<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div dir="ltr"></div><div dir="ltr">Thanks for the insight. I agree the web hosts context is not the one we want going to the cluster. </div><div dir="ltr"><br></div><div dir="ltr">This lead looks very promising! </div><div dir="ltr"><br></div><div dir="ltr">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. </div><div dir="ltr"><br></div><div dir="ltr">John-Paul</div><div dir="ltr"><br>On Dec 8, 2018, at 5:50 PM, Jeremy Nicklas <<a href="mailto:jeremywnicklas@gmail.com">jeremywnicklas@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div dir="ltr"><div dir="ltr">Hi all,<div><br></div><div>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:</div><div><br></div><div>- sets the environment variable `SBATCH_EXPORT=NONE`</div><div>- adds the command line argument `--parsable` for easier parsing of the job id</div><div><br></div><div>The relevant snippet of code can be seen here:</div><div><br></div><div><a href="https://github.com/OSC/ood_core/blob/866db98e3b3ba574a5799a3af84d2b5ffc010ff8/lib/ood_core/job/adapters/slurm.rb#L128-L138">https://github.com/OSC/ood_core/blob/866db98e3b3ba574a5799a3af84d2b5ffc010ff8/lib/ood_core/job/adapters/slurm.rb#L128-L138</a><br></div><div><br></div><div>I purposely set the `SBATCH_EXPORT=NONE` for a few reasons:</div><div><br></div><div>- 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`</div><div>- the library paths LD_LIBRARY_PATH and binary paths PATH could be different between the web node and the cluster node</div><div>- if you use `SBATCH_EXPORT=NONE`, the Slurm documentation states:</div><div><br> > Slurm will then implicitly attempt to load the user's environment on the node where the script is being executed<br></div><div><br></div><div> which is what we would want.</div><div><br></div><div>I do not recommend setting this environment variable to `ALL` for the reasons listed above. It may cause more headaches down the road.</div><div><br></div><div>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:</div><div><br></div><div><a href="https://github.com/SchedMD/slurm/blob/d128eb21583fe80b808ce64667cd89d209cd62ab/NEWS#L532">https://github.com/SchedMD/slurm/blob/d128eb21583fe80b808ce64667cd89d209cd62ab/NEWS#L532</a><br></div><div><br></div><div>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:</div><div><br></div><div><a href="https://github.com/SchedMD/slurm/commit/72b2355ca8d6f4381b4e417f76649712881f45b7">https://github.com/SchedMD/slurm/commit/72b2355ca8d6f4381b4e417f76649712881f45b7</a><br></div><div><br></div><div>I am not sure if this is what you are experiencing. But could you test OnDemand using Slurm 17.11.11?</div><div><br></div><div>- Jeremy Nicklas</div></div><br><div class="gmail_quote"><div dir="ltr">On Sat, Dec 8, 2018 at 5:33 PM John-Paul Robinson via OOD-users <<a href="mailto:ood-users@lists.osc.edu">ood-users@lists.osc.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto"><div dir="ltr"></div><div dir="ltr">Ok. </div><div dir="ltr"><br></div><div dir="ltr">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. </div><div dir="ltr"><br></div><div dir="ltr">What’s odd is that desktop jobs did work before and now don’t, suggesting slurm has changed wrt the ood assumptions. </div><div dir="ltr"><br></div><div dir="ltr">Leaving the question, where are those ood assumptions made and can we just add ALL to the front of the list?</div><div dir="ltr"><br></div><div dir="ltr">Is the conclusion of the github issue? </div></div><div dir="auto"><div dir="ltr"><br>On Dec 8, 2018, at 1:54 PM, Michael Coleman <<a href="mailto:mcolema5@uoregon.edu" target="_blank">mcolema5@uoregon.edu</a>> wrote:<br><br></div><blockquote type="cite"><div dir="ltr">
<p>The key change is what happens if you use a flag like<br>
</p>
<p><br>
</p>
<p> --export=MYVAR1,MYVAR2<br>
</p>
<p><br>
</p>
<p>The behavior mentioned in the man page (see <a href="https://github.com/OSC/ood_core/issues/109" target="_blank">https://github.com/OSC/ood_core/issues/109</a>) says that no other environment variables will be passed. In other words, this is equivalent to<br>
</p>
<p><br>
</p>
<p> --export=NONE,MYVAR1,MYVAR2<br>
</p>
<p><br>
</p>
<p>The recent fix actually makes sbatch behave this way. Previously, the implementation of this case was incorrectly equivalent to<br>
</p>
<p><br>
</p>
<p> --export=ALL,MYVAR1,MYVAR2<br>
</p>
<p><br>
</p>
<p>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:<br>
</p>
<p><br>
</p>
<p> <a href="https://slurm.schedmd.com/sbatch.html" target="_blank">https://slurm.schedmd.com/sbatch.html</a><br>
</p>
<p><br>
</p>
<p>Mike<br>
</p>
<p><br>
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<div id="m_8653619640025940478Signature">
<div name="divtagdefaultwrapper">
<p class="m_8653619640025940478MsoAutoSig"><font size="2" face="Consolas, monospace">Michael Coleman (<a href="mailto:mcolema5@uoregon.edu" id="m_8653619640025940478NoLP" target="_blank">mcolema5@uoregon.edu</a>), Computational Scientist</font></p>
<p class="m_8653619640025940478MsoAutoSig"><font size="2" face="Consolas, monospace">Research Advanced Computing Services</font></p>
<div style="color:rgb(33,33,33);background-color:rgb(255,255,255)"><font size="2" face="Consolas, monospace">6235 University of Oregon</font></div>
