[Kernel-packages] [Bug 159356] Re: System freeze on high memory usage when DMA is disabled

2018-08-31 Thread Ubuntu Foundations Team Bug Bot
** Tags added: patch

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Title:
  System freeze on high memory usage when DMA is disabled

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  I run a batch matlab job server here at my lab, running Dapper 6.06 (for the 
LTS). One of the users has submitted a very memory-consuming job, which 
successfully crashes the server. Upon closer inspection, the crash happens like 
this:
  1. I run matlab with the given file (as an ordinary, unpriveleged user)
  2. RAM usage quickly fills up
  3. Once the RAM meter hits 100%, the system freezes: All SSH connections 
freeze up, and while switching VTs directly on the machine works, no new 
processes run - so one can't log in, or do anything if he is logged in. 
(Sometimes typing doesn't work at all)

  Note that the swap - while 7 gigs of it are available - is never used.
  (The machine has 7 gigs of RAM as well)

  I've tried the same on my Gutsy 32-bit box, and there was no system
  freezeup - matlab simply notified that the system was out of memory.
  However, it did this once memory was 100% in use - and still, swap
  didn't get used at all! (Though it is mounted correctly and shows up
  in "top" and "free").

  So first thing's first - I'd like to eliminate the crash issue. I
  suppose I could switch the server to 32-bit, but I think that would be
  a performance loss, considering that it does a lot of heavy
  computation. There is no reason, however, that this should happen on a
  64-bit machine anyway. Why does it?

  WORKAROUND: Enabling DMA in the BIOS

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[Kernel-packages] [Bug 159356] Re: System freeze on high memory usage when DMA is disabled

2018-08-31 Thread jecks
It is also possible, since we now know how the bug is triggered, should
Marcus open a new report?

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Title:
  System freeze on high memory usage when DMA is disabled

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  I run a batch matlab job server here at my lab, running Dapper 6.06 (for the 
LTS). One of the users has submitted a very memory-consuming job, which 
successfully crashes the server. Upon closer inspection, the crash happens like 
this:
  1. I run matlab with the given file (as an ordinary, unpriveleged user)
  2. RAM usage quickly fills up
  3. Once the RAM meter hits 100%, the system freezes: All SSH connections 
freeze up, and while switching VTs directly on the machine works, no new 
processes run - so one can't log in, or do anything if he is logged in. 
(Sometimes typing doesn't work at all)

  Note that the swap - while 7 gigs of it are available - is never used.
  (The machine has 7 gigs of RAM as well)

  I've tried the same on my Gutsy 32-bit box, and there was no system
  freezeup - matlab simply notified that the system was out of memory.
  However, it did this once memory was 100% in use - and still, swap
  didn't get used at all! (Though it is mounted correctly and shows up
  in "top" and "free").

  So first thing's first - I'd like to eliminate the crash issue. I
  suppose I could switch the server to 32-bit, but I think that would be
  a performance loss, considering that it does a lot of heavy
  computation. There is no reason, however, that this should happen on a
  64-bit machine anyway. Why does it?

  WORKAROUND: Enabling DMA in the BIOS

To manage notifications about this bug go to:
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[Kernel-packages] [Bug 159356] Re: System freeze on high memory usage when DMA is disabled

2018-08-31 Thread jecks
This also explains the reason a person with a USB drive was seeing
thrashing (constant blinking) when using the fedora live environment
with many tabs open.

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Title:
  System freeze on high memory usage when DMA is disabled

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  I run a batch matlab job server here at my lab, running Dapper 6.06 (for the 
LTS). One of the users has submitted a very memory-consuming job, which 
successfully crashes the server. Upon closer inspection, the crash happens like 
this:
  1. I run matlab with the given file (as an ordinary, unpriveleged user)
  2. RAM usage quickly fills up
  3. Once the RAM meter hits 100%, the system freezes: All SSH connections 
freeze up, and while switching VTs directly on the machine works, no new 
processes run - so one can't log in, or do anything if he is logged in. 
(Sometimes typing doesn't work at all)

  Note that the swap - while 7 gigs of it are available - is never used.
  (The machine has 7 gigs of RAM as well)

  I've tried the same on my Gutsy 32-bit box, and there was no system
  freezeup - matlab simply notified that the system was out of memory.
  However, it did this once memory was 100% in use - and still, swap
  didn't get used at all! (Though it is mounted correctly and shows up
  in "top" and "free").

