...and now something completely different.

Mike, do you need more information about actual behaviour of your predicting models? Just to fine tune the energy function, folding procedure etc.?

One thing we all now is that some models of particular WU take much more time than the others. It's clearly seen when we have "long running WUs", however it is quite often as well in WUs which have very short models. In these cases you need to actually watch it or have good logs to see, that, i.e. most of models run in 5 minutes, and one takes 15-20.

I've been having such a task right now: testC_cc_1_8_nocst4_hb_t288__IGNORE_THE_REST_2FNEA_2_6976_1_0.
For many minutes the accepted screen was showing a very simple chain split on two, longer and shorter, and the shorter was standing still, showing some quite folded structure. It took over 400,000 steps to get something semifolded and more complicated on a "accepted" screen and go further.
This model (12th) took much more time and as the forecast runtime of a model increased, it was the last decoy allowed by the scheduler.

All of these looked like the procedure needed much more time to hit something acceptable to start with.

I'm sure you know about this issue but I have seen such a behaviour a couple times before and just wanted to let you know it is quite common.

P.S. Besided that everything - except checkpointing, see my posts above - is working like a charm.

P.S.S. Great work Feel1st!

Hello mtyka,

- Do the graphics behave properly again ?

After having problems with the graphics running minrosetta 1.52,
the combination of minrosetta 1.53 & minrosetta graphics 1.53 seems to work smoothly again.
Thanks and a good weekend,
Path7.

After Rosetta 1.47 totally crashing on my MacBook on 27 Dec 2008 (after one week of faultless computing, within hours after connecting to the Rosetta server; still haven't recovered) I have waited for an opportunity to test what is happening on Ralph. At last I received two 1.53-tasks - however, they show exactly the same symptoms as observed using 1.47 on Rosetta:

abinitio_norelax_homfrag_natfrag_129_B_1pxuA_SAVE_ALL_OUT_7037_1_0

<![CDATA[
<message>
process exited with code 193 (0xc1, -63)
</message>

This one crashed after 30 sec.

----

abinitio_norelax_homfrag_natfrag_129_B_1ctf__SAVE_ALL_OUT_7037_1_0

<![CDATA[
<message>
process exited with code 193 (0xc1, -63)
</message>
<stderr_txt>

This one is reported using Boinc 6.6.2 but computed with 6.6.1.

It started out relatively normally. But after about one hour’s computing time, steadily increasing "To completion" time, progress stuck at 0.240%, I had to conclude that this wu would turn into an everlasting task. "Show graphics" did not respond, even "Quit Boinc" was greyed out. After rebooting to install Boinc 6.6.2, and logging on as administrative and non-administrative user the wu quit after restarting using 32 sec.


I should add that I mostly use this computer as a non-administrator, which may have some bearing (on my PPC it influences my graphics display at least). However, I do not receive more units to check, so I can not test the behaviour when changing configurations.

----

PS
For the curious:
This is the report from the first wu crashing on Dec 27 2008 on Rosetta (I haven't too much time analyzing such data....). The error message is a bit more extensive than the messages for the rest of the bunch:

https://boinc.bakerlab.org/rosetta/result.php?resultid=216101560 (obsolete link)

Task ID
216101560
Name
1r9pA_BOINC_MPZN_vanilla_abrelax_5901_6648_0
Workunit
196949149
Created
21 Dec 2008 12:53:24 UTC
Sent
21 Dec 2008 13:16:26 UTC
Received
27 Dec 2008 14:15:44 UTC
Server state
Over
Outcome
Client error
Client state
Compute error
Exit status
193 (0xc1)
Computer ID
936507
Report deadline
31 Dec 2008 13:16:26 UTC
CPU time
20.36099
stderr out
<core_client_version>6.5.0</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)
</message>
<stderr_txt>
minirosetta_1.47_i686-apple-darwin(69428,0xa031b720) malloc: *** error for object 0x1748220: Non-aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
minirosetta_1.47_i686-apple-darwin(69428,0xa031b720) malloc: *** error for object 0x1748220: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
SIGBUS: bus error

Crashed executable name: minirosetta_1.47_i686-apple-darwin
built using BOINC library version 6.5.0
Machine type Intel 80486 (32-bit executable)
System version: Macintosh OS 10.5.6 build 9G55
Sat Dec 27 14:45:29 2008

Why not grab the set and issue them to us with high replication counts ... then if they fail for everyone, that tells us one thing ... if they only fail for some and not others ... that tells us something else ...

we already submit identical jobs to many many machines - and they only fail *sometimes*. Even when the same random number seed is used.

