From rkaufman at andrew.cmu.edu  Thu Aug  4 09:38:31 2022
From: rkaufman at andrew.cmu.edu (Roman Kaufman)
Date: Thu, 4 Aug 2022 09:38:31 -0400
Subject: [PIZZA] Summer Send-Off - Friday (TOMORROW) at 6 PM
Message-ID: <CAGFDa2dn4PRwhZ5AQJ4b=ccoYo2uFACWjdfOBbW5Mo1LKF7NQQ@mail.gmail.com>

Howdy Autonians!

This Friday (tomorrow!!) after Professor Dubrawski's ML Primer from 4:30 to
6 PM in NSH 3305, we'll be having *pizza in NSH 3305 at 6 PM* as a
celebration for the folks that have joined this summer, RISS and interns
alike.

Come one come all, bring a board game and a smile and we hope to see you
there!
Roman
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From awd at cs.cmu.edu  Fri Aug  5 11:25:05 2022
From: awd at cs.cmu.edu (Artur Dubrawski)
Date: Fri, 5 Aug 2022 11:25:05 -0400
Subject: "Safe and Pleasant ML": today 4:30-6pm
In-Reply-To: <CAJvAoyvtk-Gq60hyuxkpGT=JRsMkYLeSEJ+MN7DBc-UOva=ikg@mail.gmail.com>
References: <CAJvAoyvoBsYhd6OmXAj5oHpbuun7efNtTovUXJOQ-LcX77iSYA@mail.gmail.com>
 <CAJvAoysP+HedvD37V_TczCOtAuBvFLtRXXXtLvzfcvg5fSM=jg@mail.gmail.com>
 <CAJvAoyuWjiifARL6xrH0wTeTWE78zo0X1NARaRk_o_hzF=Lscw@mail.gmail.com>
 <CAJvAoyvtk-Gq60hyuxkpGT=JRsMkYLeSEJ+MN7DBc-UOva=ikg@mail.gmail.com>
Message-ID: <CAJvAoyt_b-LHyzmVJg0gSYekYVwDGQfw=RPSb24skFzPHBu9Xg@mail.gmail.com>

We will try to finish covering the material in Session 2.

We will be meeting in NSH 3305.

The slides are posted on:
https://drive.google.com/drive/folders/1wd2DHkDBIgWzBjwiDFr0FWRVVESfhhEg?usp=sharing

Cheers,
Artur Dubrawski

On Fri, Jul 22, 2022 at 11:44 AM Artur Dubrawski <awd at cs.cmu.edu> wrote:

> We will continue into Session 2 today, contents of which include:
> * The elusive concept of ?perfect data? and getting our real-world data
> closer to perfection
> * Basic feature selection algorithms
> * Feature reduction with Principal Components Analysis (PCA)
>   - Additional uses of PCA
>   - Related techniques
> * Feature reduction with Autoencoders (AE)
> * Folding data with Multi-Dimensional Scaling (MDS)
> * Unfolding data with ?Kernel trick?
> * A quick look at preparing textual data for ML
>
> We will probably not be able to cover everything in one seating, so expect
> the session to be continued in the next meetings.
>
> Cheers
> Artur
>
> On Fri, Jul 15, 2022 at 2:48 PM Artur Dubrawski <awd at cs.cmu.edu> wrote:
>
>> We are continuing today, 4:30pm, NSH 3305 and zoom.
>>
>> Artur
>>
>> On Thu, Jul 7, 2022 at 6:32 PM Artur Dubrawski <awd at cs.cmu.edu> wrote:
>>
>>> We will continue our introduction to safe and pleasant machine
>>> learning tomorrow as scheduled.
>>> This time, we will talk about bootstrapping, finish the coverage of ROC
>>> methodology, and briefly talk about McNemar's tests and classifier
>>> calibration.
>>>
>>> Slides from this and previous meetings are available at
>>> https://drive.google.com/drive/folders/1wd2DHkDBIgWzBjwiDFr0FWRVVESfhhEg
>>>
>>> (I'd like to give Dr. Gisolfi credit for coming up with the apt title of
>>> the above directory)
>>> (So please let him know if you have any trouble accessing it :P )
>>>
>>> Cheers,
>>> Artur
>>>
>>>>
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From vanl at andrew.cmu.edu  Fri Aug  5 15:35:54 2022
From: vanl at andrew.cmu.edu (Van Le)
Date: Fri, 5 Aug 2022 15:35:54 -0400
Subject: [PIZZA] Summer Send-Off - Friday (TOMORROW) at 6 PM
In-Reply-To: <CAGFDa2dn4PRwhZ5AQJ4b=ccoYo2uFACWjdfOBbW5Mo1LKF7NQQ@mail.gmail.com>
References: <CAGFDa2dn4PRwhZ5AQJ4b=ccoYo2uFACWjdfOBbW5Mo1LKF7NQQ@mail.gmail.com>
Message-ID: <CAEPaZwQfUrAz2iXuGiG6wny68Juj4Vthij+G1-DXFtm7Lo-gAQ@mail.gmail.com>

Hello Autonians,
Besides Pizza for tonight send-off, I also have cookies for all as well.
It's my great honor to have the opportunity to be a member of the lab this
summer. See you then!

On Thu, 4 Aug 2022 at 09:39 Roman Kaufman <rkaufman at andrew.cmu.edu> wrote:

> Howdy Autonians!
>
> This Friday (tomorrow!!) after Professor Dubrawski's ML Primer from 4:30
> to 6 PM in NSH 3305, we'll be having *pizza in NSH 3305 at 6 PM* as a
> celebration for the folks that have joined this summer, RISS and interns
> alike.
>
> Come one come all, bring a board game and a smile and we hope to see you
> there!
> Roman
>
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From awd at cs.cmu.edu  Mon Aug  8 13:12:59 2022
From: awd at cs.cmu.edu (Artur Dubrawski)
Date: Mon, 8 Aug 2022 13:12:59 -0400
Subject: Check out this cool blog post by our own Chirag and Willa
Message-ID: <CAJvAoyuxetKrw8RTpk_=28BkjZo=geJbwxD9AMN25nSJPvEX=w@mail.gmail.com>

It is already getting traction in the internet media:

https://blog.ml.cmu.edu/2022/08/05/auton-survival-an-open-source-package-for-regression-counterfactual-estimation-evaluation-and-phenotyping-censored-time-to-event-data/

Way to go Willa and Chirag!

Cheers,
Artur
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From awd at cs.cmu.edu  Wed Aug 10 10:33:00 2022
From: awd at cs.cmu.edu (Artur Dubrawski)
Date: Wed, 10 Aug 2022 10:33:00 -0400
Subject: Andy Gao's MSR Thesis Talk: Addressing Time-series Signal Quality in
 Healthcare Data
In-Reply-To: <CA+BzVUj8Ly_bpHYWyTwerJvnK=dOUm_G6J4gXqWvrF77TaXvgg@mail.gmail.com>
References: <CA+BzVUhoCLRono193Fj6TiwhyUHVD=40W=Wm+shKTdduSONMGQ@mail.gmail.com>
 <CA+BzVUj8Ly_bpHYWyTwerJvnK=dOUm_G6J4gXqWvrF77TaXvgg@mail.gmail.com>
Message-ID: <CAJvAoytThtueSiJocxu+Sbf9TwhrRnVzc5UN+Ju8wyooEbVMPw@mail.gmail.com>

Autonians,

If you are available please join this important talk by Andy who will be
delivering his MS thesis presentation tomorrow at 3pm.

