Rosetta 4.1+ and 4.2+

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Meerb

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Message 93238 - Posted: 3 Apr 2020, 15:57:08 UTC

I have 3 computers running Darwin 19.4.0 (macOS 10.15.4) and BOINC 7.14.4 with Rosetta 4.12. Two of three computers are running WU's just fine and contain 7th gen and 9th generation Intel CPUs, but the computer with the 4th gen CPU seems to be consistently encountering computation errors less than 60 seconds after the start of run, like many other have reported. I am seeing the same issue with two other computers containing a 2nd gen and two 4th gen Intel CPUs. The crash report seems to indicate that there is an illegal instruction, with exception type: EXC_BAD_INSTRUCTION (SIGILL).

Crash Log Excerpt:
Process: rosetta_4.12_x86_64-apple-darwin [78172]
Path: /Library/Application Support/BOINC Data/*/rosetta_4.12_x86_64-apple-darwin
Identifier: rosetta_4.12_x86_64-apple-darwin
Version: 0
Code Type: X86-64 (Native)
Parent Process: ??? [70780]
Responsible: BOINCManager [70776]
User ID: 505

Date/Time: 2020-04-02 18:27:51.869 -0500
OS Version: Mac OS X 10.15.4 (19E266)
Report Version: 12
Anonymous UUID:


Time Awake Since Boot: 4000 seconds

System Integrity Protection: enabled

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_INSTRUCTION (SIGILL)
Exception Codes: 0x0000000000000001, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY

Termination Signal: Illegal instruction: 4
Termination Reason: Namespace SIGNAL, Code 0x4
Terminating Process: rosetta_4.12_x86_64-apple-darwin [78172]

Application Specific Information:
dyld2 mode
abort() called
rosetta_4.12_x86_64-apple-darwin(78172,0x119c54dc0) malloc: *** error for object 0x116998000: pointer being freed was not allocated
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RT

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Message 93245 - Posted: 3 Apr 2020, 16:31:25 UTC - in response to Message 93238.  
Last modified: 3 Apr 2020, 16:33:04 UTC

Looking at the issue, it appears the client thinks the zip files for the work units are corrupt? Nearly all tasks that have failed so far have the same error: zip file probably corrupt (illegal instruction)

<core_client_version>7.14.2</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 jhr_boinc.xml @flags -in:file:silent 3ho6nx2y_jhr_design1_COVID-19.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 3ho6nx2y_jhr_design1_COVID-19.zip -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 -constant_seed -jran 3644681
Starting watchdog...
Watchdog active.
error: zipfile probably corrupt (illegal instruction)

</stderr_txt>
]]>
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Message 93251 - Posted: 3 Apr 2020, 17:02:03 UTC

same here on older iMac with c2d cpu. Rosetta 4.12
all my tasks fail due to computation error second after it starts



Application
Rosetta 4.12 
Name
hugh2020_HHH_rd4_0628_E18W_fragments_abinitio_SAVE_ALL_OUT_905068_626
State
Computation error
Received
Friday, 03 April 2020 at 18:55:40
Report deadline
Monday, 06 April 2020 at 18:55:40
Estimated computation size
80,000 GFLOPs
CPU time
---
Elapsed time
00:00:02
Executable
rosetta_4.12_x86_64-apple-darwin



Fri  3 Apr 18:59:24 2020 | Rosetta@home | Started download of hugh2020_HHH_rd4_0628_K6F_fragments_fold_data.zip
Fri  3 Apr 18:59:27 2020 | Rosetta@home | Finished download of hugh2020_HHH_rd4_0628_K6F_fragments_fold_data.zip
Fri  3 Apr 18:59:30 2020 | Rosetta@home | Starting task hugh2020_HHH_rd4_0628_K6F_fragments_abinitio_SAVE_ALL_OUT_905059_813_1
Fri  3 Apr 18:59:31 2020 | Rosetta@home | Computation for task hugh2020_HHH_rd4_0628_K6F_fragments_abinitio_SAVE_ALL_OUT_905059_813_1 finished
Fri  3 Apr 18:59:31 2020 | Rosetta@home | Output file hugh2020_HHH_rd4_0628_K6F_fragments_abinitio_SAVE_ALL_OUT_905059_813_1_r987270243_0 for task hugh2020_HHH_rd4_0628_K6F_fragments_abinitio_SAVE_ALL_OUT_905059_813_1 absent
Fri  3 Apr 19:00:39 2020 | Rosetta@home | Sending scheduler request: To fetch work.
Fri  3 Apr 19:00:39 2020 | Rosetta@home | Reporting 1 completed tasks
Fri  3 Apr 19:00:39 2020 | Rosetta@home | Requesting new tasks for CPU
Fri  3 Apr 19:00:40 2020 | Rosetta@home | Scheduler request completed: got 0 new tasks
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Message 93257 - Posted: 3 Apr 2020, 18:12:05 UTC
Last modified: 3 Apr 2020, 18:25:16 UTC