To my mind, the cases that fail are the ones that you should be saving and using as your issue tasks for each round of testing. Not to keep making new tasks in all cases, but to use those tasks that have proven their ability to cause a problem.

again .. we're already doing that. But the errors are sporadic in nature so submitting the same task might not throw an error "this time".

I have noticed though that some of the problems seem to be highly machine specific. Like one user will always produce this one kind of an error and nithing else. weired. something strange about their setup ? No idea.

You might want to try classifying such failures by the specific type of CPU they ran on, and what operating system they ran under. At least one other BOINC project I'm participating in found at least one problem where the results came out one way on Intel CPUs, and a different way on AMD CPUs. And more than one have found problems where workunits come out OK if run under one operating system, but not if they're run under another operating system.

Should the name of this thread be editted to include 1.51, or should a new thread be started for 1.51?

Same for 1.53, the version used in the last workunit I got. Also, this could be reflected in the description of the latest version being tested on the home page.

Thank you all for reporting the problems! The problem divides it self into three parts, firstly cornering the error, turning it into an erro message, reproducing it here and then finding the root of the problem.

<core_client_version>6.2.19</core_client_version>
<![CDATA[
<message>
There are no child processes to wait for. (0x80) - exit code 128 (0x80)
</message>
<stderr_txt>
BOINC:: Initializing ... ok.
[2009- 1-22 4:45: 1:] :: 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.


Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x7C81BD02 read attempt to address 0x00000002

Engaging BOINC Windows Runtime Debugger...



Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x7C81BD02 read attempt to address 0x00000002

Engaging BOINC Windows Runtime Debugger...


</stderr_txt>
]]>

These are random segfault that occured somewhere. I can do virtually nothing from here. If i rerun the *exact same commandline* from here all runs fine. So these ones i can only tentatively bracket with stderr statemenets.

I wonder if a significant number of these are problems with restarting after suspending the task, so if you run them on a machine that doesn't participate in enough other BOINC projects to even cause the suspension, the code with problems won't even be used?

Also, have you checked if this problem is restricted to certain BOINC versions, but not certain others?

Also, it may matter whether the Leave In Memory option is used, and thus whether the restart is from what is left in memory or from a checkpoint.

On my machine, I found that minirosetta ran better after I enabled Leave In Memory, increased the upper limit on how much disk space BOINC could use, and increased the percentage of the available swap space BOINC could use. The new upper limits are high enough to suggest that BOINC divides the available disk space and swap space equally between BOINC projects before deciding how much to give to each workunit, instead of letting the more demanding BOINC projects have more than an equal share if they need it. This does have a side effect, though - I'll probably need to run about 10 workunits of any new minirosetta version to have enough results to guess whether it is better than 1.47, unless it's significantly worse instead.

Yeah guess what. I just found a bug in the BOINC API! . Holy crap. Basically as far as i can see there's a memory leak when it's trying to unzip files. Mostly all you see is the application dying kicking and screaming just after initialization. One RALPH user though produced a suspicious trace (thank you philip in hongkong!). I have to stress that this is the only job out of hundreds such failures that has returned with a trace.

It fails in the unzip code ! OMG.
Been tinkering with the code, the bug probably stems froma single byte not being set to 0. This explains the sporadic nature - if the relevant byte happens to already be 0 then all is fine. I'll push out a version soon to see if the fix works. Its all stipulation at this point.

Mike

Is the place with the bad code part of BOINC, instead of part of minirosetta? If it is, I'd expect a number of variations of the fix to be needed, depending on which version of BOINC is used.

Could some of your problems with RALPH@home be due to it looking like an alpha test project, thus driving away participants willing to participate in beta test projects but not alpha test projects?

I looked down the list of top participants, and found that I entered this list within days after adding RALPH@home to my list of BOINC projects, and not even giving it a very high percentage of the available CPU time on my machine. It then rose rapidly in the list the next few days. Is this due to the current updates being sent only to machines of specific types, or due to a very small number of people actually currently trying to be active in RALPH@home (I'd guess around 500)?

At least the results I'm getting from RALPH@home don't look significantly worse than I'm getting at Rosetta@home, so I'll stay active for now.

