.properties.template
>
> Can you try to re-deploy upgrading the version number in it (as in the
> template)?

I removed everything and started over, but the results are still the 
same: "Opal Version: 	2.4" in the Server Info tab.  I'm not using any 
configuration files from our production system.  All the .property files 
copied from the .template files and the only changes made are 
catalina.home in build.properties and tomcat.url in opal.properties.

build.properties has "version = 2.5" in it.  In fact, since I've never 
actually installed Opal 2.4, I cannot even imagine where the dashboard 
is finding that version number.  Our current production version is 2.2.

I've been cleaning up the Opal source tree with "ant clean".  Is that 
the proper command?  As for tomcat, I actually delete the directory and 
recopy everything when I start over from scratch.

>> 2. When I first tried to deploy an application (I copied the
>> clustalw_config.xml file and changed the binary path), I got:
>>
>
> No, the new opal has a new deployment method.
> No need to run any command, just drop the file inside $CATALINA_HOME/deploy.
> To undeply rm the file from the folder.
> This is one of the new feature of opal 2.5.
>
> See the docs in dockboot (I know it is not very readable :-():
> https://github.com/nbcrrolls/opaltoolkit/blob/master/opal/opal2-core/docbook/serversetup.sgml#L314
>
> In particular:
> <para>Deploy the services inside Tomcat, by copying the
> <emphasis>date.xml</emphasis> file inside the
> directory specified in
> <emphasis>$OPAL_HOME/etc/opal.properties</emphasis> with the keyword
> <emphasis>opal.deploy.path</emphasis>.
> If you have not changed this property the default directory is
> <emphasis>$CATALINA_HOME/deploy</emphasis>.
> <screen>
>      cp configs/date.xml $CATALINA_HOME/deploy
> </screen>
> </para>

I missed that one.  Now, in opal.properties, I have:
	opal.deploy.path=deploy
My CATALINA_HOME is /usr/local/opal-tomcat6 and I copied 
clustalw_config.xml to /usr/local/opal-tomcat6/deploy.  Going to the 
dashboard, I do not see the service.  However, I did see in 
$CATALINA_HOME/logs/catalina.out the following:

> Jan 8, 2014 7:19:34 PM org.apache.catalina.startup.Catalina start
> INFO: Server startup in 2500 ms
> 2014-01-08 19:19:36,967 INFO  edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer
> .run(OpalDeployService.java:160) - initDeployServlet: axis URL: http://crick.cgl
> .ucsf.edu:8080/opal2/servlet/AxisServlet
> 2014-01-08 19:19:36,968 INFO  edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer
> .run(OpalDeployService.java:161) - initDeployServlet: deploy path: deploy
> Exception in thread "OpalDeployer" java.lang.NullPointerException
>         at edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer.run(OpalDeployServ
> ice.java:177)

>
> Luca
>

Conrad

Re: [Opaltoolkit-users] Opal 2.4 and Tomcat

[Luca C. <luc...@gm...>]

Hey Conrad,
I'm re-adding the list...

On Wed, Jan 8, 2014 at 2:10 PM, Conrad Huang <co...@cg...> wrote:
> We're close, but not quite there yet.  I got an instance of Opal 2.5 running
> under Tomcat6 by simply following the instructions.  I can reach the
> dashboard.  That's the good news.  The bad news are:
>
> 1. The "Server Info" tab says I'm still running Opal version 2.4.

You must have copied you old build.properties from the previous installation.
The template in the repo seems correct:
https://github.com/nbcrrolls/opaltoolkit/blob/master/opal/opal2-core/build.properties.template

Can you try to re-deploy upgrading the version number in it (as in the
template)?

> 2. When I first tried to deploy an application (I copied the
> clustalw_config.xml file and changed the binary path), I got:
>

No, the new opal has a new deployment method.
No need to run any command, just drop the file inside $CATALINA_HOME/deploy.
To undeply rm the file from the folder.
This is one of the new feature of opal 2.5.

See the docs in dockboot (I know it is not very readable :-():
https://github.com/nbcrrolls/opaltoolkit/blob/master/opal/opal2-core/docbook/serversetup.sgml#L314

In particular:
<para>Deploy the services inside Tomcat, by copying the
<emphasis>date.xml</emphasis> file inside the
directory specified in
<emphasis>$OPAL_HOME/etc/opal.properties</emphasis> with the keyword
<emphasis>opal.deploy.path</emphasis>.
If you have not changed this property the default directory is
<emphasis>$CATALINA_HOME/deploy</emphasis>.
<screen>
    cp configs/date.xml $CATALINA_HOME/deploy
</screen>
</para>

Luca

Re: [Opaltoolkit-users] Opal 2.4 and Tomcat

[Luca C. <luc...@gm...>]

On Tue, Jan 7, 2014 at 10:06 AM, Conrad Huang <co...@cg...> wrote:
> We're finally upgrading from Opal 2.2 over Tomcat 5.0.  I have 2.4
> downloaded but am not clear on which version of Tomcat we should use.
> We have an old 5.5 install, but that's been end-of-life for over a year
> now.  We have 6.0 as part of Redhat Enterprise Linux.  We do not have
> 7.0 installed yet.  The Opal documentation only mentions 5.5, but I'm
> somewhat reluctant to use an end-of-life product.  Any suggestions and
> tips will be greatly appreciated.  Thanks.
>
> Conrad Huang
>

Hey Conrad,
if you use 2.4 it still supports only 5.5.

If you check out the tip of the source code there is a 2.5beta which
has support for 6.x and 7.x.
It also include a much simpler mechanism to deploy services, you can
simple drop config.xml inside a folder to get the service deployed.

I'm looking for a beta tester and if you don't find any problem I will
tag that version as 2.5.
I can send you the code if you'd like.

Luca

[Opaltoolkit-users] Opal 2.4 and Tomcat

[Conrad H. <co...@cg...>]

We're finally upgrading from Opal 2.2 over Tomcat 5.0.  I have 2.4 
downloaded but am not clear on which version of Tomcat we should use. 
We have an old 5.5 install, but that's been end-of-life for over a year 
now.  We have 6.0 as part of Redhat Enterprise Linux.  We do not have 
7.0 installed yet.  The Opal documentation only mentions 5.5, but I'm 
somewhat reluctant to use an end-of-life product.  Any suggestions and 
tips will be greatly appreciated.  Thanks.

Conrad Huang

Re: [Opaltoolkit-users] Opal security question

[Luca C. <luc...@gm...>]

On Wed, Apr 10, 2013 at 4:07 AM, Guillermo Marco Puche <
gui...@si...> wrote:

>  Hello,
>
> I've managed to secure my whole Tomcat server with HTTPS with user
> certificate.
> It's working awesome !
>
> Connection is required in port 8443 and also asks user for certificate
> when trying to access website.
>
> The problem I got now is that I cannot deploy Opal apps.
> I didn't change any of my app *.xml or *.sh that have been working for
> some time.
>
> As I said I just changed Tomcat security.
>
> I've edited the following parameters in config files in Opal, but still
> cannot deploy my app.
>
>
Guillermo,
you should not use the "ant deploy and undeploy" target with the latest
code.

You should copy your app xml files in $CATALINA_HOME/deploy folder and they
will get automatically deployed.

If you use and deploy when you restart your tomcat the application will get
un-deployed.

To be able to deploy and undeploy app, you need to be able to establish a
connection to

tomcat.url + "/opal2/servlet/AxisServlet"

Where tomcat.url is the one you defined in etc/opal.properties

To verify that you should be able to run
java org.apache.axis.client.AdminClient
-lhttps://localhost:8443/opal2/servlet/AxisServlet list

I think you might need to add a valid client certificate to your local key
store.

Luca

Re: [Opaltoolkit-users] Opal security question

[Guillermo M. P. <gui...@si...>]

Hello,

I've managed to secure my whole Tomcat server with HTTPS with user 
certificate.
It's working awesome !

Connection is required in port 8443 and also asks user for certificate 
when trying to access website.

The problem I got now is that I cannot deploy Opal apps.
I didn't change any of my app *.xml or *.sh that have been working for 
some time.

As I said I just changed Tomcat security.

I've edited the following parameters in config files in Opal, but still 
cannot deploy my app.

*build.properties:*

# port number used by the tomcat server
tomcat.port = 8443


*opal.properties:*

tomcat.url=https://1xx.19.0.12:8443


I've added the same connector i'm already using (working) on tomcat 
config to my tomcat opal config, *server.xml:*

      <Connector
                 protocol="HTTP/1.1"
                 port="8443" maxThreads="200"
                 scheme="https" secure="true" SSLEnabled="true"
                 keystoreFile="/home/mastablasta/tomcat7/conf/tomcat.keystore" keystorePass="passsword"
                 truststoreFile="/home/mastablasta/tomcat7/conf/cacerts.jks" truststorePass="password"
                 clientAuth="true" sslProtocol="TLS"/>

When I deploy app i'm getting a build succesfull message, but that's not 
true. It seems that it must be an issue with connection to app database. 
I think it must be something arround https or connector.

URL with complete log of ant deploy command: http://pastebin.com/A5wv80BZ


Thank you !

Best regards,
Guillermo.


