Posts by computezrmle

1) Message boards : Number crunching : Disk usage limit exceeded (Message 108374)
Posted 18 May 2023 by computezrmle
Post:
A disk usage limit can be set by the project via <rsc_disk_bound> (in bytes).
It is thought to protect the disk from being filled by endless loops.
You may check client_state.xml for the current values.

If the error happens regularly the project people may need to increase the value.
Otherwise it may indicate a program error.
2) Message boards : Number crunching : Multiattach mode disk images (Message 107680)
Posted 6 Nov 2022 by computezrmle
Post:
Right.
:-)

It's now up to the Rosetta developers to make use of the multiattach feature.
Just in case they don't know where to download the required vboxwrapper.

Apple:
https://boinc.berkeley.edu/dl/vboxwrapper_26206_x86_64-apple-darwin.zip

Linux:
https://boinc.berkeley.edu/dl/vboxwrapper_26206_x86_64-pc-linux-gnu

Windows:
https://boinc.berkeley.edu/dl/vboxwrapper_26206_windows_x86_64.exe.zip
3) Message boards : Number crunching : Multiattach mode disk images (Message 106796)
Posted 17 Aug 2022 by computezrmle
Post:
I just checked the RPC replies.
Looks like the project sends the vdi info with each WU.
This means that you need a modified (development) client to get this working.

<edit>
... or a project that behaves more friendly, like LHC.
</edit>
4) Message boards : Number crunching : Multiattach mode disk images (Message 106793)
Posted 17 Aug 2022 by computezrmle
Post:
Looks fine.

You may add this option in cc_config.xml and try it again:
<dont_check_file_sizes>1</dont_check_file_sizes>
5) Message boards : Number crunching : Multiattach mode disk images (Message 106785)
Posted 16 Aug 2022 by computezrmle
Post:
Post the app_info.xml.
Is it located in the Rosetta projects dir?
Does your BOINC client log mention an app_info (or anonymous platform) is loaded?

Are there any <file> or <file_signature> tags in the Rosetta section of client_state.xml before you restart the BOINC client?
6) Message boards : Number crunching : Multiattach mode disk images (Message 106781)
Posted 13 Aug 2022 by computezrmle
Post:
A "file" must be there (in the slots directory).
Beside that, in this special case the "file" has not other function any more.


With "<open_name>vm_image.vdi</open_name>" the file is a "softlink" called vm_image.vdi and pointing back to AIMNet_vm_v2.vdi in the project directory.
BOINC doesn't care but it may confuse users looking through the slots directories.

Without "<open_name>vm_image.vdi</open_name>" the softlink file will be called AIMNet_vm_v2.vdi.


In both cases the softlink file's size is just a few bytes.
7) Message boards : Number crunching : Multiattach mode disk images (Message 106776)
Posted 12 Aug 2022 by computezrmle
Post:
VERR_ALREADY_EXISTS tells you there's a disk registered with this name/UUID

Try
vboxmanage list hdds

if AIMNet_vm_v2.vdi is in the list, try
vboxmanage closemedium UUID


In addition, check the owner/group of the files.
Compare that with files from other projects.


<edit>
If you run vboxmanage commands or if you use the GUI, use the account of your BOINC user as each user on your box has it's own vbox environment.
</edit>
8) Message boards : Number crunching : Multiattach mode disk images (Message 106773)
Posted 12 Aug 2022 by computezrmle
Post:
how do you shutdown BOINC?

In your BOINC Manager (GUI) isnt' there a menu entry like "File -> Shutdown the currently connected client".
(Sorry I'm running the German GUI, hence don't know the exact term)


On Linux you may run "[sudo] systemctl stop boinc-client".


I get the following error message at Step 5,
.
.
.
So the original .vdi file apparently still exists.

The file isn't the problem.
Open your VirtualBox GUI -> Media Manager and remove the disk entry there (it shouldn't be connected to a VM).
You will be asked if you also want to remove the file. Don't remove the file.
9) Message boards : Number crunching : Multiattach mode disk images (Message 106768)
Posted 12 Aug 2022 by computezrmle
Post:
Pause BOINC's network activity, pause Rosetta or do both before you reset the project and shutdown BOINC.
Then copy the required files back before you restart BOINC.
See:
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=14930&postid=106758


Using the "anonymous platform" is a rather old method, hence not perfectly user friendly.
But once it is correctly set up it is as reliable as an app_version from the server.
10) Message boards : Number crunching : Multiattach mode disk images (Message 106766)
Posted 12 Aug 2022 by computezrmle
Post:
Files listed in app_info.xml must be present in Rosetta's project dir before the BOINC client starts (including app_info.xml itself).
My guess would be that after the project reset your client contacted the server and got an app_version update from there.

