minirosetta 1.58

Message boards : RALPH@home bug list : minirosetta 1.58

To post messages, you must log in.

1 · 2 · 3 · 4 . . . 5 · Next

AuthorMessage
mtyka
Volunteer moderator
Project developer
Project scientist

Send message
Joined: 19 Mar 08
Posts: 79
Credit: 0
RAC: 0
Message 4642 - Posted: 1 Feb 2009, 23:33:22 UTC

Hopefully all the graphics work now (no more blackout current windows).

As always, your feedback is highly appreciated !

Mike
ID: 4642 · Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 13 Jan 09
Posts: 80
Credit: 246,177
RAC: 0
Message 4644 - Posted: 1 Feb 2009, 23:53:12 UTC - in response to Message 4642.  

In the Message Boards: RALPH@home bug list forum, you might want to check if some of the older threads still need stickies, such as:

Bug Reports for Ralph Server Update to BOINC version 5.9.2
ID: 4644 · Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 13 Jan 09
Posts: 80
Credit: 246,177
RAC: 0
Message 4648 - Posted: 2 Feb 2009, 6:44:05 UTC - in response to Message 4642.  

Looks like you don't have a link to the 1.58 bugs thread on your home page yet.
ID: 4648 · Report as offensive    Reply Quote
Profile feet1st

Send message
Joined: 7 Mar 06
Posts: 312
Credit: 110,522
RAC: 0
Message 4654 - Posted: 2 Feb 2009, 20:44:31 UTC
Last modified: 2 Feb 2009, 20:48:31 UTC

I finally decided to take the time to report this petty issue. Note that I didn't have a v1.58 task to take the screen shot from at the time, but seems to be the same scaling issue there from what I've seen so far. This has been the case for quite some time in the graphic. At least on my machines. The specific machine, Rosetta version, task type all seem to have the same problem.

I use Windows XP, and display resolution of 1024 x 768 which is pretty standard I believe. By default, when I open the graphic of a running task, it comes up to a less then full screen window (see image below). And if you note the title bar seems to be scaled in as part of the low energy and the RMSD, perhaps all boxes on the top half of the graphic. The low energy box and the Native box should have the same displayable height. But they don't.

As this one ran on 1.56, it wasn't showing an RMSD history at all. But if it were, you'd see it take longer to appear in the display then the energy graph. And if you maximize to full screen, you will see more of the RMSD history (the title bar being scaled to less of the window leaves more room to show the RMSD), then with the original window size.

Let me know if I'm the lone wolf on this issue or what further video or other details may be relevant.


ID: 4654 · Report as offensive    Reply Quote
I _ quit

Send message
Joined: 13 Jan 09
Posts: 44
Credit: 88,562
RAC: 0
Message 4655 - Posted: 2 Feb 2009, 21:58:17 UTC - in response to Message 4654.  
Last modified: 2 Feb 2009, 21:58:39 UTC

Feet1st, both ralph and rosie open the graphics in a reduced window on my system and i am running wide screen 1680 x1050.

once i click on the the windows box to bring it to full screen it does.
ID: 4655 · Report as offensive    Reply Quote
Profile feet1st

Send message
Joined: 7 Mar 06
Posts: 312
Credit: 110,522
RAC: 0
Message 4656 - Posted: 2 Feb 2009, 22:30:33 UTC

"...it does" what when maximized? Scale properly? My "square" boxes still aren't square, they are short by the thickness of the titlebar.
ID: 4656 · Report as offensive    Reply Quote
Aegis Maelstrom

Send message
Joined: 19 Jan 09
Posts: 12
Credit: 4,751
RAC: 0
Message 4657 - Posted: 2 Feb 2009, 23:02:31 UTC
Last modified: 2 Feb 2009, 23:07:24 UTC

@Feel1st: Hi there, I haven't noticed it before but I have the same on my widescreen, Win XP SP2, task lr6_E_score12.

It looks as if the top of the Ralph graphics is consumed by the title (usually blue) bar of the viewer application.

The same model when displayed as a screensaver (without the title bar) looks O.K.
ID: 4657 · Report as offensive    Reply Quote
Evan

Send message
Joined: 23 Dec 07
Posts: 75
Credit: 69,584
RAC: 0
Message 4658 - Posted: 2 Feb 2009, 23:11:41 UTC - in response to Message 4654.  

