Posts by Pepo

1) Message boards : RALPH@home bug list : Minirosetta 1.67 (Message 4820)
Posted 15 May 2009 by Pepo
Post:
an error occured in this task:
http://ralph.bakerlab.org/result.php?resultid=1439583

with exit code:
- exit code -1073741819 (0xc0000005)

Apparently the same error happened to my task lb_alnmatrix_brokerthread_hb_t328__IGNORE_THE_REST_9664_17_0 - error 1073741819 (0xffffffffc0000005), "Access Violation (0xc0000005) at address 0x0088A3C2 write attempt to address 0x00000000", broken stack for the errored thread, BOINC Windows Runtime Debugger dump is available.

Windows XP SP3, BOINC 6.6.23.
2) Message boards : RALPH@home bug list : minirosetta v1.54 bug thread (Message 4549)
Posted 26 Jan 2009 by Pepo
Post:
And it ges on...
test_cc2_1_8_mammoth_mix_cen_cst_hb_t327__IGNORE_THE_REST_1YYVA_3_6860_1_2 failed (0x1):

<core_client_version>6.6.2</core_client_version>

Incorrect function. (0x1) - exit code 1 (0x1)

BOINC:: Initializing ... ok.
[2009- 1-26 12:40:10:] :: 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 core...
Initializing options.... ok
ERROR: Option matching -loop:close_loops not found in command line top-level context


One peer of mine failed few days ago using mini 1.51 with other error:

ERROR: unknown model name: 2FRHA_10
ERROR:: Exit from: d:boinc_buildminirosetta_windowsminisrcprotocols/abinitio/PairingStatistics.hh line: 170
called boinc_finish


Peter
3) Message boards : RALPH@home bug list : minirosetta v1.54 bug thread (Message 4546)
Posted 26 Jan 2009 by Pepo
Post:
Thumbs up! I keep the fingers crossed and look forward...

Peter
4) Message boards : RALPH@home bug list : minirosetta v1.48-1.51 bug thread (Message 4450)
Posted 19 Jan 2009 by Pepo
Post:
As a first preliminary report:
This (long anticipated, yes i know ) new release ...
... is mistakenly dated to December 12, 2008 (probably a copy of the 1.47 release).

Peter
5) Message boards : RALPH@home bug list : Server upgrade issues (Message 4371)
Posted 1 Dec 2008 by Pepo
Post:
The message's header, like this one:
Message 4365 - Posted 27 Nov 2008 3:54:25 UTC
Last modified: 27 Nov 2008 6:03:12 UTC
or Message 4239, is being sometimes clipped as much, that I can see just upper 1-2 points of the second line. This happens with IE7, but does not with SeaMonkey.

It probably happens to all Modified messages, which contain more lines than the height of the user's description at its left side. Message 4251 is just in-between.

On this my message, I do not see even the upper 1-2 points of the second "Last modified: 1 Dec 2008 11:49:XX UTC" header line.

Peter
6) Message boards : RALPH@home bug list : minirosetta v1.41 bug thread (Message 4351)
Posted 21 Nov 2008 by Pepo
Post:
rlb_test_ralph_splitterms2_rlb_2d4f_IGNORE_THE_REST_DECOY_5551_1_1 prematurely exited after 2.2 sec runtime with code 1 (Linux 2.6.9-42.0.2.EL host, BCC 6.3.21):

process exited with code 1 (0x1, -255)
ERROR: Unable to open weights. Neither ./2nd_iter_high_atr.wts nor minirosetta_database/scoring/weights/2nd_iter_high_atr.wts exist
ERROR:: Exit from: src/core/scoring/ScoreFunctionFactory.cc line: 57



loopbuild_minimalist_core_control_standardloopfiles_homo_bench_looprelax_cheat_chunk_control_standard_loopfiles_t306__olange_IGNORE_THE_REST_1B70B_2_5522_1_0 exited after nearly 2 hours runtime (Win XP SP3 host, BCC 6.4.0):

# cpu_run_time_pref: 7200
WARNING! attempt to create gzipped file ../../projects/ralph.bakerlab.org/loopbuild_minimalist_core_control_standardloopfiles_homo_bench_looprelax_cheat_chunk_control_standard_loopfiles_t306__olange_IGNORE_THE_REST_1B70B_2_5522_1_0_0 failed.
======================================================
DONE :: 1 starting structures 7048.28 cpu seconds
This process generated 31 decoys from 31 attempts
======================================================
BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down...
called boinc_finish

<file_xfer_error>
<file_name>loopbuild_minimalist_core_control_standardloopfiles_homo_bench_looprelax_cheat_chunk_control_standard_loopfiles_t306__olange_IGNORE_THE_REST_1B70B_2_5522_1_0_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>


As someone noted few days ago in other thread, these file names (on my system, path 88 + filename 160 chars) are everything but short...

