Difference between revisions of "Quick Guide to Dirac"

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(Dirac client installation)
 
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'''Note: These instructions have been updated to use the 'new' dirac server at dirac.gridpp.ac.uk. If you are using the 'old' dirac server at dirac.grid.hep.ph.ic.ac.uk, please email [mailto:janusz.martyniak@imperial.ac.uk Janusz] with a cc to lcg-site-admin@imperial.ac.uk in case of problems.'''
+
These instruction are for the dirac server at https://dirac.gridpp.ac.uk/DIRAC.
  
 
= Introduction =  
 
= Introduction =  
This document describes how to quickly set up a simple Dirac UI client, create a job script and then submit it to a Dirac server for execution. You need to have a valid grid certificate and be a member of a supported VO. You '''do not''' need root access to the machine you are installing the Dirac UI on.
+
This document describes how to quickly set up a simple Dirac UI client, create a job script and then submit it to a Dirac server for execution. '''You need to have a valid grid certificate and be a member of a [https://www.gridpp.ac.uk/wiki/VOs_supported_by_gridpp_dirac supported VO].''' You '''do not''' need root access to the machine you are installing the Dirac UI on.
  
* [[DIRAC new user checklist|Checklist for new users]]
+
''Note: new users may wish to start with the [https://www.gridpp.ac.uk/userguide/getting-on-the-grid/getting-on-the-grid.html GridPP UserGuide], which includes complete instructions for getting setup with GridPP DIRAC.''
  
 
===Getting support===
 
===Getting support===
* Please consider signing up to the gridpp dirac users mailing list: [https://mailman.ic.ac.uk/mailman/listinfo/gridpp-dirac-users Sign up !]
+
* Please consider signing up to the gridpp dirac users mailing list: [https://mailman.ic.ac.uk/mailman/listinfo/gridpp-dirac-users Sign up !] (It's fairly low traffic.) If you are using a non-institutional email, please let us know, it's hard to seperate the spam from the real requests. Thank you.
* For operational issues please consider filing a [https://ggus.eu/ GGUS ticket]. If you set "Notify site" to UKI-LT2-IC-HEP, we'll see it quicker. If you don't know if your issue is operational, just use the mailing list :-)
+
* If something isn't working, please try the mailing list first. It may help to include the output from your commands using the debug flag, which can be done with the <code>-ddd</code> flag, e.g.: dirac-proxy-init -ddd -g gridpp_user -M
* If something isn't working, it may help to include the output from your commands using the debug flag, which can be done with the <code>-ddd</code> flag, e.g.
+
* For operational issues ("Dirac server has died") please consider filing a [https://ggus.eu/ GGUS ticket]. If you set "Notify site" to UKI-LT2-IC-HEP, we'll see it quicker. If you don't know if your issue is operational, just use the mailing list :-)
 
+
* If your jobs don't run at a ''specific'' site that you think they should be running at (but run on ''other'' sites), please email lcg-site-admin at imperial.ac.uk. Please include your DN and VO. We will then check if it is a configuration issue on the dirac side and either fix it, or advise you whom to contact instead. Alternatively you can use GGUS for this issue. Please set "Notify site" to UKI-LT2-IC-HEP, we will reroute it to the appropriate site, if applicable.
<pre>
+
$ dirac-proxy-init -ddd -g gridpp_user -M
+
</pre>
+
  
 
= Server URL =  
 
= Server URL =  
The Dirac server is installed at Imperial College. The Web interface is at:
+
The GridPP DIRAC server is installed at Imperial College. The Web interface can be found at:
  
 
   https://dirac.gridpp.ac.uk
 
   https://dirac.gridpp.ac.uk
Line 24: Line 21:
  