<div style="color:rgb(33,33,33);background-color:rgb(255,255,255)"><font size="2" face="Consolas, monospace">Eugene, OR 97403</font></div>
<p class="m_8653619640025940478MsoAutoSig" style="font-family:Calibri,Arial,Helvetica,sans-serif"><span style="font-size:10.0pt;font-family:Courier"><br>
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<div id="m_8653619640025940478divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> John-Paul Robinson <<a href="mailto:jprorama@gmail.com" target="_blank">jprorama@gmail.com</a>><br>
<b>Sent:</b> Saturday, December 8, 2018 10:54<br>
<b>To:</b> Michael Coleman<br>
<b>Cc:</b> User support mailing list for Open OnDemand<br>
<b>Subject:</b> Re: [OOD-users] no environment set for HPC desktop -- job fails</font>
<div> </div>
</div>
<div>
<div dir="ltr"></div>
<div dir="ltr">I gotta say, I am trying to read it very very carefully but don’t seem to be able to parse out the subtlety. 😐</div>
<div dir="ltr"><br>
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<div dir="ltr">Not sure how to miss read this, emphasis on all theirs:</div>
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<div dir="ltr"><dl><dt><span><b style="margin:0px;padding:0px;border:0px;font-style:inherit;line-height:inherit;vertical-align:baseline">--export</b>=<<span style="margin:0px;padding:0px;border:0px;font-style:italic;line-height:inherit;vertical-align:baseline">environment
variables [ALL] | NONE</span>></span></dt><dd><span>Identify which environment variables from the submission environment are propagated to the launched application. By default, <span style="margin:0px;padding:0px;border:0px;font-style:italic;line-height:inherit;vertical-align:baseline">all</span> are
propagated. Multiple environment variable names should be comma separated. </span></dd></dl></div>
<div dir="ltr"><br>
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<div dir="ltr"><br>
On Dec 7, 2018, at 10:24 PM, Michael Coleman <<a href="mailto:mcolema5@uoregon.edu" target="_blank">mcolema5@uoregon.edu</a>> wrote:<br>
<br>
</div>
<blockquote type="cite">
<div dir="ltr"><span>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.</span><br>
<br>
<span>Michael Coleman (<a href="mailto:mcolema5@uoregon.edu" target="_blank">mcolema5@uoregon.edu</a>), Computational Scientist</span><br>
<span>Research Advanced Computing Services</span><br>
<span>6235 University of Oregon</span><br>
<span>Eugene, OR 97403</span><br>
<br>
<br>
<span>________________________________________</span><br>
<span>From: John-Paul Robinson <<a href="mailto:jprorama@gmail.com" target="_blank">jprorama@gmail.com</a>></span><br>
<span>Sent: Friday, December 7, 2018 17:19</span><br>
<span>To: Michael Coleman</span><br>
<span>Cc: User support mailing list for Open OnDemand</span><br>
<span>Subject: Re: [OOD-users] no environment set for HPC desktop -- job fails</span><br>
<br>
<span>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. :/</span><br>
<br>
<blockquote type="cite"><span>On Dec 7, 2018, at 6:59 PM, John-Paul Robinson <<a href="mailto:jprorama@gmail.com" target="_blank">jprorama@gmail.com</a>> wrote:</span><br>
</blockquote>
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<blockquote type="cite"><span>Its a pretty alarming change to have happened in three ticks of the minor release number.</span><br>
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<blockquote type="cite"><span>Any insights from others on this?</span><br>
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<blockquote type="cite"><span>On Dec 7, 2018, at 6:37 PM, Michael Coleman <<a href="mailto:mcolema5@uoregon.edu" target="_blank">mcolema5@uoregon.edu</a>> wrote:</span><br>
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<blockquote type="cite"><span>Hi John-Paul,</span><br>
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<blockquote type="cite"><span>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.</span><br>
</blockquote>
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<blockquote type="cite"><span>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.</span><br>
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<blockquote type="cite"><span>Good luck,</span><br>
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<blockquote type="cite"><span>Mike</span><br>
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<blockquote type="cite"><span>-----Original Message-----</span><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><span>From: John-Paul Robinson <<a href="mailto:jprorama@gmail.com" target="_blank">jprorama@gmail.com</a>></span><br>
</blockquote>
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<blockquote type="cite">
<blockquote type="cite"><span>Sent: Friday, December 7, 2018 03:56 PM</span><br>
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<blockquote type="cite">
<blockquote type="cite"><span>To: Michael Coleman <<a href="mailto:mcolema5@uoregon.edu" target="_blank">mcolema5@uoregon.edu</a>>; User support mailing list for Open OnDemand <<a href="mailto:ood-users@lists.osc.edu" target="_blank">ood-users@lists.osc.edu</a>></span><br>
</blockquote>
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<blockquote type="cite">
<blockquote type="cite"><span>Subject: Re: [OOD-users] no environment set for HPC desktop -- job fails</span><br>
