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Yifan Song
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Message 67780 - Posted 21 Sep 2010 21:55:20 UTC

minirosetta is updated to add new protocols for symmetrical oligomers and membrane proteins.

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Message 67782 - Posted 21 Sep 2010 22:09:51 UTC

Here is some more information about Oligomers and Membrane proteins from Wikipedia for those who are interested. If I hang around these forums for another 20 years I might learn enough Biochemistry to consider a pre-retirement career change.
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Message 67789 - Posted 23 Sep 2010 5:09:25 UTC
Last modified: 23 Sep 2010 5:09:47 UTC

Even though the second attempt at this task ran fine, I'm reporting this compute error.

http://boinc.bakerlab.org/rosetta/result.php?resultid=366882461

<core_client_version>6.10.58</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>

|
|
|

ERROR: Option matching -docking:fake_native not found in command line top-level context
</stderr_txt>
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Message 67804 - Posted 24 Sep 2010 9:35:50 UTC

Does this version ignore the limit of 100 models per workunit?

I have a workunit which has reached 300 models and another has done 200. Both are only about 20% complete.
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Message 67810 - Posted 24 Sep 2010 13:36:37 UTC

The 100 model limit is only for certain protocols that are expected to complete models very rapidly. The main reason (to my knowledge anyway) for the imposition of that limit was due to large upload file sizes. Do you happen to know how large the uploads are getting? Size is shown in the transfers tab. But you'd have to catch one before it is sent (suspend network activity for a short time until one completes would be a simple way to orchestrate keeping one around).
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Message 67811 - Posted 24 Sep 2010 13:50:19 UTC
Last modified: 24 Sep 2010 13:50:43 UTC

Thanks for the response, Mod.Sense. My concern was that I had workunits which needed to be aborted.

I have some time yet before my first 2.15 task completes as I have selected a 10-hour run time option.

I'll try to catch the upload but may miss it.

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Message 67815 - Posted 24 Sep 2010 19:25:37 UTC

The upload is only 231KB, which is insignificant.

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Message 67817 - Posted 24 Sep 2010 22:23:38 UTC
Last modified: 24 Sep 2010 22:26:26 UTC

Today i had me first WU http://boinc.bakerlab.org/rosetta/workunit.php?wuid=333863670 with V2.15, i see 1,1GB memmory beeing used, is this normal? And if so, why does is say 512MB minimal memmory requirment on the site?

I have 4 GB machine but with 2 other WU form other projects that exceed 1GB memory requirments, i have to start watching these mmemory requirments to stil do normal work with the machine.
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Message 67820 - Posted 25 Sep 2010 6:22:27 UTC

1+ GB is not normal. I seldom monitor the memory being used by a task, but I've never seen this much memory being used before. I think it is particular to this type of task.
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Message 67825 - Posted 25 Sep 2010 20:41:44 UTC

I have this WU which uses about 900 MB of RAM, but cpu usage is down to 0%:
T0611_t4_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22276_368_0

Yesterday I had a WU with the exact same behaviour, eating lots of RAM, but no cpu use, so it must have crashed or something... Pausing and resuming does not fix the problem by the way.

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Message 67834 - Posted 26 Sep 2010 9:32:04 UTC

This one crashed yesterday after 40 minutes:
T0528_t4_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22246_78_0

When it crashed the memory consumption was 1.5 GB. The message says 'Directory not found'.


<message>
Das System kann den angegebenen Pfad nicht finden. (0x3) - exit code 3 (0x3)
</message>


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Message 67839 - Posted 27 Sep 2010 3:21:17 UTC

Yeah, I have one Rosetta processing using 1.5 Gb of RAM at 2.3% completion and another using 1.15 Gb of RAM at 16% completion. All together Rosetta is using 70% of my 8 gigs of RAM. Granted I have a 6-core processor and therefore 6 threads running, but still, that's a lot of RAM.

The biggest RAM hogs currently, are named T0523_t4_rs_stg0_lrlxjcst_t000_casp9_SAVE_ALL_OUT_22242_375_0 and
T0520_t4_rs_stg0_lrlxjcst_t000_casp9_SAVE_ALL_OUT_22239_376_0


I was away for the weekend. Looking back at my results I show over 20 results that ended as "Compute Error" since 2.15, most of which came Friday or after. Never had one Compute Error in any work unit before that.
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Message 67846 - Posted 27 Sep 2010 20:49:25 UTC

I also appear to be having problems with WU's starting with T05**. They end up using almost 1.3GB of RAM.

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Message 67847 - Posted 28 Sep 2010 0:59:42 UTC - in response to Message ID 67846.

I also appear to be having problems with WU's starting with T05**. They end up using almost 1.3GB of RAM.


I think i have a problem with the T0549_t4_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22255_997
he run since 21 hours and reach 0.099% when i look at the properties, the calculating time is only 25 second !!!

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Message 67849 - Posted 28 Sep 2010 11:01:35 UTC

T0605_t2_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22177_296_1
ERROR: Error in traceback: pointer doesn't go anywhere!

ERROR:: Exit from: ..\..\src\core\sequence\Aligner.cc line: 79
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

T0605_t2_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22177_1921_0
RROR: Error in traceback: pointer doesn't go anywhere!