Cheers,
Artur

---------- Forwarded message ---------
From: Chufan Gao <chufang at andrew.cmu.edu>
Date: Wed, Aug 10, 2022 at 10:28 AM
Subject: Re: MSR Thesis Talk: Addressing Time-series Signal Quality in
Healthcare Data
To: <ri-people at lists.andrew.cmu.edu>, Artur Dubrawski <awd at cs.cmu.edu>,
Jeff Schneider <jeff4 at andrew.cmu.edu>, Clermont, Gilles <cler at pitt.edu>,
Benedikt Boecking <boecking at andrew.cmu.edu>, Barbara (B.J.) Fecich <
barbarajean at cmu.edu>


Hi All,

A gentle reminder that this is happening tomorrow at 3pm EST in NSH A507!
*Zoom:* https://cmu.zoom.us/j/5223311585
<https://www.google.com/url?q=https://cmu.zoom.us/j/5223311585&sa=D&source=calendar&ust=1660068159564898&usg=AOvVaw36AlMyStV4M9wAJcfGvQ2R>


Sincerely,
Chufan Gao
Robotics Institute, AutonLab, Carnegie Mellon University


On Thu, Aug 4, 2022 at 2:30 PM Chufan Gao <chufang at andrew.cmu.edu> wrote:

>
>
> I will be giving my MSR thesis talk on *Thursday, August 11th, 2022 at
> 3:00 PM - 4:00 PM EST in NSH A507*. Everyone is invited!
>
> *Date: *Thursday, August 11th, 2022
> *Time: *3:00 PM - 4:00 PM EST
> *Location: *Newell-Simon Hall (NSH) A507
> *Zoom:* https://cmu.zoom.us/j/5223311585
> <https://www.google.com/url?q=https://cmu.zoom.us/j/5223311585&sa=D&source=calendar&ust=1660068159564898&usg=AOvVaw36AlMyStV4M9wAJcfGvQ2R>
>
>
> *Title:* Addressing Time-series Signal Quality in Healthcare Data
>
> *Abstract: *Healthcare data time-series signal quality assessment (SQA)
> plays a vital role in the accuracy and reliability of machine learning
> algorithms to analyze health metrics. However, these signals are often
> corrupted with different kinds of noises and artifacts, including Baseline
> Wander, Muscle Artifacts, Powerline Interference, and Equipment Failure.
> This can lead to vital, potentially deadly, errors in the medical domain.
> This can include inaccurate calculation of basic health features like Heart
> Rate, clinical alarm burnout from bedside monitors, as well as disrupting
> general downstream machine learning tasks. While some work has been done in
> the area of open-source signal quality analysis in general, there are very
> few open source implementations of signal quality analysis frameworks that
> attempt to reproduce and expand on existing results on open source
> datasets.
>
> First, we propose an open-source implementation of signal quality indices
> (SQIs) for analysis of electrocardiogram (ECG), plethysmography, and more.
> We aim to codify and reproduce SQIs and results from The Physionet Signal
> Quality Classification 2011 Challenge. We show that these SQIs may be used
> for signal quality outlier detection in a real world clinical dataset from
> University of Pittsburgh Medical Center (UPMC). Secondly, in the case of
> another common healthcare SQA issue: ECG denoising, we compare Wavelet,
> EMD, and Convolutional Autoencoder denoising techniques. We show that
> Convolutional Autoencoder denoising performs the best on the open MIT-BIH
> Arrhythmia Noise Stress Test dataset, and evaluate it on the UPMC dataset.
> To our knowledge, we are the first to provide an open source implementation
> of these two SQA tasks that is validated on public datasets. Ideally, this
> work serves as an accessible, open source, toolkit for signal quality
> analysis and ECG denoising.
>
> *Committee:*
> Professor Artur Dubrawski (advisor)
> Professor Jeff Schneider
> Professor Gilles Clermont
> PhD Student Benedikt Boecking
>
> Sincerely,
> Chufan Gao
> Robotics Institute, AutonLab, Carnegie Mellon University
>
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From predragp at andrew.cmu.edu  Thu Aug 11 18:29:03 2022
From: predragp at andrew.cmu.edu (Predrag Punosevac)
Date: Thu, 11 Aug 2022 18:29:03 -0400
Subject: lion.auton.cs.cmu.edu decommissioned
Message-ID: <CAEFFt-GaT-W5BdDh0H8C0hG9A+akK_29e0_-RkACmbrYQvMy+A@mail.gmail.com>

Dear Autonians,

The shell gateway lion.auton.cs.cmu.edu is decommissioned due to faulty
hardware. I replaced it with a new shell gateway

upload.autonlab.org  SHA256:oe00OEWRq8QneX+NEzMVQV/++1H3Hywy/VjCXqaurh4

The documentation is updated accordingly. I apologize for any
inconvenience. Make sure you clear your ~/.ssh/known_hosts file before
reporting problems.

Best,
Predrag
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From awd at cs.cmu.edu  Fri Aug 12 07:35:04 2022
From: awd at cs.cmu.edu (Artur Dubrawski)
Date: Fri, 12 Aug 2022 07:35:04 -0400
Subject: Auton Lab Walk in the Park: TODAY, 6pm start (after pizza in NSH 3305)
In-Reply-To: <CAJvAoyverLmtE7tdmYDE7K3BPzzAoZj7QF24L5+HUTNXcZThKw@mail.gmail.com>
References: <CAJvAoyt35MQvsR801LvWGs+q=jMMBRGZSj+HB4r_HiLG8nxnhg@mail.gmail.com>
 <CAJvAoyvXANuMihpU9e6kYfUUEBmuakrP2BVjFa_0yXKdi3L3zg@mail.gmail.com>
 <CAJvAoyv1=nmb==AysF5R63bngHLUP8Pxpvu8aQu8H2C-v=AkLw@mail.gmail.com>
 <CAJvAoytAGAebk96qe1hDMm4j4Uu7rF9Hb5AmPAGWOc5zAMQYSw@mail.gmail.com>
 <CAJvAoyverLmtE7tdmYDE7K3BPzzAoZj7QF24L5+HUTNXcZThKw@mail.gmail.com>
Message-ID: <CAJvAoyt30dsa2n2j69oMtyzHa8jDBcMjjFmz4Z_RO_anO1t6Qg@mail.gmail.com>

Team,

We will have a pizza farewell party for the remaining summer interns at 5pm
in NSH 3305. Everyone is welcome to join.

After that, we will go for a walk in Schenley Park, approximate start time
6pm.

Cheers
Artur

On Fri, Jul 29, 2022 at 11:53 AM Artur Dubrawski <awd at cs.cmu.edu> wrote:

> the usual deal for tonight, see you then and there!
>
> On Fri, Jul 22, 2022 at 1:49 PM Artur Dubrawski <awd at cs.cmu.edu> wrote:
>
>> Team, if you are interested please join the walking group at the NSH
>> entryway.
>>
>> 6pm.
>>
>> Cheers,
>> Artur
>>
>> On Fri, Jul 15, 2022 at 4:02 PM Artur Dubrawski <awd at cs.cmu.edu> wrote:
>>
>>> Team, i will not be able to join the walk today, but whomever is
>>> free and willing to keep our new tradition going, please do!
>>>
>>> Cheers
>>> Artur
>>>
>>> On Fri, Jul 8, 2022, 11:49 AM Artur Dubrawski <awd at cs.cmu.edu> wrote:
>>>
>>>> Team,
>>>>
>>>> The weather forecast has improved enough for us to go for a walk this
>>>> evening.
>>>>
>>>> Let's meet in front of NSH at 6pm.
>>>>
>>>> Cheers
>>>> Artur
>>>>
>>>
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From awd at cs.cmu.edu  Fri Aug 12 10:41:45 2022
From: awd at cs.cmu.edu (Artur Dubrawski)
Date: Fri, 12 Aug 2022 10:41:45 -0400
Subject: There will be NO "Safe and Pleasant ML" today
In-Reply-To: <CAJvAoyt_b-LHyzmVJg0gSYekYVwDGQfw=RPSb24skFzPHBu9Xg@mail.gmail.com>
References: <CAJvAoyvoBsYhd6OmXAj5oHpbuun7efNtTovUXJOQ-LcX77iSYA@mail.gmail.com>
 <CAJvAoysP+HedvD37V_TczCOtAuBvFLtRXXXtLvzfcvg5fSM=jg@mail.gmail.com>
 <CAJvAoyuWjiifARL6xrH0wTeTWE78zo0X1NARaRk_o_hzF=Lscw@mail.gmail.com>
 <CAJvAoyvtk-Gq60hyuxkpGT=JRsMkYLeSEJ+MN7DBc-UOva=ikg@mail.gmail.com>
 <CAJvAoyt_b-LHyzmVJg0gSYekYVwDGQfw=RPSb24skFzPHBu9Xg@mail.gmail.com>
Message-ID: <CAJvAoys_mfv9wGbVw8Eofd4bpFE0XThq1t0W8KJ0boc+RT+WfQ@mail.gmail.com>

I guess our miniseries have come to a closure last week.