  So first thing's first - I'd like to eliminate the crash issue. I
  suppose I could switch the server to 32-bit, but I think that would be
  a performance loss, considering that it does a lot of heavy
  computation. There is no reason, however, that this should happen on a
  64-bit machine anyway. Why does it?

  WORKAROUND: Enabling DMA in the BIOS

To manage notifications about this bug go to:
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[Kernel-packages] [Bug 159356] Re: System freeze on high memory usage when DMA is disabled

2018-08-31 Thread jecks
Do you think this could eventually be merged into a kernel? Has anyone
filed a kernel bugzilla with the patch so we can improve it, and get it
merged to the kernel?

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Title:
  System freeze on high memory usage when DMA is disabled

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  I run a batch matlab job server here at my lab, running Dapper 6.06 (for the 
LTS). One of the users has submitted a very memory-consuming job, which 
successfully crashes the server. Upon closer inspection, the crash happens like 
this:
  1. I run matlab with the given file (as an ordinary, unpriveleged user)
  2. RAM usage quickly fills up
  3. Once the RAM meter hits 100%, the system freezes: All SSH connections 
freeze up, and while switching VTs directly on the machine works, no new 
processes run - so one can't log in, or do anything if he is logged in. 
(Sometimes typing doesn't work at all)

  Note that the swap - while 7 gigs of it are available - is never used.
  (The machine has 7 gigs of RAM as well)

  I've tried the same on my Gutsy 32-bit box, and there was no system
  freezeup - matlab simply notified that the system was out of memory.
  However, it did this once memory was 100% in use - and still, swap
  didn't get used at all! (Though it is mounted correctly and shows up
  in "top" and "free").

  So first thing's first - I'd like to eliminate the crash issue. I
  suppose I could switch the server to 32-bit, but I think that would be
  a performance loss, considering that it does a lot of heavy
  computation. There is no reason, however, that this should happen on a
  64-bit machine anyway. Why does it?

  WORKAROUND: Enabling DMA in the BIOS

To manage notifications about this bug go to:
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[Kernel-packages] [Bug 159356] Re: System freeze on high memory usage when DMA is disabled

2018-08-31 Thread Marcus Linsner
The attached kernel patch (applied on top of 4.18.5) that I've tried,
almost completely eliminates the disk thrashing(the constant reading of
executable(and .so) files on every context switch) associated with
freezing the OS and so, with this patch, the OOM-killer is triggered
within a maxium of 1 second when it is needed, rather than, without this
patch, freeze the OS for minutes(or just a long time, it may even auto
reboot depending on your kernel .config options set to panic(reboot) on
hang after xx seconds) with constant disk reading well before OOM-killer
gets triggered.

More info as to why OS freezes with constant disk reading when running
out of RAM, here: https://unix.stackexchange.com/a/463469/306023

The patch is from inside this question:
https://stackoverflow.com/q/52067753/10239615

Note: I don't recommend using this patch in production, without actual
programmers saying that it's ok first. I'm not a programmer. Maybe some
programmer could improve it?

I am using the patch currently inside a Qubes OS R4.0 Fedora 28 AppVM
where I can easily reproduce freezing the VM's OS (+ the constant disk
thrashing, seen from `sudo iotop` in dom0) without the patch, while
attempting to compile firefox with 4000MB max RAM setting for the VM,
and with the patch basically no freezing and little to no disk thrashing
during the 1 second it takes for OOM-killer to kill the offending
process(es).