On 03/08/13 02:44, Luca Clementi wrote:
> On Thu, Mar 7, 2013 at 12:10 AM, Guillermo Marco Puche
> <gui...@si...> wrote:
>> Hello Luca,
>>
>> I've already tried to install Globus with no success. From my pov the guide
>> on Globus toolkit website is very confusing. I'm looking for an alternative
>> guide/tutorial for Globus 5+ but I can't find any.
>>
> I'm not surprised (Globus is always a pain to install).
> You can try using self signed certificate
> http://stackoverflow.com/questions/1180397/tomcat-server-client-self-signed-ssl-certificate
>
> You will get the same as with globus but with less problem.
>
> Moreover I never tested the globus libraries in tomcat 6/7 they might not work.
>
> Luca


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Re: [Opaltoolkit-users] Heap Size for big input/output files

[Luca C. <luc...@gm...>]

On Fri, Mar 22, 2013 at 12:57 AM, Guillermo Marco Puche
<gui...@si...> wrote:
> Hello,
>
> 100MB is the maximum size that worked for me.

If you use the command line client you can overcome that:
http://www.nbcr.net/data/docs/opal/docs/2.X/usingclient.html

with the option: -b (uses binary attachment).

But unfortunately from the web interface that is the limit.

Luca

Re: [Opaltoolkit-users] Opal security question

[Luca C. <luc...@gm...>]

On Tue, Mar 5, 2013 at 7:19 AM, Guillermo Marco Puche
<gui...@si...> wrote:
> Hello,
>
> Since it seems that my Opal setup is running now I’m interested in user
> authentication for web services.
>
> Is GSI globus security the only security available for Opal?
>
> I would like to maybe try out a different thing since Globus certificate
> manual pages are very confused and I was unable to set it up a few weeks
> ago.
>

If you are referring to the Web Service interface yes.
Unfortunately Opal support only GSI authentication type.

The next improvement for opal should be upgrading Axis to Axis 2.x
which will support different protocol for web service security out of
the box.
Unfortunately at the moment we don't have time to look at that.

If you are referring to the web GUI interface for that you can use
apache in front of Opal (
http://tomcat.apache.org/connectors-doc/webserver_howto/apache.html )
and then you can relay on Apache and use simple HTTP authentication
and do all sort of things (use NTLM as a source of authentication
credential).


Luca

Re: [Opaltoolkit-users] Opal job scheduler benefits

[Luca C. <luc...@gm...>]

On Tue, Mar 5, 2013 at 8:21 AM, Nadya Williams <na...@sd...> wrote:
>
> Hi Guillermo,
>
> On Mar 5, 2013, at 3:19 AM, Guillermo Marco Puche wrote:
>
> Hello Nadya,
>
> I remade my XML and created a wrapper as you told me.
> Asking user for Condor input file works great !
>
> glad it works.
>
>
> The only I thing I don't like about this is that user gets status 8
> (execution completed) right after submitting the job. I mean you cannot
> track the real job status from Opal because of Fork Job Manager.
>
> This is true.
> you still can do something about it in your shell wrapper. After
> condor_submit command you have  to parse stout
> and find a jobid for your submission. you can query with condor_queue and
> looking for a specific jobid
> in a loop and check for the job status on some interval. When a job is
> done you exit the loop.  The interval value is hard to
> guess and may need to depend on overall expected job time. But one can
> choose an intelligent default since condor
> is "high throughput" and not "high performance". May be waiting for
> minutes is not a big deal. So putting a "sleep X"
> in your loop will work fine.
>

Why don't you try to use the condor_wait logfile to do that?

condor_wait should block till the job logging in the logfile is finished.

Luca

Re: [Opaltoolkit-users] Opal job scheduler benefits

[Nadya W. <na...@sd...>]

Hi Guillermo,

On Mar 5, 2013, at 3:19 AM, Guillermo Marco Puche wrote:

> Hello Nadya,
>
> I remade my XML and created a wrapper as you told me.
> Asking user for Condor input file works great !
glad it works.

>
> The only I thing I don't like about this is that user gets status 8  
> (execution completed) right after submitting the job. I mean you  
> cannot track the real job status from Opal because of Fork Job  
> Manager.
This is true.
you still can do something about it in your shell wrapper. After  
condor_submit command you have  to parse stout
and find a jobid for your submission. you can query with condor_queue  
and looking for a specific jobid
in a loop and check for the job status on some interval. When a job is  
done you exit the loop.  The interval value is hard to
guess and may need to depend on overall expected job time. But one can  
choose an intelligent default since condor
is "high throughput" and not "high performance". May be waiting for  
minutes is not a big deal. So putting a "sleep X"
in your loop will work fine.

The other option is to edit opal src and adapt Condor job manager to  
use grid universe.
We have not done this yet. It will be worse doing if you are going to  
submit many jobs of this
type, otherwise the wrapper should be sufficient.

>
> I'll try working on streaming input/output files but I think those  
> not work in grid universe.
i think you are right. you may need to use condor transfer protocol   
with "transfer_if_needed"  syntax.
Condor is pretty smart about knowing when to transfer or not transfer  
files depending on the filesystem
used (local or remote).

