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Large # of rotatable bonds, and download page failure. #128
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I could not replicate on Actual. So, it's intermittent? I am building 64
conformers now. Not all are done.
If we have all just tried to build 64 conformers on different sites, things
might be slow for a minute.
…On Tue, Mar 14, 2023 at 9:25 AM Dan Wenworth ***@***.***> wrote:
Did replicate on actual. It is possible this will resolve when we update
glycam.org to match test.glycam.org.
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:-) Lachele
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I'm happy people are learning that sleep is important. Now, please stop
trying to kill the nocturnal folks.
|
Suspect this relates to the size of the queue prior to this request? |
No. That's not the issue. I found the problem. I think the bug is in
GEMS. There is trouble on LiveTest, too. The queue is empty.
…On Tue, Mar 14, 2023 at 10:09 AM Dan Wenworth ***@***.***> wrote:
Suspect this relates to the size of the queue prior to this request?
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It wasn't in GEMS. It was in GMML. I believe this is fixed. Re-open if I am wrong. |
I'll take a look again. I might need to finish what I was doing in GEMS in the sequence Entity. This could be anything. The "load balancing" might simply be that the structures are never being submitted. That's what was happening before. It could be a systems issue, etc. But, it is probably related to the following. Note that if more than 64 structs are available, then the default 64 always get built and minimized. This is what my changes in GEMS will fix. I made a summary here: GLYCAM-Web/gems#74 (comment) |
In the future, copy in the sequence :-) |
Thank you Oliver, for taking such detailed notes. At a glance, I can see multiple issues. After lunch, Charles and I will break this up into separate tickets and do proper assessments.
|
I need to finish my work in GEMS. It appeared that the GMML fix was all that was really needed. The jobs that aren't building are never even getting their simulation and slurm submission files made. They are never being submitted for minimization. Let's talk during or after the meeting this morning. BTW - yes, Oliver's details are great. But, a sequence would help. :-) |
And... yeah... the sequence was up there at the top. My bad. I did read all the new stuff, though. :-) Anyhow, this appears (again) to be a thing in GEMS. It seems to be a problem with the accounting when GEMS is deciding which structures exist and which need building. For example (in my DevEnv where I can control things more), I requested 4 structures. The website shows me four structures, but in the project directory, I have two new builds and three existing builds - so, five structures. The work I was doing before in GEMS will be needed. I'll get back to that immediately. |
Some of the structures I selected are left in a minimizing state: |
Tool:
Carbohydrate Builder
Bug Description:
From Rob:
"Hi Guys, when I try to build this (or anything similar) it tells me that there are too many rotatable bods. But when I select an allowable number of rotamers, the download page doesn't update and I am unable to build it. This happens whether I select it from a library or build from text."
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2[DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-4]DManpa1-3[DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2[DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-OH
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