ERROR:: Exit from: ..\..\src\core\sequence\Aligner.cc line: 79
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

T0528_tj_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_21880_4843_2
<core_client_version>6.10.58</core_client_version>
<![CDATA[
<message>
The system cannot find the path specified. (0x3) - exit code 3 (0x3)
</message>



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Message 67850 - Posted 28 Sep 2010 16:01:11 UTC - in response to Message ID 67847.


I think i have a problem with the T0549_t4_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22255_997
he run since 21 hours and reach 0.099% when i look at the properties, the calculating time is only 25 second !!!


Ademers, double check the status shown in BOINC for that task. Does BOINC say it is "running"? And does the task manager show some other, higher priority task consuming your available CPU?

But otherwise that sounds like another issue that we see crop up once and a while. Best way to move it along seems to be to exit (not close) and restart BOINC.
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Message 67853 - Posted 28 Sep 2010 20:09:28 UTC - in response to Message ID 67850.
Last modified: 28 Sep 2010 20:10:43 UTC


I think i have a problem with the T0549_t4_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22255_997
he run since 21 hours and reach 0.099% when i look at the properties, the calculating time is only 25 second !!!


Ademers, double check the status shown in BOINC for that task. Does BOINC say it is "running"? And does the task manager show some other, higher priority task consuming your available CPU?

But otherwise that sounds like another issue that we see crop up once and a while. Best way to move it along seems to be to exit (not close) and restart BOINC.


Good, I exit from BOINC and restart and the application is at 1.8% in 7 minutes and continue to go up !!!

Thank you Mod.Sense

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Message 67854 - Posted 28 Sep 2010 21:58:41 UTC

This one failed after 20sec.

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=336639766

T0524_t3_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22207_1756_0

<core_client_version>6.2.14</core_client_version>
<![CDATA[
<message>
process got signal 11
</message>
<stderr_txt>

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Message 67858 - Posted 29 Sep 2010 5:24:03 UTC
Last modified: 29 Sep 2010 5:26:47 UTC

I too am seeing an unusually high number of errors on 3 different machines (and 3 different operating systems) for Rosetta 2.15. 16 WU's in the last few days failed on various errors:

"The system cannot find the path specified. (0x3) - exit code 3 (0x3)"

"Reason: Access Violation (0xc0000005) at address 0x00581B5C write attempt to address 0x00000024"

"Incorrect function. (0x1) - exit code 1 (0x1)" (many different root causes per detailed error messages in the log. <ERROR: Error in traceback: pointer doesn't go anywhere!> occurred multiple times.)

"Reason: Out Of Memory (C++ Exception) (0xe06d7363) at address 0x759AB727"

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Message 67865 - Posted 29 Sep 2010 11:13:06 UTC

I am repeatedly getting this message since the upgrade:

"Microsoft Visual C++ Runtime Library

Runtime Error

....Bakerlab.org\minirosetta_2.15_windows_intelx86.exe

This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information."

It is difficult to remove the message which sometimes locks up the computer. What can be done to prevent this?

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Message 67872 - Posted 29 Sep 2010 11:52:39 UTC
Last modified: 29 Sep 2010 11:55:23 UTC

+1 to problems with "Txxxx_" tasks on minirosetta 2.15.
Some of them crash and others consume very higt amount of RAM (like 800-1400 Mb per task)
I think crashes was due to lack of memory too - when two such tasks run concurrently (have 2 Gb of RAM on 2 core CPU)

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Message 67881 - Posted 29 Sep 2010 22:42:47 UTC

I too have recently seen messages indicating shortage of virtual memory, so have suspended Rosetta.
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Message 67892 - Posted 1 Oct 2010 4:10:03 UTC

There are quite a few reports here on large memory usage with the latest jobs. Due to the ongoing post-CASP analysis, I think a lot of the jobs are for difficult targets, which means large proteins. And they tend to eat up more memory than normal jobs do. I'll double check with the people submitting these jobs.

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Message 67897 - Posted 1 Oct 2010 7:18:40 UTC

I also have been getting daily error messages about lack of virtual memory on all three computers i have running. One machine in particular really bogs down, until i shut off Rosetta.

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Message 67900 - Posted 1 Oct 2010 7:27:36 UTC

I had to stop Rosetta as well. My two working rigs (3.4 GB each) got unusable and even my gaming rig (12 GB) was having memory issues.
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Message 67915 - Posted 1 Oct 2010 14:31:05 UTC
Last modified: 1 Oct 2010 14:35:06 UTC

Greetings:

I knew something wasn't right when I saw my Rosetta screensaver wasn't displaying the normal graphic.

It showed only the blank chart form, with no activity, even though the displayed work unit numbers indicated that activity had, and was taking place.

I exited BOINC, and then reloaded it, figuring that might solve the problem.

Alas, now the Rosetta screensaver wouldn't display ANY graphic, not even the blank chart form.

So, I aborted Rosetta, and went to another project, which was operating normally.

Up popped an alert notice from the Norton anti-virus program, saying Rosetta had caused a HIGH security risk in my computer.