So after someone mentioned that they had 4.12 tasks running fine on a more recent MacOS machine, I did a fresh install (BOINC 7.14.4) on the most recent iMac I have access to, a 2017 iMac 5K running a i7 7700K Kaby Lake chip @ 4.2GHz. 32GB ram, latest Catalina OS X build. It is running Rosetta 4.12 tasks just fine (at least fine for the last 45 minutes or so).

So there's something about older CPU's running OS X that the new Rosetta 4.12 doesn't seem to like.
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Message 93258 - Posted: 3 Apr 2020, 18:17:25 UTC

Version 4.12 seem under Ubuntu 18.04 faulty, first i wonder about 12 hours runtime instead of 8 hours, then i see only 20 Credits for the work.

looking in the Stderr output shows

Stderr Ausgabe

<core_client_version>7.9.3</core_client_version>
<![CDATA[
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.12_i686-pc-linux-gnu -run:protocol jd2_scripting -parser:protocol predictor_v11_boinc--fuse--covid_spike_design_boinc_v1.xml @flags_jhr_cv -in:file:silent 9au6ic2s_Junior_HalfRoid_vs_COVID-19_design1_dev.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 9au6ic2s_Junior_HalfRoid_vs_COVID-19_design1_dev.zip @9au6ic2s_Junior_HalfRoid_vs_COVID-19_design1_dev.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.
BOINC:: CPU time: 43777.2s, 14400s + 28800s[2020- 4- 3 11:11:53:] :: BOINC
WARNING! cannot get file size for default.out.gz: could not open file.
Output exists: default.out.gz Size: -1
InternalDecoyCount: 0 (GZ)
-----
0
-----
Stream information inconsistent.
Writing W_0000001
======================================================
DONE :: 1 starting structures 43777.2 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
11:11:53 (4726): called boinc_finish(0)

</stderr_txt>
]]>

Only 1 structure calculated in 12 hours, the Windows CPU Pendant shows over 70 structures in 8 hours.
It seem that the Linux App doesnt really calculate.
All 12 Results show this behaviour.
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Sid Celery

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Message 93273 - Posted: 3 Apr 2020, 19:31:00 UTC - in response to Message 93258.  

BOINC:: CPU time: 43777.2s, 14400s + 28800s[2020- 4- 3 11:11:53:] :: BOINC
WARNING! cannot get file size for default.out.gz: could not open file.
Output exists: default.out.gz Size: -1
InternalDecoyCount: 0 (GZ)
-----
0
-----
Stream information inconsistent.
Writing W_0000001
======================================================
DONE :: 1 starting structures 43777.2 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
11:11:53 (4726): called boinc_finish(0)

Only 1 structure calculated in 12 hours, the Windows CPU Pendant shows over 70 structures in 8 hours.
It seem that the Linux App doesnt really calculate.
All 12 Results show this behaviour.

Streaming information inconsistent, but this time on an 8hr task +4hrs for the watchdog to cut in and the 1st decoy still isn't complete :(
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Message 93277 - Posted: 3 Apr 2020, 19:48:16 UTC - in response to Message 93055.  

I received 9 tasks on rosetta 4.12 a few hours ago. They seem to use a lot of RAM compared to the older tasks (over 1.5 GB after 15 minutes of working on them).
After a while I noticed one of the task was 'Waiting to run", probably due to the fact that all my RAM was used. And then all tasks started getting this error:
2/4/2020 13:04:58 | Rosetta@home | Task rb_04_01_20072_19955__t000__2_C1_SAVE_ALL_OUT_IGNORE_THE_REST_904939_93_0 exited with zero status but no 'finished' file
2/4/2020 13:04:58 | Rosetta@home | If this happens repeatedly you may need to reset the project.
Now I'm resetting the project hoping this doesn't happen again when I get new tasks.

