[OOD-users] no environment set for HPC desktop -- job fails
John-Paul Robinson
jprorama at gmail.com
Sat Dec 8 19:18:30 EST 2018
Thanks for the insight. I agree the web hosts context is not the one we want going to the cluster.
This lead looks very promising!
We will test 17.11.11 and see if our original success with ood HPC desktops returns. If so, the fix should be for ohpc to at least update to slurm 17.11.11.
John-Paul
> On Dec 8, 2018, at 5:50 PM, Jeremy Nicklas <jeremywnicklas at gmail.com> wrote:
>
> Hi all,
>
> Original developer of the Slurm adapter in Open OnDemand here. I want first clear up any confusion about environment variables here. Behind the scenes when OnDemand calls the `sbatch` command to submit a job it actually:
>
> - sets the environment variable `SBATCH_EXPORT=NONE`
> - adds the command line argument `--parsable` for easier parsing of the job id
>
> The relevant snippet of code can be seen here:
>
> https://github.com/OSC/ood_core/blob/866db98e3b3ba574a5799a3af84d2b5ffc010ff8/lib/ood_core/job/adapters/slurm.rb#L128-L138
>
> I purposely set the `SBATCH_EXPORT=NONE` for a few reasons:
>
> - as these are Passenger apps running below a `sudo` user switch, the environment is already drastically different from the user's login shell environment when they call `sbatch`
> - the library paths LD_LIBRARY_PATH and binary paths PATH could be different between the web node and the cluster node
> - if you use `SBATCH_EXPORT=NONE`, the Slurm documentation states:
>
> > Slurm will then implicitly attempt to load the user's environment on the node where the script is being executed
>
> which is what we would want.
>
> I do not recommend setting this environment variable to `ALL` for the reasons listed above. It may cause more headaches down the road.
>
> Now I am not entirely sure why you are seeing this issue after updating Slurm, but taking a look at the NEWS file for Slurm, one particular bugfix stands out:
>
> https://github.com/SchedMD/slurm/blob/d128eb21583fe80b808ce64667cd89d209cd62ab/NEWS#L532
>
> That particular commit in 17.11.11 fixes an issue in `src/common/env.c` which was introduced in 17.11.10. The exact commit is here:
>
> https://github.com/SchedMD/slurm/commit/72b2355ca8d6f4381b4e417f76649712881f45b7
>
> I am not sure if this is what you are experiencing. But could you test OnDemand using Slurm 17.11.11?
>
> - Jeremy Nicklas
>
>> On Sat, Dec 8, 2018 at 5:33 PM John-Paul Robinson via OOD-users <ood-users at lists.osc.edu> wrote:
>> Ok.
>>
>> My experience has been the behavior with the second export below and not the third. That is, spec an env and you only get those specific vars. Don’t spec any and you get the ALL behavior.
>>
>> What’s odd is that desktop jobs did work before and now don’t, suggesting slurm has changed wrt the ood assumptions.
>>
>> Leaving the question, where are those ood assumptions made and can we just add ALL to the front of the list?
>>
>> Is the conclusion of the github issue?
>>
>>> On Dec 8, 2018, at 1:54 PM, Michael Coleman <mcolema5 at uoregon.edu> wrote:
>>>
>>> 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), 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> 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), Computational Scientist
>>>> Research Advanced Computing Services
>>>> 6235 University of Oregon
>>>> Eugene, OR 97403
>>>>
>>>>
>>>> ________________________________________
>>>> From: John-Paul Robinson <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> 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> 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>
>>>>>> Sent: Friday, December 7, 2018 03:56 PM
>>>>>> To: Michael Coleman <mcolema5 at uoregon.edu>; User support mailing list for Open OnDemand <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> On Behalf Of John-Paul Robinson via OOD-users
>>>>>>> Sent: Wednesday, December 5, 2018 02:49 PM
>>>>>>> To: 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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> OOD-users mailing list
>>>>>>> OOD-users at lists.osc.edu
>>>>>>> https://lists.osu.edu/mailman/listinfo/ood-users
>>>>>>
>> _______________________________________________
>> OOD-users mailing list
>> OOD-users at lists.osc.edu
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