But if I hear a lot of strong arguments on if and why we should continue,
I'd consider doing that.

Cheers
Artur

On Fri, Aug 5, 2022 at 11:25 AM Artur Dubrawski <awd at cs.cmu.edu> wrote:

> We will try to finish covering the material in Session 2.
>
> We will be meeting in NSH 3305.
>
> The slides are posted on:
> https://drive.google.com/drive/folders/1wd2DHkDBIgWzBjwiDFr0FWRVVESfhhEg?usp=sharing
>
> Cheers,
> Artur Dubrawski
>
> On Fri, Jul 22, 2022 at 11:44 AM Artur Dubrawski <awd at cs.cmu.edu> wrote:
>
>> We will continue into Session 2 today, contents of which include:
>> * The elusive concept of ?perfect data? and getting our real-world data
>> closer to perfection
>> * Basic feature selection algorithms
>> * Feature reduction with Principal Components Analysis (PCA)
>>   - Additional uses of PCA
>>   - Related techniques
>> * Feature reduction with Autoencoders (AE)
>> * Folding data with Multi-Dimensional Scaling (MDS)
>> * Unfolding data with ?Kernel trick?
>> * A quick look at preparing textual data for ML
>>
>> We will probably not be able to cover everything in one seating, so
>> expect the session to be continued in the next meetings.
>>
>> Cheers
>> Artur
>>
>> On Fri, Jul 15, 2022 at 2:48 PM Artur Dubrawski <awd at cs.cmu.edu> wrote:
>>
>>> We are continuing today, 4:30pm, NSH 3305 and zoom.
>>>
>>> Artur
>>>
>>> On Thu, Jul 7, 2022 at 6:32 PM Artur Dubrawski <awd at cs.cmu.edu> wrote:
>>>
>>>> We will continue our introduction to safe and pleasant machine
>>>> learning tomorrow as scheduled.
>>>> This time, we will talk about bootstrapping, finish the coverage of ROC
>>>> methodology, and briefly talk about McNemar's tests and classifier
>>>> calibration.
>>>>
>>>> Slides from this and previous meetings are available at
>>>> https://drive.google.com/drive/folders/1wd2DHkDBIgWzBjwiDFr0FWRVVESfhhEg
>>>>
>>>> (I'd like to give Dr. Gisolfi credit for coming up with the apt title
>>>> of the above directory)
>>>> (So please let him know if you have any trouble accessing it :P )
>>>>
>>>> Cheers,
>>>> Artur
>>>>
>>>>>
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From predragp at andrew.cmu.edu  Sat Aug 13 15:32:37 2022
From: predragp at andrew.cmu.edu (Predrag Punosevac)
Date: Sat, 13 Aug 2022 15:32:37 -0400
Subject: updates
Message-ID: <CAEFFt-EmcBHm04ZHNJQ50GRjP=rNtayZMoD=CtSv-n6CahdQ3g@mail.gmail.com>

Dear Autonians,

I just updated and rebooted all files servers. Some of you have noticed a
brief 15 min description in availability of shell gateways due
to unavailability of home directories.

Some of you who were taxing NFS in-spite of all my appeals to use scratch
for data experiments will have to restart your scripts. I also had to
reboot foxconn due to the same reason.

Cheers,
Predrag
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From predragp at andrew.cmu.edu  Mon Aug 15 00:37:34 2022
From: predragp at andrew.cmu.edu (Predrag Punosevac)
Date: Mon, 15 Aug 2022 00:37:34 -0400
Subject: Xen Dom0 upgrade gone wrong
Message-ID: <CAEFFt-FuC07RXt1vqM5YxmCaTYwoMp=oHTWH5NP6iVCUaTtnGw@mail.gmail.com>

Dear Autonians,

I tried to upgrade the OS on the Xen Dom0 host from Alpine Linux 16.1 to
recently released 16.2. The upgrade also involved a minor xen server
upgrade. Unfortunately, I hit

xl create

infinite loop bug. I can't create/launch DomU guests. The number of virtual
guests are affected. Most notably shell gateway

lop2.autonlab.org

as well as

edshat
tracker
observium
comp
gitlab


This problem is not fixable tonight. I will have to deal with upstream and
submit a proper bug report.

I apologize for any inconvenience.

Best,
Predrag
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From predragp at andrew.cmu.edu  Mon Aug 15 01:00:21 2022
From: predragp at andrew.cmu.edu (Predrag Punosevac)
Date: Mon, 15 Aug 2022 01:00:21 -0400
Subject: Xen Dom0 upgrade gone wrong
In-Reply-To: <CAEFFt-FuC07RXt1vqM5YxmCaTYwoMp=oHTWH5NP6iVCUaTtnGw@mail.gmail.com>
References: <CAEFFt-FuC07RXt1vqM5YxmCaTYwoMp=oHTWH5NP6iVCUaTtnGw@mail.gmail.com>
Message-ID: <CAEFFt-EfjjDSFf+RpBb8HSAKjDk0Xze=zd4QzL1Z0qwa09mqNg@mail.gmail.com>

In case, anyone wants to follow the debugging process

https://gitlab.alpinelinux.org/alpine/aports/-/issues/14090

I should have been a bit more careful and checked bug reports before
upgrading.

Best,
Predrag

On Mon, Aug 15, 2022 at 12:37 AM Predrag Punosevac <predragp at andrew.cmu.edu>
wrote:

> Dear Autonians,
>
> I tried to upgrade the OS on the Xen Dom0 host from Alpine Linux 16.1 to
> recently released 16.2. The upgrade also involved a minor xen server
> upgrade. Unfortunately, I hit
>
> xl create
>
> infinite loop bug. I can't create/launch DomU guests. The number of
> virtual guests are affected. Most notably shell gateway
>
> lop2.autonlab.org
>
> as well as
>
> edshat
> tracker
> observium
> comp
> gitlab
>
>
> This problem is not fixable tonight. I will have to deal with upstream and
> submit a proper bug report.
>
> I apologize for any inconvenience.
>
> Best,
> Predrag
>
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From ngisolfi at cs.cmu.edu  Tue Aug 16 09:59:47 2022
From: ngisolfi at cs.cmu.edu (Nicholas Gisolfi)
Date: Tue, 16 Aug 2022 09:59:47 -0400
Subject: Push for updating the website
Message-ID: <CANmms2TVEEAd222tPKDCxX5ramO25Js9E+b1nkDbYUXdDdzNYw@mail.gmail.com>

Hi Everyone,

We are pushing to get the Auton website in better shape before the start of
the semester.

Please take a look at the links below.  *I will be updating content on
Sunday night 8-21*, so if you add your thoughts before then, I will
incorporate it into the site on your behalf.  After Sunday, you will need
to make any updates yourself.

Link to the website in its current state: https://autonlab.org

Link to website content (everyone can edit/comment):
https://docs.google.com/document/d/1SMwjGXMkkEuTX-MzeEMK0aH4ppxvyZSpOrNu7XByizE/edit?usp=sharing

Link to folder for images to add (everyone can upload):
https://drive.google.com/drive/folders/1_Av0LPEffkznQA4ss401ou5T1lM9gPOM?usp=sharing

*Things that I need each Autonian's help with:*
*1)* A link to your current homepage. Please post a link under your name in
the content document (and add your name to the list if you are not on there
-- currently it is just Artur's group on the list)
*2)* Pictures that are relevant to your work or motivate your work.  Plots,
videos, etc.  Please add to the image folder link above
*3)* Edits on summary text for applications areas, research thrusts, and
impact areas.  Snippets from abstracts, blog posts, etc are all helpful.
Please add to the content link above.
*4)* A list of publications (in bibtex format) to include on the site (2021
and 2022 look like they may have gaps).  Please add these to the end of the
content document.