thanks
nadya

>
> Thank you.
>
> Best regards,
> Guillermo.
>
> On 03/04/2013 06:34 PM, nadya williams wrote:
>> Guillermo,
>> what is your xml file now? Your xml file should define a wrapper  
>> script  that will call your bwa.sh
>> and define a  Fork job manager.
>>
>> On Mar 4, 2013, at 7:52 AM, Guillermo Marco Puche wrote:
>>
>>> Hello,
>>>
>>> I've been following your guideline.
>>>
>>> I don't get opal errors now, even though job stays on state 1:
>>>
>>> Date and time :	3/4/2013 4:45:09 PM
>>> JobId :	appBWA_SH13623864602351552853141
>>> Status code:	1
>>> Message:	Launching executable
>>> Here's my opal/etc/condor.expr:
>>>
>>> universe = grid
>>> grid_resource = batch sge mastablasta@cacique
>>> output = test.out
>>> error = test.error
>>> log = test.log
>>> should_transfer_files = YES
>>> transfer_output = true
>>> stream_output = true
>>> when_to_transfer_output = ON_EXIT_OR_EVICT
>>> queue
>> It looks like you are mixing calling condor and sge which should  
>> not be the case.
>>
>> you need to look at the resulting submit file that is produced by  
>> opal.
>> Opal "knows" only vanila and parallel. I don't know how condor will  
>> treat a submit file where
>> universe  or queue is defined multiple times.   This is why i think  
>> the condor job manager will not
>> work for your specific case and you need to submit your condor job  
>> via Fork job manager
>>>
>>> And here my bwa.sh (executable called inside bwa_sh.xml):
>>>
>>> #!/bin/bash
>>> #$ -V
>>> ### nombre
>>> #$ -N bwa_bosco
>>> ### directorio de trabajo
>>> #$ -cwd
>>> ### juntar los output
>>> #####$ -j y
>>> ### seleccionar all.q
>>> #$ -q all.q
>>>
>>> cd /home/mastablasta
>>> bwa aln /home/mastablasta/ref/hg19.fa /home/mastablasta/input/ 
>>> HapMap_2.fastq -t 8 > /home/mastablasta/output/tmp/HapMap.right.sai
>> not quite right.  This is a submit file for sge job, not for a  
>> fork  fork job.  Your wrapper script should check for the input file
>> (your condor submit  file) that you upload via opal dashboard  and  
>> call condor submit with it.
>>
>>> This should work. I've tested submitting it with condor_submit and  
>>> works well, job is queued on remote SGE cluster.
>> the command you use here for a command line needs to be reproduced  
>> in your wrapper script.
>>
>>>
>>> But with Opal I’m getting glideinjobs in condor_q when no glidein  
>>> universe has been specified in condor.expr and 4 jobs being  
>>> spawned in remote SGE queue, which is very weird. But no signs of  
>>> BWA process.
>>>
>>> local condor_q Opal machine:
>>>
>>> $ condor_q
>>> -- Submitter: brugal : <192.168.6.2:11000?sock=2009_e522_3> : brugal
>>>  ID      OWNER            SUBMITTED     RUN_TIME ST PRI SIZE CMD
>>>    9.0   mastablasta     3/4  09:41   0+00:00:00 I  0   0.0  bwa.sh
>>>    9.1   mastablasta     3/4  09:41   0+00:00:00 I  0   0.0  bwa.sh
>> you submitted 2 jobs here via your opal interface (different job ids)
>>>
>>>   10.0   mastablasta     3/4  09:41   0+00:16:39 R  0   0.0   
>>> glidein_wrapper.sh
>>>   11.0   mastablasta     3/4  09:41   0+00:16:39 R  0   0.0   
>>> glidein_wrapper.sh
>>>   12.0   mastablasta     3/4  09:41   0+00:16:11 R  0   0.0   
>>> glidein_wrapper.sh
>>>   13.0   mastablasta     3/4  09:41   0+00:16:10 R  0   0.0   
>>> glidein_wrapper.sh
>> i can only guess here, but your condor submit file may have two  
>> queue statements, one form your condor.expr and
>> one that opal writes, hence condor submits 2 jobs per 2 queue  
>> statements.
>>
>>> 6 jobs; 0 completed, 0 removed, 2 idle, 4 running, 0 held, 0  
>>> suspended
>>>
>>> Here's remote SGE queue:
>>>
>>> $ qstat
>>> job-ID  prior   name       user         state submit/start at      
>>> queue                          slots ja-task-ID
>>> -----------------------------------------------------------------------------------------------------------------
>>>      61 0.55500 bl_a29aa29 mastablasta  r     03/04/2013 17:31:30 all.q@compute-0-0.local 
>>>             1
>>>      62 0.55500 bl_f1cbb6c mastablasta  r     03/04/2013 17:31:30 all.q@compute-0-0.local 
>>>             1
>>>      63 0.55500 bl_1dc49f4 mastablasta  r     03/04/2013 17:32:00 all.q@compute-0-0.local 
>>>             1
>>>      64 0.55500 bl_ced1f94 mastablasta  r     03/04/2013 17:32:00 all.q@compute-0-0.local 
>>>             1
>>
>> what is the output of "qstat -j 61" ?
>>
>> nadya
>>
>>>
>>> On 03/01/2013 09:02 AM, Guillermo Marco Puche wrote:
>>>> Hello Nadya,
>>>>
>>>> Thank you for the information. This starts to make sense.
>>>> I had no idea on how to pass Opal my Condor config.
>>>>
>>>> I'm going to try to make this work with Grid universe. I'll  
>>>> report asap.
>>>>
>>>>
>>>> Once again, thank you very much.
>>>>
>>>> Best regards,
>>>> Guillermo.
>>>>
>>>> On 02/28/2013 06:32 PM, nadya williams wrote:
>>>>> Hi Guillermo,
>>>>>
>>>>> there are a few issues here.
>>>>> On Feb 28, 2013, at 12:47 AM, Guillermo Marco Puche wrote:
>>>>>
>>>>>> Hello Luca,
>>>>>>
>>>>>> I currently can't run Opal jobs with Condor job scheduler:
>>>>>>
>>>>>> Here's my basic app: bwa.xml --> http://pastebin.com/uGqvvBki
>>>>>> I know it has empty parameters but it's for testing purposes at  
>>>>>> this moment. All parameters and flags are run in a shell script  
>>>>>> invoked by condor job file.
>>>>> your xml file is not correct. You are using your condor.submit  
>>>>> file  in place of an executable:
>>>>> <binaryLocation>/opt/web/opal_scripts/bwa/bwa.condor</ 
>>>>> binaryLocation>
>>>>> Instead, here you need to use your /opt/web/opal_scripts/bwa/ 
>>>>> bwa.sh
>>>>> and any other parameters from which opal will make condor_submit  
>>>>> file.  Opal v 2.5 has condor.expr.file
>>>>> variable in opal.properties file:
>>>>> # Enable if there are server-specific condor expressions. Put  
>>>>> expressions in the file
>>>>> #condor.expr.file=/opt/opal/etc/condor.expr
>>>>>
>>>>> This is a file  (condor submit syntax) that needs to be used to  
>>>>> tell opal to add extra parameters  to every submit file that is  
>>>>> generated.
>>>>> This allows for server-side specific variables to be added.
>>>>>
>>>>>>
>>>>>> I want opal to execute my bwa.condor file (condor job file)  
>>>>>> which currently works with condor_submit command but not with  
>>>>>> Opal.
>>>>> this is not going to happen using your current xml file. The way  
>>>>> condor+opal work is opal generates condor submit file
>>>>> from the parameters given in xml file. You have a universe that  
>>>>> we did not test with condor before.
>>>>> Currently, opal+condor is working with  vanila or parallel  
>>>>> universe only.
>>>>>
>>>>> You can use a workaround:
>>>>>
>>>>> I suggest you try to make a wrapper script and use it in  
>>>>> <binaryLocation> in xml file.
>>>>> In you xml file add properties like
>>>>> (1)  condor submit file (untagged parameter for upload of  the  
>>>>> submit file) as
>>>>>           <param>
>>>>>                 <id>submitFile</id>
>>>>>                 <paramType>FILE</paramType>
>>>>>                 <ioType>INPUT</ioType>
>>>>>                 <required>true</required>
>>>>>                 <textDesc>upload a condor submit file </textDesc>
>>>>>             </param>
>>>>>
>>>>> (2)  use  Fork Job Manager   as   
>>>>> <jobManagerFQCN>edu.sdsc.nbcr.opal.manager.ForkJobManager</ 
>>>>> jobManagerFQCN>
>>>>> (3)  use  <parallel>false</parallel>
>>>>>
>>>>> please see apbs_parallel_1.3.xml  in the opal distro for an  
>>>>> example.
>>>>> Your wrapper script need to understand that it supposed to look  
>>>>> for a submit file (check for presence)
>>>>>  and then  condor submission via "condor_submit yourfile"
>>>>>
>>>>> This way you will have a flexibility to create "any"  submit  
>>>>> file and use any universe  and other specifics of the
>>>>> condor submission that we currently don't handle for simple cases.
>>>>>
>>>>> Regards,
>>>>> Nadya
>>>>>
>>>>>
>>>>>>
>>>>>> Here's the content of bwa.condor: http://pastebin.com/P9GNwriJ
>>>>>> And here the bwa.sh invoked by bwa.condor to be executed on  
>>>>>> remote cluster: http://pastebin.com/dWzQa92E
>>>>>>
>>>>>> Best regards,
>>>>>> Guillermo.
>>>>>>
>>>>>>
>>>>>> On 02/27/2013 11:17 PM, Luca Clementi wrote:
>>>>>>> On Wed, Feb 27, 2013 at 4:46 AM, Guillermo Marco Puche
>>>>>>> <gui...@si...> wrote:
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I would like to know what are the benefits/extras of using  
>>>>>>>> Condor
>>>>>>>> job.scheduler with Opal.
>>>>>>> The jobs you submit to Opal will be executed using Condor.
>>>>>>> Opal simply gives you a web service interface and then it has
>>>>>>> different back-end to actually execute your jobs (condor, sge,  
>>>>>>> pbs,
>>>>>>> etc.).
>>>>>>>
>>>>>>>> What's the difference between job scheduler and submitting  
>>>>>>>> jobs to Condor
>>>>>>>> straight with condor_submit?
>>>>>>> you mean the difference between using Opal vs using  
>>>>>>> condor_submit?
>>>>>>> If you use Opal you can invoke the lanuchJob operation using
>>>>>>> web-service standard (we provide python and java client side
>>>>>>> libraries).
>>>>>>> If you use condor you have to ssh to a machine (aka have an  
>>>>>>> account)
>>>>>>> and then you need to create a submission script and execute
>>>>>>> condor_submit.
>>>>>>>
>>>>>>>
>>>>>>> In NBCR We use Opal to submit job from web portal (where you  
>>>>>>> have 1
>>>>>>> user the web portal which is in charge of running different  
>>>>>>> simulation
>>>>>>> and opal takes care of creating working directories staging  
>>>>>>> input and
>>>>>>> outputs etc.).
>>>>>>>
>>>>>>>
>>>>>>> Luca
>>>>>>
>>>>>>
>>>>>> -- 
>>>>>> <1MjpCpe.png> G.MARCO: Informatician at Sistemas Genómicos S.L
>>>>>> phone: 0034635197460
>>>>>> web: www.sistemasgenomicos.com
>>>>>> ------------------------------------------------------------------------------
>>>>>> Everyone hates slow websites. So do we.
>>>>>> Make your web apps faster with AppDynamics
>>>>>> Download AppDynamics Lite for free today:
>>>>>> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
>>>>>> Opaltoolkit-users mailing list
>>>>>> Opa...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>>>>>
>>>>> Nadya Williams                 University of California, San Diego
>>>>> na...@sd...             9500 Gilman Dr. MC 0446
>>>>> +1 858 534 1820 (ofc)      La Jolla, CA 92093-0446
>>>>> +1 858 822 1619 (fax)      USA
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Everyone hates slow websites. So do we.
>>>> Make your web apps faster with AppDynamics
>>>> Download AppDynamics Lite for free today:
>>>> http://p.sf.net/sfu/appdyn_d2d_feb
>>>>
>>>>
>>>> _______________________________________________
>>>> Opaltoolkit-users mailing list
>>>> Opa...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
>>> Opaltoolkit-users mailing list
>>> Opa...@li...
>>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>>
>> Nadya Williams                 University of California, San Diego
>> na...@sd...             9500 Gilman Dr. MC 0446
>> +1 858 534 1820 (ofc)      La Jolla, CA 92093-0446
>> +1 858 822 1619 (fax)      USA
>>
>>
>>

[Opaltoolkit-users] Opal security question

[Guillermo M. P. <gui...@si...>]

Hello,

Since it seems that my Opal setup is running now I’m interested in user 
authentication for web services.

Is GSI globus security the only security available for Opal?

I would like to maybe try out a different thing since Globus certificate 
manual pages are very confused and I was unable to set it up a few weeks 
ago.


Thank you.

Best regards,
Guillermo.

[Opaltoolkit-users] Fwd: Re: Opal job scheduler benefits

[Guillermo M. P. <gui...@si...>]

Guillermo,
what is your xml file now? Your xml file should define a wrapper script 
  that will call your bwa.sh
and define a  Fork job manager.

On Mar 4, 2013, at 7:52 AM, Guillermo Marco Puche wrote:

> Hello,
>
> I've been following your guideline.
>
> I don't get opal errors now, even though job stays on state 1:
>
> Date and time : 	*3/4/2013 4:45:09 PM*
> JobId : 	appBWA_SH13623864602351552853141
> Status code: 	1
> Message: 	Launching executable
>
>
> Here's my opal/etc/condor.expr:
>
> universe = grid
> grid_resource = batch sge mastablasta@cacique
> output = test.out
> error = test.error
> log = test.log
> should_transfer_files = YES
> transfer_output = true
> stream_output = true
> when_to_transfer_output = ON_EXIT_OR_EVICT
> queue
It looks like you are mixing calling condor and sge which should not be 
the case.

you need to look at the resulting submit file that is produced by opal.
Opal "knows" only vanila and parallel. I don't know how condor will 
treat a submit file where
universe  or queue is defined multiple times.   This is why i think the 
condor job manager will not
work for your specific case and you need to submit your condor job via 
Fork job manager
>
> And here my bwa.sh (executable called inside bwa_sh.xml):
>
> #!/bin/bash
> #$ -V
> ### nombre
> #$ -N bwa_bosco
> ### directorio de trabajo
> #$ -cwd
> ### juntar los output
> #####$ -j y
> ### seleccionar all.q
> #$ -q all.q
>
> cd /home/mastablasta
> bwa aln /home/mastablasta/ref/hg19.fa /home/mastablasta/input/HapMap_2.fastq -t 8 > /home/mastablasta/output/tmp/HapMap.right.sai
not quite right.  This is a submit file for sge job, not for a fork 
  fork job.  Your wrapper script should check for the input file
(your condor submit  file) that you upload via opal dashboard  and call 
condor submit with it.

