Minirosetta 1.97

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Mike Tyka

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Message 63009 - Posted: 22 Aug 2009, 3:41:11 UTC

1.95/1.96 Repackaged again as 1.97 including minirosetta.linuxgccrelese

http://beautifulproteins.blogspot.com/
http://www.miketyka.com/
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Profile AdeB
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Message 63011 - Posted: 22 Aug 2009, 11:54:18 UTC

ERROR: Option matching -in:detect_disulfides not found in command line top-level context
in task 275059313

AdeB
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svincent

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Message 63016 - Posted: 22 Aug 2009, 17:17:45 UTC

Task 275103009
Name : 2lzm_L_7_A_ddg_predictions_82009_003_MUT.2lzm_L_7_A_.out_14642_1_0

has been running for 2.5 hours on a Mac with 0% progress. The Graphics show its still initializing (Model 0: Step 0.

Aborting.
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svincent

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Message 63017 - Posted: 22 Aug 2009, 18:20:28 UTC

Same thing on the next WU (task 275109083), 1stn_E_96_G_ddg_predictions_82009_002_MUT.1stn_E_96_G_.out_14641_2_0

Its been initailising for over an hour on Mac with zero progress,
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Michael G.R.

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Message 63018 - Posted: 22 Aug 2009, 18:45:15 UTC

Too many tasks are stalling. I'm switching my resources to World Community Grid for a while, hoping this will be fixed.

Is it my imagination or are new versions of Rosetta@home getting less testing on Ralph before being released here? Maybe that would help to find the stability problems...
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Message 63020 - Posted: 22 Aug 2009, 23:08:53 UTC

It doesn't look like Vista likes something with these or the new app all are

resends to me. We'll see if ubuntu does any better!
=================================================================
https://boinc.bakerlab.org/rosetta/workunit.php?wuid=250873853

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=250874256

<core_client_version>6.6.36</core_client_version>
<![CDATA[
<message>
CreateProcess() failed - Toegang geweigerd. (0x5)
</message>
]]>
=================================================================
https://boinc.bakerlab.org/rosetta/workunit.php?wuid=250882153

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=250882152

<core_client_version>6.6.36</core_client_version>
<![CDATA[
<message>
CreateProcess() failed - Access is denied. (0x5)
</message>
]]>

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Profile bruce

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Message 63028 - Posted: 23 Aug 2009, 12:20:29 UTC

Getting "exited with zero status but no 'finished' file" messages.

the WU remains in memory, dead/idle, taking up resources that could be used by others. Will not exit until killed or reboot.
Also, at this point, even though it is in memory, it does not show on the boinc manager task list.