Here is what Norton detected and quarantined:

c:\documents and settings\all users\application data\boinc\projects\boinc.bakerlab.org_rosetta\minirosetta_2.15_windows_intelx86.exe

Note the reverse slashes.

Is that normal?

Norton did not specify if this HIGH security risk was a virus, worm, or trojan.

Norton did indicate the threat had been fully removed.

Thank you.
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John Robert Mallernee
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Message 67919 - Posted 1 Oct 2010 16:29:49 UTC

Looks like a false alarm. Symantec needs to fix this. There is no virus or any other malware in Rosetta's executable.

But I don't know, whether Rosetta restores the application automatically, once the servers are back online, or whether you have to reset the project.
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Message 67923 - Posted 1 Oct 2010 20:47:28 UTC - in response to Message ID 67919.

Looks like a false alarm. Symantec needs to fix this. There is no virus or any other malware in Rosetta's executable.

But I don't know, whether Rosetta restores the application automatically, once the servers are back online, or whether you have to reset the project.


Greetings:

I took another look at my Norton program's history details (I'm still learning how it works), and I noticed that it had done the same thing with another BOINC project I run, Climate Prediction, over and over and over again.

Norton repeatedly identified Climate Prediction work units as a "HIGH" security threat.

The Rosetta screensaver, which is what got my attention, usually runs as it should.

But, sometimes, the Rosetta screensaver appears either as a blank form graphic, with no activity, or it simply appears as a totally blank screen, without displaying even the blank form.

So, if the problem is a software conflict with Symantec, I don't know how that can be resolved.

I'm wondering if BOINC technicians can't investigate further and maybe coordinate something?

Thank you.

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Message 67927 - Posted 1 Oct 2010 22:35:19 UTC

One solution is to add Rosetta/Climateprediction to the exceptions, programs which will not be checked. That does require some faith, I suppose.
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Message 67929 - Posted 1 Oct 2010 23:55:05 UTC

The T0x series is having troubles.
Getting traceback errors and pointer errors.
T05 and T06 series.

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Message 67931 - Posted 2 Oct 2010 4:21:16 UTC

Further to my post of yesterday, on my gaming rig which is a dual core with 4GB of ram, Rosetta was running normally on one core, however, on the second it was not running. The annotation stated Rosetta was "waiting for memory". Definitely an issue with the 2.15 version i would say, if there is not enough memory on a 4GB machine.

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Message 67934 - Posted 2 Oct 2010 17:30:05 UTC

Agreed, something buggy with 2.15 They quickly rise to over 1.5 GB of memory use, at which point they are shut down and wait for memory to free up.
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Message 67935 - Posted 2 Oct 2010 18:25:15 UTC

I don't agree. It is not a problem with the application. The problem is a type of WU that needs more memory than your average WU. But since I'm only a cruncher here, I can't be any more certain than you are. :)
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Message 67936 - Posted 2 Oct 2010 18:40:40 UTC - in response to Message ID 67934.
Last modified: 2 Oct 2010 19:06:20 UTC

They quickly rise to over 1.5 GB of memory use, at which point they are shut down and wait for memory to free up.
If you haven't already done so, you should review the BOINC memory limits set up in Advanced->Preferences->Disk and Memory Usage. A 4GB machine could be adequate to (barely) run two 1.5GB WU's at once. On a 2GB machine, it might be impossible though.

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Message 67937 - Posted 3 Oct 2010 0:05:50 UTC - in response to Message ID 67935.

I don't agree. It is not a problem with the application. The problem is a type of WU that needs more memory than your average WU. But since I'm only a cruncher here, I can't be any more certain than you are. :)


As a guess I would say it is a mixture of both. The ones that are using the most memory seem to be reruns of the Casp9 targets. Those ones used up a lot of memory the first time round but didn't seem to get as high as 1.5GB.

It is probably a combination of high-memory targets and new memory-hungry code. Hopefully they can track down the second problem and implement some less hungry code in mini 2.16.
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Message 67939 - Posted 3 Oct 2010 13:37:40 UTC

Greetings:

Unfortunately, just like everyone else who's been posting recently, I'm starting to have similar difficulty with the new version of Rosetta.

I'm using a Toshiba Satellite notebook computer with nearly a hundred gigabytes of memory.

Yet, I just now woke up to see the Rosetta screensaver graphic displaying a blank form, and frozen in place.

An alert on my task bar indicated I was out of virtual memory.

Regretfully, I'm going to have to disconnect from the Rosetta project.

Thank you.
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John Robert Mallernee
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Message 67940 - Posted 3 Oct 2010 14:35:51 UTC

I think you should try tweaking your settings before giving up. I'm running on a dual core iMac with only 2 GB of memory installed, and I have had no memory problems at all, including with casp9 units. Every once in a while, I'll get the "Waiting for memory" message in the status column, but it clears up.

Maybe an idiotic suggestion, but if you shortened the runtime per unit, would it use less ram? If the ram usage gradually increases as the unit runs, perhaps this would work?

Also, I would think that running the graphic all the time increases the ram usage. Perhaps shutting off the graphic when memory issues crop up would do the trick.

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Message 67941 - Posted 3 Oct 2010 16:04:24 UTC - in response to Message ID 67940.