Feet1st I am also using XP with the same resolution. On full screen the native box is approximately 6 cm high while the low energy box is about 5 cm. The energy graph takes a fair time to appear from the left and the rmsd graph takes even longer as you have described. It is probably being exemplified because I am going through some slow moving proteins (csttest)on 1.57.
ID: 4658 · Report as offensive    Reply Quote
I _ quit

Send message
Joined: 13 Jan 09
Posts: 44
Credit: 88,562
RAC: 0
Message 4659 - Posted: 3 Feb 2009, 1:06:44 UTC
Last modified: 3 Feb 2009, 1:14:15 UTC

i see in the rosie graphics the same size of boxes for low energy and native models as those here on ralph. 6cm for low energy and 7cm for native(not including the extra mm's) on both rosie and here on ralph. the low energy model here on ralph looks a bit close to the top of the box vs rosie. but then again its hard to compare two different proteins and their rotations to each other.

i am noticing that the top of the model for low energy is getting clipped by the title bar here on ralph. this is in the 1.54 rosie and the 1.56 ralph. I also started my first 1.58 and see the same dimensions and the same issue that the top of whatever strand is at the top of the low energy box gets a few mm's cut off of it if it happens to be a ribbon strand that is in a long vertical loop. in stick form the model fits into the box. box size did not change.
ID: 4659 · Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 13 Jan 09
Posts: 80
Credit: 246,177
RAC: 0
Message 4681 - Posted: 11 Feb 2009, 12:47:19 UTC - in response to Message 4642.  

1.58 errors are still being reported in the thread for 1.55 errors, since there's no reference to the 1.58 errors thread on the home page.
ID: 4681 · Report as offensive    Reply Quote
Profile Conan
Avatar

Send message
Joined: 16 Feb 06
Posts: 345
Credit: 1,333,577
RAC: 5
Message 4685 - Posted: 12 Feb 2009, 3:51:02 UTC
Last modified: 12 Feb 2009, 3:55:55 UTC

Have just had 9 errors for 1.58 with this error

process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
[2009- 2-11 13:51:53:] :: BOINC:: Initializing ... ok.
[2009- 2-11 13:51:53:] :: 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..
Trying to access options object.
Success.
src/protocols/abinitio/AbrelaxApplication.cc:217
src/protocols/abinitio/AbrelaxApplication.cc:237
src/protocols/abinitio/AbrelaxApplication.cc:295
src/protocols/abinitio/AbrelaxApplication.cc:317
src/protocols/abinitio/AbrelaxApplication.cc:324
src/protocols/abinitio/AbrelaxApplication.cc:326
src/protocols/abinitio/AbrelaxApplication.cc:328
src/protocols/abinitio/AbrelaxApplication.cc:330
src/protocols/abinitio/AbrelaxApplication.cc:335
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/ralph.bakerlab.org/minirosetta_database_rev26003.zip
Unpacking WU data ...
Unpacking data: ../../projects/ralph.bakerlab.org/cst_1_8_nativecst_b1.0_cen_0.1.foldcst_chunk_general.t373_.mtyka.boinc_files.zip
Setting database description ...
Setting up checkpointing ...
Setting up folding (abrelax) ...

ERROR: [ERROR] Unable to open constraints file: .pdb.distances.csts.bounded_1.0
ERROR:: Exit from: src/core/scoring/constraints/ConstraintIO.cc line: 330
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

they are dying almost as soon as they start (after 14 to 20 minutes).

See this result as an example.
ID: 4685 · Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 13 Jan 09
Posts: 80
Credit: 246,177
RAC: 0
Message 4686 - Posted: 12 Feb 2009, 16:20:10 UTC - in response to Message 4642.  
Last modified: 12 Feb 2009, 16:22:56 UTC

This 1.58 workunit:

http://ralph.bakerlab.org/workunit.php?wuid=1151935

keeps giving me error messages like these:

2/12/2009 9:34:00 AM|ralph@home|Task loopbuild_fcst_hb_t374__IGNORE_THE_REST_1VHSA_6_7770_3_0 exited with zero status but no 'finished' file
2/12/2009 9:34:00 AM|ralph@home|If this happens repeatedly you may need to reset the project.
2/12/2009 9:34:00 AM|ralph@home|Restarting task loopbuild_fcst_hb_t374__IGNORE_THE_REST_1VHSA_6_7770_3_0 using minirosetta version 158
2/12/2009 9:34:41 AM|ralph@home|Task loopbuild_fcst_hb_t374__IGNORE_THE_REST_1VHSA_6_7770_3_0 exited with zero status but no 'finished' file
2/12/2009 9:34:41 AM|ralph@home|If this happens repeatedly you may need to reset the project.
2/12/2009 9:34:41 AM|ralph@home|Restarting task loopbuild_fcst_hb_t374__IGNORE_THE_REST_1VHSA_6_7770_3_0 using minirosetta version 158
2/12/2009 9:35:22 AM|ralph@home|Task loopbuild_fcst_hb_t374__IGNORE_THE_REST_1VHSA_6_7770_3_0 exited with zero status but no 'finished' file
2/12/2009 9:35:22 AM|ralph@home|If this happens repeatedly you may need to reset the project.
2/12/2009 9:35:23 AM|ralph@home|Restarting task loopbuild_fcst_hb_t374__IGNORE_THE_REST_1VHSA_6_7770_3_0 using minirosetta version 158
2/12/2009 9:36:04 AM|ralph@home|Task loopbuild_fcst_hb_t374__IGNORE_THE_REST_1VHSA_6_7770_3_0 exited with zero status but no 'finished' file
2/12/2009 9:36:04 AM|ralph@home|If this happens repeatedly you may need to reset the project.
2/12/2009 9:36:04 AM|ralph@home|Restarting task loopbuild_fcst_hb_t374__IGNORE_THE_REST_1VHSA_6_7770_3_0 using minirosetta version 158
2/12/2009 9:36:45 AM|ralph@home|Task loopbuild_fcst_hb_t374__IGNORE_THE_REST_1VHSA_6_7770_3_0 exited with zero status but no 'finished' file
2/12/2009 9:36:45 AM|ralph@home|If this happens repeatedly you may need to reset the project.
2/12/2009 9:36:45 AM|ralph@home|Restarting task loopbuild_fcst_hb_t374__IGNORE_THE_REST_1VHSA_6_7770_3_0 using minirosetta version 158
2/12/2009 9:37:26 AM|ralph@home|Task loopbuild_fcst_hb_t374__IGNORE_THE_REST_1VHSA_6_7770_3_0 exited with zero status but no 'finished' file
2/12/2009 9:37:26 AM|ralph@home|If this happens repeatedly you may need to reset the project.

Also, when I start its graphics window within the Simple View, the window comes up bit with solid black where the graphics should be. If I hover my cursor over this window, I get the circle indicating that it is waiting for something, although without indicating what. If I then try to close the graphics window, the graphics program doesn't respond to this attempt, and must be aborted. The CPU time used so far is frozen at 0:26:55, and this workunit doesn't seem to be using the CPU even though it's listed as Running. If I try to start the graphics from within the Tasks tab of the Advanced View, the results are similar except that after a second or so, there's a white block near the center of the black graphics window.

Since I've finally succeeded in setting the percentage of CPU time used to 90% instead of 100%, this could a factor in triggering the problem.

During this time, the task monitor shows one CPU core running normally, and different views disagree on how the other is running except that they all agree that it's using significantly less than the requested 90% of the CPU time. An actual usage of about 30% is typical for these views, but one shows about 50% instead.

This workunit looks like it needs to be aborted, but is there something else I need to try first?

I'm using BOINC 6.2.28 under Vista SP1.
ID: 4686 · Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 13 Jan 09
Posts: 80
Credit: 246,177
RAC: 0
Message 4688 - Posted: 12 Feb 2009, 17:55:05 UTC - in response to Message 4686.  

This workunit went into Compute error status before anyone replied, so I decided to return it with an Update.

It had the lockfile problem, repeatedly, but didn't make any information about that visible to the user before the workunit finished.

