Posts by Snagletooth

1) Message boards : Cafe RALPH : 5 years with Ralph (Message 6528)
Posted 12 Apr 2018 by Snagletooth
Post:
I was using a ppc Mac on Rosetta and there was some bug that only effected the particular os I was on so to Ralph I came. That old Mac has been gone a while now.
2) Message boards : Cafe RALPH : 5 years with Ralph (Message 6526)
Posted 10 Apr 2018 by Snagletooth
Post:
Coming up on 11 years for me. How time flies.

Snags
3) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6069)
Posted 19 Mar 2016 by Snagletooth
Post:
So far all "des5ralph_design5" tasks have failed and two of the three currently processing are exhibiting some curious behavior. Those that failed ended with:

std::cerr: Exception was thrown:
Cannot normalize xyzVector of length() zero


My target runtime is four hours. All of the tasks currently processing have exceeded that by two, eight and twenty-seven hours. According to the properties tab no checkpoints have been taken. I have confirmed via the computers' Activity Managers that all tasks are currently using the cpu. In the stderr out of the tasks that failed the lines "Starting watchdog...Watchdog active." do appear so presumably the watchdog is set but not working in the tasks I'm running now.

Even more curious, two of the tasks on two different machines, with different versions of the Mac OS and different versions of BOINC, are recording elapsed times of less than the cpu times. Even my usually creative imagination is stumped by this.

It seems fairly obvious that these tasks will have to be aborted but I'll hold off a bit in case anyone has any questions or DEK wants to try and retrieve a file for closer examination.

Best,
Snags
4) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6042)
Posted 5 Feb 2016 by Snagletooth
Post:
I'm getting quick client/computer errors for the backrub_design tasks. From the stderr out:

minirosetta_3.71_x86_64-apple-darwin(50310,0x7fff732a2300) malloc: *** error for object 0x4b4fc3ef02e87d9a: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug


Also gaurav_rsmn_0161_65_daa2_2_SAVE_ALL_OUT_20296_50_0 is claiming a file transfer error:

# cpu_run_time_pref: 14400
reached end of minirosetta::main()
======================================================
DONE :: 2 starting structures 13443.3 cpu seconds
This process generated 13 decoys from 13 attempts
======================================================
BOINC :: WS_max 2.65622e+08

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

</stderr_txt>
<message>
upload failure: <file_xfer_error>
<file_name>gaurav_rsmn_0161_65_daa2_2_SAVE_ALL_OUT_20296_50_0_0</file_name>
<error_code>-161 (not found)</error_code>
</file_xfer_error>


Are those results truly lost?
5) Message boards : Number crunching : Rosetta mini 3.68 about 50% of WUs in "Validate error" state (Message 5964)
Posted 6 Jan 2016 by Snagletooth
Post:
!00% success rate (completed and validated) so far on my Mac. One of mine (there may be more, haven't time to trawl through the whole list) was a resend which had ended quickly (68.02 cpu sec) on a Windows machine and received a validate error. The sderr out included this bit:

ERROR: Can't create a polymer bond after residue 4 due to incompatible type: LYS:CtermProteinFull
ERROR:: Exit from: ..\..\..\src\core\conformation\Conformation.cc line: 845
DummyMover::apply() should never have been called! (JobDistributor/Parser should have replaced DummyMover.)

ERROR: false
ERROR:: Exit from: ..\..\..\src\apps\public\boinc\minirosetta.cc line: 96
DummyMover::apply() should never have been called! (JobDistributor/Parser should have replaced DummyMover.)


repeat, repeat, repeat...before ending with:

DONE :: 99 starting structures 1201 cpu seconds
This process generated 99 decoys from 99 attempts



It ran 5248 cpu seconds on my machine successfully generating two decoys from two attempts. Click the link above ("one of mine") to see the details.
6) Message boards : RALPH@home bug list : MiniRosetta Beta 3.26 (Message 5547)
Posted 29 Jun 2012 by Snagletooth
Post:
I'm running 3.26 version. Why not 3.31??