Peter
7) Message boards : RALPH@home bug list : Bug Reports for Minirosetta v1.36 (Message 4283)
Posted 16 Oct 2008 by Pepo
Post:
The new 'hombench_mtyka' work units seem to now be working ok, as none of my latest have gone past my 6 hour preference.

Some do, but some do not...


Yes Pepo, you are correct, the ones I was referring to were the "hombench_mtyka_looprelax" work units which seem to run ok.

The "hombench_mtyka_foldcst" work units all seem to fail, in my case by running well past the set preference times.

EDIT:: Have changed my mind after seeing that our reports seem to be on deaf ears at the moment, I have just checked todays returned work units and it appears I was incorrect about the "hombench_mtyka_looprelax" work units being ok.
I did get a response on the Rosetta forums but they seem to think the "hombench_mtyka" type work units are all ok, I say try processing a few and see what happens.

I've indeed got no errored "homebench_mtyka_looprelax", but crunched just a little bit. From what I've crunched in last weeks (both ralph and rosetta), 63 x homebench_mtyka_* (came since 22.9., 6 failed - 10% failure ratio), 6 x homebench_tex_* (since 2 deays ago, and all failed):

03 x homebench_mtyka_foldcst_boinc_test* - 2 failed,
11 x homebench_mtyka_foldcst_loopbuild_boinctest* - 0 failed,
03 x homebench_mtyka_foldcst_loopbuild_test1* - 1 failed,
04 x homebench_mtyka_foldcst_loopbuild_tex_cst_* - 3 failed,
03 x homebench_mtyka_foldcst_simple_* - 0 failed,
09 x homebench_mtyka_looprelax_ccd_close_* - 0 failed,
21 x homebench_mtyka_looprelax_ccd_moves_* - 0 failed,
09 x homebench_mtyka_looprelax_test_full_* - 0 failed,
06 x homebench_tex_looprelax_tex* - 6 failed,

The list is sorted alphabetically, it'd be probably better to sort them according to their time of appearance.

Peter
8) Message boards : RALPH@home bug list : Bug Reports for Minirosetta v1.36 (Message 4281)
Posted 16 Oct 2008 by Pepo
Post:
The new 'hombench_mtyka' work units seem to now be working ok, as none of my latest have gone past my 6 hour preference.

Some do, but some do not...

One more hombench_mtyka_foldcst_ task with "Maximum disk usage exceeded" and error -177, on WinXP SP3, 6.3.14 client :

hombench_mtyka_foldcst_loopbuild_tex_cst_foldcst_loopbuild_tex_cst_t286__IGNORE_THE_REST_1ZITA_1_5159_1_1 exited after 5916.234 seconds with -177 (0xffffffffffffff4f)
<core_client_version>6.3.14</core_client_version>
Maximum disk usage exceeded

sin_cos_range ERROR: 1.#QNAN00 is outside of [-1,+1] sin and cos value legal range
sin_cos_range ERROR: 1.#QNAN00 is outside of [-1,+1] sin and cos value legal range
sin_cos_range ERROR: 1.#QNAN00 is outside of [-1,+1] sin and cos value legal range
[...] (again repeated hundreds times)
sin_cos_range ERROR: 1.#QNAN00 is outside of [-1,+1] sin and cos value legal range

Unhandled Exception Detected...
- Unhandled Exception Record -
Reason: Breakpoint Encountered (0x80000003) at address 0x7C90120E
Engaging BOINC Windows Runtime Debugger...

According to dbg output, I'd again bet on a broken stack...

Peter
9) Message boards : RALPH@home bug list : Bug Reports for Minirosetta v1.36 (Message 4278)
Posted 15 Oct 2008 by Pepo
Post:
some are invalid :
resultid=1130000
hombench_tex_looprelax_tex_cst_oneparam_looprelax_tex_cst_t322__IGNORE_THE_REST_2GVHA_6_5150_1_1
ERROR: NANs occured in hbonding!
ERROR:: Exit from: ....srccorescoringhbondshbonds_geom.cc line: 763

hombench_tex_looprelax_tex_cst_oneparam_looprelax_tex_cst_t325__IGNORE_THE_REST_1DPMA_12_5151_1_1 exited with error 1.