 
= Dirac client installation =  
 
= Dirac client installation =  
You need an SL6 machine, with your user cert and key located in the $HOME/.globus directory. You also need to be a member of a dirac supported VO. <br>
+
'''16/11/2020: Major version upgrade. Please update your UI.''' <br>
You can try and run this python script (chmod u+x install_dirac_ui.py, ./install_dirac_ui.py): [https://raw.github.com/ic-hep/DIRAC-tools/master/install_dirac_ui.py dirac ui install script]. <br>
+
You need an '''SL7''' (SL6 might still work, but we do not recommned it) machine, with your user cert and key located in the $HOME/.globus directory. You also need to be a member of a GridPP supported VO. <br>
Or you can run the command sequence by hand in a bash shell: <br>
+
Please check that your firewall is open on the appropriate ports: <br>
 +
nc -v dirac01.grid.hep.ph.ic.ac.uk 9135 <br>
 +
Connection to dirac01.grid.hep.ph.ic.ac.uk 9135 port [tcp/*] succeeded!
 +
 
 +
 
 +
''Note: the installation works on SL7 only. If your cluster does not support SL7, you may wish to consider using a [https://www.gridpp.ac.uk/userguide/gridpp-cernvm/gridpp-cernvm.html GridPP CernVM].''
 +
 
 +
To install the UI, run this command sequence in a bash shell:
 +
 
 
<pre>
 
<pre>
 
mkdir dirac_ui
 
mkdir dirac_ui
 
cd dirac_ui
 
cd dirac_ui
wget -np -O dirac-install http://lhcbproject.web.cern.ch/lhcbproject/dist/Dirac_project/dirac-install
+
wget -np -O dirac-install https://raw.githubusercontent.com/DIRACGrid/DIRAC/integration/Core/scripts/dirac-install.py
 +
# add --no-check-certificate to wget if needed
 
chmod u+x dirac-install
 
chmod u+x dirac-install
./dirac-install -r v6r14p5 -i 27 -g 2015-09-03
+
./dirac-install -r v7r1p17
 
.  bashrc  
 
.  bashrc  
dirac-proxy-init -x (needs user cert password)
+
dirac-proxy-init -x # (needs user cert password)
 
dirac-configure -F -S GridPP -C dips://dirac01.grid.hep.ph.ic.ac.uk:9135/Configuration/Server -I
 
dirac-configure -F -S GridPP -C dips://dirac01.grid.hep.ph.ic.ac.uk:9135/Configuration/Server -I
dirac-proxy-init -g [your_vo_goes_here]_user -M (e.g. dirac-proxy-init -g comet.j-parc.jp_user -M)
+
dirac-proxy-init -g [your_vo_goes_here]_user -M -U # (e.g. dirac-proxy-init -g comet.j-parc.jp_user -M -U)
 +
</pre>
  
  
</pre>
+
If you see an error like below then you probably are not registered with the dirac instance. Usually you are automatically registered, but there is a delay of several hours between registering with the VO and the dirac server picking this up. If after 24h you still get the same error message, please send an email to lcg-site-admin -at- imperial.ac.uk and we'll have a look.
  
If you see an error like below then you probably are not registered with the dirac instance.
 
 
<pre>
 
<pre>
 
Could not sync dir Cannot get URL for Framework/BundleDelivery in setup MyDIRAC-Production: Option /DIRAC/Setups/MyDIRAC-Production/Framework is not defined
 
Could not sync dir Cannot get URL for Framework/BundleDelivery in setup MyDIRAC-Production: Option /DIRAC/Setups/MyDIRAC-Production/Framework is not defined
 
</pre>
 
</pre>
 
== A note on CA certificates ==
 
When you install the dirac UI, the script will automatically download a current copy of these certs for you and store them in [dirac_ui_dir]/etc/grid-security/certificates. This will be sufficient for a couple of weeks of  testing. If you are planning on using your dirac UI for longer, you need to update these certificates regularly. Most grid sites maintain a current copy of these files somewhere on their systems and you should link to those (try /etc/grid-security/certificates or at Imperial /vols/grid/certificates -- if in doubt ask your friendly sys admin :-) instead. <br>
 
 
If there is no regularly maintained set of CAs available, run the following command periodically:
 
 
source bashrc; dirac-admin-get-CAs
 
 
It is convenient to this this once per day using a cron job.
 