EDIT:
I done a reset and now I'm getting new errors besides the previous one:
2/4/2020 15:06:19 | Rosetta@home | Output file rb_04_02_17128_19982_ab_t000__h001_robetta_IGNORE_THE_REST_04_13_904952_11_0_r1478835244_0 for task rb_04_02_17128_19982_ab_t000__h001_robetta_IGNORE_THE_REST_04_13_904952_11_0 absent

Any idea what's the problem or how can I stop getting 4.12 tasks? If I can't run them on my system I want at least to stop receiving them so someone else can complete them.

I'm not sure you can shut down only the 4.12 tasks.

You may find it more useful to tell BOINC to run fewer tasks at once, so it will have more memory available for each of them.
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Message 93279 - Posted: 3 Apr 2020, 20:02:01 UTC - in response to Message 93154.  
Last modified: 3 Apr 2020, 20:02:56 UTC

Hey I'm having issues with R@h. For some reason, I am not receiving any tasks from R@h. I've updated it multiple times, and still no tasks. My friend next to me, who is also Running R@H, is saying he's getting tasks. So I don't know what I should do to start receiving tasks. Is there a way for me to fix this?
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Message 93280 - Posted: 3 Apr 2020, 20:08:47 UTC - in response to Message 93279.  

Hey I'm having issues with R@h. For some reason, I am not receiving any tasks from R@h. I've updated it multiple times, and still no tasks. My friend next to me, who is also Running R@H, is saying he's getting tasks. So I don't know what I should do to start receiving tasks. Is there a way for me to fix this?


Scroll to the bottom of the server status page and look at the "Tasks by application". ( https://boinc.bakerlab.org/rosetta/server_status.php ) Then note the number of tasks available to send. If it says 0, then there's no work to send out. The status page isn't the fastest to update, but should give you a rough idea of what's available. Occasionally tasks time out and get sent back, so people occasionally are getting some random tasks here or there, but currently (as of me writing this) there aren't any in the queue to send out so until they dump a big load of work into the pipeline we are waiting.

Leave it running, it will grab something eventually.
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Meerb

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Message 93283 - Posted: 3 Apr 2020, 21:03:16 UTC - in response to Message 93277.  

I was poking around a bit more and chatting with others on our team, and discovered something after reading Aurum's post to this morning's COVID-19 update (https://boinc.bakerlab.org/rosetta/forum_thread.php?id=13702&postid=93202#93202). He mentioned something about the misuse of the L3 cache that was causing issues he was noticing on Xeon E5's (didn't specify which architecture, and the computers are hidden). I looked at the 2nd, 4th, 7th and 9th gen Intel processors we have on our project, and found that the 2nd and 4th gen both have 3MB of L3 cache, and the 7th and 9th gen Intel processors have 4MB of L3 cache per each two physical cores (4 MB for the 7th gen core i5, and a 12MB SmartCache for the 9th gen core i7). Maybe it's coincidence; but I find it curious. Hope this helps someone track down what's going on. Cheers!
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Message 93289 - Posted: 3 Apr 2020, 21:47:50 UTC - in response to Message 93283.  

I was poking around a bit more and chatting with others on our team, and discovered something after reading Aurum's post to this morning's COVID-19 update (https://boinc.bakerlab.org/rosetta/forum_thread.php?id=13702&postid=93202#93202). He mentioned something about the misuse of the L3 cache that was causing issues he was noticing on Xeon E5's (didn't specify which architecture, and the computers are hidden). I looked at the 2nd, 4th, 7th and 9th gen Intel processors we have on our project, and found that the 2nd and 4th gen both have 3MB of L3 cache, and the 7th and 9th gen Intel processors have 4MB of L3 cache per each two physical cores (4 MB for the 7th gen core i5, and a 12MB SmartCache for the 9th gen core i7). Maybe it's coincidence; but I find it curious. Hope this helps someone track down what's going on. Cheers!

I've been seeing this in several threads recently. This is a response we got at WCG from the MIP project developers 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!"
[/code]
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Message 93297 - Posted: 3 Apr 2020, 22:09:14 UTC - in response to Message 93283.  
Last modified: 3 Apr 2020, 22:10:01 UTC

I was poking around a bit more and chatting with others on our team, and discovered something after reading Aurum's post to this morning's COVID-19 update (https://boinc.bakerlab.org/rosetta/forum_thread.php?id=13702&postid=93202#93202). He mentioned something about the misuse of the L3 cache that was causing issues he was noticing on Xeon E5's (didn't specify which architecture, and the computers are hidden). I looked at the 2nd, 4th, 7th and 9th gen Intel processors we have on our project, and found that the 2nd and 4th gen both have 3MB of L3 cache, and the 7th and 9th gen Intel processors have 4MB of L3 cache per each two physical cores (4 MB for the 7th gen core i5, and a 12MB SmartCache for the 9th gen core i7). Maybe it's coincidence; but I find it curious. Hope this helps someone track down what's going on. Cheers!