Task: 275255448

Seeing the following info in locations as noted:
--===Messages from BOINC Manager:===--
8/22/2009 10:08:40 PM Starting BOINC client version 6.10.0 for windows_intelx86
8/22/2009 10:08:40 PM log flags: task, file_xfer, sched_ops
8/22/2009 10:08:40 PM Libraries: libcurl/7.19.4 OpenSSL/0.9.8k zlib/1.2.3
8/22/2009 10:08:40 PM Running as a daemon
8/22/2009 10:08:40 PM Data directory: C:ProgramDataBOINC
8/22/2009 10:08:40 PM Running under account boinc_master
8/22/2009 10:08:40 PM Processor: 2 AuthenticAMD AMD Athlon Dual-Core QL-62 [x86 Family 17 Model 3 Stepping 1]
8/22/2009 10:08:40 PM Processor: 512.00 KB cache
8/22/2009 10:08:40 PM Processor features: fpu tsc pae nx sse sse2 pni 3dnow mmx
8/22/2009 10:08:40 PM OS: Microsoft Windows Vista: Home Premium x86 Edition, Service Pack 2, (06.00.6002.00)
8/22/2009 10:08:40 PM Memory: 1.75 GB physical, 3.74 GB virtual
8/22/2009 10:08:40 PM Disk: 222.00 GB total, 134.45 GB free
8/22/2009 10:08:40 PM Local time is UTC -7 hours
8/22/2009 10:08:40 PM No CUDA-capable NVIDIA GPUs found
8/22/2009 10:08:40 PM No CAL Runtime Libraries installed.
8/22/2009 10:08:40 PM No coprocessors
8/22/2009 10:08:40 PM Not using a proxy
8/22/2009 10:08:41 PM rosetta@home URL: https://boinc.bakerlab.org/rosetta/; Computer ID: 1069956; location: home; project prefs: default
8/22/2009 10:08:41 PM SETI@home URL: http://setiathome.berkeley.edu/; Computer ID: 4950525; location: (none); project prefs: default
8/22/2009 10:08:41 PM PrimeGrid URL: http://www.primegrid.com/; Computer ID: 118872; location: (none); project prefs: default
8/22/2009 10:08:41 PM PrimeGrid General prefs: from PrimeGrid (last modified 17-Aug-2009 03:56:52)
8/22/2009 10:08:41 PM PrimeGrid Computer location: home
8/22/2009 10:08:41 PM PrimeGrid General prefs: no separate prefs for home; using your defaults
8/22/2009 10:08:41 PM Reading preferences override file
8/22/2009 10:08:41 PM Preferences limit memory usage when active to 715.88MB
8/22/2009 10:08:41 PM Preferences limit memory usage when idle to 1163.30MB
8/22/2009 10:08:44 PM Preferences limit disk usage to 20.00GB
8/22/2009 10:08:46 PM PrimeGrid Restarting task psp_llr_33339978_1 using llrPSP version 509
8/22/2009 10:08:56 PM rosetta@home Restarting task lr8_A_seq_score12_ss1.7_rlbd_2hng_IGNORE_THE_REST_DECOY_14637_298_0 using minirosetta version 197
8/22/2009 10:55:18 PM PrimeGrid Computation for task psp_llr_33339978_1 finished
8/22/2009 10:55:18 PM rosetta@home Starting 1irnA_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1irnA-_14632_6900_0
8/22/2009 10:55:20 PM rosetta@home Starting task 1irnA_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1irnA-_14632_6900_0 using minirosetta version 197
8/22/2009 10:55:21 PM PrimeGrid Started upload of psp_llr_33339978_1_0
8/22/2009 10:55:22 PM PrimeGrid Finished upload of psp_llr_33339978_1_0
8/22/2009 11:00:13 PM rosetta@home Restarting task 1irnA_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1irnA-_14632_6900_0 using minirosetta version 197
8/22/2009 11:00:54 PM rosetta@home Task 1irnA_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1irnA-_14632_6900_0 exited with zero status but no 'finished' file
8/22/2009 11:00:54 PM rosetta@home If this happens repeatedly you may need to reset the project.
...etc...etc...etc...
8/22/2009 11:31:12 PM rosetta@home Restarting task 1irnA_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1irnA-_14632_6900_0 using minirosetta version 197
8/22/2009 11:31:53 PM rosetta@home Task 1irnA_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1irnA-_14632_6900_0 exited with zero status but no 'finished' file
8/22/2009 11:31:53 PM rosetta@home If this happens repeatedly you may need to reset the project.
8/22/2009 11:31:59 PM rosetta@home Sending scheduler request: To fetch work.
8/22/2009 11:31:59 PM rosetta@home Requesting new tasks
8/22/2009 11:32:04 PM rosetta@home Scheduler request completed: got 1 new tasks
8/22/2009 11:32:34 PM rosetta@home Task 1irnA_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1irnA-_14632_6900_0 exited with zero status but no 'finished' file
8/22/2009 11:32:34 PM rosetta@home If this happens repeatedly you may need to reset the project.
...etc...etc...etc...
8/23/2009 12:08:48 AM rosetta@home Restarting task 1irnA_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1irnA-_14632_6900_0 using minirosetta version 197
8/23/2009 12:09:29 AM rosetta@home Computation for task 1irnA_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1irnA-_14632_6900_0 finished
8/23/2009 12:09:29 AM rosetta@home Output file 1irnA_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1irnA-_14632_6900_0_0 for task 1irnA_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1irnA-_14632_6900_0 absent