** Patch added: "le9b.patch"
   
https://bugs.launchpad.net/ubuntu/+source/linux/+bug/159356/+attachment/5183022/+files/le9b.patch

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https://bugs.launchpad.net/bugs/159356

Title:
  System freeze on high memory usage when DMA is disabled

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  I run a batch matlab job server here at my lab, running Dapper 6.06 (for the 
LTS). One of the users has submitted a very memory-consuming job, which 
successfully crashes the server. Upon closer inspection, the crash happens like 
this:
  1. I run matlab with the given file (as an ordinary, unpriveleged user)
  2. RAM usage quickly fills up
  3. Once the RAM meter hits 100%, the system freezes: All SSH connections 
freeze up, and while switching VTs directly on the machine works, no new 
processes run - so one can't log in, or do anything if he is logged in. 
(Sometimes typing doesn't work at all)

  Note that the swap - while 7 gigs of it are available - is never used.
  (The machine has 7 gigs of RAM as well)

  I've tried the same on my Gutsy 32-bit box, and there was no system
  freezeup - matlab simply notified that the system was out of memory.
  However, it did this once memory was 100% in use - and still, swap
  didn't get used at all! (Though it is mounted correctly and shows up
  in "top" and "free").

  So first thing's first - I'd like to eliminate the crash issue. I
  suppose I could switch the server to 32-bit, but I think that would be
  a performance loss, considering that it does a lot of heavy
  computation. There is no reason, however, that this should happen on a
  64-bit machine anyway. Why does it?

  WORKAROUND: Enabling DMA in the BIOS

To manage notifications about this bug go to:
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[Kernel-packages] [Bug 159356] Re: System freeze on high memory usage when DMA is disabled

2018-07-01 Thread Christopher M. Penalver
jecks (slayerproof32), it is most unhelpful to post comments or
attachments here, or give pastebin links. If you want to motivate
developers to want to look into your issue, file a new report. If you
want developers to ignore your problem, continue posting here.

marco (nazgul17), one may always file a report manually via
https://bugs.launchpad.net/ubuntu/+source/linux/+filebug . For more on
this, please see https://help.ubuntu.com/community/ReportingBugs .

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https://bugs.launchpad.net/bugs/159356

Title:
  System freeze on high memory usage when DMA is disabled

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  I run a batch matlab job server here at my lab, running Dapper 6.06 (for the 
LTS). One of the users has submitted a very memory-consuming job, which 
successfully crashes the server. Upon closer inspection, the crash happens like 
this:
  1. I run matlab with the given file (as an ordinary, unpriveleged user)
  2. RAM usage quickly fills up
  3. Once the RAM meter hits 100%, the system freezes: All SSH connections 
freeze up, and while switching VTs directly on the machine works, no new 
processes run - so one can't log in, or do anything if he is logged in. 
(Sometimes typing doesn't work at all)

  Note that the swap - while 7 gigs of it are available - is never used.
  (The machine has 7 gigs of RAM as well)

  I've tried the same on my Gutsy 32-bit box, and there was no system
  freezeup - matlab simply notified that the system was out of memory.
  However, it did this once memory was 100% in use - and still, swap
  didn't get used at all! (Though it is mounted correctly and shows up
  in "top" and "free").

  So first thing's first - I'd like to eliminate the crash issue. I
  suppose I could switch the server to 32-bit, but I think that would be
  a performance loss, considering that it does a lot of heavy
  computation. There is no reason, however, that this should happen on a
  64-bit machine anyway. Why does it?

  WORKAROUND: Enabling DMA in the BIOS

To manage notifications about this bug go to:
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[Kernel-packages] [Bug 159356] Re: System freeze on high memory usage when DMA is disabled

2018-06-30 Thread jecks
Consider also posting the output of 
Sudo parted -l

Here are my results if these commands. Iam running top right now and
will be posted soon.

https://pastebin.com/8q75EXyz 1 ā€“ Inxi-Fzxc0
https://pastebin.com/mnj4Bamu ā€“ Lspci -V
https://pastebin.com/KqpKuCa3 1 --Dmesg

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https://bugs.launchpad.net/bugs/159356