I've seen some other BOINC projects offer a "test" option for running workunits that are between their beta tests and their final release, but need a higher volume of workunits completed to check for performance problems in any new sections of the code used. Are you interested in adding this option on Rosetta@home, to restrict some of the testing done on Rosetta@home to people willing to tolerate a high bug level, and thus help attract more participants that object to the high bug level currently seen on Rosetta@home? You could even enable this option for users who haven't tried to set it at all, not not for new participants, if you're worried about getting enough participants willing to use it.

Hmmm, shouldn't that be a test? When it writes to the file it should check to see if it is hearing the limit, and if so, stop ... I mean, 24 hours worth of work down the tubes other than we discovered the error ... (thank you) ...

Paul, I think you are saying "shouldn't it have detected the problem much sooner?". It dawned on me later looking at how far over the file size was, that there must be much more to it then just the last model. It was actually wrapping up the entire task when it failed.

There are file size limits in BOINC, and it does check them as the task runs (so far as I know anyway). But this one may not have been detected because I'll bet the last thing the task did was zip it all up to send in. So, there was no way to know the final size until the compression completed.

But yes, seems to indicate that the task is producing too many models. And perhaps that there is some intermediate file size that could be further limited to assure the compressed size does not exceed the limit there. The other way around it would be to limit the number of models the task is allowed to produce. But this would mess up my runtime preference, and my future requests for work, because it would end significantly sooner then my 24hr preference.

Actually, this would be another good factor for the watchdog to keep tabs on. (or the logic about whether to start the next model) If he sees a problem, then he could get the current work reported rather then losing it.

---

Is this due to the current updates being sent only to machines of specific types, or due to a very small number of people actually currently trying to be active in RALPH@home (I'd guess around 500)?

Here's some numbers

BOINC Stats for RALPH

642 active users out of 3073

HTH

---

[quote]
Hmmm, shouldn't that be a test? When it writes to the file it should check to see if it is hearing the limit, and if so, stop ... I mean, 24 hours worth of work down the tubes other than we discovered the error ... (thank you) ...

Paul, I think you are saying "shouldn't it have detected the problem much sooner?". It dawned on me later looking at how far over the file size was, that there must be much more to it then just the last model. It was actually wrapping up the entire task when it failed./quote]

Yes that is what I was trying to say. Again, not being aware of the exact circumstances and what stage you were in at the time of the issue, it seems that the system should have been more graceful. If it was trying to wrap up the model at the end is it possible that it should have been able to make several upload files rather than just one?

There are file size limits in BOINC, and it does check them as the task runs (so far as I know anyway). But this one may not have been detected because I'll bet the last thing the task did was zip it all up to send in. So, there was no way to know the final size until the compression completed./quote]

True, but you can make estimates based on input sizes and normal compression ratios. And if the system errors, back off and try smaller sets ... again, you did try to press the system and found an issue that needs some thinking ... after all it is *MY* understanding that they want us to run the tasks for longer periods (my setting on Rosetta is 6 hours) to get more attempts per issued task ...

[quote]But yes, seems to indicate that the task is producing too many models. And perhaps that there is some intermediate file size that could be further limited to assure the compressed size does not exceed the limit there. The other way around it would be to limit the number of models the task is allowed to produce. But this would mess up my runtime preference, and my future requests for work, because it would end significantly sooner then my 24hr preference./quote]

Or they would package the end data differently. Again, you stressed the system in a way they likely did not expect.

[quote]Actually, this would be another good factor for the watchdog to keep tabs on. (or the logic about whether to start the next model) If he sees a problem, then he could get the current work reported rather then losing it.

Agreed.

---

Could some of your problems with RALPH@home be due to it looking like an alpha test project, thus driving away participants willing to participate in beta test projects but not alpha test projects?

This is common for ALL BOINC projects. If you start any BOINC project you will see that you will leap up the lists if you run on that project for only a couple weeks. At some point you start to hit the level where the dedicated are accumulating work... then your rise will level off and will rise and fall depending on how many computers you have and what speed they are ...

I tend to have more machines than most people that BOINC, less than the really dedicated and so I am now solidly in the middle of the pack of participants though still rising slowly (at one point I was number 411 in the world for all projects)

But at the end of the day, test projects, Alpha or Beta needs people that will not only do the work, but are willing to report errors, try things out and run the risk of doing work and never getting "paid" for the effort because of failures.