Thank you for your help!  Let's get the website to reflect all the great
work we are doing in the Auton Lab!

- Nick
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From awd at cs.cmu.edu  Tue Aug 16 11:44:19 2022
From: awd at cs.cmu.edu (Artur Dubrawski)
Date: Tue, 16 Aug 2022 11:44:19 -0400
Subject: IMPORTANT [Re: Push for updating the website]
In-Reply-To: <CANmms2TVEEAd222tPKDCxX5ramO25Js9E+b1nkDbYUXdDdzNYw@mail.gmail.com>
References: <CANmms2TVEEAd222tPKDCxX5ramO25Js9E+b1nkDbYUXdDdzNYw@mail.gmail.com>
Message-ID: <CAJvAoyu1VWhj0Aq8x8mVWy4DLr+g-PAcDAKWO7+vB-gk-+Hu3Q@mail.gmail.com>

This is a very good and important endeavor, please contribute to making it
- finally - successful.

I do not recall when was the last time we had a passably decent website for
the lab. Maybe in the 1990-ies... Let's end the misery!

Cheers,
Artur

On Tue, Aug 16, 2022 at 10:00 AM Nicholas Gisolfi <ngisolfi at cs.cmu.edu>
wrote:

> Hi Everyone,
>
> We are pushing to get the Auton website in better shape before the start
> of the semester.
>
> Please take a look at the links below.  *I will be updating content on
> Sunday night 8-21*, so if you add your thoughts before then, I will
> incorporate it into the site on your behalf.  After Sunday, you will need
> to make any updates yourself.
>
> Link to the website in its current state: https://autonlab.org
>
> Link to website content (everyone can edit/comment):
> https://docs.google.com/document/d/1SMwjGXMkkEuTX-MzeEMK0aH4ppxvyZSpOrNu7XByizE/edit?usp=sharing
>
> Link to folder for images to add (everyone can upload):
> https://drive.google.com/drive/folders/1_Av0LPEffkznQA4ss401ou5T1lM9gPOM?usp=sharing
>
> *Things that I need each Autonian's help with:*
> *1)* A link to your current homepage. Please post a link under your name
> in the content document (and add your name to the list if you are not on
> there -- currently it is just Artur's group on the list)
> *2)* Pictures that are relevant to your work or motivate your work.
> Plots, videos, etc.  Please add to the image folder link above
> *3)* Edits on summary text for applications areas, research thrusts, and
> impact areas.  Snippets from abstracts, blog posts, etc are all helpful.
> Please add to the content link above.
> *4)* A list of publications (in bibtex format) to include on the site
> (2021 and 2022 look like they may have gaps).  Please add these to the end
> of the content document.
>
> Thank you for your help!  Let's get the website to reflect all the great
> work we are doing in the Auton Lab!
>
> - Nick
>
>
>
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From awd at cs.cmu.edu  Tue Aug 16 22:51:02 2022
From: awd at cs.cmu.edu (Artur Dubrawski)
Date: Tue, 16 Aug 2022 22:51:02 -0400
Subject: Fwd: DARPA Competition Invite to D3M Alumni
In-Reply-To: <1bc10d065b7a46529609b7e22831641a@SDEXCHP-11.darpa.mil>
References: <1bc10d065b7a46529609b7e22831641a@SDEXCHP-11.darpa.mil>
Message-ID: <CAJvAoyt=tsx_867xsj8tARwKdmGj64YLHCer2pd7FMpSX5+cuQ@mail.gmail.com>

Fyi, this may be of interest to some Autonians.

Cheers
Artur

---------- Forwarded message ---------
From: Sandberg, Brian (contr-i2o) <brian.sandberg.ctr at darpa.mil>
Date: Tue, Aug 16, 2022, 9:47 PM
Subject: DARPA Competition Invite to D3M Alumni
To: jan.silovsky at raytheon.com <jan.silovsky at raytheon.com>,
michael.crystal at raytheon.com <michael.crystal at raytheon.com>,
man-hung.siu at raytheon.com <man-hung.siu at raytheon.com>, daynefreitag at sri.com
<daynefreitag at sri.com>, cy438 at cornell.edu <cy438 at cornell.edu>,
udell at cornell.edu <udell at cornell.edu>, ramcha1994 at gmail.com <
ramcha1994 at gmail.com>, davjoh at umich.edu <davjoh at umich.edu>,
jjcorso at eecs.umich.edu <jjcorso at eecs.umich.edu>, mteng at robots.ox.ac.uk <
mteng at robots.ox.ac.uk>, fwood at robots.ox.ac.uk <fwood at robots.ox.ac.uk>,
Gunes <gunes at robots.ox.ac.uk>, zinkov at robots.ox.ac.uk <
zinkov at robots.ox.ac.uk>, cuiz3 at rpi.edu <cuiz3 at rpi.edu>, jiq at rpi.edu <
jiq at rpi.edu>, plin at vencorelabs.com <plin at vencorelabs.com>,
rizmailov at vencorelabs.com <rizmailov at vencorelabs.com>,
boecking at andrew.cmu.edu <boecking at andrew.cmu.edu>, sray at cs.cmu.edu <
sray at cs.cmu.edu>, awd at cs.cmu.edu <awd at cs.cmu.edu>, kyao at isi.edu <
kyao at isi.edu>, szekely1401 at gmail.com <szekely1401 at gmail.com>,
kalyan at csail.mit.edu <kalyan at csail.mit.edu>, benjaminschreck93 at gmail.com <
benjaminschreck93 at gmail.com>, max.kanter at featurelabs.com <
max.kanter at featurelabs.com>, bjschoenfeld at gmail.com <bjschoenfeld at gmail.com>,
cgc at cs.byu.edu <cgc at cs.byu.edu>, rlaboulaye at gmail.com <rlaboulaye at gmail.com>,
jonathon at newknowledge.io <jonathon at newknowledge.io>,
slangevin at uncharted.software <slangevin at uncharted.software>,
cepjhu at gmail.com <cepjhu at gmail.com>, emanuel_zgraggen at brown.edu <
emanuel_zgraggen at brown.edu>, eliupfal at gmail.com <eliupfal at gmail.com>,
zeyuanxy at gmail.com <zeyuanxy at gmail.com>, kraska at mit.edu <kraska at mit.edu>,
remirampin at gmail.com <remirampin at gmail.com>, yamuna at nyu.edu <yamuna at nyu.edu>,
idrori at nyu.edu <idrori at nyu.edu>, jorgehpo at nyu.edu <jorgehpo at nyu.edu>,
apfeffer at cra.com <apfeffer at cra.com>, djonker at uncharted.software
<djonker at uncharted.software>, cbethune at uncharted.software
<cbethune at uncharted.software>, mitar at tnode.com <mitar at tnode.com>,
pszekely at isi.edu <pszekely at isi.edu>, hu at cse.tamu.edu <hu at cse.tamu.edu>,
bc2699 at columbia.edu <bc2699 at columbia.edu>, eli_upfal at brown.edu <
eli_upfal at brown.edu>, scott.langevin at uncharted.software
<scott.langevin at uncharted.software>, james at hona.kr <james at hona.kr>,
dorazio at utdallas.edu <dorazio at utdallas.edu>, mmahoney at icsi.berkeley.edu <
mmahoney at icsi.berkeley.edu>, cep at jhu.edu <cep at jhu.edu>, saman at csail.mit.edu
<saman at csail.mit.edu>, juliana.freire at nyu.edu <juliana.freire at nyu.edu>,
wsc at purdue.edu <wsc at purdue.edu>, qji at ecse.rpi.edu <qji at ecse.rpi.edu>,
kunle at stanford.edu <kunle at stanford.edu>, remco at cs.tufts.edu <
remco at cs.tufts.edu>, dawnsong at cs.berkeley.edu <dawnsong at cs.berkeley.edu>,
ishanu <ishanu at uchicago.edu>, girasole at umich.edu <girasole at umich.edu>,
rizmailov at appcomsci.com <rizmailov at appcomsci.com>, carsten_binnig at brown.edu
<carsten_binnig at brown.edu>, tim_kraska at brown.edu <tim_kraska at brown.edu>,
bapoczos at cs.cmu.edu <bapoczos at cs.cmu.edu>, ehn at cs.cmu.edu <ehn at cs.cmu.edu>,
mgrabmai at andrew.cmu.edu <mgrabmai at andrew.cmu.edu>, Man-hung.siu at raytheon.com
<Man-hung.siu at raytheon.com>, vjdorazio at gmail.com <vjdorazio at gmail.com>
Cc: Elliott, Joshua <joshua.elliott at darpa.mil>



All,

Hope all are doing well!

