Posts by Dr Who Fan

1) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 102728)
Posted 19 Sep 2021 by Dr Who Fan
Post:
How can I make it stop? I have been a long time supporter of RH, but will disconnect from the project if it keeps wasting my bandwidth with 2GB failed downloads.

Temporarily STOP REQUESTING NEW WORK FOR THE PROJET by settling NO NEW WORK for Rosetta on your PC(S) in BOINC until the project fixes the problem.
2) Message boards : Number crunching : Rosetta needs 6675.72 MB RAM: is the restriction really needed? (Message 101172)
Posted 8 Apr 2021 by Dr Who Fan
Post:
Got the same message at the RALPH project site on one of my PC's about 1 hour ago. Did not see any active task sent there.
3) Message boards : Cafe Rosetta : Pfizer says COVID-19 vaccine over 90% effective (Message 99625)
Posted 9 Nov 2020 by Dr Who Fan
Post:
'Great day for humanity': Pfizer says COVID-19 vaccine over 90% effective
4) Message boards : Cafe Rosetta : Nobel Prize in chemistry goes to pioneers of the CRISPR gene-editing tool (Message 99317)
Posted 11 Oct 2020 by Dr Who Fan
Post:
It's in their DNA: Nobel Prize in chemistry goes to pioneers of the CRISPR gene-editing tool
Emmanuelle Charpentier, Jennifer Doudna will split $1m+ winnings

Two biochemistry professors who led the groundbreaking development of CRISPR, the controversial "genetic scissors" DNA-editing tool, have been awarded the Nobel Prize in chemistry.

“There is enormous power in this genetic tool, which affects us all. It has not only revolutionised basic science, but also resulted in innovative crops and will lead to ground-breaking new medical treatments,” said Claes Gustafsson, chair of the Nobel Committee for Chemistry, on Wednesday.
5) Message boards : Cafe Rosetta : Covid-19 (Message 98318)
Posted 25 Jul 2020 by Dr Who Fan
Post:
Possible ‘Breakthrough’ Coronavirus Treatment With Natural Protein Cuts Risk of Death and Serious Symptoms by 79%

An aerosol-based protein inhalant has been shown in trials to reduce the risk of death from SARS-CoV-2 and reduce the chance of developing serious symptoms by 79% compared to patients given a placebo.

Results also showed that patients were more than twice as likely to make a full recovery from Covid-19, meaning they had no lasting respiratory weakness or other damages.
6) Message boards : Cafe Rosetta : Covid-19 (Message 98097)
Posted 15 Jul 2020 by Dr Who Fan
Post:
First COVID-19 vaccine tested in US poised for final testing
The first COVID-19 vaccine tested in the U.S. revved up people’s immune systems just the way scientists had hoped, researchers reported Tuesday -- as the shots are poised to begin key final testing.

... The experimental vaccine, developed by Fauci’s colleagues at the National Institutes of Health and Moderna Inc., will start its most important step around July 27: A 30,000-person study to prove if the shots really are strong enough to protect against the coronavirus.
7) Message boards : Cafe Rosetta : Covid-19 (Message 98021)
Posted 11 Jul 2020 by Dr Who Fan
Post:
A new coronavirus mutation is taking over the world. Here's what that means.
... A new paper, published July 2 in the journal Cell, argues that the rise in the "G" variation of the new coronavirus is due to natural selection. The study finds that virus particles with this mutation have an easier time making their way into cells, suggesting that it is outcompeting other strains of the virus to become the dominant version of SARS-CoV-2.
8) Message boards : Cafe Rosetta : Covid-19 (Message 97999)
Posted 10 Jul 2020 by Dr Who Fan
Post:
To understand COVID’s spread in Dallas-Fort Worth, 45,000 will be tested in study

Read more here: https://www.star-telegram.com/news/coronavirus/article244048537.html?

To better understand the novel coronavirus’ prevalence among racial groups and occupations, approximately 45,000 Dallas-Fort Worth residents will be tested as part of a study from UT Southwestern Medical Center and Texas Health Resources.
9) Message boards : Cafe Rosetta : Covid-19 (Message 97556)
Posted 24 Jun 2020 by Dr Who Fan
Post:
Bald men might be at greater risk of dying from COVID-19, studies say. Here’s why:
International researchers studying global data on COVID-19 patients have found that in general, the more male hormones called androgens someone has, the easier it is for SARS-CoV-2 to enter and take over their immune systems.

