Problem with Rosetta@home Vbox

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dcdc
Posts: 9
Joined: 20. Jan 2022, 22:50

Problem with Rosetta@home Vbox

Post by dcdc »

Hi, I am seeing the same issue on some machines. It seems to be machine specific, so maybe something to do with hardware or firmware settings? The two machines that won't successfully run Rosetta@home VirtualBox tasks are a new-to-me Dell Optiplex 3040 and a Dell R410 server. Both will run non-Virtualbox Rosetta tasks, and the Optiplex will run other BOINC VirtualBox tasks successfully (I've only tried LHC so far but that worked fine). The tasks start to run but then CPU utilisation drops to 0% after about 15s of processor time and stays there.
Other details:
[*] The Leomoon CPU-V app says everything is working for Virtualisation on both machines.
[*] I have tried Ubuntu 20.04 and Windows 10 on both, and now Windows 11 Pro on the Optiplex
[*] I have tried installing AVG to replace Windows Defender on Win11, turning off AVG, and then uninstalling AVG again, with reboots.
[*] Drivers and firmware all up to date on the Optiplex.
[*] My other machines are all running the VBox tasks more successfully, although they're not always successful.

Can anyone point to anything that doesn't look right in the log, or elsewhere? The logs are attached.

thanks
Danny
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VBoxHardening.log.txt.zip
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VBox.log.txt
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dcdc
Posts: 9
Joined: 20. Jan 2022, 22:50

Re: Problem with Rosetta@home Vbox

Post by dcdc »

Also, here's the spec of the Optiplex in case it helps: https://boinc.bakerlab.org/rosetta/show ... id=6171984

And the PowerEdge R410: https://boinc.bakerlab.org/rosetta/show ... id=6171375

I couldn't post links for the first 24 hours...
dcdc
Posts: 9
Joined: 20. Jan 2022, 22:50

Re: Problem with Rosetta@home Vbox

Post by dcdc »

This looks suspicious to my untrained eye - in the vbox_trace.txt file in the BOINC slots folder:

Working PC says:

Code: Select all

Parent UUID:    base
State:          created
Type:           normal (base)
Location:       F:\ProgramData\BOINC\slots\0\vm_image.vdi
Storage format: VDI
Format variant: dynamic default
Capacity:       8192 MBytes
Size on disk:   7115 MBytes
Encryption:     disabled

2022-01-22 12:22:52 (79248): 
Command: VBoxManage -q showhdinfo "F:\ProgramData\BOINC\slots\0/vm_image.vdi" 
Exit Code: 0
Output:
UUID:           ef35dff9-d482-48f8-9519-fef6c1b23a3b
Parent UUID:    base
State:          created
Type:           normal (base)
Location:       F:\ProgramData\BOINC\slots\0\vm_image.vdi
Storage format: VDI
Format variant: dynamic default
Capacity:       8192 MBytes
Size on disk:   7115 MBytes
Encryption:     disabled

Non-working PC says:

Code: Select all

Parent UUID:    base
State:          inaccessible
Access Error:   UUID {ef35dff9-d482-48f8-9519-fef6c1b23a3b} of the medium 'C:\ProgramData\BOINC\slots\3\vm_image.vdi' does not match the value {9cb7b2ea-5a86-4be3-9a8c-3017ec7a8c71} stored in the media registry ('C:\Users\Danny\.VirtualBox\VirtualBox.xml')
Type:           normal (base)
Location:       C:\ProgramData\BOINC\slots\3\vm_image.vdi
Storage format: VDI
Format variant: dynamic default
Capacity:       8192 MBytes
Size on disk:   7115 MBytes
Encryption:     disabled
In use by VMs:  boinc_4419dee6319d4423 (UUID: d87d9e9b-71c6-41f4-888c-bfeca68422da)

That "State: inaccessible" doesn't look right. Any ideas what might cause that?
scottgus1
Site Moderator
Posts: 20965
Joined: 30. Dec 2009, 20:14
Primary OS: MS Windows 10
VBox Version: PUEL
Guest OSses: Windows, Linux

Re: Problem with Rosetta@home Vbox

Post by scottgus1 »

Do either of the hosts that have trouble running the BOINC VMs run Virtualbox VMs that you personally make?

Please download an Ubuntu or Mint ISO, and try making a new Linux VM in the main Virtualbox window on each host without relying on a BOINC script. If the VM will not run correctly and install the Linux OS so you can get to the Ubuntu/Mint desktop and browse the web inside the VM, zip and post the hardening and vbox logs from the failing host for the Linux VM after the VM window and any popups have been fully closed.
dcdc
Posts: 9
Joined: 20. Jan 2022, 22:50

Re: Problem with Rosetta@home Vbox

Post by dcdc »

Thanks - installing Ubuntu as a test in a new VM now.

One thing I've just noticed is that under "Details" in VirtualBox Manager, on the working machine there are three entries: "Name", "Operating System", and "Settings File Location".

"Settings File Location" has a path to the appropriate "slots" folder under "General" heading. On the machine that won't run tasks, that entry doesn't exist. Also, on the working machine under the "Description" heading it shows the task name, but it's blank on the non-working machine.