> This should work. I've tested submitting it with condor_submit and 
> works well, job is queued on remote SGE cluster.
the command you use here for a command line needs to be reproduced in 
your wrapper script.

>
> But with Opal I’m getting glideinjobs in condor_q when no glidein 
> universe has been specified in condor.expr and 4 jobs being spawned in 
> remote SGE queue, which is very weird. But no signs of BWA process.
>
> local condor_q Opal machine:
>
> $ condor_q
> -- Submitter: brugal : <192.168.6.2:11000?sock=2009_e522_3> : brugal
>   ID      OWNER            SUBMITTED     RUN_TIME ST PRI SIZE CMD
>     9.0   mastablasta     3/4  09:41   0+00:00:00 I  0   0.0  bwa.sh
>     9.1   mastablasta     3/4  09:41   0+00:00:00 I  0   0.0  bwa.sh
you submitted 2 jobs here via your opal interface (different job ids)
>       
>    10.0   mastablasta     3/4  09:41   0+00:16:39 R  0   0.0  glidein_wrapper.sh
>    11.0   mastablasta     3/4  09:41   0+00:16:39 R  0   0.0  glidein_wrapper.sh
>    12.0   mastablasta     3/4  09:41   0+00:16:11 R  0   0.0  glidein_wrapper.sh
>    13.0   mastablasta     3/4  09:41   0+00:16:10 R  0   0.0  glidein_wrapper.sh
i can only guess here, but your condor submit file may have two queue 
statements, one form your condor.expr and
one that opal writes, hence condor submits 2 jobs per 2 queue statements.

> 6 jobs; 0 completed, 0 removed, 2 idle, 4 running, 0 held, 0 suspended
>
> Here's remote SGE queue:
>
> $ qstat
> job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID
> -----------------------------------------------------------------------------------------------------------------
>       61 0.55500 bl_a29aa29 mastablasta  r     03/04/2013 17:31:30all.q@compute-0-0.local             1
>       62 0.55500 bl_f1cbb6c mastablasta  r     03/04/2013 17:31:30all.q@compute-0-0.local             1
>       63 0.55500 bl_1dc49f4 mastablasta  r     03/04/2013 17:32:00all.q@compute-0-0.local             1
>       64 0.55500 bl_ced1f94 mastablasta  r     03/04/2013 17:32:00all.q@compute-0-0.local             1

what is the output of "qstat -j 61" ?

nadya

>
> On 03/01/2013 09:02 AM, Guillermo Marco Puche wrote:
>> Hello Nadya,
>>
>> Thank you for the information. This starts to make sense.
>> I had no idea on how to pass Opal my Condor config.
>>
>> I'm going to try to make this work with Grid universe. I'll report asap.
>>
>>
>> Once again, thank you very much.
>>
>> Best regards,
>> Guillermo.
>>
>> On 02/28/2013 06:32 PM, nadya williams wrote:
>>> Hi Guillermo,
>>>
>>> there are a few issues here.
>>> On Feb 28, 2013, at 12:47 AM, Guillermo Marco Puche wrote:
>>>
>>>> Hello Luca,
>>>>
>>>> I currently can't run Opal jobs with Condor job scheduler:
>>>>
>>>> Here's my basic app: bwa.xml --> http://pastebin.com/uGqvvBki
>>>> I know it has empty parameters but it's for testing purposes at 
>>>> this moment. All parameters and flags are run in a shell script 
>>>> invoked by condor job file.
>>> your xml file is not correct. You are using your condor.submit file 
>>>  in place of an executable:
>>> <binaryLocation>/opt/web/opal_scripts/bwa/bwa.condor</binaryLocation>
>>> Instead, here you need to use your /opt/web/opal_scripts/bwa/bwa.sh
>>> and any other parameters from which opal will make condor_submit 
>>> file.  Opal v 2.5 has condor.expr.file
>>> variable in opal.properties file:
>>> # Enable if there are server-specific condor expressions. Put 
>>> expressions in the file
>>> #condor.expr.file=/opt/opal/etc/condor.expr
>>>
>>> This is a file  (condor submit syntax) that needs to be used to tell 
>>> opal to add extra parameters  to every submit file that is generated.
>>> This allows for server-side specific variables to be added.
>>>
>>>>
>>>> I want opal to execute my bwa.condor file (condor job file) which 
>>>> currently works with condor_submit command but not with Opal.
>>> this is not going to happen using your current xml file. The way 
>>> condor+opal work is opal generates condor submit file
>>> from the parameters given in xml file. You have a universe that we 
>>> did not test with condor before.
>>> Currently, opal+condor is working with  vanila or parallel universe 
>>> only.
>>>
>>> You can use a workaround:
>>>
>>> I suggest you try to make a wrapper script and use it in 
>>> <binaryLocation> in xml file.
>>> In you xml file add properties like
>>> (1) condor submit file (untagged parameter for upload of  the submit 
>>> file) as
>>>           <param>
>>> <id>submitFile</id>
>>> <paramType>FILE</paramType>
>>> <ioType>INPUT</ioType>
>>> <required>true</required>
>>>                 <textDesc>upload a condor submit file </textDesc>
>>>             </param>
>>>
>>> (2)  use  Fork Job Manager   as 
>>>  <jobManagerFQCN>edu.sdsc.nbcr.opal.manager.ForkJobManager</jobManagerFQCN>
>>> (3)  use  <parallel>false</parallel>
>>>
>>> please see apbs_parallel_1.3.xml  in the opal distro for an example.
>>> Your wrapper script need to understand that it supposed to look for 
>>> a submit file (check for presence)
>>>  and then  condor submission via "condor_submit yourfile"
>>>
>>> This way you will have a flexibility to create "any"  submit file 
>>> and use any universe  and other specifics of the
>>> condor submission that we currently don't handle for simple cases.
>>>
>>> Regards,
>>> Nadya
>>>
>>>
>>>>
>>>> Here's the content of bwa.condor: http://pastebin.com/P9GNwriJ
>>>> And here the bwa.sh invoked by bwa.condor to be executed on remote 
>>>> cluster: http://pastebin.com/dWzQa92E
>>>>
>>>> Best regards,
>>>> Guillermo.
>>>>
>>>>
>>>> On 02/27/2013 11:17 PM, Luca Clementi wrote:
>>>>> On Wed, Feb 27, 2013 at 4:46 AM, Guillermo Marco Puche
>>>>> <gui...@si...>  wrote:
>>>>>> Hello,
>>>>>>
>>>>>> I would like to know what are the benefits/extras of using Condor
>>>>>> job.scheduler with Opal.
>>>>> The jobs you submit to Opal will be executed using Condor.
>>>>> Opal simply gives you a web service interface and then it has
>>>>> different back-end to actually execute your jobs (condor, sge, pbs,
>>>>> etc.).
>>>>>
>>>>>> What's the difference between job scheduler and submitting jobs to Condor
>>>>>> straight with condor_submit?
>>>>> you mean the difference between using Opal vs using condor_submit?
>>>>> If you use Opal you can invoke the lanuchJob operation using
>>>>> web-service standard (we provide python and java client side
>>>>> libraries).
>>>>> If you use condor you have to ssh to a machine (aka have an account)
>>>>> and then you need to create a submission script and execute
>>>>> condor_submit.
>>>>>
>>>>>
>>>>> In NBCR We use Opal to submit job from web portal (where you have 1
>>>>> user the web portal which is in charge of running different simulation
>>>>> and opal takes care of creating working directories staging input and
>>>>> outputs etc.).
>>>>>
>>>>>
>>>>> Luca
>>>>
>>>>
>>>> -- 
>>>> <1MjpCpe.png> <http://i.imgur.com/1MjpCpe.png> *g.marco*: 
>>>> Informatician at Sistemas Genómicos S.L <x-msg://69/#>
>>>> phone: 0034635197460 <callto:0034635197460>
>>>> web: www.sistemasgenomicos.com <http://www.sistemasgenomicos.com/>
>>>> ------------------------------------------------------------------------------
>>>> Everyone hates slow websites. So do we.
>>>> Make your web apps faster with AppDynamics
>>>> Download AppDynamics Lite for free today:
>>>> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
>>>> Opaltoolkit-users mailing list
>>>> Opa...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>>>
>>> Nadya Williams  University of California, San Diego
>>> na...@sd... <mailto:na...@sd...>             9500 Gilman Dr. 
>>> MC 0446
>>> +1 858 534 1820 (ofc)      La Jolla, CA 92093-0446
>>> +1 858 822 1619 (fax)      USA
>>>
>>>
>>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_feb
>>
>>
>> _______________________________________________
>> Opaltoolkit-users mailing list
>> Opa...@li...
>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users

Nadya Williams              University of California, San Diego
na...@sd... <mailto:na...@sd...>             9500 Gilman Dr. MC 0446
+1 858 534 1820 (ofc)      La Jolla, CA 92093-0446
+1 858 822 1619 (fax)      USA

Re: [Opaltoolkit-users] Opal job scheduler benefits

[nadya w. <na...@sd...>]

Guillermo,
what is your xml file now? Your xml file should define a wrapper script  that will call your bwa.sh
and define a  Fork job manager. 