<core_client_version>6.3.14</core_client_version>
Incorrect function. (0x1) - exit code 1 (0x1)
# cpu_run_time_pref: 7200
No heartbeat from core client for 30 sec - exiting
# cpu_run_time_pref: 7200

ERROR: NANs occured in hbonding!
ERROR:: Exit from: ....srccorescoringhbondshbonds_geom.cc line: 763
called boinc_finish


Peter
10) Message boards : RALPH@home bug list : Bug Reports for Minirosetta v1.36 (Message 4277)
Posted 15 Oct 2008 by Pepo
Post:
I've noticed that my hombench_mtyka_looprelax_ccd_close_looprelax_t286__IGNORE_THE_REST_1BWP__13_5163_1_0 is still running (now at 03:02:29, 76.011%, 01:25:16 to go), although was meant to be preempted approx. 1:18 hours (or 39 CPU minutes) ago. Linux P-III, 6.2.4 client.

Peter

[edit]It finished correctly.[/edit]
11) Message boards : RALPH@home bug list : Bug Reports for Minirosetta v1.36 (Message 4276)
Posted 15 Oct 2008 by Pepo
Post:
Two hombench_mtyka_foldcst_ tasks with "Maximum disk usage exceeded" and error -177, both on WinXP SP3, client 6.3.14:

hombench_mtyka_foldcst_loopbuild_tex_cst_foldcst_loopbuild_tex_cst_t286__IGNORE_THE_REST_2APJA_3_5159_1_0 exited after 0 seconds with -177 (0xffffffffffffff4f)
<core_client_version>6.3.14</core_client_version>
Maximum disk usage exceeded


hombench_mtyka_foldcst_loopbuild_tex_cst_foldcst_loopbuild_tex_cst_t286__IGNORE_THE_REST_1ZITA_10_5159_1_0 exited after 4972.422 seconds with -177 (0xffffffffffffff4f)
<core_client_version>6.3.14</core_client_version>
Maximum disk usage exceeded

sin_cos_range ERROR: 1.#QNAN00 is outside of [-1,+1] sin and cos value legal range
sin_cos_range ERROR: 1.#QNAN00 is outside of [-1,+1] sin and cos value legal range
sin_cos_range ERROR: 1.#QNAN00 is outside of [-1,+1] sin and cos value legal range
[...] (repeated ~720 x)
sin_cos_range ERROR: 1.#QNAN00 is outside of [-1,+1] sin and cos value legal range

.Unhandled Exception Detected...
- Unhandled Exception Record -
Reason: Breakpoint Encountered (0x80000003) at address 0x7C90120E
#Engaging BOINC Windows Runtime Debugger...

According to dbg output, I'd bet the running thread's got a broken stack...

----

A bunch of hombench_tex_ tasks failed with "Incorrect function. - exit code 1" after 60-800 seconds; WinXP SP3, client 6.3.14 and Linux client 6.2.4:

hombench_tex_looprelax_tex_cst_oneparam_looprelax_tex_cst_t288__IGNORE_THE_REST_1T2MA_5_5137_1_1
hombench_tex_looprelax_tex_cst_oneparam_looprelax_tex_cst_t328__IGNORE_THE_REST_2CFXA_4_5154_1_0
hombench_tex_looprelax_tex_cst_oneparam_looprelax_tex_cst_t328__IGNORE_THE_REST_2CFXA_3_5154_1_0
hombench_tex_looprelax_tex_cst_oneparam_looprelax_tex_cst_t315__IGNORE_THE_REST_1KCXA_17_5148_1_0
hombench_tex_looprelax_tex_cst_oneparam_looprelax_tex_cst_t293__IGNORE_THE_REST_1VQ1A_2_5139_1_0

Peter
12) Message boards : RALPH@home bug list : Bug Reports for Minirosetta version 1.35 (Message 4232)
Posted 30 Sep 2008 by Pepo
Post:
One more -1073741819 (0xffffffffc0000005) error for hombench_mtyka_foldcst_boinc_test2_foldcst_simple_t317___4997_3_2, with large BOINC Windows Runtime Debugger output.

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x006AA016 read attempt to address 0x403E8A08

And the callstack looks weird - the accvio happened at the same address as in the Path7's case, but the call stacks are definitely different.

