Posts by AdeB

21) Message boards : RALPH@home bug list : minirosetta 1.90 (Message 4922)
Posted 11 Aug 2009 by AdeB
Post:
Big task?
1574065

<message>
Maximum memory exceeded
</message>


AdeB
22) Message boards : RALPH@home bug list : minirosetta 1.90 (Message 4920)
Posted 10 Aug 2009 by AdeB
Post:
5azu_I_20_T_ddg_predictions_lm_0.5_0.8_10_8709_run10_MUT.5azu_I_20_T_.out_12066_1_1

...
Setting up checkpointing ...
Setting up graphics native ...
ERROR:: Exit from: src/core/pack/task/ResfileReader.cc line: 987
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


AdeB
23) Message boards : RALPH@home bug list : minirosetta 1.90 (Message 4903)
Posted 2 Aug 2009 by AdeB
Post:
Add this one: 1573370 to the list.

1573375
lr8_rama_map_all_ss_iter08_rlbn_1bkr_IGNORE_THE_REST_NATIVE_12056_1_1


<core_client_version>6.4.5</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>

...
...
...

Native pose needed for OptionKeys::relax::constrain_relax_to_native_coords
ERROR:: Exit from: ..\..\src\protocols\relax\ClassicRelax.cc line: 544
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>

24) Message boards : RALPH@home bug list : minirosetta 1.90 (Message 4899)
Posted 1 Aug 2009 by AdeB
Post:
All recent workunits are failing quickly on Mac on file errors

1572293
1572221

(plus some others)

Sample output:

</stderr_txt>
<message>
<file_xfer_error>
<file_name>1a2p_A_30_S_ddg_predictions_0.3_1_8_local_min_test_sc_min_input_73009__12047_1_0_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>


I have the same error in these two tasks (Linux):
1572053
1572278

All these tasks finish after exactly 1201 seconds!

reached end of minirosetta::main()
======================================================
DONE ::     1 starting structures     1201 cpu seconds
This process generated      1 decoys from       1 attempts
======================================================

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

</stderr_txt>
<message>
<file_xfer_error>
  <file_name>1ten_L_61_A_ddg_predictions_0.2_10_8_local_min_test_sc_min_input_73009__12046_1_0_0</file_name>
  <error_code>-161</error_code>
</file_xfer_error>

</message>


AdeB
25) Message boards : RALPH@home bug list : Minirosetta 1.83-1.85 (Message 4888)
Posted 26 Jul 2009 by AdeB
Post:
1.85 error

Task: 1563379
Workunit: lr8_seq_score12_noss_rlbn_1vkk_IGNORE_THE_REST_NATIVE_11954_1

[color=red]ERROR: Option matching -in:detect_disulfides not found in command line top-level context
[/color]


AdeB
26) Message boards : RALPH@home bug list : Minirosetta 1.81 (Message 4882)
Posted 23 Jul 2009 by AdeB
Post:
This is a 1.83 WU error

<core_client_version>6.4.7</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
[2009- 7-23 9:34:44:] :: BOINC:: Initializing ... ok.
[2009- 7-23 9:34:44:] :: 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 -detect_disulphides not found in command line top-level context

See this WU


The same error here

AdeB
27) Message boards : RALPH@home bug list : Minirosetta 1.81 (Message 4880)
Posted 16 Jul 2009 by AdeB
Post:
I never saw this error before:
In task 1548231 (frb_0_8_cl1_5_hb_t305__IGNORE_THE_REST_2G59A_7_11642_1_0):

<![CDATA[
<message>
Maximum memory exceeded
</message>


This is on a PC with 512MB memory, AMD Athlon XP running linux.

AdeB
28) Message boards : RALPH@home bug list : Minirosetta 1.81 (Message 4876)
Posted 14 Jul 2009 by AdeB
Post:
Error in task 1543648.

Hbond tripped: [2009- 7-13  0:35: 0:]

ERROR: dis==0 in pairtermderiv!
ERROR:: Exit from: src/core/scoring/methods/PairEnergy.cc line: 334
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

AdeB
29) Message boards : RALPH@home bug list : minirosetta 1.80 (Message 4853)
Posted 1 Jul 2009 by AdeB
Post:
same here: task 1523280
ERROR: in::file::boinc_wu_zip /work/rvernon/disulfides/TARGETS/zipfiles/zipfile.1yl2.cs.set1.zip does not exist!
ERROR:: Exit from: src/apps/public/boinc/minirosetta.cc line: 114
BOINC:: Error reading and gzipping output datafile: default.out


AdeB
30) Message boards : RALPH@home bug list : minirosetta_1.72 (Message 4831)
Posted 5 Jun 2009 by AdeB
Post:
SIGSEGV: segmentation violation in all tasks i've got.

tasks: 1472182, 1472199 and 1472248.

This is on AMD Athlon XP running Linux.