</blockquote>
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<blockquote type="cite"><span>MIke,</span><br>
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<blockquote type="cite"><span>Thanks for pointing us to this issue.</span><br>
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<blockquote type="cite"><span>This does appear to be similar to what's happening in our dev</span><br>
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<blockquote type="cite"><span>environment. (Note our still-working prod environment is Bright CM with</span><br>
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<blockquote type="cite"><span>slurm 17.02.2).</span><br>
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<blockquote type="cite"><span>The odd thing with our dev environment (built on OpenHPC) is that it was</span><br>
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<blockquote type="cite"><span>working in October and only started failing in builds over the past</span><br>
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<blockquote type="cite"><span>month. This appears to coincide with the OpenHPC 1.3.5 to 1.3.6 update</span><br>
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<blockquote type="cite"><span>(going from slurm 17.11.7 to 17.11.10).</span><br>
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<blockquote type="cite"><span>We've had some success in restoring the original working configuration</span><br>
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<blockquote type="cite"><span>in one of our test stacks by reverting to the OpenHPC 1.3.5 release.</span><br>
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<blockquote type="cite"><span>What's odd is this implies the problem is not with OOD but in the</span><br>
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<blockquote type="cite"><span>OpenHPC system env. As far as we can determine, our OOD remains</span><br>
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<blockquote type="cite">
<blockquote type="cite"><span>identical. We are setting up dev in vagrant with ansible provisioning</span><br>
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<blockquote type="cite"><span>the openhpc + ood cluster based on the CRI_XSEDE work extended to add an</span><br>
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<blockquote type="cite"><span>OOD node via vagrant + ansible (not as a warewulf provision).</span><br>
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<blockquote type="cite"><span><a href="https://github.com/jprorama/CRI_XCBC" target="_blank">https://github.com/jprorama/CRI_XCBC</a></span><br>
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<blockquote type="cite"><span>I've read through the github issue below but haven't teased out all the</span><br>
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<blockquote type="cite"><span>details.</span><br>
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<blockquote type="cite"><span>Is there an obvious transition point where this export behavior could be</span><br>
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<blockquote type="cite"><span>impacted by the underlying system versions OOD is running on?</span><br>
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<blockquote type="cite"><span>We'll contribute insights on the github issue as we find them.</span><br>
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<blockquote type="cite"><span>Thanks,</span><br>
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<blockquote type="cite"><span>John-Paul</span><br>
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<blockquote type="cite"><span>On 12/5/18 5:15 PM, Michael Coleman wrote:</span><br>
</blockquote>
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<blockquote type="cite">
<blockquote type="cite"><span>Hi John-Paul,</span><br>
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<blockquote type="cite"><span>We worked through something similar. You might find some useful hints on this ticket.</span><br>
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<blockquote type="cite">
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<blockquote type="cite"><span> <a href="https://github.com/OSC/ood_core/issues/109" target="_blank">https://github.com/OSC/ood_core/issues/109</a></span><br>
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<blockquote type="cite"><span>Cheers,</span><br>
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<blockquote type="cite"><span>Mike</span><br>
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<blockquote type="cite"><span>-----Original Message-----</span><br>
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<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><span>From: OOD-users <<a href="mailto:ood-users-bounces+mcolema5=uoregon.edu@lists.osc.edu" target="_blank">ood-users-bounces+mcolema5=uoregon.edu@lists.osc.edu</a>> On Behalf Of John-Paul Robinson via OOD-users</span><br>
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<blockquote type="cite"><span>Sent: Wednesday, December 5, 2018 02:49 PM</span><br>
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<blockquote type="cite"><span>To: <a href="mailto:ood-users@lists.osc.edu" target="_blank">ood-users@lists.osc.edu</a></span><br>