I have this question as well. The 3.30 version included the fix for the Mac slowdown problem which effected every type of work unit. It (the fix) presumably will be included in every new version going forward so why would it not be used on Ralph?
7) Message boards : RALPH@home bug list : MiniRosetta Beta 3.26 (Message 5514)
Posted 5 Apr 2012 by Snagletooth
Post:
CASP9_bv_benchmark_hybridization_run48_T0518_0_C2_SAVE_ALL_OUT_IGNORE_THE_REST_17843_2_0
ERROR: [ERROR] Error opening symmetry file '/work/dimaio/projects/casp9/T0518/run_12/symmdef/3h3lA_201_C2.symm'
ERROR:: Exit from: src/core/conformation/symmetry/SymmData.cc line: 535
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

CASP9_bv_benchmark_hybridization_run48_T0563_0_C3_SAVE_ALL_OUT_IGNORE_THE_REST_17886_5_0
ERROR: [ERROR] Error opening symmetry file '/work/dimaio/projects/casp9/T0563/run_12/symmdef/1unbA_301_C3.symm'
ERROR:: Exit from: src/core/conformation/symmetry/SymmData.cc line: 535
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

CASP9_bv_benchmark_hybridization_run48_T0521_0_C2_SAVE_ALL_OUT_IGNORE_THE_REST_17845_6_0
ERROR: [ERROR] Error opening symmetry file '/work/dimaio/projects/casp9/T0521/run_12/symmdef/3l19B_102_C2.symm'
ERROR:: Exit from: src/core/conformation/symmetry/SymmData.cc line: 535
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

The C1 units appear to be fine on my Mac.
CASP9_bv_benchmark_hybridization_run48_T0561_2_C1_SAVE_ALL_OUT_IGNORE_THE_REST_17884_5_0

Currently crunching another C1 so we'll see if it holds up. It's about 45 minutes in with a cpu preferred runtime of 4 hours.

Best,
Snags

8) Message boards : RALPH@home bug list : RosettaMini Beta 3.24 (Message 5497)
Posted 1 Apr 2012 by Snagletooth
Post:
t7_fd.c.82-85.i.3-74_abinitio_SAVE_ALL_OUT_17707_xxx

All of these are failing immediately on my mac with:

ERROR: in::file::boinc_wu_zip design_62_data.zip does not exist!
ERROR:: Exit from: src/apps/public/boinc/minirosetta.cc line: 162
9) Message boards : RALPH@home bug list : RosettaMini Beta 3.24 (Message 5487)
Posted 27 Mar 2012 by Snagletooth
Post:
test_pose_BB_perturbation_JOBID_SAVE_ALL_OUT_17702_91_0

process exited with code 1 (0x1, -255)

ERROR: Cannot open PDB file "pose_BB"
ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 184
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish



10) Message boards : RALPH@home bug list : Rosetta Mini Beta 3.19 (Message 5447)
Posted 28 Jan 2012 by Snagletooth
Post:
Looks like a bad batch:

2XY2_boinc_01af25c3445c8a72c5666274d71d0bc4_abinitio_cmiles_IGNORE_THE_REST_16338_6

ERROR: unrecognized aa NAG
ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 643
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


2XZR_boinc_2XZR_abinitio_a14fd156c09cffe3e75b353e016d12e9_abinitio_cmiles_IGNORE_THE_REST_16356_7

ERROR: ERROR: FragmentIO: could not open file aa2XZR.9mers
ERROR:: Exit from: src/core/fragment/FragmentIO.cc line: 233
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


Best,
Snags
11) Message boards : RALPH@home bug list : Minirosetta 3.00 (Message 5248)
Posted 31 Mar 2011 by Snagletooth
Post:
celldivs_RL5_1de2_1iu9_ProteinInterfaceDesign_21Feb2011_15159_1_0

cpu time: 10.81717 seconds

exit code 1

ERROR: hashing_constraints is not known to the MoverFactory. Was it registered via a MoverRegistrator in one of the init.cc files (devel/init.cc or protocols/init.cc)?
ERROR:: Exit from: src/protocols/moves/MoverFactory.cc line: 80
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

