Rosetta 4.12+

Message boards : RALPH@home bug list : Rosetta 4.12+

To post messages, you must log in.

1 · 2 · 3 · 4 · Next

AuthorMessage
Profile [VENETO] boboviz

Send message
Joined: 9 Apr 08
Posts: 680
Credit: 1,314,914
RAC: 337
Message 6636 - Posted: 27 Mar 2020, 9:54:57 UTC

First error also on Windows platform
4923240
194 (0x000000C2) EXIT_ABORTED_BY_CLIENT
Watchdog active.
======================================================
DONE :: 22 starting structures 7118.89 cpu seconds
This process generated 22 decoys from 22 attempts
======================================================
BOINC :: WS_max 4.05647e+08

BOINC :: Watchdog shutting down...
10:47:52 (10496): called boinc_finish(0)

</stderr_txt>
<message>
finish file present too long</message>
ID: 6636 · Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 9 Apr 08
Posts: 680
Credit: 1,314,914
RAC: 337
Message 6637 - Posted: 27 Mar 2020, 16:53:31 UTC

Windows version seems good for me: 110 valid wus, only 2 errors
ID: 6637 · Report as offensive    Reply Quote
declis

Send message
Joined: 28 Mar 20
Posts: 1
Credit: 0
RAC: 0
Message 6645 - Posted: 28 Mar 2020, 9:30:09 UTC

Is it possible to run it on Odroid XU4 with Ubuntu 18.04.4 LTS? At the moment the log says:


45 ralph@home 28.03.2020 09:26:46 Requesting new tasks for CPU and Mali-T628 and Mali-T628
46 ralph@home 28.03.2020 09:26:49 Scheduler request completed: got 0 new tasks
47 ralph@home 28.03.2020 09:26:49 This project doesn't support computers of type arm-unknown-linux-gnueabihf


System:

4.14.165-172 #1 SMP PREEMPT Wed Jan 15 20:20:27 -03 2020 armv7l armv7l armv7l GNU/Linux
Operating System: Ubuntu 18.04.4 LTS
Kernel: Linux 4.14.165-172
Architecture: arm
ID: 6645 · Report as offensive    Reply Quote
Fritzhuber

Send message
Joined: 23 Mar 20
Posts: 2
Credit: 11,958
RAC: 0
Message 6646 - Posted: 28 Mar 2020, 11:24:32 UTC

Windows version seems good for me as well: 127 valid WUs, 0 errors
ID: 6646 · Report as offensive    Reply Quote
JacquesVoogt

Send message
Joined: 28 Mar 20
Posts: 3
Credit: 4,417
RAC: 78
Message 6650 - Posted: 28 Mar 2020, 23:52:15 UTC

Are there any Ubuntu work units?


