[OOD-users] no environment set for HPC desktop -- job fails

Sat Dec 8 14:54:28 EST 2018

The key change is what happens if you use a flag like

    --export=MYVAR1,MYVAR2

The behavior mentioned in the man page (see https://github.com/OSC/ood_core/issues/109) says that no other environment variables will be passed.  In other words, this is equivalent to

    --export=NONE,MYVAR1,MYVAR2

The recent fix actually makes sbatch behave this way.  Previously, the implementation of this case was incorrectly equivalent to

    --export=ALL,MYVAR1,MYVAR2

And just to make us all completely insane, it looks like they're changing this further in a newer release (that we don't yet use at our site).  See the new man page here:

    https://slurm.schedmd.com/sbatch.html

Mike

Michael Coleman (mcolema5 at uoregon.edu<mailto:mcolema5 at uoregon.edu>), Computational Scientist

Research Advanced Computing Services

6235 University of Oregon
Eugene, OR 97403

________________________________
From: John-Paul Robinson <jprorama at gmail.com>
Sent: Saturday, December 8, 2018 10:54
To: Michael Coleman
Cc: User support mailing list for Open OnDemand
Subject: Re: [OOD-users] no environment set for HPC desktop -- job fails

I gotta say, I am trying to read it very very carefully but don’t seem to be able to parse out the subtlety. 😐

Not sure how to miss read this, emphasis on all theirs:

--export=<environment variables [ALL] | NONE>
Identify which environment variables from the submission environment are propagated to the launched application. By default, all are propagated. Multiple environment variable names should be comma separated.

On Dec 7, 2018, at 10:24 PM, Michael Coleman <mcolema5 at uoregon.edu<mailto:mcolema5 at uoregon.edu>> wrote:

If you read the man page very, very carefully, I think the new behavior actually matches what it always said.  The old behavior didn't actually match.  But I definitely agree that it's a pretty significant change.

Michael Coleman (mcolema5 at uoregon.edu<mailto:mcolema5 at uoregon.edu>), Computational Scientist
Research Advanced Computing Services
6235 University of Oregon
Eugene, OR 97403

________________________________________
From: John-Paul Robinson <jprorama at gmail.com<mailto:jprorama at gmail.com>>
Sent: Friday, December 7, 2018 17:19
To: Michael Coleman
Cc: User support mailing list for Open OnDemand
Subject: Re: [OOD-users] no environment set for HPC desktop -- job fails

I’m also scratching my head because documentation (even for the 18 release) still says the default of export is to propagate all environment variables.  :/

On Dec 7, 2018, at 6:59 PM, John-Paul Robinson <jprorama at gmail.com<mailto:jprorama at gmail.com>> wrote:

Its a pretty alarming change to have happened in three ticks of the minor release number.

Any insights from others on this?

On Dec 7, 2018, at 6:37 PM, Michael Coleman <mcolema5 at uoregon.edu<mailto:mcolema5 at uoregon.edu>> wrote:

Hi John-Paul,

As you say, I believe the key event was the transition in SLURM versions.  They apparently made a change in the behavior of export of environment variables from the submitting environment to the job environment (the stuff --export controls).  There was much wailing of our users here when their sbatch scripts broke as a result.  Generally, the "fix" was simply for users that were already using the --export flag to add the "ALL" keyword to that list, which seemed to restore the old behavior.

Ultimately, OOD is calling 'sbatch' to create jobs, and this change affects the environment those jobs see.  At least in our environment, the --export=ALL flag seems to cure OOD issues.  There are probably other ways to change things, but this seemed the simplest.

Good luck,
Mike

-----Original Message-----
From: John-Paul Robinson <jprorama at gmail.com<mailto:jprorama at gmail.com>>
Sent: Friday, December 7, 2018 03:56 PM
To: Michael Coleman <mcolema5 at uoregon.edu<mailto:mcolema5 at uoregon.edu>>; User support mailing list for Open OnDemand <ood-users at lists.osc.edu<mailto:ood-users at lists.osc.edu>>
Subject: Re: [OOD-users] no environment set for HPC desktop -- job fails

MIke,

Thanks for pointing us to this issue.

This does appear to be similar to what's happening in our dev
environment.  (Note our still-working prod environment is Bright CM with
slurm 17.02.2).

The odd thing with our dev environment (built on OpenHPC) is that it was
working in October and only started failing in builds over the past
month.  This appears to coincide with the OpenHPC 1.3.5 to 1.3.6 update
(going from slurm 17.11.7 to 17.11.10).

We've had some success in restoring the original working configuration
in one of our test stacks by reverting to the OpenHPC 1.3.5 release.

What's odd is this implies the problem is not with OOD but in the
OpenHPC system env.  As far as we can determine, our OOD remains
identical.  We are setting up dev in vagrant with ansible provisioning
the openhpc + ood cluster based on the CRI_XSEDE work extended to add an
OOD node via vagrant + ansible (not as a warewulf provision).

https://github.com/jprorama/CRI_XCBC

I've read through the github issue below but haven't teased out all the
details.

Is there an obvious transition point where this export behavior could be
impacted by the underlying system versions OOD is running on?

We'll contribute insights on the github issue as we find them.

Thanks,

John-Paul

On 12/5/18 5:15 PM, Michael Coleman wrote:
Hi John-Paul,

We worked through something similar.  You might find some useful hints on this ticket.

  https://github.com/OSC/ood_core/issues/109

Cheers,
Mike

-----Original Message-----
From: OOD-users <ood-users-bounces+mcolema5=uoregon.edu at lists.osc.edu<mailto:ood-users-bounces+mcolema5=uoregon.edu at lists.osc.edu>> On Behalf Of John-Paul Robinson via OOD-users
Sent: Wednesday, December 5, 2018 02:49 PM
To: ood-users at lists.osc.edu<mailto:ood-users at lists.osc.edu>
Subject: [OOD-users] no environment set for HPC desktop -- job fails

In our dev environment (slurm with ohpc) we have started to see this
error when trying to launch interactive desktops:

/tmp/slurmd/job00079/slurm_script: line 3: module: command not found
Setting VNC password...
Error: no HOME environment variable
Starting VNC server...
vncserver: The HOME environment variable is not set.
vncserver: The HOME environment variable is not set.
vncserver: The HOME environment variable is not set. vncserver: The HOME
environment variable is

As we understand it, the PUN nginx worker launches the batch job that
starts the desktop batch job.

The problem seems to be that the environment for the job is empty, hence
no module function or HOME env or anything else.   We checked the env of
the users nginx worker under /proc and it is completely empty.   Because
our job env is inherited from the caller (the nginx worker in this case)
the attempt to run the module command and vncserver commands naturally fail.

When we launch an interactive terminal, it runs just fine, but I'm
guessing that's because the interactive session actually reads the
normal shell startup and builds its environment, even if it happened to
be missing in the proxy.

Do you have any pointers on what could cause this situation.   We
noticed it after we started adding additional interactive apps but don't
have a clear time point.  It was working fine originally and still
functions fine in our prod env (without any of the additional
interactive apps).

Thanks,

John-Paul

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