Posts by Ivailo Bonev

1) Message boards : Number crunching : If You Don't Know Where to Put it, Post it here. (Message 99611)
Posted 7 Nov 2020 by Ivailo Bonev
Post:
I don't see any new Ryzen in the CPU list. Hmm...
https://boinc.bakerlab.org/rosetta/cpu_list.php
2) Message boards : Number crunching : Rosetta 4.1+ and 4.2+ (Message 96555)
Posted 16 May 2020 by Ivailo Bonev
Post:
Same for all my "split" tasks:
split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509193616_0001_0001_fragments_fold_SAVE_ALL_OUT_929541_939_0
split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509213503_0001_0001_fragments_fold_SAVE_ALL_OUT_929546_715_1
split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200509235721_0001_0001_fragments_fold_SAVE_ALL_OUT_929550_594_0
split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200510030335_0001_0001_fragments_fold_SAVE_ALL_OUT_929553_645_0
split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200510085851_0001_0001_fragments_fold_SAVE_ALL_OUT_929563_363_1

All with the error:
<message>
upload failure: <file_xfer_error>
<file_name>split_pass_bp_agba--rlx_aln_c1_aln_pass_build.bp_20200508201700.pdb-edge1-4-6_renumbered_obj01_polA-3-5.pdb.blue.bp_20200510085851_0001_0001_fragments_fold_SAVE_ALL_OUT_929563_363_1_r550533968_0</file_name>
<error_code>-240 (stat() failed)</error_code>
</file_xfer_error>
</message>
3) Message boards : Number crunching : Rosetta 4.1+ and 4.2+ (Message 96357)
Posted 11 May 2020 by Ivailo Bonev
Post:
https://boinc.bakerlab.org/rosetta/result.php?resultid=1176852042

<core_client_version>7.16.5</core_client_version>
<![CDATA[
<message>
Incorrect function.
 (0x1) - exit code 1 (0x1)</message>
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol jhr_boinc_v4.xml @flags -in:file:silent Junior_HalfRoid_design5_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_6gx3kn9p.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 Junior_HalfRoid_design5_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_6gx3kn9p.zip @Junior_HalfRoid_design5_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_6gx3kn9p.flags -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 3876534
Using database: database_357d5d93529_n_methylminirosetta_database

ERROR: [ERROR] Unable to open constraints file: f39b38c813752ceb1e616c99588b316d_n0_c0_1_0001.MSAcst
ERROR:: Exit from: ......srccorescoringconstraintsConstraintIO.cc line: 457
BOINC:: Error reading and gzipping output datafile: default.out
11:22:22 (11520): called boinc_finish(1)

</stderr_txt>
]]>
4) Message boards : Number crunching : Rosetta 4.1+ and 4.2+ (Message 95932)
Posted 3 May 2020 by Ivailo Bonev
Post:
Same error
3cl_9aa_6lu7_modified_AVLstub_relaxed_renumbered_0004_76_extract_B_SAVE_ALL_OUT_926264_295_1

https://boinc.bakerlab.org/rosetta/result.php?resultid=1168836107

Probably these are "bad" units.
5) Message boards : Number crunching : RALPH@Home ? (Message 95591)
Posted 30 Apr 2020 by Ivailo Bonev
Post:
New 4.18 version at Ralph@Home.
6) Message boards : Number crunching : 0 new tasks, Rosetta? (Message 93548)
Posted 5 Apr 2020 by Ivailo Bonev
Post:
Please join http://ralph.bakerlab.org/ Ralph@Home - alpha test project for Rosetta@Home
New version needs to be tested on a different platforms (x86,AMD64, ARM) and different OSes (Windows, MacOS, Linux).
https://ralph.bakerlab.org/forum_thread.php?id=839&postid=6672#6672
Thank you!

Are there about to be more tasks available for Ralph@Home? I've already joined, but haven't seen any tasks there for months.


I hope so, I received a dozen new tasks today.
7) Message boards : Number crunching : 0 new tasks, Rosetta? (Message 93544)
Posted 5 Apr 2020 by Ivailo Bonev
Post:
Please join http://ralph.bakerlab.org/ Ralph@Home - alpha test project for Rosetta@Home
New version needs to be tested on a different platforms (x86,AMD64, ARM) and different OSes (Windows, MacOS, Linux).
https://ralph.bakerlab.org/forum_thread.php?id=839&postid=6672#6672
Thank you!
8) Message boards : Number crunching : Error while computing (Message 93494)
Posted 5 Apr 2020 by Ivailo Bonev
Post:
Hello, i've got 32Gb RAM and used is 15Gb. The RAM has no problems.
I don't overclock my RAM and CPU.
At the moment 15 tasks which were running long already are broken. That's a lot of time and cpu resources wasted, not to speak of the energy they used.
When it continues like this i'll get out.