Host Project Date Message
fah01 ralph@home 29/03/2020 6:36:55 AM No tasks sent
fah01 ralph@home 29/03/2020 6:36:55 AM Scheduler request completed: got 0 new tasks
fah01 ralph@home 29/03/2020 6:36:52 AM Requesting new tasks for CPU
fah01 ralph@home 29/03/2020 6:36:52 AM Sending scheduler request: To fetch work.
fah01 ralph@home 28/03/2020 11:16:43 PM project resumed by user
fah01 ralph@home 28/03/2020 11:16:32 PM No tasks sent
fah01 ralph@home 28/03/2020 11:16:32 PM Scheduler request completed: got 0 new tasks
fah01 ralph@home 28/03/2020 11:16:30 PM Requesting new tasks for CPU
fah01 ralph@home 28/03/2020 11:16:30 PM Sending scheduler request: Requested by user.
fah01 ralph@home 28/03/2020 11:16:28 PM update requested by user
fah01 ralph@home 28/03/2020 11:15:45 PM work fetch resumed by user
fah01 ralph@home 28/03/2020 10:59:57 PM No tasks sent
fah01 ralph@home 28/03/2020 10:59:57 PM Scheduler request completed: got 0 new tasks
fah01 https://ralph.bakerlab.org/ 28/03/2020 10:59:55 PM Requesting new tasks for CPU
fah01 https://ralph.bakerlab.org/ 28/03/2020 10:59:55 PM Sending scheduler request: Project initialization.
fah01 https://ralph.bakerlab.org/ 28/03/2020 10:59:49 PM Master file download succeeded
fah01 --- 28/03/2020 7:25:38 AM Internet access OK - project servers may be temporarily down.
fah01 --- 28/03/2020 7:25:36 AM Project communication failed: attempting access to reference site
fah01 --- 28/03/2020 2:41:24 AM Internet access OK - project servers may be temporarily down.
fah01 --- 28/03/2020 2:41:21 AM Project communication failed: attempting access to reference site
fah01 --- 27/03/2020 8:48:50 PM Internet access OK - project servers may be temporarily down.
fah01 --- 27/03/2020 8:48:49 PM Project communication failed: attempting access to reference site
fah01 --- 27/03/2020 4:54:53 PM Internet access OK - project servers may be temporarily down.
fah01 --- 27/03/2020 4:54:51 PM Project communication failed: attempting access to reference site
fah01 --- 27/03/2020 3:02:45 PM Internet access OK - project servers may be temporarily down.
fah01 --- 27/03/2020 3:02:43 PM Project communication failed: attempting access to reference site
fah01 --- 27/03/2020 2:16:48 PM Internet access OK - project servers may be temporarily down.
fah01 --- 27/03/2020 2:16:47 PM Project communication failed: attempting access to reference site
fah01 --- 27/03/2020 1:46:06 PM Internet access OK - project servers may be temporarily down.
fah01 --- 27/03/2020 1:46:02 PM Project communication failed: attempting access to reference site
fah01 --- 27/03/2020 1:27:21 PM Internet access OK - project servers may be temporarily down.
fah01 --- 27/03/2020 1:27:18 PM Project communication failed: attempting access to reference site
fah01 --- 27/03/2020 1:15:31 PM Internet access OK - project servers may be temporarily down.
fah01 --- 27/03/2020 1:15:28 PM Project communication failed: attempting access to reference site
fah01 --- 27/03/2020 1:06:21 PM Internet access OK - project servers may be temporarily down.
fah01 --- 27/03/2020 1:06:20 PM Project communication failed: attempting access to reference site
fah01 --- 26/03/2020 3:29:25 PM Checking presence of 65 project files
fah01 --- 26/03/2020 3:29:25 PM Setting up GUI RPC socket
fah01 --- 26/03/2020 3:29:25 PM Checking active tasks
fah01 --- 26/03/2020 3:29:25 PM Setting up project and slot directories
fah01 --- 26/03/2020 3:29:25 PM (to change preferences, visit a project web site or select Preferences in the Manager)
fah01 --- 26/03/2020 3:29:25 PM suspend work if non-BOINC CPU load exceeds 25%
fah01 --- 26/03/2020 3:29:25 PM don't use GPU while active
fah01 --- 26/03/2020 3:29:25 PM max CPUs used: 20
fah01 --- 26/03/2020 3:29:25 PM max disk usage: 11.19 GB
fah01 --- 26/03/2020 3:29:21 PM max memory usage when idle: 43463.84 MB
fah01 --- 26/03/2020 3:29:21 PM max memory usage when active: 24146.58 MB
fah01 --- 26/03/2020 3:29:21 PM Preferences:
fah01 --- 26/03/2020 3:29:21 PM Reading preferences override file


System info:
Dell R720
2x Intel Xeon E5-2640 6C/12T CPU
64GB RAM
OS: Ubuntu Server 18.04 LTS 64-bit

Runs the Rosetta project just fine.
ID: 6650 · Report as offensive    Reply Quote
Tom Rinehart

Send message
Joined: 31 Mar 20
Posts: 4
Credit: 0
RAC: 0
Message 6657 - Posted: 1 Apr 2020, 19:29:54 UTC
Last modified: 1 Apr 2020, 20:04:01 UTC

Linux ARM64 Memory Needs

I have an odroidc2 running Armbian for aarch64. The odroid C2 has 2 GB of RAM. I get this error message and no work units are received:

Rosetta for Portable Devices needs 1907.35 MB RAM but only 1770.35 MB is available for use.

Unless there is some work around, the ARM64 devices will need to have 4 GB of RAM to run work units. If one work unit needs this amount of memory, it will limit the usefulness of most ARM64 devices. Most don’t have much memory - Raspberry Pi 2 v1.2, 3, and 3+ only have 1 GB of RAM - many other ARM64 devices have 1 or 2 GB of RAM.
ID: 6657 · Report as offensive    Reply Quote
Tom Rinehart

Send message
Joined: 31 Mar 20
Posts: 4
Credit: 0
RAC: 0
Message 6659 - Posted: 3 Apr 2020, 0:36:47 UTC
Last modified: 3 Apr 2020, 1:14:51 UTC

Mac 4.12 Computation Error

I started getting 4.12 work units on my Macs in Rosetta@home. They all end in computation errors:

<core_client_version>7.14.3</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)</message>
<stderr_txt>
command: rosetta_4.12_x86_64-apple-darwin -run:protocol jd2_scripting -parser:protocol predictor_v11_boinc--fuse--covid_spike_design_boinc_v1.xml @flags_jhr_cv -in:file:silent 3xc3uf2h_Junior_HalfRoid_vs_COVID-19_design1.silent -in:file:silent_struct_type binary -silent_gz -mute all -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip 3xc3uf2h_Junior_HalfRoid_vs_COVID-19_design1.zip @3xc3uf2h_Junior_HalfRoid_vs_COVID-19_design1.flags -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937
Starting watchdog...
Watchdog active.
error: zipfile probably corrupt (illegal instruction)