DARPA and USGS partnered to host a competition to enhance USGS critical
mineral assessments.

https://criticalminerals.darpa.mil/

Registration Opens Today!

Best,
Brian Sandberg
DARPA
703-209-6295
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From predragp at andrew.cmu.edu  Thu Aug 25 07:37:16 2022
From: predragp at andrew.cmu.edu (Predrag Punosevac)
Date: Thu, 25 Aug 2022 07:37:16 -0400
Subject: Xen Dom0 upgrade gone wrong
In-Reply-To: <CAEFFt-EfjjDSFf+RpBb8HSAKjDk0Xze=zd4QzL1Z0qwa09mqNg@mail.gmail.com>
References: <CAEFFt-FuC07RXt1vqM5YxmCaTYwoMp=oHTWH5NP6iVCUaTtnGw@mail.gmail.com>
 <CAEFFt-EfjjDSFf+RpBb8HSAKjDk0Xze=zd4QzL1Z0qwa09mqNg@mail.gmail.com>
Message-ID: <CAEFFt-Exr6Ja8o49U4yR1wRTxTEvKL-=3SpPT5CA-7HqpRkBpA@mail.gmail.com>

Dear Autonians,

It appears that a small group of Alpine Linux Xen users have been able to
locate the offensive patch in two million lines of code which was added to
Linux Kernel between branches 5.15.x and 5.19.x. The current 5.15.62-1-lts
kernel our Xen Dom0 uses appears to be stable. In practical terms that mean
that shell gateway

lop2.autonlab.org

as well as

edshat
tracker
observium
comp
gitlab

are all available and running as expected.

Cheers,
Predrag




On Mon, Aug 15, 2022 at 1:00 AM Predrag Punosevac <predragp at andrew.cmu.edu>
wrote:

> In case, anyone wants to follow the debugging process
>
> https://gitlab.alpinelinux.org/alpine/aports/-/issues/14090
>
> I should have been a bit more careful and checked bug reports before
> upgrading.
>
> Best,
> Predrag
>
> On Mon, Aug 15, 2022 at 12:37 AM Predrag Punosevac <
> predragp at andrew.cmu.edu> wrote:
>
>> Dear Autonians,
>>
>> I tried to upgrade the OS on the Xen Dom0 host from Alpine Linux 16.1 to
>> recently released 16.2. The upgrade also involved a minor xen server
>> upgrade. Unfortunately, I hit
>>
>> xl create
>>
>> infinite loop bug. I can't create/launch DomU guests. The number of
>> virtual guests are affected. Most notably shell gateway
>>
>> lop2.autonlab.org
>>
>> as well as
>>
>> edshat
>> tracker
>> observium
>> comp
>> gitlab
>>
>>
>> This problem is not fixable tonight. I will have to deal with upstream
>> and submit a proper bug report.
>>
>> I apologize for any inconvenience.
>>
>> Best,
>> Predrag
>>
>
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From awd at cs.cmu.edu  Thu Aug 25 10:00:03 2022
From: awd at cs.cmu.edu (Artur Dubrawski)
Date: Thu, 25 Aug 2022 10:00:03 -0400
Subject: a tool that can help us structure our ML projects (more) correctly
Message-ID: <CAJvAoys30A1XkJjg50Fy7h2=WN45qw4csijL1rCucvSv=z18Gg@mail.gmail.com>

https://arxiv.org/abs/2207.07048
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From predragp at andrew.cmu.edu  Thu Aug 25 12:03:06 2022
From: predragp at andrew.cmu.edu (Predrag Punosevac)
Date: Thu, 25 Aug 2022 12:03:06 -0400
Subject: "Stale file handle" error
In-Reply-To: <CALg9avJcWh8T9e8vEtL+1OBBNVEvXQwAVKJi=HbHOFQ1GcfMrQ@mail.gmail.com>
References: <CALg9avJcWh8T9e8vEtL+1OBBNVEvXQwAVKJi=HbHOFQ1GcfMrQ@mail.gmail.com>
Message-ID: <CAEFFt-HERjG92xO0aywyLyYpCCpLamUK5dTuHmdciDQGSSFJAQ@mail.gmail.com>

Which computer are you using? The stale file handles is NFS client problem
which can be only fix by rebooting the host. I might need to reboot file
server hosting project and data folders as well but that will not fix the
client side.. I was unable the other day to clear stale ZFS snapshots from
the same server. In spite of  the fact that the file server was trashed in
June by a fellow grad student I take a full responsibility for being a fool
and allowing lab members to create and excessively use public directory.
Will not happen in the future.

I did apply multiple bandaids but it appears that more invasive procedure
will be necessary to fix the fallout. Thanks for you report.


Predrag

On Thu, Aug 25, 2022, 11:50 AM Emma Erickson <eerickso at andrew.cmu.edu>
wrote:

> Hello Predrag,
>
> I am trying to access some data from the '/zfsauton/data' folder. Though
> it shows up when I list directories in zfsauton, I get a "stale file
> handle" error when trying to access its contents. Rachel had the same
> issue. Is there any way to access the files in this folder?
>
> Thank you,
> Emma
>
>
>
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From predragp at andrew.cmu.edu  Thu Aug 25 12:25:24 2022
From: predragp at andrew.cmu.edu (Predrag Punosevac)
Date: Thu, 25 Aug 2022 12:25:24 -0400
Subject: "Stale file handle" error
In-Reply-To: <CALg9avL+FN_=p2NkbQept2Yt32S-GsGB4X0PFv3nqz4hdnFW3w@mail.gmail.com>
References: <CALg9avJcWh8T9e8vEtL+1OBBNVEvXQwAVKJi=HbHOFQ1GcfMrQ@mail.gmail.com>
 <CAEFFt-HERjG92xO0aywyLyYpCCpLamUK5dTuHmdciDQGSSFJAQ@mail.gmail.com>
 <CALg9avL+FN_=p2NkbQept2Yt32S-GsGB4X0PFv3nqz4hdnFW3w@mail.gmail.com>
Message-ID: <CAEFFt-EUYDz9G=KL3Fe+LBJDsQqnBN=16DjNSG-dkZJSwv_zOg@mail.gmail.com>

This will require very invasive action. I need to do a bit of planning
before I pull the trigger on this. Are you sure you see this on your
desktop. IIRC zfsauton is not mounted on you personal workstation. You can
always try to reboot it.

