Posts by Brotherbard

1) Message boards : RALPH@home bug list : minirosetta v1.55 bug thread (Message 4610)
Posted 30 Jan 2009 by Profile Brotherbard
Post:
The 4 workunits have run to completion successfully. http://ralph.bakerlab.org/results.php?userid=82

--Nathan
2) Message boards : RALPH@home bug list : minirosetta v1.55 bug thread (Message 4608)
Posted 29 Jan 2009 by Profile Brotherbard
Post:
I have 4 1.55 workunits that all start great even with weekday time limits set. Still waiting for them to finish.

Looking at the graphics app it looks like it has the same error as the main app. Here is the gdb output:

Initializing options.... ok 
Loaded options.... ok 
Processed options.... ok 
core.init: command: /Library/Application Support/BOINC Data/projects/ralph.bakerlab.org/minirosetta_graphics_1.54_i686-apple-darwin
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1656248255 seed_offset=0 real_seed=-1656248255
Initializing random generators... ok 
core.init.random: RandomGenerator:init: Normal mode, seed=-1656248255 RG_type=mt19937
Initialization complete. 
Opened semaphore

Breakpoint 1, 0x9603b4a9 in malloc_error_break ()
(gdb) bt
#0  0x9603b4a9 in malloc_error_break ()
#1  0x96036497 in szone_error ()
#2  0x95f60463 in szone_free ()
#3  0x95f602cd in free ()
#4  0x000a7cb6 in WEEK_PREFS::~WEEK_PREFS ()
#5  0x007d24a9 in GLOBAL_PREFS::~GLOBAL_PREFS ()
#6  0x001ad5a8 in get_shmem_name ()
#7  0x001ad634 in boinc_graphics_get_shmem ()
#8  0x00085dd8 in protocols::boinc::Boinc::attach_shared_memory ()
#9  0x000074b9 in app_graphics_init ()
#10 0x0000ca75 in boinc_graphics_loop ()
#11 0x000087f6 in main ()

And the stderrgfx.txt has a "Non-aligned pointer being freed (2)" error for each of the weekday setting just like the science app did.

The graphics start up fine if the weekday prefs are not set when BOINC first starts up. But if the prefs were set when I started BOINC then even if I reset the preferences the graphics apps will still not start up.

--Nathan

3) Message boards : RALPH@home bug list : minirosetta v1.54 bug thread (Message 4595)
Posted 28 Jan 2009 by Profile Brotherbard
Post:
I have 8 minirosetta 1.54 workunits from r@h that have completed successfully now without failures.

--Nathan

4) Message boards : RALPH@home bug list : minirosetta v1.54 bug thread (Message 4590)
Posted 28 Jan 2009 by Profile Brotherbard
Post:
I ran the minirosetta 1.54 app in gdb and here is the stack trace:

Breakpoint 1, 0x9603b4a9 in malloc_error_break ()
(gdb) bt
#0  0x9603b4a9 in malloc_error_break ()
#1  0x96036497 in szone_error ()
#2  0x95f60463 in szone_free ()
#3  0x95f602cd in free ()
#4  0x005d8576 in WEEK_PREFS::~WEEK_PREFS () at /usr/include/c++/4.0.0/bits/basic_string.h:227
#5  0x00d13e76 in GLOBAL_PREFS::~GLOBAL_PREFS ()
#6  0x00103d8d in protocols::boinc::Boinc::initialize_worker () at /usr/include/c++/4.0.0/bits/basic_string.h:227
#7  0x000034a1 in main () 

And here is the beginning of stderr.txt

BOINC:: Initializing ... ok.
[2009- 1-28  8:51: 4:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
minirosetta_1.54_i686-apple-darwin(1142,0xa07b2720) malloc: *** error for object 0x1a3d2e0: Non-aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
minirosetta_1.54_i686-apple-darwin(1142,0xa07b2720) malloc: *** error for object 0x1a3c270: Non-aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully.

I do have two day-of-the-week overrides set and turning them off fixed the problem! I had one weekday set in CPU Usage and one in Network Usage and there were two malloc errors, a quick test shows you get one error from each weekday set. The only reason I had them set was because I was playing with the GUI-RPCs, I don't actually need them for anything. Also the daily time settings do not have this problem.

I'm not sure if minirosetta is doing anything special with the global prefs, I would suspect this is a BOINC defect. I'm running BOINC 6.2.18, and have not tested this on other versions, nor do I have work from any other project on this machine at the moment so cannot test if other projects fail like this too.

--Nathan

5) Message boards : RALPH@home bug list : minirosetta v1.54 bug thread (Message 4589)
Posted 28 Jan 2009 by Profile Brotherbard
Post:
I ran the minirosetta 1.54 app in gdb and here is the stack trace:

[code]Breakpoint 1, 0x9603b4a9 in malloc_error_break ()
(gdb
6) Message boards : RALPH@home bug list : minirosetta v1.54 bug thread (Message 4587)
Posted 28 Jan 2009 by Profile Brotherbard
Post:
My Mac Pro was set to:
	kern.sysv.shmall: 8192
	kern.sysv.shmseg: 32
	kern.sysv.shmmni: 128
	kern.sysv.shmmin: 1
	kern.sysv.shmmax: 33554432

I changed it to match what Paul has on his Mac but that did not fix anything.