Just to tie into this, I managed to test on my 2015 iMac (8 core 4GHz Core i7, 6700K Skylake based 8MB L3) and it's now running 4.12 tasks. Any machine running OSX that's pre-Skylake seems to crash on 4.12 tasks, including several Xeon MacPro's. Oddly my lone Window's box is running 4.12 fine with the same XEON processor family my MacPro has, so it's a OS code bug.
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Message 93356 - Posted: 4 Apr 2020, 8:02:10 UTC - in response to Message 93297.  
Last modified: 4 Apr 2020, 8:05:04 UTC

I was poking around a bit more and chatting with others on our team, and discovered something after reading Aurum's post to this morning's COVID-19 update (https://boinc.bakerlab.org/rosetta/forum_thread.php?id=13702&postid=93202#93202). He mentioned something about the misuse of the L3 cache that was causing issues he was noticing on Xeon E5's (didn't specify which architecture, and the computers are hidden). I looked at the 2nd, 4th, 7th and 9th gen Intel processors we have on our project, and found that the 2nd and 4th gen both have 3MB of L3 cache, and the 7th and 9th gen Intel processors have 4MB of L3 cache per each two physical cores (4 MB for the 7th gen core i5, and a 12MB SmartCache for the 9th gen core i7). Maybe it's coincidence; but I find it curious. Hope this helps someone track down what's going on. Cheers!


Just to tie into this, I managed to test on my 2015 iMac (8 core 4GHz Core i7, 6700K Skylake based 8MB L3) and it's now running 4.12 tasks. Any machine running OSX that's pre-Skylake seems to crash on 4.12 tasks, including several Xeon MacPro's. Oddly my lone Window's box is running 4.12 fine with the same XEON processor family my MacPro has, so it's a OS code bug.


That is interesting to hear, I've tested two 4.12 tasks on my early 2015 Macbook Pro equipped with a 14 nm "Broadwell" CPU welding 2 cores and 4 threads clocked at 2.9GHz (got the 512GB/8GB variant, I believe the CPU is an i5-5257U, which has 3MB of cache) and they ran fine, netting slightly over 1000 credits/day per core. I am running MacOS Catalina, however. Which version of MacOS/OSX are you using? If it is an OS bug it might have been fixed in the latest MacOS releases.
That being said, I only run one BOINC task at a time to prevent overheating.
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Message 93363 - Posted: 4 Apr 2020, 10:05:42 UTC - in response to Message 93356.  
Last modified: 4 Apr 2020, 10:10:34 UTC

To prevent overheating, it is much more productive on such a cooling constrained system to run on all cores, but sleep often. For the same fan RPM, you could produce at least twice the amount of RAC this way. This is caused by: turbo boost increasing voltage if running a single core, causing square thermal output and also package power saving not kicking in if a core is constantly active. Somehow BOIC's runtime % preference isn't as power efficient, so I simply set everything to 100% and run something like this: (but with temperature control, deprivileged user, logging and whatnot)

sudo su
while true; do
killall -em -CONT apple-darwin
sleep 0.5
killall -em -STOP apple-darwin
sleep 0.5 # adjust this
done


Feel free to adjust the sleep to fit your fan RPM target (don't increase the one after CONT to help dissipate heat).

Although for the sake of responsiveness, you may still opt to only use 50% of the cores (threads) or to suspend while the computer is active. I found the "suspend when other processes use the CPU" to be not operable on OS X.
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Message 93364 - Posted: 4 Apr 2020, 11:24:48 UTC

No 4.12 WU works on my Linux Ubuntu System all got the same problem:

Stderr Ausgabe

<core_client_version>7.9.3</core_client_version>
<![CDATA[
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.12_i686-pc-linux-gnu -run:protocol jd2_scripting -parser:protocol predictor_v11_boinc--fuse--covid_spike_design_boinc_v1.xml @flags_jhr_cv -in:file:silent 6cp3nh2c_Junior_HalfRoid_vs_COVID-19_design1_dev.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 6cp3nh2c_Junior_HalfRoid_vs_COVID-19_design1_dev.zip @6cp3nh2c_Junior_HalfRoid_vs_COVID-19_design1_dev.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.
BOINC:: CPU time: 43776.6s, 14400s + 28800s[2020- 4- 4 11:33:34:] :: BOINC
WARNING! cannot get file size for default.out.gz: could not open file.
Output exists: default.out.gz Size: -1
InternalDecoyCount: 0 (GZ)
-----
0
-----
Stream information inconsistent.
Writing W_0000001
======================================================
DONE :: 1 starting structures 43776.6 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
11:33:34 (18264): called boinc_finish(0)

</stderr_txt>
]]>

I stopped all 4.12 WU's on the Linux system, waiting for a bugfix. Switches this machine to TN-Grid, They have also Workunits special for the Corona problem.
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Message 93401 - Posted: 4 Apr 2020, 18:31:07 UTC - in response to Message 93356.  

That is interesting to hear, I've tested two 4.12 tasks on my early 2015 Macbook Pro equipped with a 14 nm "Broadwell" CPU welding 2 cores and 4 threads clocked at 2.9GHz (got the 512GB/8GB variant, I believe the CPU is an i5-5257U, which has 3MB of cache) and they ran fine, netting slightly over 1000 credits/day per core. I am running MacOS Catalina, however. Which version of MacOS/OSX are you using? If it is an OS bug it might have been fixed in the latest MacOS releases.
That being said, I only run one BOINC task at a time to prevent overheating.

I should have phrased that better. The OS doesn't crash, the Rosetta 4.12 tasks all fail with a "Error while computing" seconds after being downloaded. If you take a peek at my account you will see I run a range of MacOS machines, mostly on Catalina but a few Mojave and High Sierras. The newest machines (2015 and later, both Catalina) run 4.12 tasks fine. Anything older then the 2015 Macs won't run 4.12 tasks regardless of OS. (2012 Mac mini running latest Catalina won't). So it's not a MacOS problem, it's just a coding issue in Rosetta for older CPU's running OS X. Hopefully a simple fix. All my machines pre-4.12 ran full load, 24/7 without issue.
That said, as I mentioned before my MacPro's run the same CPU family (Intel Xeon X5670, X5690, all circa 2012) as my lone Windows 10 machine (Xeon X5675), and the windows machine is happily crunching away on 4.12 tasks.
Tasks running on Rosetta pre-4.12 ran (and continue to run) fine on every single machine. Mini-Rosetta also continues to run to completion without error on all machines.
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Message 93512 - Posted: 5 Apr 2020, 16:26:03 UTC

Can people please join Ralph@home http://ralph.bakerlab.org/. I'm trying to test an updated build which may fix the OSX issue but there are not enough active participants. This application update includes some code related to COVID-19 that we'd like to push out to R@h.

Thanks
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Message 93519 - Posted: 5 Apr 2020, 17:09:18 UTC - in response to Message 93512.  

Can people please join Ralph@home http://ralph.bakerlab.org/. I'm trying to test an updated build which may fix the OSX issue but there are not enough active participants. This application update includes some code related to COVID-19 that we'd like to push out to R@h.

Thanks


I have done so.
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Message 93520 - Posted: 5 Apr 2020, 17:10:44 UTC - in response to Message 93512.  

Can people please join Ralph@home http://ralph.bakerlab.org/. I'm trying to test an updated build which may fix the OSX issue but there are not enough active participants. This application update includes some code related to COVID-19 that we'd like to push out to R@h.

Thanks


I'm registered for both, on all my devices - got 4 WUs crunching on my tablet right now.
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Message 93522 - Posted: 5 Apr 2020, 17:25:42 UTC - in response to Message 93512.  
Last modified: 5 Apr 2020, 18:04:15 UTC

Can people please join Ralph@home http://ralph.bakerlab.org/. I'm trying to test an updated build which may fix the OSX issue but there are not enough active participants. This application update includes some code related to COVID-19 that we'd like to push out to R@h.

Thanks

I've tried to sign up (New user, inside the boinc software using the URL you list above) and it won't let me join....

/edit OSX Catalina, i7, BOINC 7.14.4. When I try and sign up from both the BOINC software, and the website, it says my email is not formatted properly, must be <name>@domain.<xxx>. Which is weird as I'm typing my email in correctly and it's the same one I used for the normal Rosetta site/Project.

/edit2. Apparently it didn't like my VPN. I shut that off and it let me sign up fine.
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