Only three files remain in the slots# folders associated with this task:
boinc_lockfile
stderr.txt
stdout.txt
--===Messages from stderr.txt:===--
[2009- 8-22 22:55:20:] :: BOINC:: Initializing ... ok.
[2009- 8-22 22:55:20:] :: 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 ...
Setting up folding (abrelax) ...
Beginning folding (abrelax) ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
Starting work on structure: _00001
[2009- 8-22 23: 0:13:] :: BOINC:: Initializing ... ok.
Can't acquire lockfile - exiting
...etc...etc...etc...
[2009- 8-23 0: 8:48:] :: BOINC:: Initializing ... ok.
Can't acquire lockfile - exiting
--===Messages from stdout.txt:===--
Created shared memory segment
Created semaphore
--=== ===--
With the task still in memory, the boinc_lockfile is still locked, has not been released by the task. Once the task has been killed, or the system rebooted, the boinc_lockfile can be removed.

Any suggestions?

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Profile macko
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Message 63033 - Posted: 24 Aug 2009, 20:18:06 UTC

Task ID 275700999
Name lr8_A_seq_score12_ss1.7_rlbd_1ugh_IGNORE_THE_REST_DECOY_14637_734_0
Workunit 251299403
Created 24 Aug 2009 18:56:13 UTC
Sent 24 Aug 2009 19:08:29 UTC
Received 24 Aug 2009 20:18:43 UTC
Server state Over
Outcome Client error
Client state Compute error
Exit status -226 (0xffffff1e)
Computer ID 1096769
Report deadline 3 Sep 2009 19:08:29 UTC
CPU time 0
stderr out

<core_client_version>6.2.28</core_client_version>
<![CDATA[
<message>
too many exit(0)s
</message>
]]>

Validate state Invalid
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P . P . L .

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Message 63036 - Posted: 24 Aug 2009, 23:44:01 UTC

Hi.

The four tasks i reported earlier, that had a problem on win Vista rigs

have ran fine on my Ubuntu rig.

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Profile Eric

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Message 63040 - Posted: 25 Aug 2009, 19:01:34 UTC
Last modified: 25 Aug 2009, 19:01:52 UTC

Is anyone else with a Mac with OS X (not sure what other information needed, ask away- sorry!) getting


"core.scoring.rms_util: WARNING: CA_rmsd out of range... range1 90 requested but only 89 CA atoms found in fill_rmsd_coordinates "
in Console.app when the BOINC screensaver is running?
Thanks!
-Eric
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Profile robertmiles

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Message 63044 - Posted: 26 Aug 2009, 0:03:28 UTC - in response to Message 63018.  

Too many tasks are stalling. I'm switching my resources to World Community Grid for a while, hoping this will be fixed.

Is it my imagination or are new versions of Rosetta@home getting less testing on Ralph before being released here? Maybe that would help to find the stability problems...


I've seen some of the recent versions get tested on Ralph@home only after a more recent version is already in use on Rosetta@home. Let's at least hope that those tests are for parts recently added, and therefore not tested enough to use on Rosetta@home.
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Message 63045 - Posted: 26 Aug 2009, 0:09:51 UTC
Last modified: 26 Aug 2009, 0:16:28 UTC

Some workunits (probably all 1.97) that appear to have been lost on my 64-bit computer during a power failure today:

Task ID 275856608
Name lr8_A_seq_score12_ss1.7_rlbd_1ugh_IGNORE_THE_REST_DECOY_14637_804_0
Workunit 251443492

Task ID 275835549
Name 2f09_NNMAKE_CONSTRAINT_BOINC_abinitio.v3_SAVE_ALL_OUT_14648_70_1
Workunit 251413484
This one already failed for a wingmate.

Task ID 275795579
Name lr8_A_seq_score12_ss1.7_rlbd_1ail_IGNORE_THE_REST_DECOY_14637_780_0
Workunit 251387536

Task ID 275587800
Name 1co4A_ZNMP_ABRELAX_tetraL_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1co4A-_14631_11872_0
Workunit 251195929

Task ID 275580265
Name lr8_combine_smooth_torsion_it00_A_rlbd_2chf_IGNORE_THE_REST_DECOY_14638_182_0
Workunit 251189829

If you can't tell your server to send them to the same computer again the next time it asks for workunits, you might as well reissue them to someone else.