  
 
= Submitting a 'Hello World' job via dirac =
 
= Submitting a 'Hello World' job via dirac =
  
 
== Create a proxy ==
 
== Create a proxy ==
 +
 +
If you don't already have a valid proxy you should create one:
  
 
<pre>
 
<pre>
. bashrc  
+
source bashrc  
 
dirac-proxy-init -g [your_vo_goes_here]_user -M (e.g. dirac-proxy-init -g comet.j-parc.jp_user -M)
 
dirac-proxy-init -g [your_vo_goes_here]_user -M (e.g. dirac-proxy-init -g comet.j-parc.jp_user -M)
 
 
 
</pre>
 
</pre>
  
Line 81: Line 78:
 
</pre>
 
</pre>
  
= Submit a job =
+
== Submit a job ==
 
+
  
 
<pre>
 
<pre>
Line 112: Line 108:
 
</pre>
 
</pre>
  
 +
A list of JDL parameters used by DIRAC can be found in the [https://dirac.readthedocs.io/en/latest/UserGuide/GettingStarted/UserJobs/JDLReference/index.html DIRAC documentation].
 +
 +
= Advanced job management =
 +
For any real work, we recommend that you develop your code against the DIRAC python API. Please also read the "Data Handling Within a Job" section before you produce any kind of data to be stored on a storage element.
 +
== Using the DIRAC API to submit a Job ==
 +
 +
An example of a hello world job can be found
 +
[https://github.com/ic-hep/DIRAC-tools/blob/master/user/hello_world_job.py here]. <br>
 +
Another example with more options: [https://github.com/ic-hep/DIRAC-tools/blob/master/user/job_with_more_options.py Options!]. You will also need
 +
[https://github.com/ic-hep/DIRAC-tools/blob/master/user/testapi.sh this] shell script which is used as an executable within the example. <br>
 +
The corresponding section in the DIRAC user guide can be found [http://dirac.readthedocs.io/en/latest/UserGuide/GettingStarted/UserJobs/DiracAPI/index.html here] and the Job API [https://dirac.readthedocs.io/en/latest/CodeDocumentation/Interfaces/API/Job.html here].
 +
 +
== Selecting a site platform ==
 +
 +
By default GridPP DIRAC will only run jobs at sites providing an EL7 (as in "Enterprise Linux 7", treat it as a synonym for SL7) based operating system.
 +
If you would like to submit a job that requires a different operating system (such as EL6)
 +
this can be set using the Platform option in the JDL:
 +
 +
<pre>Platform = "EL6";</pre>
 +
 +
If is also possible to specify AnyPlatform as the platform name to disable this check:
 +
 +
<pre>Platform = "AnyPlatform";</pre>
 +
 +
Note that all parts of this JDL string are case sensitive (the word Platform and the platform string itself).
 +
 +
Users of the DIRAC API can use the '''job.setPlatform("EL6")''' function to configure this behaviour.
 +
 +
Ganga users can set extra options, including the platform, via the backend settings attribute:
 +
 +
<pre>
 +
j = Job(backend=Dirac())
 +
j.backend.settings['Platform'] = "EL6"
 +
</pre>
 +
 +
== Advanced Site/CE selection ==
 +
 +
If you want to run at a specific subset of available sites for your VO, you can specify a list of Sites
 +
