# Interactive app environment in 1.7

**URL:** <https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878>\
**Category:** Get Help\
**Created:** [April 29, 2020, 4:42pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878 "2020-04-29T16:42:03Z")\
**Posts on this page:** 20\
**Page:** 1

<div class="post-metadata">

**Author:** ![mcuma](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/mcuma/32/171_2.png) [@mcuma](https://discourse.openondemand.org/u/mcuma)\
**Post date:** [April 29, 2020, 4:42pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/1 "2020-04-29T16:42:04Z")

</div>

While testing OOD 1.7, I noticed that the interactive apps seem to be starting with limited environment, which is different than in 1.6.

In our case, we source the Lmod through a series of profile.d like scripts that are called from /etc/profile.d, shown below. In 1.6 case the module.sh would get sourced, while in 1.7 it does not. We do have below a condition that UID\<500 does not source these files, so, any chance that the interactive app sessions start as non-user? I am not seeing why/how could that be but just want to make sure.

Or, any other thoughts?

Below is the profile.d files structure  
 cat /etc/profile.d/chpc.sh if [[{UID} -ge 500]]  
then  
if [-f /uufs/chpc.utah.edu/sys/etc/chpc.sh]  
then  
source /uufs/chpc.utah.edu/sys/etc/chpc.sh  
fi  
fi  
$ cat /uufs/chpc.utah.edu/sys/etc/chpc.sh  
for i in /uufs/chpc.utah.edu/sys/etc/profile.d/_.sh; do  
if [-r “$i”]; then  
if [“$PS1”]; then  
. “$i”  
else  
. "i" \>/dev/null 2\>&1 fi fi done ls /uufs/chpc.utah.edu/sys/etc/profile.d/_.sh  
/uufs/chpc.utah.edu/sys/etc/profile.d/module.sh  
(this is a bit longer file that sets up the appropriate Lmod).

Thanks,  
MC

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<div class="post-metadata">

**Author:** ![mcuma](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/mcuma/32/171_2.png) [@mcuma](https://discourse.openondemand.org/u/mcuma)\
**Post date:** [April 29, 2020, 4:44pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/2 "2020-04-29T16:44:40Z")

</div>

I should add that we do have a workaround for that, to add this to the template/script.sh.erb:  
if [-z “$LMOD\_VERSION”]; then  
source /etc/profile.d/chpc.sh  
fi

---

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**Author:** ![jeff.ohrstrom](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/jeff.ohrstrom/32/136_2.png) [@jeff.ohrstrom](https://discourse.openondemand.org/u/jeff.ohrstrom)\
**Post date:** [April 29, 2020, 5:19pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/3 "2020-04-29T17:19:48Z")

</div>

You should use `script_wrapper` or `header` in your cluster config instead of editing the template scripts (script wrapper needs the `%s` because it wraps the script and you can have things above or below it).

```auto
      batch_connect:
        vnc:
          header: "#!/bin/bash"
          script_wrapper: |
            if [-z "$LMOD_VERSION"]; then
              source /etc/profile.d/chpc.sh
            fi
            %s
        basic:
          # same result as above
          header: |
            #!/bin/bash
            if [-z "$LMOD_VERSION"]; then
              source /etc/profile.d/chpc.sh
            fi

```

As to the difference between 6 and 7, I can’t say off the top of my head why they’d be different.

---

<div class="post-metadata">

**Author:** ![mcuma](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/mcuma/32/171_2.png) [@mcuma](https://discourse.openondemand.org/u/mcuma)\
**Post date:** [April 29, 2020, 9:17pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/4 "2020-04-29T21:17:29Z")

</div>

Thanks Jeff, I did not think about the cluster configs.

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<div class="post-metadata">

**Author:** ![jeff.ohrstrom](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/jeff.ohrstrom/32/136_2.png) [@jeff.ohrstrom](https://discourse.openondemand.org/u/jeff.ohrstrom)\
**Post date:** [May 1, 2020, 9:41pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/5 "2020-05-01T21:41:37Z")

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Actually, @mcuma I can think of what’s different now, especially as it relates to environment variables. We added something to `copy_environment` for all the schedulers.

In, say, SLURM it’s `--export`. Do you set and or use `job_environment` map? (I found through some utah docs that seem to indicate you use SLURM).

The behaviour now is, if you don’t use `job_environment`, it won’t use the `--export` flag - which is what it did in 1.6.