I think you should try tweaking your settings before giving up. I'm running on a dual core iMac with only 2 GB of memory installed, and I have had no memory problems at all, including with casp9 units. Every once in a while, I'll get the "Waiting for memory" message in the status column, but it clears up.

Maybe an idiotic suggestion, but if you shortened the runtime per unit, would it use less ram? If the ram usage gradually increases as the unit runs, perhaps this would work?

Also, I would think that running the graphic all the time increases the ram usage. Perhaps shutting off the graphic when memory issues crop up would do the trick.



Mr. Gould, Et Alii:

The problem with your suggestion is that you exhibit far more knowledge of computer technology than I do.

I'm unable to do what you suggest because I don't understand what you're suggesting.

I'm just an ordinary guy with only an amateur user's ability.

Everything I've learned so far about having a personal computer and using the Internet has been through trial and error "by guess and by gosh!" experimentation.

The really sad thing about all this is that it will have a negative effect on all other BOINC projects.

Up until now, I've been enthusiastically recommending BOINC participation in my e-mails and on my web site.

But, if people suspect problems with any one of the BOINC projects (including Rosetta), then they'll be reluctant to volunteer their personal computers for any scientific research.

I really do want to participate in the Rosetta project, but these technical problems need to be resolved, and any instructions have to be simple enough for an ordinary home computer user to easily comprehend.

Thank you.
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John Robert Mallernee
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Message 67942 - Posted 3 Oct 2010 17:34:24 UTC - in response to Message ID 67941.

I really do want to participate in the Rosetta project, but these technical problems need to be resolved (...)

That are not technical problems, just the information on the Recommended System Requirements Page is not up to date, at least with recent (and even not so recent) WUs in mind.

And that are the minimum system requirements, so system like that maybe still can run rosetta, but doing anything else on that machine gets quite impossible even without those 1GB+ tasks, I know that from my 768MB machine. IMO it's time to update that information and clearly distinguish between minimum and recomended system requirements.
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Message 67945 - Posted 3 Oct 2010 22:58:54 UTC - in response to Message ID 67941.

I think you should try tweaking your settings before giving up. I'm running on a dual core iMac with only 2 GB of memory installed, and I have had no memory problems at all, including with casp9 units. Every once in a while, I'll get the "Waiting for memory" message in the status column, but it clears up.

Maybe an idiotic suggestion, but if you shortened the runtime per unit, would it use less ram? If the ram usage gradually increases as the unit runs, perhaps this would work?

Also, I would think that running the graphic all the time increases the ram usage. Perhaps shutting off the graphic when memory issues crop up would do the trick.



Mr. Gould, Et Alii:

The problem with your suggestion is that you exhibit far more knowledge of computer technology than I do.

I'm unable to do what you suggest because I don't understand what you're suggesting.

I'm just an ordinary guy with only an amateur user's ability.

Everything I've learned so far about having a personal computer and using the Internet has been through trial and error "by guess and by gosh!" experimentation.

The really sad thing about all this is that it will have a negative effect on all other BOINC projects.

Up until now, I've been enthusiastically recommending BOINC participation in my e-mails and on my web site.

But, if people suspect problems with any one of the BOINC projects (including Rosetta), then they'll be reluctant to volunteer their personal computers for any scientific research.

I really do want to participate in the Rosetta project, but these technical problems need to be resolved, and any instructions have to be simple enough for an ordinary home computer user to easily comprehend.

Thank you.



What he is saying is there is a place in your account online here on the project to shorten your run times.

If you goto the top of the screen here and click on participants and then look at preferences and then goto Resource share and graphics section and next to this line you will see on the right in blue text: Rosetta@home preferences
and then modify these settings to like what I have:

Percentage of CPU time used for graphics not selected
Number of frames per second for graphics not selected
Target CPU run time 4 hours

I have no trouble handling 4 tasks with 3.2 GB of ram while running everything else I want on my computer.

Now in the Boinc manager you should click on the projects tab and then highlight via clicking the rosetta@home project and then click on the update tab on the left. This will download your new settings into the Boinc Manager program.

Give this a try and see what happens.

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Message 67948 - Posted 4 Oct 2010 2:02:53 UTC

This one had zero run time, and died.

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=333445194

Dengue9Sept2010_3c5x_2ckk_ProteinInterfaceDesign_9Sep2010_21855_129_2

<core_client_version>6.10.58</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
[2010-10- 4 12:43:18:] :: BOINC:: Initializing ... ok.
[2010-10- 4 12:43:18:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully.
Registering options..
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize() End reached
ERROR: Option matching -docking:fake_native not found in command line top-level context

</stderr_txt>
]]>

____________


amgthis

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Message 67956 - Posted 4 Oct 2010 16:43:08 UTC
Last modified: 4 Oct 2010 16:45:24 UTC

I have a quad core Q6700 with 4 gigs of RAM and I'm having the same problem reported here. With Windoze XP SP2 I'm getting constant 'nag' bubbles about low system memory. I check the usage under task manager and one instance is using over 1 gig of memory. The other 3 running WU's are looking more typical, using
right around ~300k each of RAM, plus or minus. The work unit that is sucking over a gig is this one:

task T0592_t4_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22268_1995_0

running under 2.15.