using the usual Site clause with a list:
 +
 +
<pre>
 +
Site = {"Site1", "Site2", "Site3"};
 +
</pre>
 +
 +
It is also possible to select specific CEs (generally this is used for targeting special resources):
 +
 +
<pre>
 +
GridCE = {"ceprod05.grid.hep.ph.ic.ac.uk", "ceprod06.grid.hep.ph.ic.ac.uk"};
 +
</pre>
 +
 +
Note that selecting an invalid combination of Sites & CEs may result in your job staying in the waiting state forever.
 +
 +
= Basic data management =
 +
 +
(using the UI and proxy you just setup) <br>
 +
List files in the dirac file catalogue (please do not use the file catalogue for anything else):
 +
<pre>
 +
$ dirac-dms-filecatalog-cli
 +
Starting FileCatalog client
 +
File Catalog Client $Revision: 1.17 $Date:
 +
FC:/> ls
 +
(use 'exit' to, well, exit)
 +
</pre>
 +
 +
Add a file to an SE (here UKI-LT2-IC-HEP-disk). Please replace /gridpp with the name of the VO you are using, and firstname.lastname with your first and last name (or alias or superhero, it just has to be unique):
 +
<pre>
 +
dirac-dms-add-file /gridpp/user/f/firstname.lastname/myfile.txt myfile.txt UKI-LT2-IC-HEP-disk
 +
</pre>
 +
 +
List all replicas:
 +
<pre>
 +
dirac-dms-lfn-replicas /gridpp/user/f/firstname.lastname/myfile.txt
 +
</pre>
 +
 +
Copy file from SE to disk: <br>
 +
<pre>
 +
dirac-dms-get-file /gridpp/user/f/firstname.lastname/myfile.txt
 +
</pre>
 +
 +
Replicate file from on SE to another (file is currently at UKI-LT2-IC-HEP-disk): <br>
 +
<pre>
 +
dirac-dms-replicate-lfn /gridpp/user/f/firstname.lastname/myfile.txt UKI-LT2-QMUL2-disk
 +
</pre>
 +
 +
Ask for the access URL (you should only need this for very special cases):
 +
<pre>
 +
dirac-dms-lfn-accessURL  /gridpp/user/f/firstname.lastname/myfile.txt UKI-LT2-IC-HEP-disk
 +
</pre>
 +
 +
Remove file from a specific SE: <br>
 +
<pre>
 +
dirac-dms-remove-replicas /gridpp/user/f/firstname.lastname/myfile.txt UKI-LT2-IC-HEP-disk
 +
</pre>
 +
 +
Remove all replicas (?):
 +
<pre>
 +
dirac-dms-remove-files  /gridpp/user/f/firstname.lastname/myfile.txt
 +
</pre>
 +
 +
<hr>
 +
Using the asynchronous files transfer tools.  <br>
 +
Replicate a file to a given SE:
 +
<pre>
 +
dirac-dms-replicate-and-register-request [make up an id for this transfer] [LFN] [target SE]
 +
</pre>
 +
e.g. replicate a file to the RHUL SE (files must exist and be registered in the file catalogue):
 +
<pre>
 +
dirac-dms-replicate-and-register-request daniela1 /gridpp/user/d/daniela.bauer/small.text.file.txt UKI-LT2-RHUL-disk
 +
</pre>
 +
Querying the transfers:
 +
<pre>
 +
dirac-rms-request [transfer if from above, e.g. daniela1]
 +
dirac-rms-request--Status='Done' --Since='2016-05-05'
 +
</pre>
 +
 +
=Data Handling within a job=
 +
 +
Please see the documentation here: [[DIRAC_Data_Handling_within_a_Job]]
 +
 +
=DIRAC command reference=
 +
[http://dirac.readthedocs.io/en/rel-v6r22/UserGuide/CommandReference/index.html Docs for v6r22]
 +
 +
<br />
 