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<blockquote type="cite">
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<blockquote type="cite"><span>Subject: [OOD-users] no environment set for HPC desktop -- job fails</span><br>
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<blockquote type="cite"><span>In our dev environment (slurm with ohpc) we have started to see this</span><br>
</blockquote>
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<blockquote type="cite">
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<blockquote type="cite"><span>error when trying to launch interactive desktops:</span><br>
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<blockquote type="cite"><span>/tmp/slurmd/job00079/slurm_script: line 3: module: command not found</span><br>
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<blockquote type="cite"><span>Setting VNC password...</span><br>
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<blockquote type="cite"><span>Error: no HOME environment variable</span><br>
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<blockquote type="cite"><span>Starting VNC server...</span><br>
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<blockquote type="cite"><span>vncserver: The HOME environment variable is not set.</span><br>
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<blockquote type="cite"><span>vncserver: The HOME environment variable is not set.</span><br>
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<blockquote type="cite"><span>vncserver: The HOME environment variable is not set. vncserver: The HOME</span><br>
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<blockquote type="cite"><span>environment variable is</span><br>
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<blockquote type="cite"><span>As we understand it, the PUN nginx worker launches the batch job that</span><br>
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<blockquote type="cite"><span>starts the desktop batch job.</span><br>
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<blockquote type="cite"><span>The problem seems to be that the environment for the job is empty, hence</span><br>
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<blockquote type="cite"><span>no module function or HOME env or anything else. We checked the env of</span><br>
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<blockquote type="cite">
<blockquote type="cite"><span>the users nginx worker under /proc and it is completely empty. Because</span><br>
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<blockquote type="cite"><span>our job env is inherited from the caller (the nginx worker in this case)</span><br>
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<blockquote type="cite"><span>the attempt to run the module command and vncserver commands naturally fail.</span><br>
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<blockquote type="cite"><span>When we launch an interactive terminal, it runs just fine, but I'm</span><br>
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<blockquote type="cite"><span>guessing that's because the interactive session actually reads the</span><br>
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<blockquote type="cite"><span>normal shell startup and builds its environment, even if it happened to</span><br>
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<blockquote type="cite"><span>be missing in the proxy.</span><br>
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<blockquote type="cite"><span>Do you have any pointers on what could cause this situation. We</span><br>
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<blockquote type="cite"><span>noticed it after we started adding additional interactive apps but don't</span><br>
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<blockquote type="cite">
<blockquote type="cite"><span>have a clear time point. It was working fine originally and still</span><br>
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<blockquote type="cite"><span>functions fine in our prod env (without any of the additional</span><br>
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<blockquote type="cite"><span>interactive apps).</span><br>
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<blockquote type="cite"><span>Thanks,</span><br>
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<blockquote type="cite"><span>John-Paul</span><br>
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<blockquote type="cite"><span>_______________________________________________</span><br>
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<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><span>OOD-users mailing list</span><br>
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</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><span><a href="mailto:OOD-users@lists.osc.edu" target="_blank">OOD-users@lists.osc.edu</a></span><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><span><a href="https://lists.osu.edu/mailman/listinfo/ood-users" target="_blank">https://lists.osu.edu/mailman/listinfo/ood-users</a></span><br>
</blockquote>
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