On Mar 4, 2013, at 7:52 AM, Guillermo Marco Puche wrote:

> Hello,
> 
> I've been following your guideline.
> 
> I don't get opal errors now, even though job stays on state 1:
> 
> Date and time :	3/4/2013 4:45:09 PM
> JobId :	appBWA_SH13623864602351552853141
> Status code:	1
> Message:	Launching executable
> Here's my opal/etc/condor.expr:
> 
> universe = grid
> grid_resource = batch sge mastablasta@cacique
> output = test.out
> error = test.error
> log = test.log
> should_transfer_files = YES
> transfer_output = true
> stream_output = true
> when_to_transfer_output = ON_EXIT_OR_EVICT
> queue
It looks like you are mixing calling condor and sge which should not be the case. 

you need to look at the resulting submit file that is produced by opal.  
Opal "knows" only vanila and parallel. I don't know how condor will treat a submit file where
universe  or queue is defined multiple times.   This is why i think the condor job manager will not 
work for your specific case and you need to submit your condor job via Fork job manager
> 
> And here my bwa.sh (executable called inside bwa_sh.xml):
> 
> #!/bin/bash
> #$ -V
> ### nombre
> #$ -N bwa_bosco
> ### directorio de trabajo
> #$ -cwd
> ### juntar los output
> #####$ -j y 
> ### seleccionar all.q
> #$ -q all.q
> 
> cd /home/mastablasta
> bwa aln /home/mastablasta/ref/hg19.fa /home/mastablasta/input/HapMap_2.fastq -t 8 > /home/mastablasta/output/tmp/HapMap.right.sai
not quite right.  This is a submit file for sge job, not for a fork  fork job.  Your wrapper script should check for the input file
(your condor submit  file) that you upload via opal dashboard  and call condor submit with it. 

> This should work. I've tested submitting it with condor_submit and works well, job is queued on remote SGE cluster.
the command you use here for a command line needs to be reproduced in your wrapper script. 

> 
> But with Opal I’m getting glideinjobs in condor_q when no glidein universe has been specified in condor.expr and 4 jobs being spawned in remote SGE queue, which is very weird. But no signs of BWA process. 
> 
> local condor_q Opal machine:
> 
> $ condor_q
> -- Submitter: brugal : <192.168.6.2:11000?sock=2009_e522_3> : brugal
>  ID      OWNER            SUBMITTED     RUN_TIME ST PRI SIZE CMD               
>    9.0   mastablasta     3/4  09:41   0+00:00:00 I  0   0.0  bwa.sh            
>    9.1   mastablasta     3/4  09:41   0+00:00:00 I  0   0.0  bwa.sh       
you submitted 2 jobs here via your opal interface (different job ids)
>      
>   10.0   mastablasta     3/4  09:41   0+00:16:39 R  0   0.0  glidein_wrapper.sh
>   11.0   mastablasta     3/4  09:41   0+00:16:39 R  0   0.0  glidein_wrapper.sh
>   12.0   mastablasta     3/4  09:41   0+00:16:11 R  0   0.0  glidein_wrapper.sh
>   13.0   mastablasta     3/4  09:41   0+00:16:10 R  0   0.0  glidein_wrapper.sh
i can only guess here, but your condor submit file may have two queue statements, one form your condor.expr and
one that opal writes, hence condor submits 2 jobs per 2 queue statements. 

> 6 jobs; 0 completed, 0 removed, 2 idle, 4 running, 0 held, 0 suspended
> 
> Here's remote SGE queue:
> 
> $ qstat
> job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID 
> -----------------------------------------------------------------------------------------------------------------
>      61 0.55500 bl_a29aa29 mastablasta  r     03/04/2013 17:31:30 all.q@compute-0-0.local            1        
>      62 0.55500 bl_f1cbb6c mastablasta  r     03/04/2013 17:31:30 all.q@compute-0-0.local            1        
>      63 0.55500 bl_1dc49f4 mastablasta  r     03/04/2013 17:32:00 all.q@compute-0-0.local            1        
>      64 0.55500 bl_ced1f94 mastablasta  r     03/04/2013 17:32:00 all.q@compute-0-0.local            1   

what is the output of "qstat -j 61" ? 

nadya

> 
> On 03/01/2013 09:02 AM, Guillermo Marco Puche wrote:
>> Hello Nadya,
>> 
>> Thank you for the information. This starts to make sense. 
>> I had no idea on how to pass Opal my Condor config.
>> 
>> I'm going to try to make this work with Grid universe. I'll report asap.
>> 
>> 
>> Once again, thank you very much.
>> 
>> Best regards,
>> Guillermo.
>> 
>> On 02/28/2013 06:32 PM, nadya williams wrote:
>>> Hi Guillermo,
>>> 
>>> there are a few issues here. 
>>> On Feb 28, 2013, at 12:47 AM, Guillermo Marco Puche wrote:
>>> 
>>>> Hello Luca,
>>>> 
>>>> I currently can't run Opal jobs with Condor job scheduler:
>>>> 
>>>> Here's my basic app: bwa.xml --> http://pastebin.com/uGqvvBki
>>>> I know it has empty parameters but it's for testing purposes at this moment. All parameters and flags are run in a shell script invoked by condor job file.
>>> your xml file is not correct. You are using your condor.submit file  in place of an executable:
>>> <binaryLocation>/opt/web/opal_scripts/bwa/bwa.condor</binaryLocation>
>>> Instead, here you need to use your /opt/web/opal_scripts/bwa/bwa.sh 
>>> and any other parameters from which opal will make condor_submit file.  Opal v 2.5 has condor.expr.file
>>> variable in opal.properties file:
>>> # Enable if there are server-specific condor expressions. Put expressions in the file
>>> #condor.expr.file=/opt/opal/etc/condor.expr
>>> 
>>> This is a file  (condor submit syntax) that needs to be used to tell opal to add extra parameters  to every submit file that is generated. 
>>> This allows for server-side specific variables to be added.  
>>> 
>>>> 
>>>> I want opal to execute my bwa.condor file (condor job file) which currently works with condor_submit command but not with Opal.
>>> this is not going to happen using your current xml file. The way condor+opal work is opal generates condor submit file
>>> from the parameters given in xml file. You have a universe that we did not test with condor before. 
>>> Currently, opal+condor is working with  vanila or parallel universe only.  
>>> 
>>> You can use a workaround:  
>>> 
>>> I suggest you try to make a wrapper script and use it in <binaryLocation> in xml file. 
>>> In you xml file add properties like
>>> (1)
>>>                condor submit file (untagged parameter for upload of  the submit file) as
>>>           <param>
>>>                 <id>submitFile</id>
>>>                 <paramType>FILE</paramType>
>>>                 <ioType>INPUT</ioType>
>>>                 <required>true</required>
>>>                 <textDesc>upload a condor submit file </textDesc>
>>>             </param>
>>> 
>>> (2)  use  Fork Job Manager   as  <jobManagerFQCN>edu.sdsc.nbcr.opal.manager.ForkJobManager</jobManagerFQCN>
>>> (3)  use  <parallel>false</parallel>
>>> 
>>> please see apbs_parallel_1.3.xml  in the opal distro for an example. 
>>> Your wrapper script need to understand that it supposed to look for a submit file (check for presence) 
>>>  and then  condor submission via "condor_submit yourfile"
>>> 
>>> This way you will have a flexibility to create "any"  submit file and use any universe  and other specifics of the 
>>> condor submission that we currently don't handle for simple cases. 
>>> 
>>> Regards,
>>> Nadya
>>> 
>>> 
>>>> 
>>>> Here's the content of bwa.condor: http://pastebin.com/P9GNwriJ
>>>> And here the bwa.sh invoked by bwa.condor to be executed on remote cluster: http://pastebin.com/dWzQa92E
>>>> 
>>>> Best regards,
>>>> Guillermo.
>>>> 
>>>> 
>>>> On 02/27/2013 11:17 PM, Luca Clementi wrote:
>>>>> On Wed, Feb 27, 2013 at 4:46 AM, Guillermo Marco Puche
>>>>> <gui...@si...> wrote:
>>>>>> Hello,
>>>>>> 
>>>>>> I would like to know what are the benefits/extras of using Condor
>>>>>> job.scheduler with Opal.
>>>>> The jobs you submit to Opal will be executed using Condor.
>>>>> Opal simply gives you a web service interface and then it has
>>>>> different back-end to actually execute your jobs (condor, sge, pbs,
>>>>> etc.).
>>>>> 
>>>>>> What's the difference between job scheduler and submitting jobs to Condor
>>>>>> straight with condor_submit?
>>>>> you mean the difference between using Opal vs using condor_submit?
>>>>> If you use Opal you can invoke the lanuchJob operation using
>>>>> web-service standard (we provide python and java client side
>>>>> libraries).
>>>>> If you use condor you have to ssh to a machine (aka have an account)
>>>>> and then you need to create a submission script and execute
>>>>> condor_submit.
>>>>> 
>>>>> 
>>>>> In NBCR We use Opal to submit job from web portal (where you have 1
>>>>> user the web portal which is in charge of running different simulation
>>>>> and opal takes care of creating working directories staging input and
>>>>> outputs etc.).
>>>>> 
>>>>> 
>>>>> Luca
>>>> 
>>>> 
>>>> -- 
>>>> <1MjpCpe.png> G.MARCO: Informatician at Sistemas Genómicos S.L
>>>> phone: 0034635197460
>>>> web: www.sistemasgenomicos.com
>>>> ------------------------------------------------------------------------------
>>>> Everyone hates slow websites. So do we.
>>>> Make your web apps faster with AppDynamics
>>>> Download AppDynamics Lite for free today:
>>>> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
>>>> Opaltoolkit-users mailing list
>>>> Opa...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>>> 
>>> Nadya Williams                 University of California, San Diego
>>> na...@sd...             9500 Gilman Dr. MC 0446
>>> +1 858 534 1820 (ofc)      La Jolla, CA 92093-0446
>>> +1 858 822 1619 (fax)      USA
>>> 
>>> 
>>> 
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_feb
>> 
>> 
>> _______________________________________________
>> Opaltoolkit-users mailing list
>> Opa...@li...
>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
> 
> 
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users

Nadya Williams                 University of California, San Diego
na...@sd...             9500 Gilman Dr. MC 0446
+1 858 534 1820 (ofc)      La Jolla, CA 92093-0446
+1 858 822 1619 (fax)      USA

Re: [Opaltoolkit-users] Opal job scheduler benefits

[Guillermo M. P. <gui...@si...>]

Hello,

I've been following your guideline.