---

currently there is no monitoring of that. I'll look into putting safety stop on that. I'm not even sure how to get that info from the boinc api.

Perhaps begging? :)

---

Is this due to the current updates being sent only to machines of specific types, or due to a very small number of people actually currently trying to be active in RALPH@home (I'd guess around 500)?

Here's some numbers

BOINC Stats for RALPH

642 active users out of 3073

HTH

I got caught behind a ton of work in my buffer for Ralph and then ran up a big debt load to rosie. I have shrunk my buffer size since then. When there is work available I should get it automatically and be active in testing again.

Please mister, can I have some more?

Can't test the version with no work to do ... :)

---

Please mister, can I have some more?

Can't test the version with no work to do ... :)

No worries - there shall be more work soon. I'm preparring another update.

I just got 25 new tasks after changing my allocation percentage.

*** set a breakpoint in malloc_error_break to debug
minirosetta_1.47_i686-apple-darwin(69428,0xa031b720) malloc: *** error for object 0x1748220: incorrect checksum for freed object - object was probably modified after being freed.

Hi ramostol, thanks for joining ralph. You error is new, i've not seen it on any other machine yet, but at least now we have a chance to cathc it. Shame the trace is giving so little information.

Mike

Since the computer in question is connected to the internet only in weekends I cannot be of much use without lots of wus...

But -- in connection with modified object -- this computer isn't doing much more that computing BOINC projects at the moment, and the sole configuration made by yours truly when connecting to the Rosetta server was changing the runtime to keep within limits. Since my first (of three) Rosetta crash the last months (that one using BOINC 6.3.14) made it necessary to manually delete all project files before reattaching to get up and running, I wonder if some errors are created outside of miniRosetta itself...

My apologies in advance for this long post, but I thought it the best method of report. I know you wanted feedback on the checkpointing. Specifically the checkpoint buffering that I understand should be included in v1.53.

I have this v1.53 task, it's been running for about 11.5hrs on my 24hr preference. My BOINC client confirms my "write at most..." setting is 600 seconds. This task has generated 122 checkpoints so far (as per the boinc_checkpoint_count.txt file) and is now on model 106, and perhaps so many models is the root cause, but here is what I see in the slots file.

I believe you indicated that at the end of a model, we would see a disk write, regardless of preference and any other buffered checkpoints. But, I seem to be seeing a large number of writes in a single minute, with several file numbers.

So, showing you the directory seems the only way... (sorted by date/time, and colorized where heavy disk periods seem to be. Some just seem to have written a large number of files, others seem to have written multiple checkpoints [if that is what the numbers are], in a single minute)