Title:
  System freeze on high memory usage when DMA is disabled

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  I run a batch matlab job server here at my lab, running Dapper 6.06 (for the 
LTS). One of the users has submitted a very memory-consuming job, which 
successfully crashes the server. Upon closer inspection, the crash happens like 
this:
  1. I run matlab with the given file (as an ordinary, unpriveleged user)
  2. RAM usage quickly fills up
  3. Once the RAM meter hits 100%, the system freezes: All SSH connections 
freeze up, and while switching VTs directly on the machine works, no new 
processes run - so one can't log in, or do anything if he is logged in. 
(Sometimes typing doesn't work at all)

  Note that the swap - while 7 gigs of it are available - is never used.
  (The machine has 7 gigs of RAM as well)

  I've tried the same on my Gutsy 32-bit box, and there was no system
  freezeup - matlab simply notified that the system was out of memory.
  However, it did this once memory was 100% in use - and still, swap
  didn't get used at all! (Though it is mounted correctly and shows up
  in "top" and "free").

  So first thing's first - I'd like to eliminate the crash issue. I
  suppose I could switch the server to 32-bit, but I think that would be
  a performance loss, considering that it does a lot of heavy
  computation. There is no reason, however, that this should happen on a
  64-bit machine anyway. Why does it?

  WORKAROUND: Enabling DMA in the BIOS

To manage notifications about this bug go to:
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[Kernel-packages] [Bug 159356] Re: System freeze on high memory usage when DMA is disabled

2018-06-30 Thread jecks
Iā€™d say you probably want to start with these 4 commands and posting the results
Lspci -v
Inxi  -Fzxc0
dmesg > dmesg.log (will save to ~/dmesg.log)


top -b > top.log (run this command, then trigger the memory issue. It will save 
to ~/top.log. If you have to hard reboot, the file will still be saved)

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Title:
  System freeze on high memory usage when DMA is disabled

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  I run a batch matlab job server here at my lab, running Dapper 6.06 (for the 
LTS). One of the users has submitted a very memory-consuming job, which 
successfully crashes the server. Upon closer inspection, the crash happens like 
this:
  1. I run matlab with the given file (as an ordinary, unpriveleged user)
  2. RAM usage quickly fills up
  3. Once the RAM meter hits 100%, the system freezes: All SSH connections 
freeze up, and while switching VTs directly on the machine works, no new 
processes run - so one can't log in, or do anything if he is logged in. 
(Sometimes typing doesn't work at all)

  Note that the swap - while 7 gigs of it are available - is never used.
  (The machine has 7 gigs of RAM as well)

  I've tried the same on my Gutsy 32-bit box, and there was no system
  freezeup - matlab simply notified that the system was out of memory.
  However, it did this once memory was 100% in use - and still, swap
  didn't get used at all! (Though it is mounted correctly and shows up
  in "top" and "free").

  So first thing's first - I'd like to eliminate the crash issue. I
  suppose I could switch the server to 32-bit, but I think that would be
  a performance loss, considering that it does a lot of heavy
  computation. There is no reason, however, that this should happen on a
  64-bit machine anyway. Why does it?

  WORKAROUND: Enabling DMA in the BIOS

To manage notifications about this bug go to:
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[Kernel-packages] [Bug 159356] Re: System freeze on high memory usage when DMA is disabled

2018-06-30 Thread marco
Hi Christopher,

How does one go about providing debugging information?
Please consider the limitations of an environment that does not respond to 
commands.

Thank you!

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https://bugs.launchpad.net/bugs/159356

Title:
  System freeze on high memory usage when DMA is disabled

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  I run a batch matlab job server here at my lab, running Dapper 6.06 (for the 
LTS). One of the users has submitted a very memory-consuming job, which 
successfully crashes the server. Upon closer inspection, the crash happens like 
this:
  1. I run matlab with the given file (as an ordinary, unpriveleged user)
  2. RAM usage quickly fills up
  3. Once the RAM meter hits 100%, the system freezes: All SSH connections 
freeze up, and while switching VTs directly on the machine works, no new 
processes run - so one can't log in, or do anything if he is logged in. 
(Sometimes typing doesn't work at all)

  Note that the swap - while 7 gigs of it are available - is never used.
  (The machine has 7 gigs of RAM as well)

  I've tried the same on my Gutsy 32-bit box, and there was no system
  freezeup - matlab simply notified that the system was out of memory.
  However, it did this once memory was 100% in use - and still, swap
  didn't get used at all! (Though it is mounted correctly and shows up
  in "top" and "free").