I don't get opal errors now, even though job stays on state 1:

Date and time : 	*3/4/2013 4:45:09 PM*
JobId : 	appBWA_SH13623864602351552853141
Status code: 	1
Message: 	Launching executable


Here's my opal/etc/condor.expr:

universe = grid
grid_resource = batch sge mastablasta@cacique
output = test.out
error = test.error
log = test.log
should_transfer_files = YES

transfer_output = true
stream_output = true

when_to_transfer_output = ON_EXIT_OR_EVICT

queue


And here my bwa.sh (executable called inside bwa_sh.xml):

#!/bin/bash
#$ -V
### nombre
#$ -N bwa_bosco
### directorio de trabajo
#$ -cwd
### juntar los output
#####$ -j y
### seleccionar all.q
#$ -q all.q

cd /home/mastablasta
bwa aln /home/mastablasta/ref/hg19.fa /home/mastablasta/input/HapMap_2.fastq -t 8 > /home/mastablasta/output/tmp/HapMap.right.sai

This should work. I've tested submitting it with condor_submit and works 
well, job is queued on remote SGE cluster.

But with Opal I'm getting glideinjobs in condor_q when no glidein 
universe has been specified in condor.expr and 4 jobs being spawned in 
remote SGE queue, which is very weird. But no signs of BWA process.

local condor_q Opal machine:

$ condor_q

-- Submitter: brugal : <192.168.6.2:11000?sock=2009_e522_3> : brugal

  ID      OWNER            SUBMITTED     RUN_TIME ST PRI SIZE CMD

    9.0   mastablasta     3/4  09:41   0+00:00:00 I  0   0.0  bwa.sh

    9.1   mastablasta     3/4  09:41   0+00:00:00 I  0   0.0  bwa.sh

   10.0   mastablasta     3/4  09:41   0+00:16:39 R  0   0.0  glidein_wrapper.sh

   11.0   mastablasta     3/4  09:41   0+00:16:39 R  0   0.0  glidein_wrapper.sh

   12.0   mastablasta     3/4  09:41   0+00:16:11 R  0   0.0  glidein_wrapper.sh

   13.0   mastablasta     3/4  09:41   0+00:16:10 R  0   0.0  glidein_wrapper.sh

6 jobs; 0 completed, 0 removed, 2 idle, 4 running, 0 held, 0 suspended

Here's remote SGE queue:

$ qstat

job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID

-----------------------------------------------------------------------------------------------------------------

      61 0.55500 bl_a29aa29 mastablasta  r     03/04/2013 17:31:30 all.q@compute-0-0.local            1

      62 0.55500 bl_f1cbb6c mastablasta  r     03/04/2013 17:31:30 all.q@compute-0-0.local            1

      63 0.55500 bl_1dc49f4 mastablasta  r     03/04/2013 17:32:00 all.q@compute-0-0.local            1

      64 0.55500 bl_ced1f94 mastablasta  r     03/04/2013 17:32:00 all.q@compute-0-0.local            1


On 03/01/2013 09:02 AM, Guillermo Marco Puche wrote:
> Hello Nadya,
>
> Thank you for the information. This starts to make sense.
> I had no idea on how to pass Opal my Condor config.
>
> I'm going to try to make this work with Grid universe. I'll report asap.
>
>
> Once again, thank you very much.
>
> Best regards,
> Guillermo.
>
> On 02/28/2013 06:32 PM, nadya williams wrote:
>> Hi Guillermo,
>>
>> there are a few issues here.
>> On Feb 28, 2013, at 12:47 AM, Guillermo Marco Puche wrote:
>>
>>> Hello Luca,
>>>
>>> I currently can't run Opal jobs with Condor job scheduler:
>>>
>>> Here's my basic app: bwa.xml --> http://pastebin.com/uGqvvBki
>>> I know it has empty parameters but it's for testing purposes at this 
>>> moment. All parameters and flags are run in a shell script invoked 
>>> by condor job file.
>> your xml file is not correct. You are using your condor.submit file 
>>  in place of an executable:
>> <binaryLocation>/opt/web/opal_scripts/bwa/bwa.condor</binaryLocation>
>> Instead, here you need to use your /opt/web/opal_scripts/bwa/bwa.sh
>> and any other parameters from which opal will make condor_submit 
>> file.  Opal v 2.5 has condor.expr.file
>> variable in opal.properties file:
>> # Enable if there are server-specific condor expressions. Put 
>> expressions in the file
>> #condor.expr.file=/opt/opal/etc/condor.expr
>>
>> This is a file  (condor submit syntax) that needs to be used to tell 
>> opal to add extra parameters  to every submit file that is generated.
>> This allows for server-side specific variables to be added.
>>
>>>
>>> I want opal to execute my bwa.condor file (condor job file) which 
>>> currently works with condor_submit command but not with Opal.
>> this is not going to happen using your current xml file. The way 
>> condor+opal work is opal generates condor submit file
>> from the parameters given in xml file. You have a universe that we 
>> did not test with condor before.
>> Currently, opal+condor is working with  vanila or parallel universe 
>> only.
>>
>> You can use a workaround:
>>
>> I suggest you try to make a wrapper script and use it in 
>> <binaryLocation> in xml file.
>> In you xml file add properties like
>> (1) condor submit file (untagged parameter for upload of  the submit 
>> file) as
>>           <param>
>>                 <id>submitFile</id>
>> <paramType>FILE</paramType>
>>                 <ioType>INPUT</ioType>
>>                 <required>true</required>
>>                 <textDesc>upload a condor submit file </textDesc>
>>             </param>
>>
>> (2)  use  Fork Job Manager   as 
>>  <jobManagerFQCN>edu.sdsc.nbcr.opal.manager.ForkJobManager</jobManagerFQCN>
>> (3)  use  <parallel>false</parallel>
>>
>> please see apbs_parallel_1.3.xml  in the opal distro for an example.
>> Your wrapper script need to understand that it supposed to look for a 
>> submit file (check for presence)
>>  and then  condor submission via "condor_submit yourfile"
>>
>> This way you will have a flexibility to create "any"  submit file and 
>> use any universe  and other specifics of the
>> condor submission that we currently don't handle for simple cases.
>>
>> Regards,
>> Nadya
>>
>>
>>>
>>> Here's the content of bwa.condor: http://pastebin.com/P9GNwriJ
>>> And here the bwa.sh invoked by bwa.condor to be executed on remote 
>>> cluster: http://pastebin.com/dWzQa92E
>>>
>>> Best regards,
>>> Guillermo.
>>>
>>>
>>> On 02/27/2013 11:17 PM, Luca Clementi wrote:
>>>> On Wed, Feb 27, 2013 at 4:46 AM, Guillermo Marco Puche
>>>> <gui...@si...>  wrote:
>>>>> Hello,
>>>>>
>>>>> I would like to know what are the benefits/extras of using Condor
>>>>> job.scheduler with Opal.
>>>> The jobs you submit to Opal will be executed using Condor.
>>>> Opal simply gives you a web service interface and then it has
>>>> different back-end to actually execute your jobs (condor, sge, pbs,
>>>> etc.).
>>>>
>>>>> What's the difference between job scheduler and submitting jobs to Condor
>>>>> straight with condor_submit?
>>>> you mean the difference between using Opal vs using condor_submit?
>>>> If you use Opal you can invoke the lanuchJob operation using
>>>> web-service standard (we provide python and java client side
>>>> libraries).
>>>> If you use condor you have to ssh to a machine (aka have an account)
>>>> and then you need to create a submission script and execute
>>>> condor_submit.
>>>>
>>>>
>>>> In NBCR We use Opal to submit job from web portal (where you have 1
>>>> user the web portal which is in charge of running different simulation
>>>> and opal takes care of creating working directories staging input and
>>>> outputs etc.).
>>>>
>>>>
>>>> Luca
>>>
>>>
>>> -- 
>>> <1MjpCpe.png> <http://i.imgur.com/1MjpCpe.png> *g.marco*: 
>>> Informatician at Sistemas Genómicos S.L <x-msg://69/#>
>>> phone: 0034635197460 <callto:0034635197460>
>>> web: www.sistemasgenomicos.com <http://www.sistemasgenomicos.com/>
>>> ------------------------------------------------------------------------------
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
>>> Opaltoolkit-users mailing list
>>> Opa...@li...
>>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>>
>> Nadya Williams  University of California, San Diego
>> na...@sd... <mailto:na...@sd...>             9500 Gilman Dr. MC 
>> 0446
>> +1 858 534 1820 (ofc)      La Jolla, CA 92093-0446
>> +1 858 822 1619 (fax)      USA
>>
>>
>>
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
>
>
> _______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users

[Opaltoolkit-users] Fwd: Re: Heap Size for big input/output files

[Guillermo M. P. <gui...@si...>]

Hello,

I'm going try more settings.
I hope I can work with bigger files it's a must for me.

Best regards,
Guillermo.

