Posts by funkydude

1) Message boards : Number crunching : Rosetta now abandonware? (Message 96561)
Posted 16 May 2020 by funkydude
Post:
I think the fact that the project heard & responded to the suggestion that writing things to the slot directories that didn't need to be there was un-necessary, both here in the forums & by deploying a new application, shows that they do take notice & respond.


Sorry, but I disagree.
The issue with directories should not have had to wait until 2020 and a pandemic to resolve.
The only reason they added HTTPS protection was because of pressure from a big company. Prior to that, no thought about protecting users.

Ultimately since those (good) changes were implemented, the forums have been void of all interaction.
Poor quality tasks are regularly being allowed into the public. From failed zips to nonsensical work names.
The zip fails are evidence that tasks aren't even run on a test machine before being thrown at the public without any real care.

Users here (like you) try their best to post about faulty tasks and those tasks end up being purged before anyone responsible even looks at them.

Processing a task for 8+ hours only to have it fail to zip itself, something that would have been caught had it been tested prior to deployment, is an egregious waste of electricity.
2) Message boards : Cafe Rosetta : COVID 19 tasks released on WCG (Message 96560)
Posted 16 May 2020 by funkydude
Post:
"All tasks are verified by a wingman for safety"

Actually, after a host delivers a certain number of valid results, it becomes quorum 1.
All the AutoDock/AutoDock Vina projects have been that way.
Periodically however, quorum 2 will be re-enabled to make sure the host is doing fine.

The AutoDock software currently in use at OpenPandemics is in a way, a new version, as it includes a new "reactive docking" protocol.


Good to know, thanks.

I've also noticed that after it becomes 1, you will be randomly picked as a wingman for others. So you may still be participating in quorum 2 tasks.

Overall it's good that extra care is taken to have good results. There are multiple people on this forum who like to dismiss Rosetta's bugs as merely a fault in the donators hardware.
This form of verification can help prove otherwise.
3) Message boards : Number crunching : Rosetta now abandonware? (Message 96538)
Posted 15 May 2020 by funkydude
Post:
Had another 3 errors on my main machine.
2 memory errors and a zip error: For some reason the task was trying to zip up task specific data from the project directory instead of the slots directory where the data actually is...
The task was fully complete, but counted as an error because of its failure to zip the correct contents.

Giving up for now and moving to WCG. (Posting there to keep threads clean and on topic)

Rosetta is great but unfortunately for me it comes down to one thing: Wasting electricity on beta quality software (errors) instead of the project using Ralph for longer periods of test time.
We all want to beat this together but wasting electricity isn't an option for me like it may be for others.
4) Message boards : Cafe Rosetta : COVID 19 tasks released on WCG (Message 96537)
Posted 15 May 2020 by funkydude
Post:
This is great news. I had originally left Rosetta for WCG because of the file size issues, then came back to Rosetta when they were fixed.
But it seems there is no interest in resolving the latest issues including memory errors and zip failures, so back to WCG I go.

Here are the benefits I personally see: (It's ok if you don't agree)
    Clear and transparent, dedicated section to this specific project with all news posted in one place: https://www.worldcommunitygrid.org/research/opn1/news.do
    Promise of frequent updates
    Longer deadlines (~1 week)
    Lower completion times (~2 hours)
    Lower memory footprint (~200MB)
    All tasks are verified by a wingman for safety
    AVX support
    GPU support nearly done
    The ability to choose to work on only COVID-19
    Badges specifically for COVID-19
    Based on the free and open source AutoDock software instead of the closed source proprietary Rosetta software.
    According to Wikipedia "AutoDock is one of the most cited docking software applications in the research community"



The fact that it's used so much is probably why it's so much more stable.
Although I admit this is from very little testing of the few machines I've swapped over.

I'll give it a week to see how things go, then I'll discuss with my colleagues about moving the work fleet over.

5) Message boards : Number crunching : Rosetta now abandonware? (Message 96492)
Posted 14 May 2020 by funkydude
Post:
    <10k tasks left, previously there was over 2million and was actively being kept above 1 million
    No news/updates in regards to project progress - Folding@Home gives update almost daily
    No way to know what you've contributed to (Folding@Home puts their publications front and center. GPUGRID gives you badges according to each publication you contributed to).
    Continuing the above point: Rosetta does nothing to make you feel involved. e.g. Folding@Home now has a community Discord to keep contributors engaged to try and reduce the decline in users over time.
    Still no AVX support - Folding@Home has this
    Still no GPU support - Folding@Home has this
    Memory errors posted on forums is going unaddressed (See signal 11 for Linux/Max and ACCESS_VIOLATION for Windows.)
    In some cases, BSOD's are occurring when running these tasks at the same time as other heavy applications.
    Direct PMs unanswered, direct emails ignored, forum posts not replied to.



The lack of communication, especially in regards to the memory errors, is what annoys me the most. Work feels wasted.

6) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 96453)
Posted 13 May 2020 by funkydude
Post:
You're not the only person experiencing signal 11. Please post in the other thread: https://boinc.bakerlab.org/rosetta/forum_thread.php?id=13941
7) Message boards : Number crunching : minirosetta_database directory in slot (Message 96183)
Posted 6 May 2020 by funkydude
Post:
I'm not sure how one can update that global preference via the web site. I just edited the xml but that isn't convenient. If anyone knows, please post instructions here. I suppose I can modify the database records but I'm not completely sure that would cause problems or not and don't want to take that risk.


From what I see there are only 2 options.

1) You update the database for all users, then they gradually migrate to HTTPS the next time each user contacts the server for more work.
2) Attempt to get users to edit their BOINC preferences on rosetta themselves.

I think number 1 is the only realistic option, but if anyone wants to follow step 2, here how to do it (and how I did it).
The following steps will enable HTTPS protection for your BOINC configuration.

    > Log into the Rosetta@Home website and go to your account.
    > Click on "Computing preferences".
    > Click "Edit Preferences" at the bottom.
    > Change anything you want. e.g. "Store at least X days of work". If you don't want to change anything just change it back straight after.
    > Click "Update preferences" at the bottom.
    ---
    > At this point you can either edit your preferences again to undo your change, or you can proceed with the next step.
    > Open up your BOINC manager, select the Rosetta@Home project and click the "Update" button.


That's it. Your preferences are now encrypted with HTTPS instead of using HTTP.

While this works, it is a really convoluted method that next to no one is going to bother following.

8) Message boards : Number crunching : minirosetta_database directory in slot (Message 96122)
Posted 5 May 2020 by funkydude
Post:
There were indeed some remaining http references in some xmls and I think I traced the issue. This is hopefully fixed now but will only be active with new jobs submitted by our group. Currently queued and running jobs will still have some URLs with http. I'll check again after new jobs get submitted.


This explanation makes perfect sense for the upload_url because it appears once for every single task i.e. it appears 24 times in the config file when running 24 tasks.
So obviously this URL is tied to the generated tasks themselves and as you already said, we need to wait for brand new tasks.

However, are you sure this applies to the scheduler?
From my original post
BOINC/global_prefs.xml
<source_scheduler>http://bwsrv1.bakerlab.org/rosetta_cgi/cgi</source_scheduler>


Not only does this also only appear once, but it also appears in XML files for other projects.
For example, this is a GPUGRID XML file:
BOINC/sched_request_www.gpugrid.net.xml
<source_scheduler>http://bwsrv1.bakerlab.org/rosetta_cgi/cgi</source_scheduler>


I believe this is because I'm using the web preferences set by R@H, so the GPUGRID XML files ends up with a reference to your scheduler to know my BOINC preferences.

Are you sure this can only be fixed by more work and isn't some setting on the back end of the website?
9) Message boards : Number crunching : minirosetta_database directory in slot (Message 96067)
Posted 4 May 2020 by funkydude
Post:
Those URLs should be https. I'm not sure what is going on with your host.


Thanks for the follow up.
Unless this was fixed after I re-attached my machines then it's not just me. But I will try re-attach them again soon.

Have you tried doing a search for "http:" in all .XML files in the BOINC data directory?
10) Message boards : Number crunching : minirosetta_database directory in slot (Message 96057)
Posted 4 May 2020 by funkydude
Post:
I'd like to attract attention


Bump, admin?
11) Message boards : Number crunching : minirosetta_database directory in slot (Message 95925)
Posted 3 May 2020 by funkydude
Post:
As for the captcha, I can add it to the registration / email forms to replace the internal spam filtering when I get a chance but that's definitely low priority.


That's a shame, hopefully you can get that done and lift the filtering soon. On a positive note, I re-attached and everything is going well, so you clearly didn't need my testing.

I'd like to attract attention to my other post that got drowned out, if possible: https://boinc.bakerlab.org/rosetta/forum_thread.php?id=13894&postid=95809#95809

On a final note, I'd like to request IPv6 support be added to the boinc-files.bakerlab.org domain. The other 2 domains (boinc.bakerlab.org & bwsrv1.bakerlab.org) already support it. This will allow me to add 2 maybe 3 more hosts. But finishing the HTTPS work should be higher priority.
12) Message boards : Number crunching : This project is using an old URL - in BOINC Manager Event Log (Message 95924)
Posted 3 May 2020 by funkydude
Post:
HTTP will be dead within the next 5 years thanks to the great and gradual work the Chrome devs are doing to push for this goal.

All it does is confirm there is no man in the middle. Useful for financial stuff, passwords and so on, not so for downloads of data files.


Your western protective bubble is showing.
13) Message boards : News : Switch to using SSL (Secure Socket Layer) (Message 95809)
Posted 2 May 2020 by funkydude
Post:
Nice progress, I detached, deleted everything to be sure, and added the project again..
But you have missed some things to be fully secure:

BOINC/client_state.xml
All work uploads insecurely.
<upload_url>http ://boinc.bakerlab.org/rosetta_cgi/file_upload_handler</upload_url>


BOINC/global_prefs.xml
<source_scheduler>http ://bwsrv1.bakerlab.org/rosetta_cgi/cgi</source_scheduler>


BOINC/sched_reply_boinc.bakerlab.org_rosetta.xml
<url>http ://boinc.bakerlab.org/rosetta_cgi/file_upload_handler</url>


BOINC/sched_request_boinc.bakerlab.org_rosetta.xml
<source_scheduler>http ://bwsrv1.bakerlab.org/rosetta_cgi/cgi</source_scheduler>


EDIT: I added the spaces on purpose because some kind of rewrite rule on the forum is changing my text from http to https.
14) Message boards : Number crunching : minirosetta_database directory in slot (Message 95274)
Posted 24 Apr 2020 by funkydude
Post:
Completely agree. If there's a way, we can do it. I can look into this and test on our ralph project. But this will take some time since it will require an application update.