If this happened your client_state.xml will contain <signature_required/> tags related to Rosetta files you mentioned in app_info.xml (like AIMNet_vm_v2.vdi). These would be wrong.

In addition the client must be restarted to read app_info.xml.
11) Message boards : Number crunching : Multiattach mode disk images (Message 106763)
Posted 11 Aug 2022 by computezrmle
Post:
I suspect that you didn't reset the project.
If so, in client_state.xml there's still a signature of the original app_version files.

A project reset removes them.
12) Message boards : Number crunching : Multiattach mode disk images (Message 106758)
Posted 10 Aug 2022 by computezrmle
Post:
Remove this line from your app_info.xml
<open_name>vm_image.vdi</open_name>


Backup the following files from your Rosetta project directory:

vboxwrapper_26205_windows_x86_64.exe
AIMNet_vm_v2.vdi (the already cloned one)
app_info.xml
vbox_job_v4.xml (the already modified one)
boinc_app_v4



Disable the client's network access
Reset the Rosetta project (this removes the app_version you got from the project; must be done to avoid getting mixed versions)
Shutdown the client
Restore the backed up files
Check if executable flags are set for vboxwrapper and boinc_app_v4
Start the client
Enable network access
13) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 106755)
Posted 10 Aug 2022 by computezrmle
Post:
If you want to get rid of some nasty settings regarding the python app, try to use an app_info.xml.
See:
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=14930&postid=106754
14) Message boards : Number crunching : Multiattach mode disk images (Message 106754)
Posted 10 Aug 2022 by computezrmle
Post:
Based on the experience from LHC@home the suggestion from post https://boinc.bakerlab.org/rosetta/forum_thread.php?id=14930&postid=106452 needs to be slightly refined.


Get vboxwrapper 26205 instead of 26204.
As long as 26205 is not available on https://boinc.berkeley.edu/dl/

get it from LHC@home


Linux version:
http://lhcathome.cern.ch/lhcathome/download/vboxwrapper_26205_x86_64-pc-linux-gnu

Windows version:
http://lhcathome.cern.ch/lhcathome/download/vboxwrapper_26205_windows_x86_64.exe



Replace "vboxwrapper_26204" with "vboxwrapper_26205" in app_info.xml


The tag "<open_name>vm_image.vdi</open_name>" at the bottom of the previous post is now obsolete and shouldn't be used.


Volunteers waiting for an official release from Rosetta may wait forever.
15) Message boards : Number crunching : Multiattach mode disk images (Message 106452)
Posted 30 Jun 2022 by computezrmle
Post:
The steps below are for the impatient volunteers who want to test the differencing image method.
Use on own risk.
Expect a higher error rate.

The steps are written for Linux but can be used for Windows if the Windows vboxwrapper is used:
https://boinc.berkeley.edu/dl/vboxwrapper_26204_windows_x86_64.zip


1.
Set Rosetta to "no new tasks" and finish/report all Rosetta work

2.
Reset Rosetta and close BOINC

3.
Change the working directory to to "<BOINC_data_directory>/projects/boinc.bakerlab.org_rosetta/"

4.
Downlod the following files:
https://boinc.berkeley.edu/dl/vboxwrapper_26204_x86_64-pc-linux-gnu
https://boinc-files.bakerlab.org/rosetta/download/boinc_app_v4
https://boinc-files.bakerlab.org/rosetta/download/vbox_job_v4.xml
https://boinc-files.bakerlab.org/rosetta/download/26/AIMNet_vm_v2.vdi.gz

5.
Set executable flags:
chmod +x vboxwrapper_26204_x86_64-pc-linux-gnu
chmod +x boinc_app_v4

Extract AIMNet_vm_v2.vdi from AIMNet_vm_v2.vdi.gz
rename "AIMNet_vm_v2.vdi" to "AIMNet_vm_v2.vdi.bak"
run "vboxmanage clonemedium AIMNet_vm_v2.vdi.bak AIMNet_vm_v2.vdi" (Important: this creates a new UUID for AIMNet_vm_v2.vdi)
chmod +r AIMNet_vm_v2.vdi
move AIMNet_vm_v2.vdi.bak to a different directory