I have my preferences basically set to use any resources they can grab, which has always worked great up till now. Also, I never run the graphic screen saver. I leave my computer on 24/7 with no other restrictions on Rosetta, other
than the time it accesses my local LAN.
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Message 67957 - Posted 4 Oct 2010 18:07:41 UTC

Getting more of the ERROR: Error in traceback: pointer doesn't go anywhere!
in the T605xxxx tasks

My wingman is also getting the same issue.
Look at http://boinc.bakerlab.org/rosetta/workunit.php?wuid=335771275 and http://boinc.bakerlab.org/rosetta/workunit.php?wuid=335771175

JTKirk

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Message 67959 - Posted 5 Oct 2010 0:26:37 UTC - in response to Message ID 67865.

I am getting this error as well. Closing it doesn't help, it will reappear shortly. Anyone have any idea what is causing this?

I am repeatedly getting this message since the upgrade:

"Microsoft Visual C++ Runtime Library

Runtime Error

....Bakerlab.org\minirosetta_2.15_windows_intelx86.exe

This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information."

It is difficult to remove the message which sometimes locks up the computer. What can be done to prevent this?

Yifan Song
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Message 67961 - Posted 5 Oct 2010 3:28:17 UTC

After David Kim and TJ looked into this, we did find a problem with large memory usage with the 2.15 version. I'll do a revert first thing tomorrow. (Too tired to get it started now :p)

deesy58

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Message 67964 - Posted 5 Oct 2010 7:16:24 UTC - in response to Message ID 67939.

Greetings:

Unfortunately, just like everyone else who's been posting recently, I'm starting to have similar difficulty with the new version of Rosetta.

I'm using a Toshiba Satellite notebook computer with nearly a hundred gigabytes of memory.

Yet, I just now woke up to see the Rosetta screensaver graphic displaying a blank form, and frozen in place.

An alert on my task bar indicated I was out of virtual memory.

Regretfully, I'm going to have to disconnect from the Rosetta project.

Thank you.


I think you might have "nearly a hundred gigabytes" of hard disk space capacity, but I seriously doubt that you have that much RAM memory (Random Access Memory). Virtual memory is a combination of both types of memory, and a shortage of virtual memory is often an indication that your hard disk has become nearly full. How much disk space is available on your machine? To find out, open your "Computer" icon, then right click on "Local Disk (C:)" and select "Properties." This should tell you how much space is available on your hard disk. If you have insufficient space left, you can use the "Disk Cleanup" utility (carefully) to remove files that might no longer be needed. All of this assumes that you are using the Microsoft Windows Operating System, of course, and it appears that you are.

BTW, those "reverse slashes" you referred to in your original post are, indeed, normal in the Microsoft environment.

deesy

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Message 67966 - Posted 5 Oct 2010 10:11:25 UTC - in response to Message ID 67961.

After David Kim and TJ looked into this, we did find a problem with large memory usage with the 2.15 version. I'll do a revert first thing tomorrow. (Too tired to get it started now :p)



take a look at this thread when looking at the ram issues.

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Message 67975 - Posted 6 Oct 2010 1:27:58 UTC

This one failed after 15sec.

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=337685670

rb_10_04_377_958_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22344_973_1


Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/rb_10_04_377_958_rs_stg0_lrlxjcst_t000__casp9.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...

ERROR: Error in traceback: pointer doesn't go anywhere!

ERROR:: Exit from: src/core/sequence/Aligner.cc line: 79
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>

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Message 67988 - Posted 7 Oct 2010 23:22:01 UTC

Here is a whole batch of errors.
Pretty sure one of these errors caused a Windows BSOD.
Wingman also died on these tasks.
No fancy URL links, just raw data

T0605_t2_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22177_298_1
http://boinc.bakerlab.org/rosetta/result.php?resultid=367677827
Incorrect function. (0x1) - exit code 1 (0x1)
ERROR: Error in traceback: pointer doesn't go anywhere!
ERROR:: Exit from: ..\..\src\core\sequence\Aligner.cc line: 79
BOINC:: Error reading and gzipping output datafile: default.out


fix_disulf_v4_NMR_1eig_CONTROL__BOINC_abrelax.score12.fastrelax.v2_SAVE_ALL_OUT_22291_788_0
http://boinc.bakerlab.org/rosetta/result.php?resultid=367990336
Incorrect function. (0x1) - exit code 1 (0x1)
ERROR: rsd_type_list.size()
ERROR:: Exit from: ..\..\src\core\fragment\Frame.cc line: 62
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

fix_disulf_v4_NMR_1m12_CONTROL__BOINC_abrelax.score12.fastrelax.v2_SAVE_ALL_OUT_22291_788_0
http://boinc.bakerlab.org/rosetta/result.php?resultid=367990356
Incorrect function. (0x1) - exit code 1 (0x1)
ERROR: rsd_type_list.size()
ERROR:: Exit from: ..\..\src\core\fragment\Frame.cc line: 62
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


mem_abinitio_bench_run01_A_BRD7_SAVE_ALL_OUT_IGNORE_THE_REST_22294_290_1
http://boinc.bakerlab.org/rosetta/result.php?resultid=367990547
Incorrect function. (0x1) - exit code 1 (0x1)
ERROR: Cannot open PDB file "input_BRD7\BRD4.pdb"
ERROR:: Exit from: ..\..\src\core\io\pdb\pose_io.cc line: 182
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


fix_disulf_v4_NMR_1xu6_DISULF__BOINC_abrelax.score12.fastrelax.v2_SAVE_ALL_OUT_22292_695_1
http://boinc.bakerlab.org/rosetta/result.php?resultid=367990548
Incorrect function. (0x1) - exit code 1 (0x1)
ERROR: rsd_type_list.size()
ERROR:: Exit from: ..\..\src\core\fragment\Frame.cc line: 62
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