<hr>
 
<hr>
 
Back to [https://www.gridpp.ac.uk/wiki/Dirac GridPP Dirac] overview page.
 
Back to [https://www.gridpp.ac.uk/wiki/Dirac GridPP Dirac] overview page.

Latest revision as of 13:44, 24 November 2020

These instruction are for the dirac server at https://dirac.gridpp.ac.uk/DIRAC.

Introduction

This document describes how to quickly set up a simple Dirac UI client, create a job script and then submit it to a Dirac server for execution. You need to have a valid grid certificate and be a member of a supported VO. You do not need root access to the machine you are installing the Dirac UI on.

Note: new users may wish to start with the GridPP UserGuide, which includes complete instructions for getting setup with GridPP DIRAC.

Getting support

  • Please consider signing up to the gridpp dirac users mailing list: Sign up ! (It's fairly low traffic.) If you are using a non-institutional email, please let us know, it's hard to seperate the spam from the real requests. Thank you.
  • If something isn't working, please try the mailing list first. It may help to include the output from your commands using the debug flag, which can be done with the -ddd flag, e.g.: dirac-proxy-init -ddd -g gridpp_user -M
  • For operational issues ("Dirac server has died") please consider filing a GGUS ticket. If you set "Notify site" to UKI-LT2-IC-HEP, we'll see it quicker. If you don't know if your issue is operational, just use the mailing list :-)
  • If your jobs don't run at a specific site that you think they should be running at (but run on other sites), please email lcg-site-admin at imperial.ac.uk. Please include your DN and VO. We will then check if it is a configuration issue on the dirac side and either fix it, or advise you whom to contact instead. Alternatively you can use GGUS for this issue. Please set "Notify site" to UKI-LT2-IC-HEP, we will reroute it to the appropriate site, if applicable.

Server URL

The GridPP DIRAC server is installed at Imperial College. The Web interface can be found at:

 https://dirac.gridpp.ac.uk

You need a certificate installed in your browser.
To check that you are correctly registered with this dirac instance and that you are a member of a dirac supported VO, visit [the server] and check the bottom righthand corner. If this shows you as "visitor" and you cannot change this, you are not registered. In this case, please contact lcg-site-admin@imperial.ac.uk

Dirac client installation

16/11/2020: Major version upgrade. Please update your UI.
You need an SL7 (SL6 might still work, but we do not recommned it) machine, with your user cert and key located in the $HOME/.globus directory. You also need to be a member of a GridPP supported VO.
Please check that your firewall is open on the appropriate ports:
nc -v dirac01.grid.hep.ph.ic.ac.uk 9135
Connection to dirac01.grid.hep.ph.ic.ac.uk 9135 port [tcp/*] succeeded!


Note: the installation works on SL7 only. If your cluster does not support SL7, you may wish to consider using a GridPP CernVM.

To install the UI, run this command sequence in a bash shell:

mkdir dirac_ui
cd dirac_ui
wget -np -O dirac-install https://raw.githubusercontent.com/DIRACGrid/DIRAC/integration/Core/scripts/dirac-install.py 
# add --no-check-certificate to wget if needed
chmod u+x dirac-install
./dirac-install -r v7r1p17
.  bashrc 
dirac-proxy-init -x # (needs user cert password)
dirac-configure -F -S GridPP -C dips://dirac01.grid.hep.ph.ic.ac.uk:9135/Configuration/Server -I
dirac-proxy-init -g [your_vo_goes_here]_user -M -U # (e.g. dirac-proxy-init -g comet.j-parc.jp_user -M -U)


If you see an error like below then you probably are not registered with the dirac instance. Usually you are automatically registered, but there is a delay of several hours between registering with the VO and the dirac server picking this up. If after 24h you still get the same error message, please send an email to lcg-site-admin -at- imperial.ac.uk and we'll have a look.

Could not sync dir Cannot get URL for Framework/BundleDelivery in setup MyDIRAC-Production: Option /DIRAC/Setups/MyDIRAC-Production/Framework is not defined

Submitting a 'Hello World' job via dirac

Create a proxy

If you don't already have a valid proxy you should create one:

source  bashrc 
dirac-proxy-init -g [your_vo_goes_here]_user -M (e.g. dirac-proxy-init -g comet.j-parc.jp_user -M)

Create a JDL

Now we are ready to create a simple Dirac jdl. Put the lines below into a file Simple.jdl:

[
JobName = "Simple_Job";
Executable = "/bin/ls";
Arguments = "-ltr";
StdOutput = "StdOut";
StdError = "StdErr";
OutputSandbox = {"StdOut","StdErr"};
]

Submit a job

$ dirac-wms-job-submit -f logfile Simple.jdl 
JobID = 236

Check job status:

$ dirac-wms-job-status -f logfile

JobID=236 Status=Waiting; MinorStatus=Pilot Agent Submission; Site=ANY 

and eventually:

$ dirac-wms-job-status -f logfile 
JobID=236 Status=Done; MinorStatus=Execution Complete; Site=LCG.Glasgow.uk;

The jobs can also be monitored using the Web interface. Go to Jobs ->Job monitor You can also submit a job using the Web interface (Tools->Job Launchpad).