Predrag

On Thu, Aug 25, 2022, 12:21 PM Emma Erickson <eerickso at andrew.cmu.edu>
wrote:

> Hi Predrag,
>
> Thank you for getting back so quickly. I first encountered the issue on my
> lab desktop, but receive the same errors regardless of whether I try
> upload, bash, or lop2.
> [image: image.png]
>
> Best,
> Emma
>
>
> On Thu, Aug 25, 2022 at 12:03 PM Predrag Punosevac <
> predragp at andrew.cmu.edu> wrote:
>
>> Which computer are you using? The stale file handles is NFS client
>> problem which can be only fix by rebooting the host. I might need to reboot
>> file server hosting project and data folders as well but that will not fix
>> the client side.. I was unable the other day to clear stale ZFS snapshots
>> from the same server. In spite of  the fact that the file server was
>> trashed in June by a fellow grad student I take a full responsibility for
>> being a fool and allowing lab members to create and excessively use public
>> directory. Will not happen in the future.
>>
>> I did apply multiple bandaids but it appears that more invasive procedure
>> will be necessary to fix the fallout. Thanks for you report.
>>
>>
>> Predrag
>>
>> On Thu, Aug 25, 2022, 11:50 AM Emma Erickson <eerickso at andrew.cmu.edu>
>> wrote:
>>
>>> Hello Predrag,
>>>
>>> I am trying to access some data from the '/zfsauton/data' folder. Though
>>> it shows up when I list directories in zfsauton, I get a "stale file
>>> handle" error when trying to access its contents. Rachel had the same
>>> issue. Is there any way to access the files in this folder?
>>>
>>> Thank you,
>>> Emma
>>>
>>>
>>>
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From predragp at andrew.cmu.edu  Thu Aug 25 13:53:14 2022
From: predragp at andrew.cmu.edu (Predrag Punosevac)
Date: Thu, 25 Aug 2022 13:53:14 -0400
Subject: "Stale file handle" error
In-Reply-To: <CALg9avJcbiWBSfVfAStewVwT68Dv537+utdiP=SmYEsLQJzOpw@mail.gmail.com>
References: <CALg9avJcWh8T9e8vEtL+1OBBNVEvXQwAVKJi=HbHOFQ1GcfMrQ@mail.gmail.com>
 <CAEFFt-HERjG92xO0aywyLyYpCCpLamUK5dTuHmdciDQGSSFJAQ@mail.gmail.com>
 <CALg9avL+FN_=p2NkbQept2Yt32S-GsGB4X0PFv3nqz4hdnFW3w@mail.gmail.com>
 <CAEFFt-EUYDz9G=KL3Fe+LBJDsQqnBN=16DjNSG-dkZJSwv_zOg@mail.gmail.com>
 <CALg9avJcbiWBSfVfAStewVwT68Dv537+utdiP=SmYEsLQJzOpw@mail.gmail.com>
Message-ID: <CAEFFt-GO1NHi0ZhMMYCCcbY7vUjXgCiVyPdEtEiyFYBksWk1YQ@mail.gmail.com>

To what machine did you ssh? That computing nodes needs to be rebooted. You
have no business using shell gateways as your workstation is your personal
shell gateway so that part of your report is irrelevant. I also don't mount
data and project on shell gateways.

Predrag

On Thu, Aug 25, 2022, 12:30 PM Emma Erickson <eerickso at andrew.cmu.edu>
wrote:

> Oh I phrased that poorly, I was using ssh from my desktop to access
> zfsauton.
>
> On Thu, Aug 25, 2022 at 12:25 PM Predrag Punosevac <
> predragp at andrew.cmu.edu> wrote:
>
>> This will require very invasive action. I need to do a bit of planning
>> before I pull the trigger on this. Are you sure you see this on your
>> desktop. IIRC zfsauton is not mounted on you personal workstation. You can
>> always try to reboot it.
>>
>> Predrag
>>
>> On Thu, Aug 25, 2022, 12:21 PM Emma Erickson <eerickso at andrew.cmu.edu>
>> wrote:
>>
>>> Hi Predrag,
>>>
>>> Thank you for getting back so quickly. I first encountered the issue on
>>> my lab desktop, but receive the same errors regardless of whether I try
>>> upload, bash, or lop2.
>>> [image: image.png]
>>>
>>> Best,
>>> Emma
>>>
>>>
>>> On Thu, Aug 25, 2022 at 12:03 PM Predrag Punosevac <
>>> predragp at andrew.cmu.edu> wrote:
>>>
>>>> Which computer are you using? The stale file handles is NFS client
>>>> problem which can be only fix by rebooting the host. I might need to reboot
>>>> file server hosting project and data folders as well but that will not fix
>>>> the client side.. I was unable the other day to clear stale ZFS snapshots
>>>> from the same server. In spite of  the fact that the file server was
>>>> trashed in June by a fellow grad student I take a full responsibility for
>>>> being a fool and allowing lab members to create and excessively use public
>>>> directory. Will not happen in the future.
>>>>
>>>> I did apply multiple bandaids but it appears that more invasive
>>>> procedure will be necessary to fix the fallout. Thanks for you report.
>>>>
>>>>
>>>> Predrag
>>>>
>>>> On Thu, Aug 25, 2022, 11:50 AM Emma Erickson <eerickso at andrew.cmu.edu>
>>>> wrote:
>>>>
>>>>> Hello Predrag,
>>>>>
>>>>> I am trying to access some data from the '/zfsauton/data' folder.
>>>>> Though it shows up when I list directories in zfsauton, I get a "stale file
>>>>> handle" error when trying to access its contents. Rachel had the same
>>>>> issue. Is there any way to access the files in this folder?
>>>>>
>>>>> Thank you,
>>>>> Emma
>>>>>
>>>>>
>>>>>
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From predragp at andrew.cmu.edu  Thu Aug 25 13:57:21 2022
From: predragp at andrew.cmu.edu (Predrag Punosevac)
Date: Thu, 25 Aug 2022 13:57:21 -0400
Subject: "Stale file handle" error
In-Reply-To: <CALRGks6Lm9z4h8FH6OJPQ3nDm8_iXyGoAih=ENp7o-Z_TKWKew@mail.gmail.com>
References: <CALg9avJcWh8T9e8vEtL+1OBBNVEvXQwAVKJi=HbHOFQ1GcfMrQ@mail.gmail.com>
 <CAEFFt-HERjG92xO0aywyLyYpCCpLamUK5dTuHmdciDQGSSFJAQ@mail.gmail.com>
 <CALg9avL+FN_=p2NkbQept2Yt32S-GsGB4X0PFv3nqz4hdnFW3w@mail.gmail.com>
 <CAEFFt-EUYDz9G=KL3Fe+LBJDsQqnBN=16DjNSG-dkZJSwv_zOg@mail.gmail.com>
 <CALRGks6Lm9z4h8FH6OJPQ3nDm8_iXyGoAih=ENp7o-Z_TKWKew@mail.gmail.com>
Message-ID: <CAEFFt-GGkDVmgM8cQpDU80A3AZsi2RBuCy6xG6uKR3qtEVfZfg@mail.gmail.com>

Could you be more specific? Which node? It is NFS client error. Contrary to
widespread belief I can't read people's minds and I am not clairvoyant. You
have to give me some info to work with.


Predrag

On Thu, Aug 25, 2022, 12:35 PM Abby Turner <abigailt at andrew.cmu.edu> wrote:

> Just for the record, I've had this issue since yesterday as well.
>
> Best,
> Abby
>
> On Thu, Aug 25, 2022 at 12:26 PM Predrag Punosevac <
> predragp at andrew.cmu.edu> wrote:
>
>> This will require very invasive action. I need to do a bit of planning
>> before I pull the trigger on this. Are you sure you see this on your
>> desktop. IIRC zfsauton is not mounted on you personal workstation. You can
>> always try to reboot it.
>>
>> Predrag
>>
>> On Thu, Aug 25, 2022, 12:21 PM Emma Erickson <eerickso at andrew.cmu.edu>
>> wrote:
>>
>>> Hi Predrag,
>>>
>>> Thank you for getting back so quickly. I first encountered the issue on
>>> my lab desktop, but receive the same errors regardless of whether I try
>>> upload, bash, or lop2.
>>> [image: image.png]
>>>
>>> Best,
>>> Emma
>>>
>>>
>>> On Thu, Aug 25, 2022 at 12:03 PM Predrag Punosevac <
>>> predragp at andrew.cmu.edu> wrote:
>>>
>>>> Which computer are you using? The stale file handles is NFS client
>>>> problem which can be only fix by rebooting the host. I might need to reboot
>>>> file server hosting project and data folders as well but that will not fix
>>>> the client side.. I was unable the other day to clear stale ZFS snapshots
>>>> from the same server. In spite of  the fact that the file server was
>>>> trashed in June by a fellow grad student I take a full responsibility for
>>>> being a fool and allowing lab members to create and excessively use public
>>>> directory. Will not happen in the future.
>>>>
>>>> I did apply multiple bandaids but it appears that more invasive
>>>> procedure will be necessary to fix the fallout. Thanks for you report.
>>>>
>>>>
>>>> Predrag
>>>>
>>>> On Thu, Aug 25, 2022, 11:50 AM Emma Erickson <eerickso at andrew.cmu.edu>
>>>> wrote:
>>>>
>>>>> Hello Predrag,
>>>>>
>>>>> I am trying to access some data from the '/zfsauton/data' folder.
>>>>> Though it shows up when I list directories in zfsauton, I get a "stale file
>>>>> handle" error when trying to access its contents. Rachel had the same
>>>>> issue. Is there any way to access the files in this folder?
>>>>>
>>>>> Thank you,
>>>>> Emma
>>>>>
>>>>>
>>>>>
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From predragp at andrew.cmu.edu  Thu Aug 25 14:18:30 2022
From: predragp at andrew.cmu.edu (Predrag Punosevac)
Date: Thu, 25 Aug 2022 14:18:30 -0400
Subject: "Stale file handle" error
In-Reply-To: <CALg9avKBR=SP4ENKHBJd2GHDR-957Ep+Qp7GBCra-0a1CCx1og@mail.gmail.com>
References: <CALg9avJcWh8T9e8vEtL+1OBBNVEvXQwAVKJi=HbHOFQ1GcfMrQ@mail.gmail.com>
 <CAEFFt-HERjG92xO0aywyLyYpCCpLamUK5dTuHmdciDQGSSFJAQ@mail.gmail.com>
 <CALg9avL+FN_=p2NkbQept2Yt32S-GsGB4X0PFv3nqz4hdnFW3w@mail.gmail.com>
 <CAEFFt-EUYDz9G=KL3Fe+LBJDsQqnBN=16DjNSG-dkZJSwv_zOg@mail.gmail.com>
 <CALg9avJcbiWBSfVfAStewVwT68Dv537+utdiP=SmYEsLQJzOpw@mail.gmail.com>
 <CAEFFt-GO1NHi0ZhMMYCCcbY7vUjXgCiVyPdEtEiyFYBksWk1YQ@mail.gmail.com>
 <CALg9avKBR=SP4ENKHBJd2GHDR-957Ep+Qp7GBCra-0a1CCx1og@mail.gmail.com>
Message-ID: <CAEFFt-EW_21k-cumh=_2YFzS-Uxp5rpshowMicD1TSoFtTHrQA@mail.gmail.com>

Now that is a much more useful problem report! That is what I was
afraid of. A lot of machines will have to be rebooted but we have to be
smart about it. I will need to do some invasive surgery on the file server
so this doesn't happen again after the reboot.

Predrag

On Thu, Aug 25, 2022 at 2:09 PM Emma Erickson <eerickso at andrew.cmu.edu>
wrote:

> Hi Predrag,
>
> I tried several different machines (lov3, lov4, lov5, lov8, lov12 and
> gpu4). I encountered the same "stale file handle" issue across all of them.
>
> Thank you,
> Emma
>
> On Thu, Aug 25, 2022 at 1:53 PM Predrag Punosevac <predragp at andrew.cmu.edu>
> wrote:
>
>> To what machine did you ssh? That computing nodes needs to be rebooted.
>> You have no business using shell gateways as your workstation is your
>> personal shell gateway so that part of your report is irrelevant. I also
>> don't mount data and project on shell gateways.
>>
>> Predrag
>>
>> On Thu, Aug 25, 2022, 12:30 PM Emma Erickson <eerickso at andrew.cmu.edu>
>> wrote:
>>
>>> Oh I phrased that poorly, I was using ssh from my desktop to access
>>> zfsauton.
>>>
>>> On Thu, Aug 25, 2022 at 12:25 PM Predrag Punosevac <
>>> predragp at andrew.cmu.edu> wrote:
>>>
>>>> This will require very invasive action. I need to do a bit of planning
>>>> before I pull the trigger on this. Are you sure you see this on your
>>>> desktop. IIRC zfsauton is not mounted on you personal workstation. You can
>>>> always try to reboot it.
>>>>
>>>> Predrag
>>>>
>>>> On Thu, Aug 25, 2022, 12:21 PM Emma Erickson <eerickso at andrew.cmu.edu>
>>>> wrote:
>>>>
>>>>> Hi Predrag,
>>>>>
>>>>> Thank you for getting back so quickly. I first encountered the issue
>>>>> on my lab desktop, but receive the same errors regardless of whether I try
>>>>> upload, bash, or lop2.
>>>>> [image: image.png]
>>>>>
>>>>> Best,
>>>>> Emma
>>>>>
>>>>>
>>>>> On Thu, Aug 25, 2022 at 12:03 PM Predrag Punosevac <
>>>>> predragp at andrew.cmu.edu> wrote:
>>>>>
>>>>>> Which computer are you using? The stale file handles is NFS client
>>>>>> problem which can be only fix by rebooting the host. I might need to reboot
>>>>>> file server hosting project and data folders as well but that will not fix
>>>>>> the client side.. I was unable the other day to clear stale ZFS snapshots
>>>>>> from the same server. In spite of  the fact that the file server was
>>>>>> trashed in June by a fellow grad student I take a full responsibility for
>>>>>> being a fool and allowing lab members to create and excessively use public
>>>>>> directory. Will not happen in the future.
>>>>>>
>>>>>> I did apply multiple bandaids but it appears that more invasive
>>>>>> procedure will be necessary to fix the fallout. Thanks for you report.
>>>>>>
>>>>>>
>>>>>> Predrag
>>>>>>
>>>>>> On Thu, Aug 25, 2022, 11:50 AM Emma Erickson <eerickso at andrew.cmu.edu>
>>>>>> wrote:
>>>>>>
>>>>>>> Hello Predrag,
>>>>>>>
>>>>>>> I am trying to access some data from the '/zfsauton/data' folder.
>>>>>>> Though it shows up when I list directories in zfsauton, I get a "stale file
>>>>>>> handle" error when trying to access its contents. Rachel had the same
>>>>>>> issue. Is there any way to access the files in this folder?
>>>>>>>
>>>>>>> Thank you,
>>>>>>> Emma
>>>>>>>
>>>>>>>
>>>>>>>
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From predragp at andrew.cmu.edu  Thu Aug 25 14:19:56 2022
From: predragp at andrew.cmu.edu (Predrag Punosevac)
Date: Thu, 25 Aug 2022 14:19:56 -0400
Subject: "Stale file handle" error
In-Reply-To: <CALRGks5b48ZF=ei6dC5ZDt9aq9a6Z_x0sq4DR1VznvdWv8A8hw@mail.gmail.com>
References: <CALg9avJcWh8T9e8vEtL+1OBBNVEvXQwAVKJi=HbHOFQ1GcfMrQ@mail.gmail.com>
 <CAEFFt-HERjG92xO0aywyLyYpCCpLamUK5dTuHmdciDQGSSFJAQ@mail.gmail.com>
 <CALg9avL+FN_=p2NkbQept2Yt32S-GsGB4X0PFv3nqz4hdnFW3w@mail.gmail.com>
 <CAEFFt-EUYDz9G=KL3Fe+LBJDsQqnBN=16DjNSG-dkZJSwv_zOg@mail.gmail.com>
 <CALRGks6Lm9z4h8FH6OJPQ3nDm8_iXyGoAih=ENp7o-Z_TKWKew@mail.gmail.com>
 <CAEFFt-GGkDVmgM8cQpDU80A3AZsi2RBuCy6xG6uKR3qtEVfZfg@mail.gmail.com>
 <CALRGks5b48ZF=ei6dC5ZDt9aq9a6Z_x0sq4DR1VznvdWv8A8hw@mail.gmail.com>
Message-ID: <CAEFFt-GR1oyAPgScJSHR9PP_W0xOj=A-CD3fQ6qLetcpiKGzdw@mail.gmail.com>

Just answered Emma. Thank you so much Abbu. That is a much more useful
problem report! I need to think a bit before pulling the trigger.