Also:

*** 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.
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Message 63046 - Posted: 26 Aug 2009, 11:03:24 UTC - in response to Message 63017.  

Same thing on the next WU (task 275109083), 1stn_E_96_G_ddg_predictions_82009_002_MUT.1stn_E_96_G_.out_14641_2_0

Its been initailising for over an hour on Mac with zero progress,

Got same WU today...
It seemed that WU has stack, but finally i got result.

There's another trouble:

This WU uses 512MiB of RAM at start!!! And it's not a limit...
Step-by-step the job has eaten 1.8 gbytes of the RAM.
Look here:

thank god, i have 6 GB of memory, but present, what if all eight i7-cores receive such jobs?!
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Krasnoyarsk_TEAM

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Message 63047 - Posted: 26 Aug 2009, 12:36:26 UTC

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Message 63049 - Posted: 27 Aug 2009, 7:23:53 UTC

Hi.

This froze one of my rigs that has 1 gig of ram. It was using 970mb odd of that

and 550mb swap space it was stuck at 1hr 5min wanting for memory so i abouted it.

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=251761378

1bvc_A_15_L_ddg_predictions_82409_006_WT.1bvc_A_15_L_.out_14656_2

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Path7

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Message 63055 - Posted: 27 Aug 2009, 13:03:38 UTC

Hello all,

Another RAM hungry WU:
1u5p_D_194_G_ddg_predictions_82409_006_MUT.1u5p_D_194_G_.out_14656_1_0

At the first attempt it ran for about 17 minutes used more than 700 MB Ram and ended with: "waiting for memory".
At the second attempt I changed the setting from "use at most 50 % RAM while in use" to 75 %.
This time the WU kept on running with a peak RAM usage of 1104100 kB (some 1078 MB).

Sad thing is the WU doesn't seem to proceed, stuck at 0.000 %.
The graphics screen show me the WU still initializing.

Running a single core AMD sempron with 1471.48 MB RAM
Sorry, with my PC becoming sluggish I had to abort this WU.

Path7.
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P . P . L .

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Message 63060 - Posted: 27 Aug 2009, 21:44:25 UTC

Here's another one that i had to kill, it was stuck for an hour not moving no

graphics and using 1.2gig of ram on my quad that has 4gig.

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=251760114

2lzm_V_87_T_ddg_predictions_82409_006_WT.2lzm_V_87_T_.out_14656_2_0

This type seems to be the problem!

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Message 63062 - Posted: 27 Aug 2009, 22:37:32 UTC

Hi all

Be patient with this WUs. Altough there is no visible progression or regular grafic activity (initalizing---), they will finish after some hours. I have only 732 MB of RAM and it runs out when my host wasn't idle,but it seems to be enough.
1stn_E_70_V_ddg_predictions_82409_007_WT.1stn_E_70_V_.out_14657_1_0
https://boinc.bakerlab.org/rosetta/result.php?resultid=276277965

There are WUs in another project with similar behavior.
On the other hand I have 2 hosts. On first resetting solved the problem with app 1.97, on second still have only comp errors only after resetting, detaching and reinstalling boinc (rep. install). Same op system (win xp sp3) and near the same week hardware. Ideas?
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Message 63063 - Posted: 27 Aug 2009, 22:55:57 UTC

Here's another task different problem.

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=251841018

Fri 28 Aug 2009 07:44:35 EST|rosetta@home|Output file 2baf_NNMAKE_CONSTRAINT_BOINC_abinitio.v3_SAVE_ALL_OUT_14648_602_0_0 for task absent

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Message 63064 - Posted: 28 Aug 2009, 6:58:01 UTC

One of my computers seems to have erased its copy of each of these workunits during a recent power failure, when it got a new computer number.

275856608
275835549
275795579
251195929
251189829

I'll let you decide if it's more convenient to send me another copy of each of them, or reassign them to someone else.

Probably all 1.97 workunits, but I'm not sure.
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