</stderr_txt>
]]>

One of my other Macs is getting this error:

<core_client_version>7.14.3</core_client_version>
<![CDATA[
<message>
process got signal 4</message>
<stderr_txt>

</stderr_txt>
]]>

I have two linux boxes running Debian Buster that are working fine, so it looks like a Mac app problem.
ID: 6659 · Report as offensive    Reply Quote
JacquesVoogt

Send message
Joined: 28 Mar 20
Posts: 3
Credit: 4,417
RAC: 78
Message 6663 - Posted: 5 Apr 2020, 12:52:33 UTC - in response to Message 6659.  

Starting to see some rosetta 4.13 work on one of my Ubuntu servers since this afternoon.
So far all showing success.

I'm guessing 4.12 did not make it to prod then.

Rosetta work seems to have been depleted
ID: 6663 · Report as offensive    Reply Quote
JacquesVoogt

Send message
Joined: 28 Mar 20
Posts: 3
Credit: 4,417
RAC: 78
Message 6664 - Posted: 5 Apr 2020, 13:43:49 UTC - in response to Message 6663.  

I had few errors now with
.*Mini_Protein_binds_IL1R_COVID-19_test1_SAVE_ALL_OUT_19_4_1 and
.*Mini_Protein_binds_IL1R_COVID-19_test1_SAVE_ALL_OUT_19_3_1

Each ran for 7 and 8 seconds respectively
ID: 6664 · Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 9 Apr 08
Posts: 680
Credit: 1,314,914
RAC: 337
Message 6665 - Posted: 5 Apr 2020, 15:05:21 UTC - in response to Message 6664.  

I had few errors now with
.*Mini_Protein_binds_IL1R_COVID-19_test1_SAVE_ALL_OUT_19_4_1 and

It's better if you link the wus here, to help developers to find these errors.
Your pc is public so, i think it is, for example, this wu 4953487
ID: 6665 · Report as offensive    Reply Quote
Ivaylo Bonev

Send message
Joined: 30 Mar 20
Posts: 3
Credit: 3,702
RAC: 0
Message 6667 - Posted: 5 Apr 2020, 15:40:01 UTC

Two errors from the new 4.13 app (both me and my wingman have the errors) :
https://ralph.bakerlab.org/result.php?resultid=4953444
https://ralph.bakerlab.org/result.php?resultid=4953446
ID: 6667 · Report as offensive    Reply Quote
Admin
Project administrator

Send message
Joined: 15 Dec 17
Posts: 252
Credit: 0
RAC: 0
Message 6670 - Posted: 5 Apr 2020, 18:08:17 UTC

These look to be job specific errors and can be dealt with without an app update. I'm more concerned with general errors that would require an update so please keep an eye out for more general errors also. I had to push another build for the rosetta linux platforms to add a quick fix.
ID: 6670 · Report as offensive    Reply Quote
Admin
Project administrator

Send message
Joined: 15 Dec 17
Posts: 252
Credit: 0
RAC: 0
Message 6672 - Posted: 5 Apr 2020, 18:20:50 UTC
Last modified: 5 Apr 2020, 18:22:34 UTC

The COVID-19 related updates to the 4.13 rosetta and rosetta_for_devices and 4.14 rosetta linux versions include a new target clash energy and fold-tree options to improve the interface design protocol. It will allow sampling with the ACE2 binding helix motif fixed along with the target and a fast target clash energy check. Successful binders using this protocol are already being tested and optimized in the wet lab but this will allow us to design many more candidates to increase our chances of designing successful binders with the most promising binder properties.

Please spread to word to help our Ralph@home testing efforts for this app. A broad range of platforms is desired. Thanks!
ID: 6672 · Report as offensive    Reply Quote
Plomos

Send message
Joined: 8 Jul 12
Posts: 4
Credit: 226
RAC: 0
Message 6673 - Posted: 5 Apr 2020, 18:52:11 UTC

Hi,

I saw a post over on the main rosetta board saying that you guys needed help testing things over here so I came over. I am running Fedora 31 system that has been fully updated so kernel 5.5.13-200.fc31.x86_64. I am running BOINC as it is in the fedora repos so version 7.16.1. I am using KDE as a DE in case that is relevant.