Once the job is done, retrieve the output:

$ dirac-wms-job-get-output -f logfile

A list of JDL parameters used by DIRAC can be found in the DIRAC documentation.

Advanced job management

For any real work, we recommend that you develop your code against the DIRAC python API. Please also read the "Data Handling Within a Job" section before you produce any kind of data to be stored on a storage element.

Using the DIRAC API to submit a Job

An example of a hello world job can be found here.
Another example with more options: Options!. You will also need this shell script which is used as an executable within the example.
The corresponding section in the DIRAC user guide can be found here and the Job API here.

Selecting a site platform

By default GridPP DIRAC will only run jobs at sites providing an EL7 (as in "Enterprise Linux 7", treat it as a synonym for SL7) based operating system. If you would like to submit a job that requires a different operating system (such as EL6) this can be set using the Platform option in the JDL:

Platform = "EL6";

If is also possible to specify AnyPlatform as the platform name to disable this check:

Platform = "AnyPlatform";

Note that all parts of this JDL string are case sensitive (the word Platform and the platform string itself).

Users of the DIRAC API can use the job.setPlatform("EL6") function to configure this behaviour.

Ganga users can set extra options, including the platform, via the backend settings attribute:

j = Job(backend=Dirac())
j.backend.settings['Platform'] = "EL6"

Advanced Site/CE selection

If you want to run at a specific subset of available sites for your VO, you can specify a list of Sites using the usual Site clause with a list:

Site = {"Site1", "Site2", "Site3"};

It is also possible to select specific CEs (generally this is used for targeting special resources):

GridCE = {"ceprod05.grid.hep.ph.ic.ac.uk", "ceprod06.grid.hep.ph.ic.ac.uk"};

Note that selecting an invalid combination of Sites & CEs may result in your job staying in the waiting state forever.

Basic data management

(using the UI and proxy you just setup)
List files in the dirac file catalogue (please do not use the file catalogue for anything else):

$ dirac-dms-filecatalog-cli
Starting FileCatalog client
File Catalog Client $Revision: 1.17 $Date: 
FC:/> ls
(use 'exit' to, well, exit)

Add a file to an SE (here UKI-LT2-IC-HEP-disk). Please replace /gridpp with the name of the VO you are using, and firstname.lastname with your first and last name (or alias or superhero, it just has to be unique):

dirac-dms-add-file /gridpp/user/f/firstname.lastname/myfile.txt myfile.txt UKI-LT2-IC-HEP-disk

List all replicas:

dirac-dms-lfn-replicas /gridpp/user/f/firstname.lastname/myfile.txt

Copy file from SE to disk:

dirac-dms-get-file /gridpp/user/f/firstname.lastname/myfile.txt

Replicate file from on SE to another (file is currently at UKI-LT2-IC-HEP-disk):

dirac-dms-replicate-lfn /gridpp/user/f/firstname.lastname/myfile.txt UKI-LT2-QMUL2-disk

Ask for the access URL (you should only need this for very special cases):

dirac-dms-lfn-accessURL  /gridpp/user/f/firstname.lastname/myfile.txt UKI-LT2-IC-HEP-disk

Remove file from a specific SE:

dirac-dms-remove-replicas /gridpp/user/f/firstname.lastname/myfile.txt UKI-LT2-IC-HEP-disk

Remove all replicas (?):

dirac-dms-remove-files  /gridpp/user/f/firstname.lastname/myfile.txt

Using the asynchronous files transfer tools.
Replicate a file to a given SE:

dirac-dms-replicate-and-register-request [make up an id for this transfer] [LFN] [target SE]

e.g. replicate a file to the RHUL SE (files must exist and be registered in the file catalogue):

dirac-dms-replicate-and-register-request daniela1 /gridpp/user/d/daniela.bauer/small.text.file.txt UKI-LT2-RHUL-disk

Querying the transfers:

dirac-rms-request [transfer if from above, e.g. daniela1]
dirac-rms-request--Status='Done' --Since='2016-05-05'

Data Handling within a job

Please see the documentation here: DIRAC_Data_Handling_within_a_Job

DIRAC command reference

Docs for v6r22



Back to GridPP Dirac overview page.