Happy to see this response from you. I'll use this opportunity to ask for something else: Remove the IP address blocking from registration for ralph (and rosetta).

Please understand that this is an archaic and flawed way of preventing spam. There is nothing unique or static about an IP address. An increasing amount of ISPs are now implementing CGNAT (Carrier Grade NAT) due to IPv4 shortage, which you will be familiar with since you're a university: Many users under a same IP address.

There are multiple ways of preventing spam by not using IP blocking.
SETI chooses to use a Google Captcha (https://setiathome.berkeley.edu/signup.php)
GPUGRID chooses to force you to register via the BOINC client (https://www.gpugrid.net/create_account_form.php)
I believe Cloudflare even offers services for free which include filtering methods.

I do not know what version of the BOINC web software you are using, perhaps the captcha is an in built optional feature now?

If you can do this, I'd be happy to sign up to Ralph and help you test shared data (if you implement it)
If you don't do this, please, at least improve the error message to stop misleading people with the "incorrectly formatted email address" error.

Thanks.
15) Message boards : Number crunching : minirosetta_database directory in slot (Message 95243)
Posted 23 Apr 2020 by funkydude
Post:
Indeed this is not efficient but there currently is no easy workaround that we know of since Rosetta is dependent on the database directory structure. If anyone knows of an easy workaround, I'm all ears. The Rosetta application depends on the database directory structure. This database holds all the required score, chemical, sampling, rotamer, etc. parameters and libraries that are the backbone of all the computations and a result of many years of research and development. These parameters may or may not change with application updates. For example, for the COVID-19 specific jobs, we had to significantly increase the size of the database to include an improved local protein structure fragment library in addition to side chain motif libraries to enable the interface design protocol. These are parameters/libraries that have been developed and continue to be developed in the lab through careful analysis and research of native protein structures and molecular structures in general.


Look at WCG (World Community Grid).
They do not copy all the data into every single slot. They don't even copy the executables.
It seems they use 1KB files which I assume act as pointers/symlinks, but don't quote me on that.
Looking at the logs of WCG completed tasks, I see a reference to the /projects/ directory directly.

FYI this is the reason I gave up on this project and moved to WCG (waiting on their COVID project)
The currently implementation was obviously designed back in the 4 core days.
Not acceptable to use ~24GB of storage for 24 tasks (threads) today.

I'll come back if it's ever fixed.
16) Message boards : News : Rosetta's role in fighting coronavirus (Message 92761)
Posted 31 Mar 2020 by funkydude
Post:
3. We almost have the new update out, but not yet.


Will this new update also include 64 bit support so that 2GB tasks stop crashing with out of memory errors when there is plenty free?

Also is there plans to update the version of BOINC ran on the web server, or to update the config files the server sends to clients to point from http to https? You never know what [insert authoritarian regime] decides that running this might be offensive tomorrow. All transfers should be protected by default.
17) Message boards : Number crunching : Tired of 11 hours (Message 59232)
Posted 2 Feb 2009 by funkydude
Post:
I'm getting tired of every single model for the past 2 weeks or so being around 11 hours. I've specified 6 hours in my settings. First I thought it was for the new Rosetta Mini versions, but now I'm getting 11hour Rosetta beta's. What's going on here?
18) Message boards : Number crunching : A SINGLE Graphics Card = 1 teraFLOPS (Message 59231)
Posted 2 Feb 2009 by funkydude
Post:
http://game.amd.com/us-en/unlock_radeon4800.aspx?p=2


Yes, It can run crysis.


Also uses more than double the amount of electricity. Somehow I'd rather stick to CPU crunching.
19) Message boards : Number crunching : Minirosetta v1.47 bug thread. (Message 57935)
Posted 16 Dec 2008 by funkydude
Post:

On the first machine, NOD32 Antivirus thinks the Minirosetta .exe either contains a viral signature or looks bad heuristically (their UI doesn't say which). I have to add an exclusion to get the thing out of quarantine, every time a new version is released.


Hello, I've been using both nod32 and rosetta for years now, I've never had nod32 detect rosetta as anything malicious, make sure you are updated. v3.0.672.0 DB 3695 as of writing.
20) Message boards : Number crunching : SERVER PROBLEMS. (Message 57437)
Posted 2 Dec 2008 by funkydude
Post:
Hi David.

Did that it worked on the second try, thanks.

pete.



I wish this worked for me, but it simply does not. It keeps saying can't attach shared memory. Tried reboot, router reboot, manual update etc...

edit: It won't even update the stats like RAC.


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