And bald men have more of these hormones than men with full manes, and women.
10) Message boards : Number crunching : Rosetta 4.1+ and 4.2+ (Message 96685)
Posted 21 May 2020 by Dr Who Fan
Post:
Name: Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_2nv3om7g_929581_20_0
Task 1184606782
Application version Rosetta v4.20 arm-android-linux-gnu

Stderr output
<core_client_version>7.16.3</core_client_version>
<![CDATA[
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_arm-android-linux-gnu -run:protocol jd2_scripting -parser:protocol jhr_boinc_v4_cart.xml @flags -in:file:silent Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_2nv3om7g.silent -in:file:silent_struct_type binary -silent_gz -mute all -silent_read_through_errors true -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_2nv3om7g.zip @Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_2nv3om7g.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 2832607
Using database: database_357d5d93529_n_methyl/minirosetta_database
Too many restarts with no progress. Keep application in memory while preempted.
======================================================
DONE :: 1 starting structures 8991.99 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
BOINC :: WS_max 0
called boinc_finish(0)

</stderr_txt>
<message>
upload failure: <file_xfer_error>
<file_name>Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_2nv3om7g_929581_20_0_r1500706928_0</file_name>
<error_code>-161 (not found)</error_code>
</file_xfer_error>

</message>
]]>
11) Message boards : Cafe Rosetta : Security warning: State-backed hackers are trying to steal coronavirus research (Message 96618)
Posted 18 May 2020 by Dr Who Fan
Post:
Security warning: State-backed hackers are trying to steal coronavirus research

Joint warning from UK National Cyber Security Centre and US Department of Homeland Security warns that cyberattackers are actively targeting healthcare with a variety of hacking tricks.

Advanced Persistent Threat (APT) groups – sophisticated hacking groups generally linked to a nation-state – are looking to get hold of information about national COVID-19 responses, healthcare research or other sensitive data related to coronavirus, and are targeting organisations in sectors including healthcare, pharmaceuticals, academia, medical research and local government, says the joint advisory.
12) Message boards : News : Switch to using SSL (Secure Socket Layer) (Message 95777)
Posted 2 May 2020 by Dr Who Fan
Post:
is there a MIN version of BOINC that this will work on?? I'm using 6.12.34 and when I try to attach I get

5/1/2020 11:12:56 PM | | Fetching configuration file from https://boinc.bakerlab.org/rosetta/get_project_config.php
5/1/2020 11:12:58 PM | | Project communication failed: attempting access to reference site
5/1/2020 11:13:00 PM | | Internet access OK - project servers may be temporarily down.


or is something else going on??

Ed F

You are using a VERY OLD VERSION of BOINC and has an EXPIRED SECURITY CERTIFICATE..

To fix , DOWNLOAD AND INSTALL LATEST Windows x64 VERSION of BOINC 7.16.5 from https://boinc.berkeley.edu/dl/boinc_7.16.5_windows_x86_64.exe

NOTE: Your Linux host has the most recent recommenced version and does not need updating at this time.
13) Message boards : Number crunching : Rosetta 4.1+ and 4.2+ (Message 95216)
Posted 23 Apr 2020 by Dr Who Fan
Post:
https://boinc.bakerlab.org/rosetta/result.php?resultid=1157960758

Name 0yx8rt2q_24HGBAB0HM2HGABB24H_build_COVID-19_binder_build1_SAVE_ALL_OUT_924149_47_0
Application version Rosetta v4.15 arm-android-linux-gnu
Peak working set size 688.89 MB
Peak swap size 972.25 MB
Peak disk usage 1,098.00 MB

Stderr output

<core_client_version>7.16.3</core_client_version>
<![CDATA[
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.15_arm-android-linux-gnu -run:protocol jd2_scripting -parser:protocol design_2019CoV_boinc.xml @bp_cov_flags_24HGBAB0HM2HGABB24H -in:file:silent 0yx8rt2q_24HGBAB0HM2HGABB24H_build_COVID-19_binder_test1.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 0yx8rt2q_24HGBAB0HM2HGABB24H_build_COVID-19_binder_test1.zip @0yx8rt2q_24HGBAB0HM2HGABB24H_build_COVID-19_binder_test1.flags -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 5000 -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 3029927
Too many restarts with no progress. Keep application in memory while preempted.
======================================================
DONE :: 462 starting structures 13803.8 cpu seconds
This process generated 462 decoys from 462 attempts
======================================================
BOINC :: WS_max 0
called boinc_finish(0)

</stderr_txt>
]]>
14) Message boards : Number crunching : Stalled downloads (Message 92137)
Posted 22 Mar 2020 by Dr Who Fan
Post:
I'm fairly sure I saw a "new server version" message a short while ago - might be significant if multiple projects are showing this symptom.

<edit>
Just seen another stuck download. Oddly, the files that I see "stuck" always seem to be really small... makes me wonder if some buffer is not being filled and an end point is either missing or not seen. Anyone seeing BIG files stuck?
</edit>

So far, have not seen any BIG files stuck - only small files and ONLY "zip" extensions,

The stuck file never does download for me.
I can go about 3 or 4 days then get a new stuck file with similar name and have to kill the TASK to clear the stuck file.
If I kill the stuck FILE the task never gets removed from task list on PC.
15) Message boards : News : Rosetta's role in fighting coronavirus (Message 91996)
Posted 15 Mar 2020 by Dr Who Fan
Post:
Don't request tasks for NVIDIA GPU
Project has no apps for NVIDIA GPU

Is this CPU only?