AdeB
31) Message boards : RALPH@home bug list : minirosetta 1.58 (Message 4707)
Posted 15 Feb 2009 by AdeB
Post:
This looks like a long-running model: resultid=1309799
Name: loopbuild_chunk_2_7_B_hb_t286__IGNORE_THE_REST_1YZFA_5_7846_1_0
Outcome: Validate error
stderr out:
. . .
BOINC:: Worker startup. 
Starting watchdog...
Watchdog active.
# cpu_run_time_pref: 14400
Hbond tripped !!!
BOINC:: CPU time: 28889.1s, 14400s + 14400s[2009- 2-14 15:24: 2:] :: BOINC 
======================================================
DONE ::     2 starting structures  28889.1 cpu seconds
This process generated      3 decoys from       3 attempts
======================================================
called boinc_finish


AdeB
32) Message boards : RALPH@home bug list : minirosetta 1.58 (Message 4695)
Posted 13 Feb 2009 by AdeB
Post:
Hello,

And the same error here: loopbuild_chunk_2_7_hb_t332__IGNORE_THE_REST_1X7OA_7_7809_1_0
ERROR: [ERROR] Error opening RBSeg file 'core_1X7OA_7_noloop_loops.txt'
ERROR:: Exit from: src/protocols/loops/LoopClass.cc line: 443
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


Gentoo linux - Boinc 5.10.45

AdeB
33) Message boards : RALPH@home bug list : minirosetta v1.55 bug thread (Message 4625)
Posted 31 Jan 2009 by AdeB
Post:
since we are on 1.56 now, should there be a new thread for that?

btw..very interesting color choice for the accepted energy line and the other line above the rmsd box. what does the blue and yellow mean and isn't there a purplish color in there as well?


Nope - its just prettyness. No extra meaning i'm afraid.


Triggered by this message i tried to look at the graphics of task 1285083, but the graphics screen didn't open.
I'm running Gentoo linux on a AMD Athlon XP with 512MB memmory.

In version 1.54 the graphics did work, the only problem there (and in previous versions) was the presentation of Total credit and RAC.
34) Message boards : RALPH@home bug list : minirosetta v1.55 bug thread (Message 4619)
Posted 31 Jan 2009 by AdeB
Post:
This task was valid and it got credit, but there are some error messages in stderr out:

...
Starting work on structure: S_shuffle_00012 <--- F_00007_0000861_0
Fullatom mode .. 
Hbond tripped.

ERROR: dis==0 in pairtermderiv!
ERROR:: Exit from: src/core/scoring/methods/PairEnergy.cc line: 338
called boinc_finish
...


AdeB
35) Message boards : RALPH@home bug list : minirosetta v1.54 bug thread (Message 4585)
Posted 28 Jan 2009 by AdeB
Post:

I am using Ubuntu 8.10, two core system with 2G memory, disk space 58.5 G

shmax = 33554432
shall = 2097152
shmmni = 4096

the citation's note at the top on determining the values did work on Ubuntu ... if someone has another version of Linux could you post your numbers?

sysctl -A | grep shm

is the command to run in terminal, you may get some access errors which I suppose you could supress by running it as sudo



Both of my Gentoo Linux systems (Athlon XP with 512M memory) show exact the same numbers:

kernel.shmmax = 33554432
kernel.shmall = 2097152
kernel.shmmni = 4096
36) Message boards : RALPH@home bug list : minirosetta v1.47 bug thread (Message 4424)
Posted 17 Dec 2008 by AdeB
Post:
Another long task - over 10 hours for 1 decoy

What surprises me is that boinc during those 10 hours never switched to an other project. There was work for other projects and [Switch between applications every] is set to 120 minutes. It looks like this task 'hijacked' my PC until it was finished. Should it behave like this?

I also saw the strange values for Total Credit and RAC Phil is describing. Also on a linux PC.

AdeB
37) Message boards : RALPH@home bug list : minirosetta v1.46 bug thread (Message 4406)
Posted 13 Dec 2008 by AdeB
Post:
Error in ccc_1_8_mammoth_mix_cst_homo_bench_foldcst_chunk_general_mammoth_cst_t302__mtyka_IGNORE_THE_REST_2CRPA_8_6270_1_0.

stderr out:
<core_client_version>6.2.15</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>

ERROR: not able to build valid fold-tree in JumpingFoldConstraints::setup_foldtree
ERROR:: Exit from: src/protocols/abinitio/LoopJumpFoldCst.cc line: 108
called boinc_finish
# cpu_run_time_pref: 14400

</stderr_txt>
]]>


AdeB
38) Message boards : RALPH@home bug list : minirosetta v1.41 bug thread (Message 4354)
Posted 21 Nov 2008 by AdeB
Post:
task id: 1184232
workunit: rlb_test_ralph_splitterms2_rlb_5cro_IGNORE_THE_REST_DECOY_5551_1

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
39) Message boards : RALPH@home bug list : Bug Reports for Minirosetta v1.39 (Message 4329)
Posted 1 Nov 2008 by AdeB
Post:
resultid=1175219

stderr out:
<core_client_version>5.10.45</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)
</message>
<stderr_txt>
# cpu_run_time_pref: 14400
SIGSEGV: segmentation violation
Stack trace (9 frames):
[0x8b104a7]
[0x8b3aba0]
[0xffffe420]
[0x82c2ab0]
[0x82c171a]
[0x819f626]
[0x804c2ea]
[0x8b9669c]
[0x8048111]

Exiting...

</stderr_txt>
]]>
40) Message boards : RALPH@home bug list : Bug reports for minirosetta_split_terms v 1.02 (Message 4323)
Posted 29 Oct 2008 by AdeB
Post:
workunit 1174580

stderr out:
<core_client_version>5.10.45</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
# cpu_run_time_pref: 14400

ERROR: unknown atom_name: LEU C4*
ERROR:: Exit from: src/core/chemical/ResidueType.hh line: 960

called boinc_finish

</stderr_txt>
]]>


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