--Nathan

7) Message boards : RALPH@home bug list : minirosetta v1.54 bug thread (Message 4568)
Posted 27 Jan 2009 by Profile Brotherbard
Post:

Did you ever increase the size of the shared memory segment?

It is POSSIBLE that the original configuration is too limiting and that may be causing the error ... there are directions for increasing the size that *MAY* help ...


Yes, I did that some time ago.

When I checked it this morning, I had three workunits (1 from ralph and 2 from rosetta) that were stuck at a very low completion (around 0.111 to 0.240) and the two rosetta ones were just shy of 8 hours with my time setting at 2 hours. Show graphics does not show anything.

I needed to reboot due to installing some system updates and when BOINC came back up they started over at zero time and two of them failed right away, with one getting stuck again. I'm down to just this one workunit on my machine and I noticed that it is running around 200% CPU usage. It appears that both the main thread and the watchdog thread are stuck in __spin_lock.

--Nathan

8) Message boards : RALPH@home bug list : minirosetta v1.54 bug thread (Message 4563)
Posted 27 Jan 2009 by Profile Brotherbard
Post:
Having problems with Mac OS X on a Mac Pro on both ralph and rosetta. So far not a single 1.54 task has completed successfully. I've stopped downloading more.

http://ralph.bakerlab.org/results.php?hostid=16351
http://boinc.bakerlab.org/rosetta/results.php?hostid=585071


9) Message boards : RALPH@home bug list : removed from memory by benchmark (Message 817)
Posted 5 Mar 2006 by Profile Brotherbard
Post:
When the benchmark ran it forced RALPH out of memory. Not sure how this can be managed better.


This was a problem with BOINC not with the science apps, I'm not sure which version fixed it (it might be in the development version) but try updating to the current version for your computer.

--Nathan
10) Message boards : RALPH@home bug list : Report \"stuck at 1%\" bugs here (Message 790)
Posted 2 Mar 2006 by Profile Brotherbard
Post:
If it is a version 4.90 WU, abort it. If it is a 4.91 WU then try restarting it by restarting BOINC.


It's on a Mac OS X 10.4.5, RAPLH v 4.85

--Nathan
11) Message boards : RALPH@home bug list : Report \"stuck at 1%\" bugs here (Message 787)
Posted 2 Mar 2006 by Profile Brotherbard
Post:
The WU # 11525 1vdi_loop_1m5xA__1001_233_5 has been hung at 1% for 13 hours now.

In the graphics the model is not changing and the stats show: Stage: Relax, Model: 1, Step: 0.

The stderr file is filled with "Could not identify element type from chemical symbol. Setting as undefined". And both the stderr and sdtout files have not been modified since about a half hour from the start of the WU.

It is still running.

--Nathan
12) Message boards : Current tests : Mac OSX graphics (Message 202)
Posted 18 Feb 2006 by Profile Brotherbard
Post:
One more suggestion: When resizing the window constrain the width and height ratio to be the same as the view.

--Nathan
13) Message boards : Current tests : Mac OSX graphics (Message 201)
Posted 18 Feb 2006 by Profile Brotherbard
Post:
The graphics come up fine, but when you close them or exit the screensaver, the little icon in the dock stays there, and if you choose quit (from the menu you get when option/right-click the icon), the workunit restarts.


What you are quitting is the science application itself, there is no separate graphics application. Normally Mac OS X will not show applications that have no user interface in the Dock, so the science app has been hidden before. When you press the 'Show Graphics' button the science app creates and shows a window, therefore it's now an app with a user interface and is added to the Dock.

For OS X applications if the programmers wanted to stop the app from showing in the Dock they would set LSUIElement to 1 in the Info.plist file. This creates an Agent, a program with no menu and no Dock icon but can show a window and have user interaction. However BOINC uses UNIX processes and I'm not sure how to configure those. Here is some info on Info.plist files in flat executables that might help the developers.

--Nathan
14) Message boards : Current tests : Mac OSX graphics (Message 195)
Posted 18 Feb 2006 by Profile Brotherbard
Post:
Some suggestions:

1) After rotating/moving/zooming the native structure it would be nice to have a way to return the view back to the default position. Maybe use the spacebar or return, or just double click on it.

2) Include the work unit name and ID, also possibly include the host ID, so if someone sends in a screen capture you have all the information in case the participant forgets to include it.

3) Next to the percent complete include the status (Running, Preempted, Suspended by User, .. etc)

4) The Total credit and RAC don't need that many decimal places, the web sites and BOINC Manager only use 2 digits past the decimal point.


Question: Should the Accepted Energy be a negative value?

--Nathan
15) Message boards : Current tests : Mac OSX graphics (Message 20)
Posted 16 Feb 2006 by Profile Brotherbard
Post:
We have graphics for OSX 10.3+ now!


very cool!

just downloaded my first wu and the graphics come up. thanks :)

--Nathan






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