Minirosetta 1.97

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Profile robertmiles

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Message 63066 - Posted: 28 Aug 2009, 8:52:48 UTC - in response to Message 63045.  

*** WARNING *** - the Microsoft updates today for my second 64-bit Vista computer disabled its ability to reach the internet; fortunately, it's a laptop I don't consider ready to run BOINC projects yet, especially those that don't run well with less than 100% CPU. Recovery started, but not finished.


Note - I finally found which update; one needed for Vista SP1 just before it offers to let you install the Vista SP2 update. So if you're already at Vista SP2, ignore that part of the message. Recovery of that machine finished, except for that one failed update.
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Profile Gen_X_Accord
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Message 63072 - Posted: 29 Aug 2009, 4:03:08 UTC

I had to kill this work unit because after 40 minutes it had zero % progress and I thought that was ridiculous. The graphic part showed it still initializing. Why waste processing time something that is going nowhere. Even restarted the client to no avail.

243l_A_58_I_ddg_predictions_82409_010_WT.243l_A_58_I_.out_14659_1
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Message 63078 - Posted: 29 Aug 2009, 14:32:32 UTC
Last modified: 30 Aug 2009, 15:18:40 UTC

Just watching one of these "ddg_predictions" tasks running on my own machine. At the risk of overstepping my duties, I'm going to recommend

anyone with no more then 512MB of memory, cancel tasks with "ddg_predictions" in the name.

I've EMailed the Project Team asking about these. They have the complete picture (beyond all of the posts in this thread) of how these tasks are running to assess if they are producing useful results, and so I will expect further details will follow soon.

At this point, I feel confident these tasks are consistently using more memory then is going to be feasible for a 512MB machine. So this is why I'm making the suggestion above.
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TimL

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Message 63080 - Posted: 29 Aug 2009, 21:39:27 UTC
Last modified: 29 Aug 2009, 21:42:58 UTC

2 tasks error'd out. The 2nd task caused a c++ runtime pop up.

276192618
1aye_I_12_V_ddg_predictions_82409_005_MUT.1aye_I_12_V_.out_14655_2_0

and

276192613
1aye_H_48_A_ddg_predictions_82409_005_MUT.1aye_H_48_A_.out_14655_2_0
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Sid Celery

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Message 63093 - Posted: 31 Aug 2009, 15:08:16 UTC

Tempting fate, I know, but I thought I'd check for any errors to report in the last week and went back through every 1.97 WU I've ever received. No errors at all. Surely that can't be right... ;)

For all those people who went off in a huff over perceived problems earlier in the month, can someone tell them the coast is currently very clear.

Even credits have edged back up per WU too. Whisper it quietly...
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Profile Greg_BE
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Message 63101 - Posted: 1 Sep 2009, 8:21:03 UTC

whatever they did sure cleaned up the errors.
been clean as far back as the rosie will let me and its all perfect.
did have one group of tasks that came back as no reply, kind of odd.
no effect on credit though.
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Profile robertmiles

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Message 63111 - Posted: 1 Sep 2009, 13:41:35 UTC - in response to Message 63101.  

whatever they did sure cleaned up the errors.
been clean as far back as the rosie will let me and its all perfect.
did have one group of tasks that came back as no reply, kind of odd.
no effect on credit though.


I've had one batch of tasks that came back as no reply on one of my computers, but I thought this was the result of a recent power failure, partly since all BOINC projects this computer participates in were affected, not just Rosetta@home.
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frederick corse

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Message 63167 - Posted: 5 Sep 2009, 6:07:14 UTC

Hello I am now running 8tim_Q_178_A_ddg_predictions_82409_1252 and it calls out that it is using 1.5G of memory . It has been running for over 40 minutes and it is still initalizing. the first time it was sent out came back as no reply.
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frederick corse