  So first thing's first - I'd like to eliminate the crash issue. I
  suppose I could switch the server to 32-bit, but I think that would be
  a performance loss, considering that it does a lot of heavy
  computation. There is no reason, however, that this should happen on a
  64-bit machine anyway. Why does it?

  WORKAROUND: Enabling DMA in the BIOS

To manage notifications about this bug go to:
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[Kernel-packages] [Bug 159356] Re: System freeze on high memory usage when DMA is disabled

2018-06-30 Thread Christopher M. Penalver
jecks (slayerproof32), this report is poorly defined, and not root caused as no 
debugging logs have been provided by the original reporter. However, what 
little is known is that the issue for the original reporter was correlated to 
when DMA was disabled in the BIOS, using a now old, and unsupported version of 
Ubuntu. Hence, if you would like your issue root caused and resolved,  you will 
want to file a new report via a terminal:
ubuntu-bug linux

Please feel free to subscribe me to it.

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https://bugs.launchpad.net/bugs/159356

Title:
  System freeze on high memory usage when DMA is disabled

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  I run a batch matlab job server here at my lab, running Dapper 6.06 (for the 
LTS). One of the users has submitted a very memory-consuming job, which 
successfully crashes the server. Upon closer inspection, the crash happens like 
this:
  1. I run matlab with the given file (as an ordinary, unpriveleged user)
  2. RAM usage quickly fills up
  3. Once the RAM meter hits 100%, the system freezes: All SSH connections 
freeze up, and while switching VTs directly on the machine works, no new 
processes run - so one can't log in, or do anything if he is logged in. 
(Sometimes typing doesn't work at all)

  Note that the swap - while 7 gigs of it are available - is never used.
  (The machine has 7 gigs of RAM as well)

  I've tried the same on my Gutsy 32-bit box, and there was no system
  freezeup - matlab simply notified that the system was out of memory.
  However, it did this once memory was 100% in use - and still, swap
  didn't get used at all! (Though it is mounted correctly and shows up
  in "top" and "free").

  So first thing's first - I'd like to eliminate the crash issue. I
  suppose I could switch the server to 32-bit, but I think that would be
  a performance loss, considering that it does a lot of heavy
  computation. There is no reason, however, that this should happen on a
  64-bit machine anyway. Why does it?

  WORKAROUND: Enabling DMA in the BIOS

To manage notifications about this bug go to:
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[Kernel-packages] [Bug 159356] Re: System freeze on high memory usage when DMA is disabled

2018-06-30 Thread Christopher M. Penalver
** Package changed: linux (Arch Linux) => linux (Ubuntu)

** Changed in: linux (Ubuntu)
   Status: New => Incomplete

** No longer affects: linux (Ubuntu)

** Package changed: fedora => ubuntu

** Changed in: ubuntu
   Importance: Medium => Undecided

** Changed in: ubuntu
   Status: Won't Fix => New

** Changed in: ubuntu
 Remote watch: Red Hat Bugzilla #1472336 => None

** Changed in: ubuntu
   Importance: Undecided => Low

** Changed in: ubuntu
   Status: New => Incomplete

** Package changed: ubuntu => linux (Ubuntu)

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Title:
  System freeze on high memory usage when DMA is disabled

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  I run a batch matlab job server here at my lab, running Dapper 6.06 (for the 
LTS). One of the users has submitted a very memory-consuming job, which 
successfully crashes the server. Upon closer inspection, the crash happens like 
this:
  1. I run matlab with the given file (as an ordinary, unpriveleged user)
  2. RAM usage quickly fills up
  3. Once the RAM meter hits 100%, the system freezes: All SSH connections 
freeze up, and while switching VTs directly on the machine works, no new 
processes run - so one can't log in, or do anything if he is logged in. 
(Sometimes typing doesn't work at all)

  Note that the swap - while 7 gigs of it are available - is never used.
  (The machine has 7 gigs of RAM as well)

  I've tried the same on my Gutsy 32-bit box, and there was no system
  freezeup - matlab simply notified that the system was out of memory.
  However, it did this once memory was 100% in use - and still, swap
  didn't get used at all! (Though it is mounted correctly and shows up
  in "top" and "free").

