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How to configure LabKey server (linux) to run R scripts remotely on another server (linux)

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How to configure LabKey server (linux) to run R scripts remotely on another server (linux) Jason Leadley  2017-01-10 07:19
Status: Closed
 
Hello LabKey

We want to use labKey in an university research environment in epidemiology.
We already have a computing server to run R and we want to add a new Labkey server to our environment. This tool seems strong but a bit hard to configure. In particular when you try to run R remotly.

We would be delighted if you could help us find the appropriate documentation for this configuration. The documentation available on the website does not describe precisely this type of configuration and we have not found any information on your forum.

We're trying to configure our LabKey server (linux) to run R scripts remotly on another server (linux) on the same VLAN but we get a java null pointer exception.

We've follow this documentation : https://www.labkey.org/home/Documentation/wiki-page.view?name=LabKeyRserve#defaultremote but without success.

When we try to modify this option :

Sign in as an admin.
Go to Admin > Site > Admin Console.
Click Experimental Features.
Under Rserve Reports, click Enable.

We get a NullPointerException from java when we click on Views and Scripting Configuration :

Do you know this error ? Or do you know where we can find information about this ?

Many thanks.

Kind regards
Cordialement
 
 
Jon (LabKey DevOps) responded:  2017-01-10 14:41
Hello,

Based on the error you're receiving, it looks like you didn't setup a Site-Level File Root under the Admin Console.

Please go into LabKey and select Admin > Site > Admin Console and click "Files".

From there, you should see the Site-Level File Root field. Enter in a valid site-level directory/path there and the problem should not re-occur.

For more details about this, please read the following documentation:

https://www.labkey.org/home/Documentation/wiki-page.view?name=setRoots

In the next version of LabKey (LabKey 17.1), we will provide a better error message to address this in the future if the Site-Wide File Root is missing.

Regards,

Jon
 
pierre rathier responded:  2017-01-11 07:15
Hello Jon,

Thank you for your answer. I just checked, we correctly configured the Site-wide File Root (see attached screenshot).

From Labkey Linux server side :

[root@CIWEB-V06D-LABKEY files]# pwd
/usr/local/labkey-16.3/files
[root@CIWEB-V06D-LABKEY files]# ll
total 4
drwxr-xr-x. 2 tomcat tomcat 4096 Jan 11 02:00 @files
drwxr-xr-x. 4 tomcat tomcat 35 Dec 21 11:48 home
drwxr-xr-x. 3 tomcat tomcat 20 Dec 21 11:48 Shared
drwxr-xr-x. 3 tomcat tomcat 20 Jan 11 11:01 Test

If you have any ideas.

Kind regards,

Pierre
 
Jon (LabKey DevOps) responded:  2017-01-11 20:46
Hi Pierre,

Can you go back into that Files page and click the Save button? Then after you do that, try to reproduce the problem again.

Regards,

Jon
 
pierre rathier responded:  2017-01-12 00:43
Hello Jon,

You're my savior ! It works now. Was pretty pernicious...

Thank you very much for your help, your support has been very useful to us.

Kind regards,

Pierre