Ross2X3_SAVE_ALL_OUT_r006_010_22296_138_0
http://boinc.bakerlab.org/rosetta/result.php?resultid=368110199
- exit code -1073741819 (0xc0000005)
Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x004CF209 read attempt to address 0x20EEE6E5

Engaging BOINC Windows Runtime Debugger..

T0591_t3_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22223_1177_1
http://boinc.bakerlab.org/rosetta/result.php?resultid=368248774
The system cannot find the path specified. (0x3) - exit code 3 (0x3)
Couple of No heartbeat from client errors messages

That's a pretty big laundry list for 1 or 2 days.

Mad_Max

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Message 67996 - Posted 9 Oct 2010 2:29:06 UTC

A have few Runtime errors and crashes to destop from minirosetta_2.15_windows_intelx86.exe last days (never seen them before on previous versions of minirosetta, only "standart" errors) and even 1 BSOD too (I had forgotten BSODs since the transition from windows 98 to XP).

On this computer: http://boinc.bakerlab.org/rosetta/results.php?hostid=1252064
Not sure what concrete job caused a BSOD, there are a whole bundle of bads. Some of them with a runtime error, one with BSOD and a few were killed by BOINC for exceeding the limit of memory (after quickly after start grew up to ~ 1 GB)

Like this:
08/10/2010 23:58:52 rosetta@home Aborting task rs_stg0_lrlx_t363__run1_SAVE_ALL_OUT_19372_805_0: exceeded memory limit 1353.20MB > 1223.80MB
09/10/2010 05:51:57 rosetta@home Aborting task lr5_combined_torsion_it01_run01_A_rlbd_256b_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_18669_2770_1: exceeded memory limit 1291.75MB > 1223.80MB
09/10/2010 05:53:25 rosetta@home Aborting task rs_stg0_lrlx_t311__run1_SAVE_ALL_OUT_19356_6624_1: exceeded memory limit 1292.80MB > 1223.80MB
09/10/2010 05:55:04 rosetta@home Aborting task lr5_combined_torsion_it01_run01_A_rlbd_1eyv_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_18669_2636_1: exceeded memory limit 1269.07MB > 1223.80MB


P.S.
2.15 is the most problematic and buggy version of all that I've seen (since the connection to the project at start of this year inc. 5.98 2.03 2.05 2.10 2.11 2.14) On the forum of my team, just a lot of complaints about this version from other members too.

Brian Priebe

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Message 67997 - Posted 9 Oct 2010 5:25:48 UTC - in response to Message ID 67996.

2.15 is the most problematic and buggy version of all that I've seen

Out of my most recent 100 WU's, 22% of them blew up on one or another of the errors already posted here. The "Unusual Termination" dialog box from MSVC seems to be becoming more frequent.

Jim Martin

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Message 67998 - Posted 9 Oct 2010 5:51:18 UTC

Two enclosures:
1) system boot info.
2) error report.