On 03/02/2013 04:31 AM, Luca Clementi wrote:
> On Fri, Mar 1, 2013 at 8:45 AM, Guillermo Marco Puche
> <gui...@si...>  wrote:
>> Hello,
>>
>> I'm in need of using big input and output files. Documentation at this
>> point is very confusing.
>> I've tried to increase heapsize through Tomcat7 catalina.sh script.
>>
>> Adding the following line:
>>
>> export JAVA_OPTS="-Xms6144m -Xmx15360m -XX:PermSize=64M
>> -XX:MaxPermSize=128M"
>>
>> But i still can't upload input files bigger than 100mb through Opal.
>>
> So I know you have to set the maxPostSize:
> http://tomcat.apache.org/tomcat-6.0-doc/config/http.html
>
> I tried to do some test but if your file is really big more than 100M
> I get a very odd behavior: It's like if the request content never
> arrives to opal2, it just get discharged, and there is not trace of
> that in the log...
>
>
> Luca


-- 
<http://i.imgur.com/1MjpCpe.png> *g.marco*: Informatician at Sistemas 
Genómicos S.L <#>
phone: 0034635197460 <callto:0034635197460>
web: www.sistemasgenomicos.com <http://www.sistemasgenomicos.com>

Re: [Opaltoolkit-users] Heap Size for big input/output files

[Luca C. <luc...@gm...>]

On Fri, Mar 1, 2013 at 8:45 AM, Guillermo Marco Puche
<gui...@si...> wrote:
>
> Hello,
>
> I'm in need of using big input and output files. Documentation at this
> point is very confusing.
> I've tried to increase heapsize through Tomcat7 catalina.sh script.
>
> Adding the following line:
>
> export JAVA_OPTS="-Xms6144m -Xmx15360m -XX:PermSize=64M
> -XX:MaxPermSize=128M"
>
> But i still can't upload input files bigger than 100mb through Opal.
>

So I know you have to set the maxPostSize:
http://tomcat.apache.org/tomcat-6.0-doc/config/http.html

I tried to do some test but if your file is really big more than 100M
I get a very odd behavior: It's like if the request content never
arrives to opal2, it just get discharged, and there is not trace of
that in the log...


Luca

[Opaltoolkit-users] Heap Size for big input/output files

[Guillermo M. P. <gui...@si...>]

Hello,

I'm in need of using big input and output files. Documentation at this 
point is very confusing.
I've tried to increase heapsize through Tomcat7 catalina.sh script.

Adding the following line:

export JAVA_OPTS="-Xms6144m -Xmx15360m -XX:PermSize=64M 
-XX:MaxPermSize=128M"

But i still can't upload input files bigger than 100mb through Opal.

Tomcat dashboard shows the following info:

Free memory: 4812.64 MB Total memory: 5888.00 MB Max memory: 13653.37 MB

Memory Pool 	Type 	Initial 	Total 	Maximum 	Used
PS Eden Space 	Heap memory 	1536.00 MB 	1536.00 MB 	4608.00 MB 	1075.35 
MB (23%)
PS Old Gen 	Heap memory 	4096.00 MB 	4096.00 MB 	10240.00 MB 	0.00 MB (0%)
PS Survivor Space 	Heap memory 	256.00 MB 	256.00 MB 	256.00 MB 	0.00 MB 
(0%)
Code Cache 	Non-heap memory 	2.43 MB 	2.43 MB 	48.00 MB 	1.99 MB (4%)
PS Perm Gen 	Non-heap memory 	64.00 MB 	64.00 MB 	128.00 MB 	39.77 MB (31%)



Thank you.

Best regards,
Guillermo.

[Opaltoolkit-users] Opal & Maximum heap size

[Guillermo M. P. <gui...@si...>]

Hello,

I'm in need of using big input and output files. Documentation at this 
point is very confusing.
I've tried to increase heapsize through Tomcat7 catalina.sh script.

Adding the following line:

export JAVA_OPTS="-Xms6144m -Xmx15360m -XX:PermSize=64M 
-XX:MaxPermSize=128M"

But i still can't upload input files bigger than 100mb through Opal.

Thank you.

Best regards,
Guillermo.

Re: [Opaltoolkit-users] Opal job scheduler benefits

[Guillermo M. P. <gui...@si...>]

Hello Nadya,

Thank you for the information. This starts to make sense.
I had no idea on how to pass Opal my Condor config.

I'm going to try to make this work with Grid universe. I'll report asap.


Once again, thank you very much.

Best regards,
Guillermo.

On 02/28/2013 06:32 PM, nadya williams wrote:
> Hi Guillermo,
>
> there are a few issues here.
> On Feb 28, 2013, at 12:47 AM, Guillermo Marco Puche wrote:
>
>> Hello Luca,
>>
>> I currently can't run Opal jobs with Condor job scheduler:
>>
>> Here's my basic app: bwa.xml --> http://pastebin.com/uGqvvBki
>> I know it has empty parameters but it's for testing purposes at this 
>> moment. All parameters and flags are run in a shell script invoked by 
>> condor job file.
> your xml file is not correct. You are using your condor.submit file 
>  in place of an executable:
> <binaryLocation>/opt/web/opal_scripts/bwa/bwa.condor</binaryLocation>
> Instead, here you need to use your /opt/web/opal_scripts/bwa/bwa.sh
> and any other parameters from which opal will make condor_submit file. 
>  Opal v 2.5 has condor.expr.file
> variable in opal.properties file:
> # Enable if there are server-specific condor expressions. Put 
> expressions in the file
> #condor.expr.file=/opt/opal/etc/condor.expr
>
> This is a file  (condor submit syntax) that needs to be used to tell 
> opal to add extra parameters  to every submit file that is generated.
> This allows for server-side specific variables to be added.
>
>>
>> I want opal to execute my bwa.condor file (condor job file) which 
>> currently works with condor_submit command but not with Opal.
> this is not going to happen using your current xml file. The way 
> condor+opal work is opal generates condor submit file
> from the parameters given in xml file. You have a universe that we did 
> not test with condor before.
> Currently, opal+condor is working with  vanila or parallel universe only.
>
> You can use a workaround:
>
> I suggest you try to make a wrapper script and use it in 
> <binaryLocation> in xml file.
> In you xml file add properties like
> (1) condor submit file (untagged parameter for upload of  the submit 
> file) as
>           <param>
>                 <id>submitFile</id>
>                 <paramType>FILE</paramType>
>                 <ioType>INPUT</ioType>
>                 <required>true</required>
>                 <textDesc>upload a condor submit file </textDesc>
>             </param>
>
> (2)  use  Fork Job Manager   as 
>  <jobManagerFQCN>edu.sdsc.nbcr.opal.manager.ForkJobManager</jobManagerFQCN>
> (3)  use  <parallel>false</parallel>
>
> please see apbs_parallel_1.3.xml  in the opal distro for an example.
> Your wrapper script need to understand that it supposed to look for a 
> submit file (check for presence)
>  and then  condor submission via "condor_submit yourfile"
>
> This way you will have a flexibility to create "any"  submit file and 
> use any universe  and other specifics of the
> condor submission that we currently don't handle for simple cases.
>
> Regards,
> Nadya
>
>
>>
>> Here's the content of bwa.condor: http://pastebin.com/P9GNwriJ
>> And here the bwa.sh invoked by bwa.condor to be executed on remote 
>> cluster: http://pastebin.com/dWzQa92E
>>
>> Best regards,
>> Guillermo.
>>
>>
>> On 02/27/2013 11:17 PM, Luca Clementi wrote:
>>> On Wed, Feb 27, 2013 at 4:46 AM, Guillermo Marco Puche
>>> <gui...@si...>  wrote:
>>>> Hello,
>>>>
>>>> I would like to know what are the benefits/extras of using Condor
>>>> job.scheduler with Opal.
>>> The jobs you submit to Opal will be executed using Condor.
>>> Opal simply gives you a web service interface and then it has
>>> different back-end to actually execute your jobs (condor, sge, pbs,
>>> etc.).
>>>
>>>> What's the difference between job scheduler and submitting jobs to Condor
>>>> straight with condor_submit?
>>> you mean the difference between using Opal vs using condor_submit?
>>> If you use Opal you can invoke the lanuchJob operation using
>>> web-service standard (we provide python and java client side
>>> libraries).
>>> If you use condor you have to ssh to a machine (aka have an account)
>>> and then you need to create a submission script and execute
>>> condor_submit.
>>>
>>>
>>> In NBCR We use Opal to submit job from web portal (where you have 1
>>> user the web portal which is in charge of running different simulation
>>> and opal takes care of creating working directories staging input and
>>> outputs etc.).
>>>
>>>
>>> Luca
>>
>>
>> -- 
>> <1MjpCpe.png> <http://i.imgur.com/1MjpCpe.png> *g.marco*: 
>> Informatician at Sistemas Genómicos S.L <x-msg://69/#>
>> phone: 0034635197460 <callto:0034635197460>
>> web: www.sistemasgenomicos.com <http://www.sistemasgenomicos.com/>
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
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>> Download AppDynamics Lite for free today:
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>
> Nadya Williams  University of California, San Diego
> na...@sd... <mailto:na...@sd...>             9500 Gilman Dr. MC 0446
> +1 858 534 1820 (ofc)      La Jolla, CA 92093-0446
> +1 858 822 1619 (fax)      USA
>
>
>

Re: [Opaltoolkit-users] Opal job scheduler benefits

[Guillermo M. P. <gui...@si...>]

Sorry I forgot to paste the erro i'm getting in Opal Dashboard:

  * A remote error occured while submitting the job to the remote server
  * The remote error message is: Error while running executable via
    Condor - null