11/18/2008 12:24 PM 138 t327_.fasta
11/18/2008 01:19 PM 666 T0327.all0.T20.aln.filt.2F2EA_2.mapping
11/18/2008 01:19 PM 667 T0327.all0.T20.aln.filt.2F2EA_4.mapping
11/18/2008 01:19 PM 628 T0327.all0.T20.aln.filt.2F2EA_5.mapping
11/18/2008 01:19 PM 672 T0327.all0.T20.aln.filt.2F2EA_6.mapping
11/18/2008 01:19 PM 594 T0327.all0.T20.aln.filt.2F2EA_7.mapping
11/18/2008 01:19 PM 668 T0327.all0.T20.aln.filt.2F2EA_8.mapping
11/18/2008 01:19 PM 672 T0327.all0.T20.aln.filt.2F2EA_9.mapping
11/18/2008 01:19 PM 628 T0327.all0.T20.aln.filt.2F2EA_12.mapping
11/18/2008 01:19 PM 669 T0327.all0.T20.aln.filt.2F2EA_11.mapping
11/18/2008 01:19 PM 602 T0327.all0.T20.aln.filt.2F2EA_10.mapping
11/18/2008 01:19 PM 700 T0327.all0.T20.aln.filt.1UB9A_2.mapping
11/18/2008 01:19 PM 601 T0327.all0.T20.aln.filt.2F2EA_15.mapping
11/18/2008 01:19 PM 671 T0327.all0.T20.aln.filt.2F2EA_14.mapping
11/18/2008 01:19 PM 676 T0327.all0.T20.aln.filt.2F2EA_16.mapping
11/18/2008 01:19 PM 646 T0327.all0.T20.aln.filt.1UB9A_5.mapping
11/18/2008 01:19 PM 696 T0327.all0.T20.aln.filt.1UB9A_6.mapping
11/18/2008 01:19 PM 670 T0327.all0.T20.aln.filt.1UB9A_10.mapping
11/18/2008 01:19 PM 697 T0327.all0.T20.aln.filt.1UB9A_8.mapping
11/18/2008 01:19 PM 694 T0327.all0.T20.aln.filt.1UB9A_13.mapping
11/18/2008 01:19 PM 636 T0327.all0.T20.aln.filt.1XMAA_10.mapping
11/18/2008 01:19 PM 636 T0327.all0.T20.aln.filt.1XMAA_13.mapping
11/18/2008 01:19 PM 675 T0327.all0.T20.aln.filt.1XMAA_11.mapping
11/18/2008 01:19 PM 682 T0327.all0.T20.aln.filt.1XMAA_14.mapping
11/18/2008 01:19 PM 659 T0327.all0.T20.aln.filt.1XMAA_15.mapping
11/18/2008 01:19 PM 683 T0327.all0.T20.aln.filt.1XMAA_16.mapping
11/18/2008 01:19 PM 645 T0327.all0.T20.aln.filt.1XMAA_17.mapping
11/18/2008 01:19 PM 595 T0327.all0.T20.aln.filt.1YYVA_3.mapping
11/18/2008 01:19 PM 674 T0327.all0.T20.aln.filt.1YYVA_6.mapping
11/18/2008 01:19 PM 637 T0327.all0.T20.aln.filt.1YYVA_5.mapping
11/18/2008 01:19 PM 671 T0327.all0.T20.aln.filt.1YYVA_8.mapping
11/18/2008 01:19 PM 612 T0327.all0.T20.aln.filt.1YYVA_7.mapping
11/18/2008 01:19 PM 678 T0327.all0.T20.aln.filt.1YYVA_10.mapping
11/18/2008 01:19 PM 612 T0327.all0.T20.aln.filt.1YYVA_9.mapping
11/18/2008 01:19 PM 677 T0327.all0.T20.aln.filt.1YYVA_14.mapping
11/18/2008 01:19 PM 676 T0327.all0.T20.aln.filt.1YYVA_12.mapping
11/18/2008 01:20 PM 637 T0327.all0.T20.aln.filt.2FSWA_1.mapping
11/18/2008 01:20 PM 604 T0327.all0.T20.aln.filt.2FSWA_3.mapping
11/18/2008 01:20 PM 653 T0327.all0.T20.aln.filt.2FSWA_2.mapping
11/18/2008 01:20 PM 674 T0327.all0.T20.aln.filt.2FSWA_5.mapping
11/18/2008 01:20 PM 691 T0327.all0.T20.aln.filt.2FSWA_4.mapping
11/18/2008 01:20 PM 612 T0327.all0.T20.aln.filt.2FSWA_6.mapping
11/18/2008 01:20 PM 671 T0327.all0.T20.aln.filt.2FSWA_7.mapping
11/18/2008 01:20 PM 674 T0327.all0.T20.aln.filt.2FSWA_8.mapping
11/18/2008 01:20 PM 678 T0327.all0.T20.aln.filt.2FSWA_9.mapping
11/18/2008 01:20 PM 587 T0327.all0.T20.aln.filt.2FSWA_10.mapping