* * *
10/8/2010 11:29:55 PM Starting BOINC client version 6.10.58 for windows_intelx86
10/8/2010 11:29:55 PM log flags: file_xfer, sched_ops, task
10/8/2010 11:29:55 PM Libraries: libcurl/7.19.7 OpenSSL/0.9.8l zlib/1.2.3
10/8/2010 11:29:55 PM Data directory: C:\ProgramData\BOINC
10/8/2010 11:29:55 PM Running under account James
10/8/2010 11:29:56 PM Processor: 2 GenuineIntel Intel(R) Core(TM)2 CPU T7200 @ 2.00GHz [Family 6 Model 15 Stepping 6]
10/8/2010 11:29:56 PM Processor: 4.00 MB cache
10/8/2010 11:29:56 PM Processor features: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss htt tm pni ssse3 cx16 nx lm vmx tm2 pbe
10/8/2010 11:29:56 PM OS: Microsoft Windows Vista: Business x86 Edition, Service Pack 2, (06.00.6002.00)
10/8/2010 11:29:56 PM Memory: 2.00 GB physical, 4.23 GB virtual
10/8/2010 11:29:56 PM Disk: 142.71 GB total, 89.40 GB free
10/8/2010 11:29:56 PM Local time is UTC -4 hours
10/8/2010 11:29:56 PM No usable GPUs found
10/8/2010 11:29:57 PM rosetta@home URL http://boinc.bakerlab.org/rosetta/; Computer ID 1324493; resource share 100
10/8/2010 11:29:57 PM climateprediction.net URL http://climateprediction.net/; Computer ID 819110; resource share 100
10/8/2010 11:29:57 PM Einstein@Home URL http://einstein.phys.uwm.edu/; Computer ID 1616831; resource share 50
10/8/2010 11:29:57 PM lhcathome URL http://lhcathome.cern.ch/lhcathome/; Computer ID 9825728; resource share 100
10/8/2010 11:29:57 PM Quake-Catcher Network URL http://qcn.stanford.edu/sensor/; Computer ID 9909; resource share 100
10/8/2010 11:29:57 PM SETI@home URL http://setiathome.berkeley.edu/; Computer ID 5490317; resource share 50
10/8/2010 11:29:57 PM Einstein@Home General prefs: from Einstein@Home (last modified 08-Jul-2010 11:24:21)
10/8/2010 11:29:57 PM Einstein@Home Computer location: home
10/8/2010 11:29:57 PM General prefs: using separate prefs for home
10/8/2010 11:29:57 PM Preferences:
10/8/2010 11:29:57 PM max memory usage when active: 1022.66MB
10/8/2010 11:29:57 PM max memory usage when idle: 1840.78MB
10/8/2010 11:30:10 PM max disk usage: 50.00GB
10/8/2010 11:30:10 PM don't use GPU while active
10/8/2010 11:30:10 PM (to change preferences, visit the web site of an attached project, or select Preferences in the Manager)
10/8/2010 11:30:10 PM Not using a proxy
10/8/2010 11:30:10 PM Quake-Catcher Network Restarting task qcnk_sc300_sta200_087854_0 using qcnsensor version 562
10/8/2010 11:30:40 PM rosetta@home Restarting task rs_stg0_lrlx_t363__run1_SAVE_ALL_OUT_19372_6575_0 using minirosetta version 215
10/8/2010 11:30:40 PM climateprediction.net Sending scheduler request: To send trickle-up message.
10/8/2010 11:30:40 PM climateprediction.net Not reporting or requesting tasks
10/8/2010 11:30:44 PM climateprediction.net Scheduler request completed
10/8/2010 11:30:44 PM climateprediction.net Message from server: Project is temporarily shut down for maintenance
10/8/2010 11:32:27 PM rosetta@home Restarting task mem_widd_run02_Mevn_A_2ksy_SAVE_ALL_OUT_IGNORE_THE_REST_22157_49662_0 using minirosetta version 215
* * *
BoincLogX - History

nr / date error_txt project_name domain_name user_total_credit user_expavg_credit CPU error

1596 2010.10.08 13:10:49 rosetta@home james-pc 183398.626579 169.348558 00:00:59 true
1st Entry:

result_name

rs_stg0_lrlx_t311_run1_SAVE_ALL_OUT_19356_2623_0_0

error_txt

The system cannot find the path specified. (0x3) - exit code 3 (0x3);[2010-10-8 12:32:52]::BOINC::Initializing ...

ok. [2010-10-8 12:32-52]


* * * * *

User note:

The above error/WU failure appeared to be generated, immediately after an outputted window,
"Microsoft Visual C++ Runtime Library", was exited. Prior to deleating it, the system ran
slower than normal. Also, after exiting, normal system speed resumed.

The failures occurred on three occasions, although only one is listed, above. BoincLogX information
was entered, by hand, by this user.

Also, approx. 1.29 GB mem was accessed, max.

* * * * *

2nd entry, with the following:

Rosetta Mini 2.15 Mem_widd_run02_Mevn_A_2key_SAVE_ALL_OUT_IGNORE_THE_REST_22157_49662_0.

Used phys mem was in approx. 51%-67% range. No other WU's were run, except QCN@home.

After approx. 23+% run-time, with mem. usage varying from an average of 465 MB, to a max of 1.29 GB,

a second Rosetta Mini 2.15 WU enabled, even though it had been previously been placed in a "suspended" state:

rs_sth0_lrlx_t363_run1_SAVE_ALL_OUT_19372_6575_0.

It resulted in Used phys mem to increase to 99% range, with mem usage, by ...Mem_widd..., about 1.934GB,
and approx. 393.7MB, for rs_sth0...

The system, temporarily, locked up (cursor movement "froze"), until ...Mem_widd... was halted, by the
pgrm., and placed in a "Waiting for memory" mode.

* * * * *

Summary:

1) Rosetta Mini 2.15 WU memory requirements appear to necessitate restricting all other pgrms. from running,
to avoid maxing out memory.

2) Successful WU run not possible, because of the entry of a 2nd Rosetta WU (reason unk.).

Conclusion:

1) If possible, enable the user the option of allocating memory for Rosetta (ref. Garli, Lattice project).
This might free up memory for other projects, for those with multiple CPU's (my system has two);
Rosetta@home might lose some users, if this issue cannot be resolved. I had to drop Garli, for
this reason.

2) Again, if possible, enable the program to function within the allocated memory.

3) Determine the cause of the activation, from "suspended" state, of another Rosetta WU (If it had not
activated, the original WU pbly. would have successfully completed.).

* * *

Pardon the verbosity; hopefully, it will prove enlightening.