6.
Create the following "app_info.xml"
<app_info>
    <app>
        <name>rosetta_python_projects</name>
        <user_friendly_name>rosetta python projects</user_friendly_name>
        <non_cpu_intensive>0</non_cpu_intensive>
    </app>
    <file_info>
        <name>vboxwrapper_26204_x86_64-pc-linux-gnu</name>
        <executable/>
    </file_info>
    <file_info>
        <name>boinc_app_v4</name>
        <executable/>
    </file_info>
    <file_info>
        <name>vbox_job_v4.xml</name>
    </file_info>
    <file_info>
        <name>AIMNet_vm_v2.vdi</name>
    </file_info>
    <app_version>
        <app_name>rosetta_python_projects</app_name>
        <version_num>103</version_num>
        <avg_ncpus>1.000000</avg_ncpus>
        <plan_class>vbox64</plan_class>
        <api_version>7.7.0</api_version>
        <file_ref>
            <file_name>vboxwrapper_26204_x86_64-pc-linux-gnu</file_name>
            <main_program/>
        </file_ref>
        <file_ref>
            <file_name>boinc_app_v4</file_name>
            <open_name>shared/boinc_app</open_name>
            <copy_file/>
        </file_ref>
        <file_ref>
            <file_name>vbox_job_v4.xml</file_name>
            <open_name>vbox_job.xml</open_name>
        </file_ref>
        <file_ref>
            <file_name>AIMNet_vm_v2.vdi</file_name>
        </file_ref>
        <dont_throttle/>
    </app_version>
</app_info>



7.
Modify vbox_job_v4.xml
<vbox_job>
    <memory_size_mb>6144</memory_size_mb>
    <os_name>Debian_64</os_name>
    <enable_shared_directory/>
    <enable_remotedesktop/>
    <enable_vm_savestate_usage/>
    <disable_automatic_checkpoints/>
    <multiattach_vdi_file>AIMNet_vm_v2.vdi</multiattach_vdi_file>
</vbox_job>


8.
Restart BOINC and get fresh work (start with a small work buffer)


<edit>
May be better to add this to the file_ref section of "app_info.xml" instead of just the filename line:
        <file_ref>
            <file_name>AIMNet_vm_v2.vdi</file_name>
            <open_name>vm_image.vdi</open_name>
        </file_ref>

</edit>
16) Message boards : Number crunching : Multiattach mode disk images (Message 106376)
Posted 10 Jun 2022 by computezrmle
Post:
BOINC recently published vboxwrapper 26204 which introduces the code to deal with differencing images.
Downloads:
https://boinc.berkeley.edu/dl/vboxwrapper_26204_windows_x86_64.zip
https://boinc.berkeley.edu/dl/vboxwrapper_26204_x86_64-apple-darwin.zip
https://boinc.berkeley.edu/dl/vboxwrapper_26204_x86_64-pc-linux-gnu


It's now up to the Rosetta developers to create new app versions that make use of it.


Hint:
https://github.com/BOINC/boinc/issues/4602
17) Message boards : Number crunching : High write-rate with Pythons (Message 106346)
Posted 3 Jun 2022 by computezrmle
Post:
Yes, I know you prefer that extreme long write delay.
I just wanted to point out that there are optional methods.


I made good experience with LHC (ATLAS native) which I directly write to a tmpfs "partition" (since it has a rather bad compression rate).
This is the fastest possible method.

LHC (vbox apps like CMS) compress rather good and they run fine on a zram device.
This is comparable to Rosetta's vbox app.

All those methods crash in case of a power line outage since the data is not written to disk.
18) Message boards : Number crunching : High write-rate with Pythons (Message 106344)
Posted 3 Jun 2022 by computezrmle
Post:
Setting the write cache to an extreme delay doesn't really help since the cache daemon also writes to disk when all RAM is in use and the OS requests some more.

On Linux I prefer to mount the /slots/ dir as zram device.
It shares the same RAM with the disk cache but transparently compresses the data.
Typical savings due to compression: 40%

A process to backup/restore data to/from a real disk needs to be implemented locally but that's an easy task.


On Windows there are a couple of tools doing similar things, even freeware.
Just look for "dynamic ramdisk with compression".
19) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 105892)
Posted 9 Apr 2022 by computezrmle
Post:
robertmiles wrote:
Virtualbox has the old vbox, which handles 32-bit programs
.
.
.
Where's any evidence that the multicore Cosmology tasks use Virtualbox?

It's mentioned at the apps overview page of any project:
https://boinc.bakerlab.org/rosetta/apps.php
https://www.cosmologyathome.org/apps.php


no "()" in the "Version" col indicates a native/legacy app without special requirements like SSE, AVX ...
(vbox64) in the "Version" col indicates an app that requires VirtualBox 64-bit.
(vbox64_mt) in the "Version" col indicates an app that requires VirtualBox 64-bit and is able to run multicore VMs.
64-bit vbox apps don't run on a computer that has 32-bit vbox installed.
20) Message boards : Number crunching : Multiattach mode disk images (Message 105747)
Posted 28 Mar 2022 by computezrmle
Post:
You can also download other premade vbox images of the Rosetta environment.
https://www.osboxes.org/virtualbox-images/

VM images from that website have nothing to do with Rosetta.
They just offer plain (Linux) VMs without the required scientific environment.


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