Predrag

On Thu, Aug 25, 2022 at 2:11 PM Abby Turner <abigailt at andrew.cmu.edu> wrote:

> Alas, that makes things more difficult. I tried lov2 and lov4.
>
> On Thu, Aug 25, 2022 at 1:57 PM Predrag Punosevac <predragp at andrew.cmu.edu>
> wrote:
>
>> Could you be more specific? Which node? It is NFS client error. Contrary
>> to widespread belief I can't read people's minds and I am not clairvoyant.
>> You have to give me some info to work with.
>>
>>
>> Predrag
>>
>> On Thu, Aug 25, 2022, 12:35 PM Abby Turner <abigailt at andrew.cmu.edu>
>> wrote:
>>
>>> Just for the record, I've had this issue since yesterday as well.
>>>
>>> Best,
>>> Abby
>>>
>>> On Thu, Aug 25, 2022 at 12:26 PM Predrag Punosevac <
>>> predragp at andrew.cmu.edu> wrote:
>>>
>>>> This will require very invasive action. I need to do a bit of planning
>>>> before I pull the trigger on this. Are you sure you see this on your
>>>> desktop. IIRC zfsauton is not mounted on you personal workstation. You can
>>>> always try to reboot it.
>>>>
>>>> Predrag
>>>>
>>>> On Thu, Aug 25, 2022, 12:21 PM Emma Erickson <eerickso at andrew.cmu.edu>
>>>> wrote:
>>>>
>>>>> Hi Predrag,
>>>>>
>>>>> Thank you for getting back so quickly. I first encountered the issue
>>>>> on my lab desktop, but receive the same errors regardless of whether I try
>>>>> upload, bash, or lop2.
>>>>> [image: image.png]
>>>>>
>>>>> Best,
>>>>> Emma
>>>>>
>>>>>
>>>>> On Thu, Aug 25, 2022 at 12:03 PM Predrag Punosevac <
>>>>> predragp at andrew.cmu.edu> wrote:
>>>>>
>>>>>> Which computer are you using? The stale file handles is NFS client
>>>>>> problem which can be only fix by rebooting the host. I might need to reboot
>>>>>> file server hosting project and data folders as well but that will not fix
>>>>>> the client side.. I was unable the other day to clear stale ZFS snapshots
>>>>>> from the same server. In spite of  the fact that the file server was
>>>>>> trashed in June by a fellow grad student I take a full responsibility for
>>>>>> being a fool and allowing lab members to create and excessively use public
>>>>>> directory. Will not happen in the future.
>>>>>>
>>>>>> I did apply multiple bandaids but it appears that more invasive
>>>>>> procedure will be necessary to fix the fallout. Thanks for you report.
>>>>>>
>>>>>>
>>>>>> Predrag
>>>>>>
>>>>>> On Thu, Aug 25, 2022, 11:50 AM Emma Erickson <eerickso at andrew.cmu.edu>
>>>>>> wrote:
>>>>>>
>>>>>>> Hello Predrag,
>>>>>>>
>>>>>>> I am trying to access some data from the '/zfsauton/data' folder.
>>>>>>> Though it shows up when I list directories in zfsauton, I get a "stale file
>>>>>>> handle" error when trying to access its contents. Rachel had the same
>>>>>>> issue. Is there any way to access the files in this folder?
>>>>>>>
>>>>>>> Thank you,
>>>>>>> Emma
>>>>>>>
>>>>>>>
>>>>>>>
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From awd at cs.cmu.edu  Fri Aug 26 07:39:39 2022
From: awd at cs.cmu.edu (Artur Dubrawski)
Date: Fri, 26 Aug 2022 07:39:39 -0400
Subject: Auton Lab Walk in the Park: TODAY, 6pm start
In-Reply-To: <CAJvAoyt30dsa2n2j69oMtyzHa8jDBcMjjFmz4Z_RO_anO1t6Qg@mail.gmail.com>
References: <CAJvAoyt35MQvsR801LvWGs+q=jMMBRGZSj+HB4r_HiLG8nxnhg@mail.gmail.com>
 <CAJvAoyvXANuMihpU9e6kYfUUEBmuakrP2BVjFa_0yXKdi3L3zg@mail.gmail.com>
 <CAJvAoyv1=nmb==AysF5R63bngHLUP8Pxpvu8aQu8H2C-v=AkLw@mail.gmail.com>
 <CAJvAoytAGAebk96qe1hDMm4j4Uu7rF9Hb5AmPAGWOc5zAMQYSw@mail.gmail.com>
 <CAJvAoyverLmtE7tdmYDE7K3BPzzAoZj7QF24L5+HUTNXcZThKw@mail.gmail.com>
 <CAJvAoyt30dsa2n2j69oMtyzHa8jDBcMjjFmz4Z_RO_anO1t6Qg@mail.gmail.com>
Message-ID: <CAJvAoysk9e8MeVK8idNDw9i9gj7L6aGyij_zza5RenAW=dzJoQ@mail.gmail.com>

Even though the current forecast shows scattered thunderstorms, I am
tempted to call for our traditional Auton Lab Walk in Schenley Park.
Let's meet at the 3rd floor entryway to Newell-Simon Hall at 6pm tonight as
usual, and we'll adjust if/as necessary.
These forecasts have not been very accurate lately.

Cheers,
Artur


> On Fri, Jul 29, 2022 at 11:53 AM Artur Dubrawski <awd at cs.cmu.edu> wrote:
>
>> the usual deal for tonight, see you then and there!
>>
>> On Fri, Jul 22, 2022 at 1:49 PM Artur Dubrawski <awd at cs.cmu.edu> wrote:
>>
>>> Team, if you are interested please join the walking group at the NSH
>>> entryway.
>>>
>>> 6pm.
>>>
>>> Cheers,
>>> Artur
>>>
>>> On Fri, Jul 15, 2022 at 4:02 PM Artur Dubrawski <awd at cs.cmu.edu> wrote:
>>>
>>>> Team, i will not be able to join the walk today, but whomever is
>>>> free and willing to keep our new tradition going, please do!
>>>>
>>>> Cheers
>>>> Artur
>>>>
>>>> On Fri, Jul 8, 2022, 11:49 AM Artur Dubrawski <awd at cs.cmu.edu> wrote:
>>>>
>>>>> Team,
>>>>>
>>>>> The weather forecast has improved enough for us to go for a walk this
>>>>> evening.
>>>>>
>>>>> Let's meet in front of NSH at 6pm.
>>>>>
>>>>> Cheers
>>>>> Artur
>>>>>
>>>>
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From predragp at andrew.cmu.edu  Mon Aug 29 18:07:18 2022
From: predragp at andrew.cmu.edu (Predrag Punosevac)
Date: Mon, 29 Aug 2022 18:07:18 -0400
Subject: NFS stale file handles "fixed"
Message-ID: <CAEFFt-EdRqWZcDacx4mGkNLzbB2ftxQUfdyn8WSVoRF=Mra=7A@mail.gmail.com>

Dear Autonians,

The stale file handles exceptions some of you reported when trying to
access /zfsauton/project and /zfsauton/data folders should now be fixed. I
noticed that these two NFS shares are not mounted on some nodes. Please
report any problems and if they are not available.

I am afraid that this time the cure was worse than the disease. I had to
reboot all 42 computing nodes as well as the file server. That is a lot of
work lost.

Best,
Predrag
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