JM
____________

cleaner

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Message 67999 - Posted 9 Oct 2010 5:54:56 UTC

I would have to agree with Mad Max about the buginess of the 2.15 Rosetta.Before it was mainly lack of memory issues, but now i am starting to get Runtime errors. Hopefully they will soon come out with an updated version, or else revert back to an earlier, more stable version, because this is getting to be a little ridiculus to me.

bparker

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Message 68000 - Posted 9 Oct 2010 14:09:51 UTC - in response to Message ID 67999.
Last modified: 9 Oct 2010 14:11:04 UTC

I would have to agree with Mad Max about the buginess of the 2.15 Rosetta.Before it was mainly lack of memory issues, but now i am starting to get Runtime errors. Hopefully they will soon come out with an updated version, or else revert back to an earlier, more stable version, because this is getting to be a little ridiculus to me.


I abandoned Rosetta 2.15 until the bugs are fixed and the version changes. All my other BOINC apps work fine except for this one, and it eventually locks up the computer if I leave it running long enough without rebooting. My Window 7 machine works it without problem. My XP machine chokes on it.

Aidan & Liz Hopkins

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Message 68003 - Posted 9 Oct 2010 20:02:36 UTC

I keep getting the following:

09/10/2010 20:43:39|rosetta@home|Task lr5_combined_torsion_it01_run01_A_rlbd_2hkv_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_18669_2172_1 exited with zero status but no 'finished' file
09/10/2010 20:43:39|rosetta@home|If this happens repeatedly you may need to reset the project.

It appears to be linked to a C++ Runtime Library error message, which has inconveniently vanished. After it had kept happening all afternoon I did 'reset', but it is still happening. Original FAQ instructions were to ignore any "exited with zero status but no 'finished' file" situation, but that was a long time ago, and this may be a different problem.

It appears to be doing its regular contact with the server, and nothing is being sent or received at present.

Do I just ignore it and assume the automated updates will resolve it?
____________

Sid Celery

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Message 68012 - Posted 10 Oct 2010 4:14:53 UTC
Last modified: 10 Oct 2010 4:15:35 UTC

With all the other reports of problems I thought I'd check my own tasks:

W7-64bit Intel Core2Duo laptop 4Gb RAM - 1 error out of 36 tasks
CURATED_NMR_1k7b_CONTROL__BOINC_abrelax.score12.fastrelax.v4_SAVE_ALL_OUT_22308_425_0

<core_client_version>6.10.58</core_client_version>
<message>Incorrect function. (0x1) - exit code 1 (0x1)</message>
[...]
ERROR: Assertion failure: runtime_assert( ( begin + size - 1 ) <= pose.total_residue() );
ERROR:: Exit from: ..\..\src\protocols\abinitio\FragmentMover.cc line: 258
BOINC:: Error reading and gzipping output datafile: default.out


Vista64 AMD Phenom 9850 Quad Desktop 8Gb RAM - 2 errors out of 86 tasks
CURATED_NMR_1k7b_disulf__BOINC_abrelax.score12.fastrelax.v4_SAVE_ALL_OUT_22309_663_0

Errors exactly as above

T0591_t3_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22223_1049_1
<core_client_version>6.10.58</core_client_version>
<message> - exit code -1073741819 (0xc0000005)</message>
[...]
- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x00581B5C write attempt to address 0x00000024

Not too terrible, but I do have a decent amount of RAM to play with on each machine - possibly makes the difference.
____________

Sid Celery

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Message 68021 - Posted 11 Oct 2010 0:02:06 UTC

Spoke too soon:

lr5_combined_torsion_it01_run01_A_rlbd_1unp_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_18669_2260_0
lr5_combined_torsion_it01_run01_A_rlbd_1e6i_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_18669_2721_0
rs_stg0_lrlx_t363__run1_SAVE_ALL_OUT_19372_6878_0
All report the same:

<core_client_version>6.10.58</core_client_version>
<message> - exit code -529697949 (0xe06d7363)</message>
[...]
Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Out Of Memory (C++ Exception) (0xe06d7363) at address 0x76A4E124

Out of memory on a machine with 8Gb RAM? I doubt it.

One other:
rb_10_04_377_958_rs_stg0_lrlxjcst_t000__casp9_SAVE_ALL_OUT_22344_1087_1
<core_client_version>6.10.58</core_client_version>
<message>Incorrect function. (0x1) - exit code 1 (0x1)</message>
[...]
ERROR: Error in traceback: pointer doesn't go anywhere!

ERROR:: Exit from: ..\..\src\core\sequence\Aligner.cc line: 79
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

____________

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Message 68034 - Posted 11 Oct 2010 18:36:16 UTC

ehhh...nuts to 2.15
aborting them and moving to 2.16
every few tasks come up with ERROR: Error in traceback: pointer doesn't go anywhere!

ERROR:: Exit from: ..\..\src\core\sequence\Aligner.cc line: 79
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

or some other rubish

wolfpat

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Message 68111 - Posted 16 Oct 2010 17:07:16 UTC

I also had to abort all the 2.15 tasks. They would not run at all on my XP machine. The 2.16 tasks are running fine.

Message boards : Number crunching : minirosetta 2.15


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