rserver error after OS upgrade

[Tom Bishop]

Hi,

I have recently updated our servers to Ubuntu 18, and after doing this rserver won't start. The error in  stdout.log is:

Error: Could not find or load main class org.obiba.rserver.Application

Do I need to reinstall it?

Thanks

Tom

[Yannick Marcon]

Hi,

Check java version, maybe it was upgraded: java -version

Is this the legacy rserver application or the rock one?

Yannick 

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[Tom Bishop]

Hi Yannick,

Thanks for the quick response

I get:

java version "1.8.0_131"
Java(TM) SE Runtime Environment (build 1.8.0_131-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.131-b11, mixed mode)

It is the legacy rserver, so I was thinking that I could upgrade if all else fails....

Tom

[Yannick Marcon]

If you have Opal 4.x, yes it is preferable to switch to rock.

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[Tom Bishop]

ok, I will give that a try. Good opportunity to learn :)

[Yannick Marcon]

If you want to learn, I have also prepared a docker image that is datashield-ready (dsBase preinstalled): datashield/rock-base (an extension of image obiba/rock)

https://hub.docker.com/r/datashield/rock-base

Docker instructions:

https://rockdoc.obiba.org/en/latest/admin/installation.html#docker-image-installation

Similarly you can prepare your own docker image, if you need more R server side packages pre-installed. No more R base install to manage, and easier upgrade + better installation reproducibility.

Yannick

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[Tom Bishop]

Great! Thank you.

To begin with, because our installations are standalone, I have installed non-Docker Rock.

I have tried to find answers to my questions in the documentation, but there are still a couple of things I need help understanding:

- I expected the stdout.log to be the equivalent of /var/lib/rserver/logs/Rserve.log, but it isn't! Is there an equivalent for Rock?

- I don't see any DataSHIELD packages listed in Administration/DataSHIELD, although the methods are listed in the sections below and can be called. I can see on the opal-demo server that these are reported correctly. What I have done wrong?

More general question:

- If I created one docker for Rock with dsBase v6.1 and another with dsBase v6.2, how do you define which one a user gets assigned to? I guess the same question about the load balancing, how are users assigned to particular Rocks? Is this to come in Opal in the form of profiles?

Thanks

Tom

[Tom Bishop]

I can see in my Opal log I have:

 16:33:15,450 [qtp230816477-178] ERROR org.obiba.opal.r.rock.RockService - Error when reading installed DataSHIELD packages

[Yannick Marcon]

* rock (and legacy rserver) is a java process (rock.log/rserver-admin.log + stdout.log) that drives a R process (Reserve.log)

* opal does not extract the DS config from the R server at every request: it is stored in opal and it is sync when a package is installed or removed. In your case the R server was removed outside of Opal's control. Settings will be updated when you will reinstall the packages.

* different versions will be handled with the DS profiles. For now opal connects to a single cluster of R servers, that are assumed to be identical, and does the load balancing between these. Will look like this:

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[Yannick Marcon]

Normally there is a stack trace that comes with this error message.

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[Tom Bishop]

Ah yes here is the full message, attached. I think it must be a networking issue as I cannot browse to http://localhost:8085. So that is why there is a 400 error?

[Yannick Marcon]

Are opal and rock on the same host ?

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[Yannick Marcon]

I guess they are, otherwise you would not see it in Opal.

The bad request error can be the result of a failing R command (it takes several of them to scan the datashield-compatible packages). Do you have anything in the Rserve.log?

[Tom Bishop]

yes they are on the same host.

The Rserve.log is quite large (attached), I can see some errors but not yet understand them

[Yannick Marcon]

This is the usual R package installation verbosity... The error message at the end may indicate that you should restart the R server (to flush loaded libraries from memory): Administration > R > R Servers and then Stop + Start.

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[Yannick Marcon]

Strange. The issue you had with the legacy rserver is still there. There is something broken in your system. Another good reason to use a containerized R server.

On Fri, May 7, 2021 at 8:58 PM Tom Bishop <Tom.B...@mrc-epid.cam.ac.uk> wrote:

Hmmm, I thought I would just restart the server, but now Rock does not come back up. In stdout.log I have:

       .:: OBiBa Rock R server ::.

Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=128M; support was removed in 8.0
Error: Could not find or load main class org.springframework.boot.loader.JarLauncher
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=128M; support was removed in 8.0
Error: Could not find or load main class org.springframework.boot.loader.JarLauncher

and in the rock.log it looks like it shut down a while ago...

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[Tom Bishop]

I have managed to fix that*... so now I am back to where we were before with the 400 bad request problem. The stopping and starting the Rserver did not help.

* When I tried to install curl, it asked for libcurl4. When I installed that I missed that it had uninstalled rock! There is something odd with the dependencies on the system.

[Yannick Marcon]

I noticed that R is quite old: 3.6.3

The R error was:

Loading required package: parallel
Error in strsplit(pp, ",") : non-character argument

Is it still the case?

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[Tom Bishop]

yes that is correct

[Yannick Marcon]

parallel is not a direct dependency; maybe try to reinstall this package

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[Tom Bishop]

OK. I have taken the plunge and am upgrading to R v4.0.5. This has fixed the problem with the DS packages not being visible. I am just working through updating all the packages that stop dsBase working properly.... it's taking a while

Of course, it would be better to have this in a containerised set up. It is probably less painful to move all the data over...

Thanks for your help!

Tom