If you _do_ use `job_environment` then it’ll do `--export=NONE,FOO,BAR` if you don’t use `copy_environment` and `--export=ALL,FOO,BAR` if you do set `copy_environment` to true (I know that phrase has alot of ifs in it and may be convoluted).

This is the only thing I can think of. The sessions could not start as a non-user, OOD submits the job through slurm as the UID of the given user (unless you have some wrapper script in front of srun).

---

<div class="post-metadata">

**Author:** ![mcuma](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/mcuma/32/171_2.png) [@mcuma](https://discourse.openondemand.org/u/mcuma)\
**Post date:** [May 1, 2020, 10:03pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/6 "2020-05-01T22:03:40Z")

</div>

Hi Jeff,

I think you may be on the right track since the environment seems to be passed, but, the Lmod “module” command is an alias which probably does not pass. Though, the job should be opening a new terminal on the compute node and source the Lmod, which is what the standard SLURM job does. And there the alias is functional. So, it’s still looking like the /etc/profile.d/… part is not being sourced.

I don’t think we do anything with the job environment, and the default should be --export=ALL

Is there any documentation on the job\_environment?

Thanks,  
MC

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<div class="post-metadata">

**Author:** ![milberg](https://avatars.discourse-cdn.com/v4/letter/m/c2a13f/32.png) [@milberg](https://discourse.openondemand.org/u/milberg)\
**Post date:** [May 5, 2020, 11:57am UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/7 "2020-05-05T11:57:13Z")

</div>

In updating from 1.6 to 1.7, I had to add sourcing the module environment setup `.sh` script to `script_wrapper`.

---

<div class="post-metadata">

**Author:** ![mjbludwig](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/mjbludwig/32/684_2.png) [@mjbludwig](https://discourse.openondemand.org/u/mjbludwig)\
**Post date:** [May 21, 2020, 5:33pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/8 "2020-05-21T17:33:12Z")

</div>

Can we add this to the Docs somewhere. In the release notes maybe? This burned me as well

Thanks,  
Morgan

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<div class="post-metadata">

**Author:** ![jeff.ohrstrom](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/jeff.ohrstrom/32/136_2.png) [@jeff.ohrstrom](https://discourse.openondemand.org/u/jeff.ohrstrom)\
**Post date:** [May 21, 2020, 8:12pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/9 "2020-05-21T20:12:34Z")

</div>

☹ Well there’s clearly something awry here. Looking over the code again, the default SLURM behavior for job environments _should_ be the same. That is, the commands executed should be the same as before, with the same environment.

@milberg & @mjbludwig do you also use SLURM?

Looking at SLURM help tickets I see stuff like this. The SLURM FAQ also says something similar.  
`The user environment is re-populated from a copy of the environment taken when the job was submitted through sbatch, with the SLURM_* environment variables added in to it.`  
So somehow we corrupted the environment when we run `srun`.

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<div class="post-metadata">

**Author:** ![milberg](https://avatars.discourse-cdn.com/v4/letter/m/c2a13f/32.png) [@milberg](https://discourse.openondemand.org/u/milberg)\
**Post date:** [May 21, 2020, 8:45pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/10 "2020-05-21T20:45:20Z")

</div>

@jeff.ohrstrom Yes, we are using Slurm. Besides adding sourcing the module environment setup `.sh` script in the cluster config, I later found that I needed to add it to the Job Composer templates as well.

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<div class="post-metadata">

**Author:** ![jeff.ohrstrom](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/jeff.ohrstrom/32/136_2.png) [@jeff.ohrstrom](https://discourse.openondemand.org/u/jeff.ohrstrom)\
**Post date:** [May 21, 2020, 10:36pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/11 "2020-05-21T22:36:59Z")

</div>

OK, we clearly broke previous behavior.

We used to set `SBATCH_EXPORT=NONE` which makes it unclear to me how slurm _used_ to find this function definition? We now just use the `--export` argument, but that’s only if there are other `job_environment` variables.

There’s a lot of talk in the tickets that generated this change, but it’s likely we’ll have to patch this as it looks like the previous behavior (however it happened) is expected and indeed a much better experience.

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<div class="post-metadata">

**Author:** ![dsajdak](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/dsajdak/32/44_2.png) [@dsajdak](https://discourse.openondemand.org/u/dsajdak)\
**Post date:** [May 27, 2020, 1:00am UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/12 "2020-05-27T01:00:21Z")

</div>

Glad I found this thread. We updated to 1.7.11 in production today and found that it broke all our jupyter apps. I had forgotten to test this in dev. It doesn’t know the ‘module’ command so nothing launches.