PROJECT IS CPU ONLY
16) Message boards : Number crunching : Stalled downloads (Message 91975)
Posted 14 Mar 2020 by Dr Who Fan
Post:
It is obviously a SERVER issue.

Does not matter what operating system your computer runs.

I have had downloads stalled on Windows Vista, 7 and 8.1.
17) Message boards : Number crunching : File transfers. (Message 91972)
Posted 14 Mar 2020 by Dr Who Fan
Post:
This thread/ topic is duplicate to Message boards : Number crunching : Stalled downloads
Let's not make multiple topics on SAME issue!
18) Message boards : Number crunching : Stalled downloads (Message 91971)
Posted 14 Mar 2020 by Dr Who Fan
Post:
.... saw that after killing the stuck downloads, BOINC did not imediately try for another. .

I found out that you can't kill the stuck file(s) - you have to kill the task(s) that is that is stuck downloading - otherwise nothing gets downloaded from the project that has one or more files erroring on download.

Last I saw was a post from Mod.Sense 3+ days ago here saying:
I've sent an EMail to David Kim and asked that he look in to it, pointing out that the hung downloads are preventing machines from getting work so they can resume processing
.
19) Message boards : Number crunching : Stalled downloads (Message 91915)
Posted 10 Mar 2020 by Dr Who Fan
Post:
The stalled downloads are back.
File name rb_03_08_17831_17664_ab_t000__h002_robetta.zip

Rosetta@home	rb_03_08_17831_17664_ab_t000__h002_robetta.zip	62.399	1.93 K	00:31:10 - 12:23:13	0.00 Kbps	Download pending (Retry in: 02:47:54), retried: 10


10-Mar-2020 07:32:01 [Rosetta@home] [http] HTTP_OP::init_get(): http://boinc.bakerlab.org/rosetta/download/1cb/rb_03_08_17831_17664_ab_t000__h002_robetta.zip
10-Mar-2020 07:32:01 [Rosetta@home] [http] HTTP_OP::libcurl_exec(): ca-bundle 'C:BOINCca-bundle.crt'
10-Mar-2020 07:32:01 [Rosetta@home] [http] HTTP_OP::libcurl_exec(): ca-bundle set
10-Mar-2020 07:32:01 [Rosetta@home] Started download of rb_03_08_17831_17664_ab_t000__h002_robetta.zip
10-Mar-2020 07:32:02 [Rosetta@home] [http] [ID#44082] Info: Connection 7018 seems to be dead!
10-Mar-2020 07:32:02 [Rosetta@home] [http] [ID#44082] Info: Closing connection 7018
10-Mar-2020 07:32:02 [Rosetta@home] [http] [ID#44082] Info: Trying 128.95.160.156...
10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Info: Connected to boinc.bakerlab.org (128.95.160.156) port 80 (#7019)
10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Sent header to server: GET /rosetta/download/1cb/rb_03_08_17831_17664_ab_t000__h002_robetta.zip HTTP/1.1

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Sent header to server: Host: boinc.bakerlab.org

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Sent header to server: User-Agent: BOINC client (windows_x86_64 7.16.3)

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Sent header to server: Accept: */*

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Sent header to server: Accept-Encoding: deflate, gzip

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Sent header to server: Accept-Language: en_US

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Sent header to server:

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Sent header to server: alSign0Y0*†HÎ=*†HÎ=B
10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Received header from server: HTTP/1.1 200 OK

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Received header from server: Date: Tue, 10 Mar 2020 12:32:06 GMT

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Received header from server: Server: Apache/2.4.18

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Received header from server: Last-Modified: Mon, 09 Mar 2020 02:03:43 GMT

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Received header from server: ETag: "7b8-5a06269a96f3a"

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Received header from server: Accept-Ranges: bytes

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Received header from server: Content-Length: 1976

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Received header from server: Content-Type: application/zip

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Received header from server:

10-Mar-2020 07:32:03 [Rosetta@home] [http] [ID#44082] Received header from server: PK
10-Mar-2020 07:35:08 [Rosetta@home] [http] [ID#44082] Info: Operation too slow. Less than 10 bytes/sec transferred the last 180 seconds
10-Mar-2020 07:35:08 [Rosetta@home] [http] [ID#44082] Info: Closing connection 7019
10-Mar-2020 07:35:08 [Rosetta@home] [http] HTTP error: Timeout was reached
10-Mar-2020 07:35:08 [Rosetta@home] Temporarily failed download of rb_03_08_17831_17664_ab_t000__h002_robetta.zip: transient HTTP error
10-Mar-2020 07:35:08 [Rosetta@home] Backing off 03:06:46 on download of rb_03_08_17831_17664_ab_t000__h002_robetta.zip
20) Message boards : Number crunching : How to get only Rosetta mini ? (Message 91598)
Posted 23 Jan 2020 by Dr Who Fan
Post:
In all the years I have run this project (since May 2006) there NEVER has been any option to select what type of task you want to run.

You can look for yourself... the project preferences page in your Rosetta home page does not have any specific types of tasks to run selection options.
That is where you would find it if there was any way to select specific types of tasks to run options.


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