I'll check more machines to see if that's always the case.
dcdc
Posts: 9
Joined: 20. Jan 2022, 22:50

Re: Problem with Rosetta@home Vbox

Post by dcdc »

I've installed Ubuntu in a VM on the optiplex machine and it works fine. Can browse the web etc. The LHC BOINC tasks run fine on that machine too.
dcdc
Posts: 9
Joined: 20. Jan 2022, 22:50

Re: Problem with Rosetta@home Vbox

Post by dcdc »

I've confirmed on some more machines - those that work correctly have a path listed under "Settings File Location" and those that don't run the Vbox tasks do not have that entry. So presumably they are failing because they can't see the task they are supposed to run.

Might that be persistent even after installing a new OS because of something like the disk write speed/SATA bus speed being too slow for a time-out? Seems very strange.
scottgus1
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Re: Problem with Rosetta@home Vbox

Post by scottgus1 »

dcdc wrote:under "Details" in VirtualBox Manager, on the working machine there are three entries: "Name", "Operating System", and "Settings File Location".
I see "Name" and "Operating System", but not "Settings File Location". Please post a screenshot, using the form's Upload Attachment tab.
dcdc wrote:I've installed Ubuntu in a VM on the optiplex machine and it works fine. Can browse the web etc. The LHC BOINC tasks run fine on that machine too.
scottgus1 wrote:Do either of the hosts that have trouble running the BOINC VMs run Virtualbox VMs that you personally make?
The intent was that you try Ubuntu in a VM on the hosts that do not run the BOINC VMs well. Have you tried that? I can't tell in your reports if you did.
dcdc
Posts: 9
Joined: 20. Jan 2022, 22:50

Re: Problem with Rosetta@home Vbox

Post by dcdc »

scottgus1 wrote:Do either of the hosts that have trouble running the BOINC VMs run Virtualbox VMs that you personally make?
The intent was that you try Ubuntu in a VM on the hosts that do not run the BOINC VMs well. Have you tried that? I can't tell in your reports if you did.
Apologies - I wasn't clear. I installed and ran a Ubuntu VBox successfully on the Optiplex machine that will not run the Rosetta tasks. So that machine will successfully install and run Ubuntu and BOINC LHC tasks - it is just the Rosetta VBox tasks that fail.
dcdc
Posts: 9
Joined: 20. Jan 2022, 22:50

Re: Problem with Rosetta@home Vbox

Post by dcdc »

Comparison image attached. That is the same for all tasks that I've seen so far. I'll be able to check some more machines later today.

The machine on the left was successfully running Rosetta VBox tasks when it was running from the C:\ drive too, but ran out of space. I have other machines running Rosetta successfully from C: so I don't think that's a factor.
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scottgus1
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Re: Problem with Rosetta@home Vbox

Post by scottgus1 »

Thanks for the information.
dcdc wrote:that machine will successfully install and run Ubuntu and BOINC LHC tasks - it is just the Rosetta VBox tasks that fail.
That Virtualbox itself and other BOINC VMs run means the problem is in the Rosetta files and configuration, not in Virtualbox.

The Description line is an anything-goes setting that can manually be set to any desired content and does not influence the VM's operation.

I have never seen the Settings File Location line. It's not there in normal Virtualbox VMs. I wonder if it's an 'extradata' set in the VM's .vbox file? Maybe a forum guru knows about this one.
fth0
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Re: Problem with Rosetta@home Vbox

Post by fth0 »

scottgus1 wrote:I have never seen the Settings File Location line.
Well, then let's change that: ;)

In the right pane of the VirtualBox Manager, the VM settings are displayed in groups, and each group has a heading (e.g. General, System) and a block of lines with some of the settings below that. Position your mouse over the block of lines, not over the heading, and click the right mouse button ...

In consequence, this is a red herring here.
dcdc
Posts: 9
Joined: 20. Jan 2022, 22:50

Re: Problem with Rosetta@home Vbox

Post by dcdc »

I hadn't appreciated that I could just look at the VirtualBox script that is running by hitting "Show". On the one machine I've looked at so far, it is failing on "mk1_lapack_ps_mc3_dsytrf_l_small" if that means anything to anyone?

Screenshot:
https://ibb.co/0JX2LL6

I've cross-posted this on the Rosetta forum, but couldn't post here as I couldn't log in earlier for some reason...

Rosetta thread: https://boinc.bakerlab.org/rosetta/foru ... p?id=14886
scottgus1
Site Moderator
Posts: 20965
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Re: Problem with Rosetta@home Vbox

Post by scottgus1 »

fth0 wrote:Position your mouse over the block of lines, not over the heading, and click the right mouse button ...
Well, I'll be... I never know that was there! Thanks!
scottgus1
Site Moderator
Posts: 20965
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Re: Problem with Rosetta@home Vbox

Post by scottgus1 »

dcdc wrote:Screenshot:
Screenshots look better when screen-snipped with the host OS, and can be posted with Upload Attachment just like logs.

That error is definitely inside a working VM, and is from the VM's OS. What it is I cannot say. Could be an incompatibility in Rosetta's OVA or premade vdi file with the host's CPU.
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