If someone else finishes that workunit with a success, could you ask him or her whether he or she is using 100% CPU?
ID: 4688 · Report as offensive    Reply Quote
Evan

Send message
Joined: 23 Dec 07
Posts: 75
Credit: 69,584
RAC: 0
Message 4689 - Posted: 12 Feb 2009, 18:35:58 UTC

This one: 1150435 was a long one taking about 5 hours completing one decoy but given a validate error. I notice that its second attempt ended in immediate failure.

Also is it my imagination or are these units (cst__1_8_nativecst_b1.0_cen_0.1_hb_t313 etc) using more ram?
ID: 4689 · Report as offensive    Reply Quote
Profile Paul D. Buck

Send message
Joined: 14 Jan 09
Posts: 62
Credit: 33,293
RAC: 0
Message 4692 - Posted: 12 Feb 2009, 20:46:09 UTC - in response to Message 4686.  

This 1.58 workunit:

http://ralph.bakerlab.org/workunit.php?wuid=1151935


It looks like the second try it ran to completion ...

It looks to me like my assertion that running at less than 100% CPU causes issues ... like the "can't acquire lockfile" error ...
ID: 4692 · Report as offensive    Reply Quote
Profile Paul D. Buck

Send message
Joined: 14 Jan 09
Posts: 62
Credit: 33,293
RAC: 0
Message 4693 - Posted: 13 Feb 2009, 7:41:22 UTC
Last modified: 13 Feb 2009, 7:45:04 UTC

New error ... random, many tasks work, but I have at least 5 with this error:

ERROR: [ERROR] Error opening RBSeg file 'core_1VKBA_18_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


Not sure why the mix of success and failure ... the failures:

1308740
1308739
1307455
1307355
1307354
ID: 4693 · Report as offensive    Reply Quote
Path7

Send message
Joined: 11 Feb 08
Posts: 56
Credit: 4,974
RAC: 0
Message 4694 - Posted: 13 Feb 2009, 21:09:48 UTC

Hello all,

Having the same kind of error as Paul D. Buck:

ERROR: [ERROR] Error opening RBSeg file 'core_1B70B_12_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

loopbuild_chunk_cheat_3_5_hb_t306__IGNORE_THE_REST_1B70B_12_7794_1_0

Windows XP – Boinc 5.10.45

This WU had the same error again when it was returned by another computer.

Have a nice day,
Path7.
ID: 4694 · Report as offensive    Reply Quote
AdeB
Avatar

Send message
Joined: 22 Dec 07
Posts: 61
Credit: 121,552
RAC: 0
Message 4695 - Posted: 13 Feb 2009, 21:26:36 UTC - in response to Message 4694.  

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
ID: 4695 · Report as offensive    Reply Quote
Profile Paul D. Buck

Send message
Joined: 14 Jan 09
Posts: 62
Credit: 33,293
RAC: 0
Message 4696 - Posted: 14 Feb 2009, 10:02:43 UTC

Also had one repetition of the line 330 error:


ERROR: [ERROR] Unable to open constraints file: .pdb.distances.csts.bounded_1.0
ERROR:: Exit from: src/core/scoring/constraints/ConstraintIO.cc line: 330
BOINC:: Error reading and gzipping output datafile: default.out


Task 1309122

Just as important, have also had quite a few successes too ... though not as good as 1.54 running on Rosetta where I have not had an error in a couple weeks ...

Hmm, was this just a reissue of the task that should have been canceled? I see that the wingman also had the same error ...
ID: 4696 · Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 13 Jan 09
Posts: 80
Credit: 246,177
RAC: 0
Message 4697 - Posted: 14 Feb 2009, 16:52:36 UTC - in response to Message 4692.  

This 1.58 workunit:

http://ralph.bakerlab.org/workunit.php?wuid=1151935


It looks like the second try it ran to completion ...

It looks to me like my assertion that running at less than 100% CPU causes issues ... like the "can't acquire lockfile" error ...


Mike, have you thought of adding some debug code to the parts of the next version of minirosetta that have anything to do with the lockfile, and occasionally recording the percentage of the CPU time BOINC runs?
ID: 4697 · Report as offensive    Reply Quote
1 · 2 · 3 · 4 . . . 5 · Next

Message boards : RALPH@home bug list : minirosetta 1.58



©2018 University of Washington
http://www.bakerlab.org