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Message 63168 - Posted: 5 Sep 2009, 8:01:07 UTC

helo boinc I sampled the program core::scoring::etable::count_pair::CPCrossoverBehavior)
1 operator new(unsigned long)
1 malloc
1 std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)
1 char* std::string::_S_construct<char const*>(char const*, char const*, std::allocator<char> const&, std::forward_iterator_tag)
ore::graph::PointGraphEdgeData> >, double, utility::vector1<bool, std::allocator<bool> >)
1 operator new(unsigned long)
1 malloc
1 malloc_zone_malloc
1 szone_malloc_should_clear
1 small_malloc_from_free_list
1 0xffffffff
1 _sigtramp
1 __i686.get_pc_thunk.bx
1 core::graph::residue_point_graph_from_pose(core::pose::Pose const&, core::graph::UpperEdgeGraph<core::graph::PointGraphVertexData, core::gr 1 std::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string()
1 __i686.get_pc_thunk.bx
4 core::scoring::etable::count_pair::CountPairAll::count(int, int, double&) const
3 core::scoring::etable::count_pair::CountPairIntraRes<core::scoring::etable::count_pair::CountPairCrossover3>::count(int, int, double&) const
2 core::graph::find_neighbors_restricted(utility::pointer::owning_ptr<core::graph::UpperEdgeGraph<core::graph::PointGraphVertexData, core::graph::PointGraphEdgeData> >, d
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Astropoint

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Message 63169 - Posted: 5 Sep 2009, 9:31:16 UTC

I had a WU stuck for about 4 hours on 0% and using 1.2GB of memory before I aborted it. https://boinc.bakerlab.org/rosetta/result.php?resultid=278489672
This is the 2nd one that I remember from the past couple of weeks
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Message 63173 - Posted: 5 Sep 2009, 16:15:55 UTC

frederick, see my post on ddg_predictions tasks previously. I haven't seen any for a while, so I'm guessing they cancelled any new ones. Sounds like the one you got was reissued due to the original copy missing the deadline.

They seems to consume a lot of memory, not interact with BOINC Manager to report their progress, they seem to have rather long running models, and not to display anything more then the basic framework of the graphic... but they do seem to eventually complete.

It looks like your preferred runtime is about 4 hours. Please let that one run for at least 8hrs before considering aborting it. I believe it will be completed before that time anyway. your other ddg_predictions task finished in about 5 hrs, and it ran that long because it was only able to complete a single model (the minimum amount of useful results a task can produce).
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Profile bill Johnson@GMU

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Message 63177 - Posted: 6 Sep 2009, 14:00:02 UTC

I have now run out of tasks to work on.

However my computer is still trying to get new work units because when I checked the messages section it was listing,
“Requesting new tasks
Scheduler request completed: got 0 new tasks. “

Also under the server status the scheduler is running.

Is anyone else getting this problem?
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LizzieBarry

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Message 63180 - Posted: 6 Sep 2009, 18:36:07 UTC - in response to Message 63177.  

I have now run out of tasks to work on.

However my computer is still trying to get new work units because when I checked the messages section it was listing,
“Requesting new tasks
Scheduler request completed: got 0 new tasks. “

Also under the server status the scheduler is running.

Is anyone else getting this problem?

Sort of, yes. Eventually something came through, but it looks like the work generator is struggling to keep up again.
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P . P . L .

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Message 63198 - Posted: 7 Sep 2009, 22:03:47 UTC

This one was stuck or not making much progress. After 4hrs, 14min it was on

Model: 1 ,Step: 3. I aborted it sorry.

lr13_seq_score12_ss5.0_rlbd_1tig_IGNORE_THE_REST_DECOY_14612_3390_0

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=254147223

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AMD_is_logical

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Message 63216 - Posted: 9 Sep 2009, 1:59:54 UTC

I currently have over 100 results in my "pending" list. Also, I notice that I have quite a few results taking around 2 hours or less. (My runtime setting is 12 hours.)
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Quercus Petraea

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Message 63227 - Posted: 9 Sep 2009, 15:11:33 UTC
Last modified: 9 Sep 2009, 15:19:41 UTC

Many "pending" granted credit in my list to!
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[AF>france>pas-de-calais]symaski62