---

<div class="post-metadata">

**Author:** ![efranz](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/efranz/32/27_2.png) [@efranz](https://discourse.openondemand.org/u/efranz)\
**Post date:** [May 27, 2020, 12:00pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/13 "2020-05-27T12:00:52Z")

</div>

We will be fixing this in 1.7.13 so that the behavior is reverted. But the fixes in this PR should address the problem and be unaffected when 1.7.13 is released.

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<div class="post-metadata">

**Author:** ![dsajdak](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/dsajdak/32/44_2.png) [@dsajdak](https://discourse.openondemand.org/u/dsajdak)\
**Post date:** [May 27, 2020, 7:29pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/14 "2020-05-27T19:29:46Z")

</div>

We have an additional issue for our center in that users and groups create their own modules and source them in their .bashrc files. This work around provided doesn’t help for this issue. Any idea when you’ll be releasing version 1.7.13?

Thanks,  
Dori

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<div class="post-metadata">

**Author:** ![jeff.ohrstrom](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/jeff.ohrstrom/32/136_2.png) [@jeff.ohrstrom](https://discourse.openondemand.org/u/jeff.ohrstrom)\
**Post date:** [May 27, 2020, 10:35pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/15 "2020-05-27T22:35:00Z")

</div>

We have the patch in and we’re building now, so tomorrow we should be able to verify everything is working as it should.

Then we’ll be able to promote it to stable, so maybe tomorrow 5-28 and maybe Friday 5-29 depending (and it’s 1.7.14 now to also get a Safari/noVNC patch).

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<div class="post-metadata">

**Author:** ![dsajdak](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/dsajdak/32/44_2.png) [@dsajdak](https://discourse.openondemand.org/u/dsajdak)\
**Post date:** [May 28, 2020, 12:36pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/16 "2020-05-28T12:36:24Z")

</div>

Excellent! I can test this in our development setup too if that would help.

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<div class="post-metadata">

**Author:** ![efranz](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/efranz/32/27_2.png) [@efranz](https://discourse.openondemand.org/u/efranz)\
**Post date:** [May 28, 2020, 5:08pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/17 "2020-05-28T17:08:22Z")

</div>

1.7.14 is currently built in the latest repo [https://yum.osc.edu/ondemand/latest/web/el7/x86\_64/](https://yum.osc.edu/ondemand/latest/web/el7/x86_64/)

You can try this out on your development host by running:

```auto
yum install https://yum.osc.edu/ondemand/latest/ondemand-release-web-latest-1-6.noarch.rpm
yum clean all
yum update ondemand

```

You can undo this change by running

```auto
yum remove ondemand-release-web-latest
yum install https://yum.osc.edu/ondemand/1.7/ondemand-release-web-1.7-1.noarch.rpm
yum clean all
yum downgrade ondemand

```

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<div class="post-metadata">

**Author:** ![dsajdak](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/dsajdak/32/44_2.png) [@dsajdak](https://discourse.openondemand.org/u/dsajdak)\
**Post date:** [May 28, 2020, 9:13pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/18 "2020-05-28T21:13:09Z")

</div>

Thanks! This worked well for us in dev so we put it in production this afternoon. Appreciate the fast response on fixing this!

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<div class="post-metadata">

**Author:** ![jeff.ohrstrom](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/jeff.ohrstrom/32/136_2.png) [@jeff.ohrstrom](https://discourse.openondemand.org/u/jeff.ohrstrom)\
**Post date:** [May 29, 2020, 1:52pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/19 "2020-05-29T13:52:52Z")

</div>

This has been promoted to stable, so you don’t need to pull it off our latest repo anymore, you can get it from the regular 1.7 repo.

Sites that have implemented this fix should not have issues updating directly. There should be no issue sourcing a file a second time (if it gets sourced at all, with the if block there).

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<div class="post-metadata">

**Author:** ![mcuma](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/mcuma/32/171_2.png) [@mcuma](https://discourse.openondemand.org/u/mcuma)\
**Post date:** [May 29, 2020, 3:40pm UTC](https://discourse.openondemand.org/t/interactive-app-environment-in-1-7/878/20 "2020-05-29T15:40:37Z")

</div>

Hi Jeff,

does this update also include the Linux Host Adapter fixes that you did for us?

Also, would you mind checking [Linux Host Adapter feedback](https://discourse.openondemand.org/t/linux-host-adapter-feedback/931) and responding to the questions I have there?

Thanks,  
MC

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