If you want to quit, abort all your tasks, and then quit, it will be faster for others to do your work. I'll recommend you to abort all the tasks and reset the project, but it's your PC and you can do what you want.

I had already a few times the problem that when the client sent a screensaver it was impossible to get back. Is there a possibility to suppress this screensaver?

You can disable screensaver, or change it to show something different.
9) Message boards : Number crunching : Error while computing (Message 93483)
Posted 5 Apr 2020 by Ivailo Bonev
Post:
I had already a few times the problem that when the client sent a screensaver it was impossible to get back. Is there a possibility to suppress this screensaver?


Check your memory with Memtest for Windows. Have you overclocked your RAM, or/and CPU?
10) Message boards : News : Outage notice (Message 93475)
Posted 5 Apr 2020 by Ivailo Bonev
Post:
What I do not understand is why my computers are not getting any tasks while the Server Status says there are over 500K queued jobs?

Look at Computing->Server Status, not the front page.
11) Message boards : Number crunching : Rosetta x86 on AMD CPU (Message 93352)
Posted 4 Apr 2020 by Ivailo Bonev
Post:
We were seeing this same behavior over at WCG on the MIP project which also uses Rosetta. The MIP developers posted this reply after we had sent them some data on what we were seeing (this was a couple of years ago):

"The short version is that Rosetta, the program being used by the MIP to fold the proteins on all of your computers*, is pretty hungry when it comes to cache. A single instance of the program fits well in to a small cache. However, when you begin to run multiple instances there is more contention for that cache. This results in L3 cache misses and the CPU sits idle while we have to make a long trip to main memory to get the data we need. This behavior is common for programs that have larger memory requirements. It's also not something that we as developers often notice; we typically run on large clusters and use hundreds to thousands of cores in parallel on machines. Nothing seemed slower for us because we are always running in that regime.
We are looking to see if if we can improve the cache behavior. Rosetta is ~2 million lines of C++ and improving the cache performance might involve changing some pretty fundamental parts. We have some ideas of where to start digging, but I can't make any promises.

Long term, identifying these issues may end up improving Rosetta for everyone that uses it so pat yourselves on the back for that!"

It's that sitting idle while waiting for data from main memory that causes the temps and energy use to drop.


Thank you for the answer and explanation, I see now usual behavior from the CPU, maybe data in the first batch with 4.12 was much more different and "hungry for L3 cache".
12) Message boards : Number crunching : Question about Load Sharing (Message 93196)
Posted 3 Apr 2020 by Ivailo Bonev
Post:
My understanding is that every xx min it checks to see if it should switch or not. It may or may not switch at that time, depending on the debt owed (or not) to the other project(s).

xx being whatever you have set, or the default of 60min.


Probably you are right, I haven't had more than 2 projects on 1 PC, and mostly they use different resources (like 1 for CPU, and 1 for GPU).
13) Message boards : Number crunching : Question about Load Sharing (Message 93187)
Posted 3 Apr 2020 by Ivailo Bonev
Post:
I thought that means each get 1/3 CPU.

No, if you have 3 projects, they will share CPU time equally, but every one will use CPU for the time set in BOINC Manager,
Options-Computing Preferences(Computing tab)-Switch between tasks every ... minutes (default 60).
So every project will switch after 1 hour time if you not set it different.
14) Message boards : Number crunching : Rosetta x86 on AMD CPU (Message 93174)
Posted 3 Apr 2020 by Ivailo Bonev
Post:
I think something is off with the CPU utilization by new 4.12 app for the new Ryzen 3k systems.
I have 3800X and with 4.07 had consistent 79-80C temps under the full load (CPU Package power - 105-107W), now with 4.12 app, temps are 65-70C under full load (CPU Package power is 80-85W).
What was changed? I was under impression that new app will be somewhat more optimized for the new CPU-s.
15) Message boards : News : Rosetta's role in fighting coronavirus (Message 92117)
Posted 22 Mar 2020 by Ivailo Bonev
Post:
Here we go, my first unit for COVID-19 related research!







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