12) Message boards : RALPH@home bug list : minirosetta 2.17 (Message 5225)
Posted 29 Nov 2010 by Snagletooth
Post:
Validate errors:

lrm_je9o_combined_torsion_dun02_it01_run01_A_rlbn_1utg_IGNORE_THE_REST_NATIVE_NOCON_15096_1
13) Message boards : RALPH@home bug list : minirosetta 2.17 (Message 5219)
Posted 7 Nov 2010 by Snagletooth
Post:
@Snags

Changed a preference setting in BOINC.
Was switching tasks every 60 mins changed that to every 4hrs to try and get tasks under control. Had 6-8 open in various stages at any one time under old setting.
This could account for the bizarre clock time.


Hey, greg be - I would imagine that having fewer wus in a "waiting to run" status would lessen the reliance on a swap file and thus increase overall efficiency (assuming you've got "leave apps in memory" set to yes). Is that what you were going for? Have the times improved?

Best,
Snags
14) Message boards : RALPH@home bug list : minirosetta 2.17 (Message 5207)
Posted 4 Nov 2010 by Snagletooth
Post:
Remember that the elapsed time is wall clock time whereas the preference setting is for cpu time. Open the properties window for that particular task to see how much cpu time it has accumulated.

greg_be, that task completed 4 models in 18418.4 cpu seconds so it appears to have honored your preference of 21600 cpu seconds. If the discrepancy between cpu and elapsed time is dramatically different from from what you are used to seeing then it might be wise to open up task manager (or whatever it's called in Windows) and make sure some new or errant process isn't eating up a bunch of cpu cycles.

Best,
Snags



15) Message boards : RALPH@home bug list : Minirosetta 2.16 (Message 5198)
Posted 24 Oct 2010 by Snagletooth
Post:
validate error for WU created on the 23rd (after TJ reported a fix):

T0586_AD_rs_stg0_lrlxMultiCst_t000__casp9__aln2_SAVE_ALL_OUT_14982_111_0


Best,
Snags
16) Message boards : RALPH@home bug list : Minirosetta 2.16 (Message 5190)
Posted 21 Oct 2010 by Snagletooth
Post:
And another validate error (not a resend, created and returned today):

T0594_AB_rs_stg0_lrlxMultiCst_t000__casp9__aln1_SAVE_ALL_OUT_14971_712_0


Snags
17) Message boards : RALPH@home bug list : Minirosetta 2.14 (Message 5165)
Posted 6 Sep 2010 by Snagletooth
Post:
SAXS-rescore-1eovA__14879_15

Mon Sep 6 12:03:24 2010 ralph@home Output file SAXS-rescore-1eovA__14879_15_0_0 for task SAXS-rescore-1eovA__14879_15_0 absent

======================================================
DONE :: 1 starting structures 12857.1 cpu seconds
This process generated 6 decoys from 6 attempts
======================================================

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

</stderr_txt>
<message>
<file_xfer_error>
<file_name>SAXS-rescore-1eovA__14879_15_0_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>
18) Message boards : RALPH@home bug list : minirosetta 2.05 (Message 5100)
Posted 21 Mar 2010 by Snagletooth
Post:
compute error on my mac: placestub_alt_denovo_1zvy_2quo_ProteinInterfaceDesign_19Mar2010_14558_2_0
ERROR: Value of inactive option accessed: -holes:dalphaball
SIGSEGV: segmentation violation
19) Message boards : RALPH@home bug list : minirosetta 2.05 (Message 5064)
Posted 5 Feb 2010 by Snagletooth
Post:
one more validate error:
1l33A_boinc_70pct_loopbuild_threading_cst_relax_tex_IGNORE_THE_REST_14292_3_0
20) Message boards : RALPH@home bug list : minirosetta 2.05 (Message 5062)
Posted 5 Feb 2010 by Snagletooth
Post:
more validate errors:

dckCFA_1sq2_1xg8_0029_0002_ProteinInterfaceDesign_4Feb2010_14289_3


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