On 02/28/2013 09:47 AM, Guillermo Marco Puche wrote:
> Hello Luca,
>
> I currently can't run Opal jobs with Condor job scheduler:
>
> Here's my basic app: bwa.xml --> http://pastebin.com/uGqvvBki
> I know it has empty parameters but it's for testing purposes at this 
> moment. All parameters and flags are run in a shell script invoked by 
> condor job file.
>
> I want opal to execute my bwa.condor file (condor job file) which 
> currently works with condor_submit command but not with Opal.
>
> Here's the content of bwa.condor: http://pastebin.com/P9GNwriJ
> And here the bwa.sh invoked by bwa.condor to be executed on remote 
> cluster: http://pastebin.com/dWzQa92E
>
> Best regards,
> Guillermo.
>
>
> On 02/27/2013 11:17 PM, Luca Clementi wrote:
>> On Wed, Feb 27, 2013 at 4:46 AM, Guillermo Marco Puche
>> <gui...@si...>  wrote:
>>> Hello,
>>>
>>> I would like to know what are the benefits/extras of using Condor
>>> job.scheduler with Opal.
>> The jobs you submit to Opal will be executed using Condor.
>> Opal simply gives you a web service interface and then it has
>> different back-end to actually execute your jobs (condor, sge, pbs,
>> etc.).
>>
>>> What's the difference between job scheduler and submitting jobs to Condor
>>> straight with condor_submit?
>> you mean the difference between using Opal vs using condor_submit?
>> If you use Opal you can invoke the lanuchJob operation using
>> web-service standard (we provide python and java client side
>> libraries).
>> If you use condor you have to ssh to a machine (aka have an account)
>> and then you need to create a submission script and execute
>> condor_submit.
>>
>>
>> In NBCR We use Opal to submit job from web portal (where you have 1
>> user the web portal which is in charge of running different simulation
>> and opal takes care of creating working directories staging input and
>> outputs etc.).
>>
>>
>> Luca
>
>
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
>
>
> _______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users


-- 
<http://i.imgur.com/1MjpCpe.png> *g.marco*: Informatician at Sistemas 
Genómicos S.L <#>
phone: 0034635197460 <callto:0034635197460>
web: www.sistemasgenomicos.com <http://www.sistemasgenomicos.com>

Re: [Opaltoolkit-users] Opal job scheduler benefits

[nadya w. <na...@sd...>]

Hi Guillermo,

there are a few issues here. 
On Feb 28, 2013, at 12:47 AM, Guillermo Marco Puche wrote:

> Hello Luca,
> 
> I currently can't run Opal jobs with Condor job scheduler:
> 
> Here's my basic app: bwa.xml --> http://pastebin.com/uGqvvBki
> I know it has empty parameters but it's for testing purposes at this moment. All parameters and flags are run in a shell script invoked by condor job file.
your xml file is not correct. You are using your condor.submit file  in place of an executable:
<binaryLocation>/opt/web/opal_scripts/bwa/bwa.condor</binaryLocation>
Instead, here you need to use your /opt/web/opal_scripts/bwa/bwa.sh 
and any other parameters from which opal will make condor_submit file.  Opal v 2.5 has condor.expr.file
variable in opal.properties file:
# Enable if there are server-specific condor expressions. Put expressions in the file
#condor.expr.file=/opt/opal/etc/condor.expr

This is a file  (condor submit syntax) that needs to be used to tell opal to add extra parameters  to every submit file that is generated. 
This allows for server-side specific variables to be added.  

> 
> I want opal to execute my bwa.condor file (condor job file) which currently works with condor_submit command but not with Opal.
this is not going to happen using your current xml file. The way condor+opal work is opal generates condor submit file
from the parameters given in xml file. You have a universe that we did not test with condor before. 
Currently, opal+condor is working with  vanila or parallel universe only.  

You can use a workaround:  

I suggest you try to make a wrapper script and use it in <binaryLocation> in xml file. 
In you xml file add properties like
(1)	 condor submit file (untagged parameter for upload of  the submit file) as
          <param>
                <id>submitFile</id>
                <paramType>FILE</paramType>
                <ioType>INPUT</ioType>
                <required>true</required>
                <textDesc>upload a condor submit file </textDesc>
            </param>

(2)  use  Fork Job Manager   as  <jobManagerFQCN>edu.sdsc.nbcr.opal.manager.ForkJobManager</jobManagerFQCN>
(3)  use  <parallel>false</parallel>

please see apbs_parallel_1.3.xml  in the opal distro for an example. 
Your wrapper script need to understand that it supposed to look for a submit file (check for presence) 
 and then  condor submission via "condor_submit yourfile"

This way you will have a flexibility to create "any"  submit file and use any universe  and other specifics of the 
condor submission that we currently don't handle for simple cases. 

Regards,
Nadya


> 
> Here's the content of bwa.condor: http://pastebin.com/P9GNwriJ
> And here the bwa.sh invoked by bwa.condor to be executed on remote cluster: http://pastebin.com/dWzQa92E
> 
> Best regards,
> Guillermo.
> 
> 
> On 02/27/2013 11:17 PM, Luca Clementi wrote:
>> On Wed, Feb 27, 2013 at 4:46 AM, Guillermo Marco Puche
>> <gui...@si...> wrote:
>>> Hello,
>>> 
>>> I would like to know what are the benefits/extras of using Condor
>>> job.scheduler with Opal.
>> The jobs you submit to Opal will be executed using Condor.
>> Opal simply gives you a web service interface and then it has
>> different back-end to actually execute your jobs (condor, sge, pbs,
>> etc.).
>> 
>>> What's the difference between job scheduler and submitting jobs to Condor
>>> straight with condor_submit?
>> you mean the difference between using Opal vs using condor_submit?
>> If you use Opal you can invoke the lanuchJob operation using
>> web-service standard (we provide python and java client side
>> libraries).
>> If you use condor you have to ssh to a machine (aka have an account)
>> and then you need to create a submission script and execute
>> condor_submit.
>> 
>> 
>> In NBCR We use Opal to submit job from web portal (where you have 1
>> user the web portal which is in charge of running different simulation
>> and opal takes care of creating working directories staging input and
>> outputs etc.).
>> 
>> 
>> Luca
> 
> 
> -- 
> <1MjpCpe.png> G.MARCO: Informatician at Sistemas Genómicos S.L
> phone: 0034635197460
> web: www.sistemasgenomicos.com
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users

Nadya Williams                 University of California, San Diego
na...@sd...             9500 Gilman Dr. MC 0446
+1 858 534 1820 (ofc)      La Jolla, CA 92093-0446
+1 858 822 1619 (fax)      USA

Re: [Opaltoolkit-users] Opal job scheduler benefits

[Guillermo M. P. <gui...@si...>]

Hello Luca,

I currently can't run Opal jobs with Condor job scheduler:

Here's my basic app: bwa.xml --> http://pastebin.com/uGqvvBki
I know it has empty parameters but it's for testing purposes at this 
moment. All parameters and flags are run in a shell script invoked by 
condor job file.

I want opal to execute my bwa.condor file (condor job file) which 
currently works with condor_submit command but not with Opal.

Here's the content of bwa.condor: http://pastebin.com/P9GNwriJ
And here the bwa.sh invoked by bwa.condor to be executed on remote 
cluster: http://pastebin.com/dWzQa92E

Best regards,
Guillermo.


On 02/27/2013 11:17 PM, Luca Clementi wrote:
> On Wed, Feb 27, 2013 at 4:46 AM, Guillermo Marco Puche
> <gui...@si...> wrote:
>> Hello,
>>
>> I would like to know what are the benefits/extras of using Condor
>> job.scheduler with Opal.
> The jobs you submit to Opal will be executed using Condor.
> Opal simply gives you a web service interface and then it has
> different back-end to actually execute your jobs (condor, sge, pbs,
> etc.).
>
>> What's the difference between job scheduler and submitting jobs to Condor
>> straight with condor_submit?
> you mean the difference between using Opal vs using condor_submit?
> If you use Opal you can invoke the lanuchJob operation using
> web-service standard (we provide python and java client side
> libraries).
> If you use condor you have to ssh to a machine (aka have an account)
> and then you need to create a submission script and execute
> condor_submit.
>
>
> In NBCR We use Opal to submit job from web portal (where you have 1
> user the web portal which is in charge of running different simulation
> and opal takes care of creating working directories staging input and
> outputs etc.).
>
>
> Luca


-- 
<http://i.imgur.com/1MjpCpe.png> *g.marco*: Informatician at Sistemas 
Genómicos S.L <#>
phone: 0034635197460 <callto:0034635197460>
web: www.sistemasgenomicos.com <http://www.sistemasgenomicos.com>

Re: [Opaltoolkit-users] Opal job scheduler benefits

[Luca C. <luc...@gm...>]

On Wed, Feb 27, 2013 at 4:46 AM, Guillermo Marco Puche
<gui...@si...> wrote:
> Hello,
>
> I would like to know what are the benefits/extras of using Condor
> job.scheduler with Opal.

The jobs you submit to Opal will be executed using Condor.
Opal simply gives you a web service interface and then it has
different back-end to actually execute your jobs (condor, sge, pbs,
etc.).

> What's the difference between job scheduler and submitting jobs to Condor
> straight with condor_submit?

you mean the difference between using Opal vs using condor_submit?
If you use Opal you can invoke the lanuchJob operation using
web-service standard (we provide python and java client side
libraries).
If you use condor you have to ssh to a machine (aka have an account)
and then you need to create a submission script and execute
condor_submit.


In NBCR We use Opal to submit job from web portal (where you have 1
user the web portal which is in charge of running different simulation
and opal takes care of creating working directories staging input and
outputs etc.).


Luca