I grabbed a Rosetta 4.14 task and at least here within the first ten minutes it seems to be running fine except for the graphics. The option to view the graphics is available, but when I click on it the graphics window does not open at all. Is there a special dependancy that I need to be able to see the graphics for a task? Over the last couple of weeks I have run 4.07, and 4.08 tasks and could not access graphics from those either to be able to see how many decoys I was managing during the run. I will keep an eye on the WU for any other issues, but thought it odd the graphics do not show.
ID: 6673 · Report as offensive    Reply Quote
nastasache

Send message
Joined: 5 Apr 20
Posts: 1
Credit: 0
RAC: 0
Message 6674 - Posted: 5 Apr 2020, 18:56:35 UTC

<core_client_version>7.14.4</core_client_version>
<![CDATA[
<message>
process got signal 6</message>
<stderr_txt>
dyld: Library not loaded: /usr/local/lib/libftgl.2.dylib
Referenced from: /Library/Application Support/BOINC Data/slots/2/../../projects/ralph.bakerlab.org/rosetta_4.13_x86_64-apple-darwin
Reason: image not found

</stderr_txt>
]]>
ID: 6674 · Report as offensive    Reply Quote
Admin
Project administrator

Send message
Joined: 15 Dec 17
Posts: 252
Credit: 0
RAC: 0
Message 6676 - Posted: 5 Apr 2020, 19:29:37 UTC - in response to Message 6674.  
Last modified: 5 Apr 2020, 19:51:39 UTC

Think I fixed this with 4.14. Try updating to get the new app.
ID: 6676 · Report as offensive    Reply Quote
Admin
Project administrator

Send message
Joined: 15 Dec 17
Posts: 252
Credit: 0
RAC: 0
Message 6677 - Posted: 5 Apr 2020, 19:58:26 UTC - in response to Message 6673.  

Supporting graphics for linux is tough. The graphics uses OpenGL and GLUT but depend on some dynamic libs that may or may not be available among different linux versions. If anyone has suggestions for more general graphics support for linux, I'm all ears.
ID: 6677 · Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 13 Jan 09
Posts: 90
Credit: 317,142
RAC: 2
Message 6678 - Posted: 5 Apr 2020, 20:38:40 UTC - in response to Message 6663.  

Starting to see some rosetta 4.13 work on one of my Ubuntu servers since this afternoon.
So far all showing success.

I'm guessing 4.12 did not make it to prod then.

Rosetta work seems to have been depleted

4,12 made it over on Rosetta@home, even if it was not tested first on Ralph@home.

New users over on Rosetta@home are trying to download more tasks much faster than new tasks are created. Work over there WILL be depleted until they work out ways to generate new tasks faster.
ID: 6678 · Report as offensive    Reply Quote
Admin
Project administrator

Send message
Joined: 15 Dec 17
Posts: 252
Credit: 0
RAC: 0
Message 6680 - Posted: 5 Apr 2020, 20:54:25 UTC - in response to Message 6678.  
Last modified: 5 Apr 2020, 20:56:30 UTC

Starting to see some rosetta 4.13 work on one of my Ubuntu servers since this afternoon.
So far all showing success.

I'm guessing 4.12 did not make it to prod then.

Rosetta work seems to have been depleted

4,12 made it over on Rosetta@home, even if it was not tested first on Ralph@home.

New users over on Rosetta@home are trying to download more tasks much faster than new tasks are created. Work over there WILL be depleted until they work out ways to generate new tasks faster.


4.12 was tested on Ralph but not thoroughly enough. We wanted to get it out anyway so that we can start working on the scaffolds. Time is important. We've been trying our best to get this next app version pushed out. But want it thoroughly tested now since we are still able to get important COVID-19 work done on R@h with 4.12.

Yes, the people behind the scenes are working hard at producing work and analyzing results but there will be plenty of work to come in the near future. This app update should help. We are also trying to recruit more researchers in the IPD to use R@h for their computing rather than relying just on our local options. This new update should allow many more researchers to work on a vast range of interesting targets not just related to COVID-19 but other important targets, but of course, COVID-19 has the highest priority. We do not want to just fill the queue with jobs that we feel already have enough samples as there are other distributed projects people can help with while we are low on work (hopefully in the near future this will not be an issue even with the amount of computing we have at hand).
ID: 6680 · Report as offensive    Reply Quote
Plomos

Send message
Joined: 8 Jul 12
Posts: 4
Credit: 226
RAC: 0
Message 6681 - Posted: 5 Apr 2020, 22:16:57 UTC - in response to Message 6677.  

Supporting graphics for linux is tough. The graphics uses OpenGL and GLUT but depend on some dynamic libs that may or may not be available among different linux versions. If anyone has suggestions for more general graphics support for linux, I'm all ears.


Ok thanks, I'm glad that it isn't an issue with my machine. So far the current 4.14 task is making good progress after 3.5 hours of running. We'll see what the results end up like when it's done
ID: 6681 · Report as offensive    Reply Quote
1 · 2 · 3 · 4 · Next

Message boards : RALPH@home bug list : Rosetta 4.12+



©2020 University of Washington
http://www.bakerlab.org