  So first thing's first - I'd like to eliminate the crash issue. I
  suppose I could switch the server to 32-bit, but I think that would be
  a performance loss, considering that it does a lot of heavy
  computation. There is no reason, however, that this should happen on a
  64-bit machine anyway. Why does it?

  WORKAROUND: Enabling DMA in the BIOS

To manage notifications about this bug go to:
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[Kernel-packages] [Bug 159356] Re: System freeze on high memory usage when DMA is disabled

2018-06-30 Thread Christopher M. Penalver
** Summary changed:

- System freeze on high memory usage
+ System freeze on high memory usage when DMA is disabled

** No longer affects: linux (Ubuntu)

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Title:
  System freeze on high memory usage when DMA is disabled

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  I run a batch matlab job server here at my lab, running Dapper 6.06 (for the 
LTS). One of the users has submitted a very memory-consuming job, which 
successfully crashes the server. Upon closer inspection, the crash happens like 
this:
  1. I run matlab with the given file (as an ordinary, unpriveleged user)
  2. RAM usage quickly fills up
  3. Once the RAM meter hits 100%, the system freezes: All SSH connections 
freeze up, and while switching VTs directly on the machine works, no new 
processes run - so one can't log in, or do anything if he is logged in. 
(Sometimes typing doesn't work at all)

  Note that the swap - while 7 gigs of it are available - is never used.
  (The machine has 7 gigs of RAM as well)

  I've tried the same on my Gutsy 32-bit box, and there was no system
  freezeup - matlab simply notified that the system was out of memory.
  However, it did this once memory was 100% in use - and still, swap
  didn't get used at all! (Though it is mounted correctly and shows up
  in "top" and "free").

  So first thing's first - I'd like to eliminate the crash issue. I
  suppose I could switch the server to 32-bit, but I think that would be
  a performance loss, considering that it does a lot of heavy
  computation. There is no reason, however, that this should happen on a
  64-bit machine anyway. Why does it?

  WORKAROUND: Enabling DMA in the BIOS

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[Kernel-packages] [Bug 159356] Re: System freeze on high memory usage when DMA is disabled

2018-06-30 Thread Launchpad Bug Tracker
Status changed to 'Confirmed' because the bug affects multiple users.

** Changed in: linux (Ubuntu)
   Status: New => Confirmed

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https://bugs.launchpad.net/bugs/159356

Title:
  System freeze on high memory usage when DMA is disabled

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  I run a batch matlab job server here at my lab, running Dapper 6.06 (for the 
LTS). One of the users has submitted a very memory-consuming job, which 
successfully crashes the server. Upon closer inspection, the crash happens like 
this:
  1. I run matlab with the given file (as an ordinary, unpriveleged user)
  2. RAM usage quickly fills up
  3. Once the RAM meter hits 100%, the system freezes: All SSH connections 
freeze up, and while switching VTs directly on the machine works, no new 
processes run - so one can't log in, or do anything if he is logged in. 
(Sometimes typing doesn't work at all)

  Note that the swap - while 7 gigs of it are available - is never used.
  (The machine has 7 gigs of RAM as well)

  I've tried the same on my Gutsy 32-bit box, and there was no system
  freezeup - matlab simply notified that the system was out of memory.
  However, it did this once memory was 100% in use - and still, swap
  didn't get used at all! (Though it is mounted correctly and shows up
  in "top" and "free").

  So first thing's first - I'd like to eliminate the crash issue. I
  suppose I could switch the server to 32-bit, but I think that would be
  a performance loss, considering that it does a lot of heavy
  computation. There is no reason, however, that this should happen on a
  64-bit machine anyway. Why does it?

  WORKAROUND: Enabling DMA in the BIOS

To manage notifications about this bug go to:
https://bugs.launchpad.net/ubuntu/+source/linux/+bug/159356/+subscriptions

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