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Message 63238 - Posted: 10 Sep 2009, 10:27:41 UTC

https://boinc.bakerlab.org/rosetta/result.php?resultid=279674844


<core_client_version>6.6.36</core_client_version>
<![CDATA[
<stderr_txt>
[2009- 9-10  7: 5:29:] :: BOINC:: Initializing ... ok.
[2009- 9-10  7: 5:29:] :: 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
Loaded options.... ok 
Processed options.... ok 
Initializing random generators... ok 
Initialization complete. 
Setting WU description ...
Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev32257.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup. 
Starting watchdog...
Watchdog active.
# cpu_run_time_pref: 14400
[2009- 9-10  9:59:56:] :: BOINC:: Initializing ... ok.
[2009- 9-10  9:59:56:] :: 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
Loaded options.... ok 
Processed options.... ok 
Initializing random generators... ok 
Initialization complete. 
Setting WU description ...
Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev32257.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup. 
Starting watchdog...
Watchdog active.
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk1_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk2_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk3_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk4_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk5_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk6_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk7_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk8_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk9_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk10_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk11_fa ... success! 
# cpu_run_time_pref: 14400
======================================================
DONE ::    21 starting structures  10500.8 cpu seconds
This process generated     21 decoys from      21 attempts
======================================================

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish

</stderr_txt>
]]>


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Profile Greg_BE
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Message 63242 - Posted: 10 Sep 2009, 12:31:51 UTC - in response to Message 63238.  

there is nothing wrong with this task other than it is in pending credit queue.
please do not post so much information unless you truly have a bug to report.


https://boinc.bakerlab.org/rosetta/result.php?resultid=279674844


<core_client_version>6.6.36</core_client_version>
<![CDATA[
<stderr_txt>
[2009- 9-10  7: 5:29:] :: BOINC:: Initializing ... ok.
[2009- 9-10  7: 5:29:] :: 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
Loaded options.... ok 
Processed options.... ok 
Initializing random generators... ok 
Initialization complete. 
Setting WU description ...
Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev32257.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup. 
Starting watchdog...
Watchdog active.
# cpu_run_time_pref: 14400
[2009- 9-10  9:59:56:] :: BOINC:: Initializing ... ok.
[2009- 9-10  9:59:56:] :: 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
Loaded options.... ok 
Processed options.... ok 
Initializing random generators... ok 
Initialization complete. 
Setting WU description ...
Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev32257.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup. 
Starting watchdog...
Watchdog active.
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk1_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk2_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk3_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk4_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk5_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk6_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk7_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk8_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk9_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk10_fa ... success! 
Continuing computation from checkpoint: chk_3BDC-ALA132GLU_0001_00020_FastRelax__chk11_fa ... success! 
# cpu_run_time_pref: 14400
======================================================
DONE ::    21 starting structures  10500.8 cpu seconds
This process generated     21 decoys from      21 attempts
======================================================

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish

</stderr_txt>
]]>


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Profile JollySwagman
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Message 63247 - Posted: 10 Sep 2009, 16:27:44 UTC

Got about 16 WU,s waiting to upload and no new work yet severs say all OK
yet when you ping the srv4.bakerlab.org you get timed out

C:Program FilesSupport Tools>ping srv4.bakerlab.org

Pinging srv4.bakerlab.org [140.142.20.112] with 32 bytes of data:

Request timed out.
Request timed out.
Request timed out.
Request timed out.

Ping statistics for 140.142.20.112:
Packets: Sent = 4, Received = 0, Lost = 4 (100% loss),
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P . P . L .

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Message 63411 - Posted: 21 Sep 2009, 1:58:47 UTC

symm_lr8_seq_score12_A_rlbd_1t2i_IGNORE_THE_REST_DECOY_14880_289

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=257005065

Are we getting these again, i seem to remember this type from weeks ago.

Some of them caused problems back then to, other user had a problem with it to.

When this one restarted it had done over 3hrs and it then went back to

Model:1 / Step:0 doesn't look like it check pointed at all so i ABORTED IT.





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