Peter
13) Message boards : RALPH@home bug list : Bug Reports for Minirosetta version 1.34 (Message 4231)
Posted 30 Sep 2008 by Pepo
Post:
I recieved a similar error message, on this WU

WARNING: Override of option -out:file:silent sets a different value
WARNING: Override of option -out:file:silent sets a different value

<file_xfer_error>
<file_name>hombench_mtyka_looprelax_test_full_2_looprelax_t326__IGNORE_THE_REST_1S1MA_7_4951_1_0_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>

Me too:

<core_client_version>6.2.4</core_client_version>

WARNING: Override of option -out:file:silent sets a different value
WARNING: Override of option -out:file:silent sets a different value
# cpu_run_time_pref: 14400
======================================================
DONE :: 1 starting structures 16363.7 cpu seconds
This process generated 2 decoys from 2 attempts
======================================================

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

<file_xfer_error>
<file_name>hombench_mtyka_looprelax_test_full_2_looprelax_t374__IGNORE_THE_REST_2FE7A_5_4954_1_2_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>


Peter
14) Message boards : RALPH@home bug list : Bug Reports for Rosetta version 5.98 (Message 4230)
Posted 30 Sep 2008 by Pepo
Post:
Had the same error:
ERROR:: Exit from: options.cc line: 525

Me too: t042_1_NMRREF_1_t015_1_S_00001_0000163IGNORE_THE_REST_040000_5065_48_0.

Peter
15) Message boards : RALPH@home bug list : Bug Reports for Minirosetta version 1.34 (Message 4203)
Posted 17 Sep 2008 by Pepo
Post:
hombench_mtyka_ralph_test1_foldcst_simple_t303___4839_2_0 prematurely exited, after 200 sec runtime (Windows XP host, own modified BCC 6.3.8):

Incorrect function. (0x1) - exit code 1 (0x1)
WARNING: Override of option -out:file:silent sets a different value

ERROR: unknown atom_name: PRO H
ERROR:: Exit from: c:cygwinhomeboincboinc_buildminirosettaminirosetta_1.34minisrccore/chemical/ResidueType.hh line: 928
called boinc_finish


Peter
16) Message boards : RALPH@home bug list : Bug Reports for Minirosetta version 1.34 (Message 4200)
Posted 11 Sep 2008 by Pepo
Post:
Similarly like mentioned in the Bug Reports for Minirosetta version 1.33 thread, my task fa_dis7-t313_-2008-9-4_4786_8_1 prematurely exited, after 5 sec runtime (Linux host, stock BCC 6.2.4):

<core_client_version>6.2.4</core_client_version>
process exited with code 1 (0x1, -255)

ERROR: Cannot open file /work/tex/projects/cm/benchmark/targets/t313_/native/T0313.pdb
ERROR:: Exit from: src/core/io/pdb/pose_io.cc line: 161
called boinc_finish


James Thompson mentioned that 1.34 should fix this error, apparently it did not (or it was not exactly the same error).

My wingman processed this WU with minirosetta 1.33 and failed with "Maximum CPU time exceeded", the result was reported just yesterday. As this WU is already older, actually from before this note "...I sent out a batch with options for minirosetta version 1.32 rather than version 1.33. The offending workunits have been removed from the queue...", I wonder whether the WU was left on the system by accident and survived the deletion.

Peter
17) Message boards : RALPH@home bug list : Bug Reports for Rosetta version 5.98 (Message 4154)
Posted 3 Jul 2008 by Pepo
Post:
The FRA_t451_CASP8_HYBRID_MANUAL_1_IGNORE_THE_RESTt451_1_axmin1_0001_4594_10_0 exited with code 1: "ERROR:: Exit from: barcode_classes.cc line: 657" after 73.5 seconds runtime. The same happened to wingman (both are Windows).

Peter
18) Message boards : RALPH@home bug list : Bug report for Minirosetta version 1.29 (Message 4148)
Posted 25 Jun 2008 by Pepo
Post:
Mini 1.29 deletes old database files – old db files downloaded again after reboot.

Obviously they're still being kept listed in client_state.xml... then it is not enough to just delete them.

Peter
19) Message boards : RALPH@home bug list : Bug report for Rosetta version 5.97 (Message 4144)
Posted 24 Jun 2008 by Pepo
Post:
t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2
di 24 jun 2008 20:22:51 CEST|ralph@home|Aborting task t419N_autoalign_IGNORE_THE_REST_renumbered_4285_6_2: exceeded disk limit: 569.28MB > 476.84MB

The t419N_autoalign_IGNORE_THE_REST_renumbered_4406_8_1: "Maximum disk usage exceeded". The same happened to all 3 wingmen (Mac, Linux, Vista).

Peter
20) Message boards : RALPH@home bug list : Bug report for Rosetta version 5.97 (Message 4139)
Posted 23 Jun 2008 by Pepo
Post:
There is still a possibility of getting access violations with the t405 jobs. We have to track down and fix the cause. What we are really concerned about is fixing the client stalling issue. This is a really bad problem since without any information sent back from the client, we can't determine the status of tasks and obviously a stalled client is a very bad situation.

If my tasks will stall again (as some already did in the past), what files from my slot/project folders would interest you?

Peter


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