11/18/2008 01:20 PM 670 T0327.all0.T20.aln.filt.2FSWA_11.mapping
11/18/2008 01:20 PM 566 T0327.all0.T20.aln.filt.2FSWA_12.mapping
11/18/2008 01:20 PM 601 T0327.all0.T20.aln.filt.2FSWA_13.mapping
11/18/2008 01:20 PM 683 T0327.all0.T20.aln.filt.2ESHA_14.mapping
11/18/2008 01:21 PM 663 T0327.all0.T20.aln.filt.2FRHA_3.mapping
11/18/2008 01:21 PM 698 T0327.all0.T20.aln.filt.2FRHA_10.mapping
11/18/2008 01:24 PM 629,605 boinc_aat327_03_05.200_v1_3.gz
11/18/2008 01:25 PM 1,731,406 boinc_aat327_09_05.200_v1_3.gz
11/18/2008 01:30 PM 135,465 1ub9.pdb
11/18/2008 01:31 PM 141,309 1xma.pdb
11/18/2008 01:31 PM 149,160 1yyv.pdb
11/18/2008 01:32 PM 154,587 2esh.pdb
11/18/2008 01:33 PM 180,600 2f2e.pdb
11/18/2008 01:34 PM 175,317 2frh.pdb
11/18/2008 01:35 PM 141,402 2fsw.pdb
11/18/2008 01:35 PM 39,881 2F2EA_2.pdb
11/18/2008 01:35 PM 39,881 2F2EA_4.pdb
11/18/2008 01:35 PM 39,881 2F2EA_5.pdb
11/18/2008 01:35 PM 39,881 2F2EA_6.pdb
11/18/2008 01:35 PM 39,881 2F2EA_7.pdb
11/18/2008 01:35 PM 39,881 2F2EA_8.pdb
11/18/2008 01:35 PM 39,881 2F2EA_10.pdb
11/18/2008 01:35 PM 39,881 2F2EA_9.pdb
11/18/2008 01:35 PM 39,881 2F2EA_11.pdb
11/18/2008 01:35 PM 39,881 2F2EA_12.pdb
11/18/2008 01:35 PM 39,881 2F2EA_14.pdb
11/18/2008 01:35 PM 39,881 2F2EA_16.pdb
11/18/2008 01:35 PM 39,881 2F2EA_15.pdb
11/18/2008 01:35 PM 39,881 1UB9A_2.pdb
11/18/2008 01:35 PM 39,881 1UB9A_5.pdb
11/18/2008 01:35 PM 39,881 1UB9A_6.pdb
11/18/2008 01:35 PM 39,881 1UB9A_8.pdb
11/18/2008 01:35 PM 39,881 1UB9A_10.pdb
11/18/2008 01:35 PM 39,881 1UB9A_13.pdb
11/18/2008 01:35 PM 39,881 1XMAA_10.pdb
11/18/2008 01:35 PM 39,881 1XMAA_11.pdb
11/18/2008 01:35 PM 39,881 1XMAA_13.pdb
11/18/2008 01:35 PM 39,881 1XMAA_15.pdb
11/18/2008 01:35 PM 39,881 1XMAA_14.pdb
11/18/2008 01:35 PM 39,881 1XMAA_16.pdb
11/18/2008 01:36 PM 39,881 1XMAA_17.pdb
11/18/2008 01:36 PM 39,881 1YYVA_3.pdb
11/18/2008 01:36 PM 39,881 1YYVA_5.pdb
11/18/2008 01:36 PM 39,881 1YYVA_6.pdb
11/18/2008 01:36 PM 39,881 1YYVA_7.pdb
11/18/2008 01:36 PM 39,881 1YYVA_8.pdb
11/18/2008 01:36 PM 39,881 1YYVA_9.pdb
11/18/2008 01:36 PM 39,881 1YYVA_10.pdb
11/18/2008 01:36 PM 39,881 1YYVA_12.pdb
11/18/2008 01:36 PM 39,881 1YYVA_14.pdb
11/18/2008 01:37 PM 39,881 2FSWA_1.pdb
11/18/2008 01:37 PM 39,881 2FSWA_2.pdb
11/18/2008 01:37 PM 39,881 2FSWA_3.pdb
11/18/2008 01:37 PM 39,881 2FSWA_4.pdb
11/18/2008 01:37 PM 39,881 2FSWA_6.pdb
11/18/2008 01:37 PM 39,881 2FSWA_5.pdb
11/18/2008 01:37 PM 39,881 2FSWA_7.pdb
11/18/2008 01:37 PM 39,881 2FSWA_8.pdb
11/18/2008 01:37 PM 39,881 2FSWA_10.pdb
11/18/2008 01:37 PM 39,881 2FSWA_9.pdb
11/18/2008 01:37 PM 39,881 2FSWA_11.pdb
11/18/2008 01:37 PM 39,881 2FSWA_13.pdb
11/18/2008 01:37 PM 39,881 2ESHA_14.pdb
11/18/2008 01:38 PM 39,881 2FRHA_3.pdb
11/18/2008 01:38 PM 39,881 2FRHA_10.pdb
11/20/2008 05:14 PM 94,689 native.pdb
12/01/2008 01:11 PM 43 core_2F2EA_16_noloop_loops.txt
12/01/2008 01:11 PM 43 core_2F2EA_14_noloop_loops.txt
12/01/2008 01:11 PM 66 core_2F2EA_11_noloop_loops.txt
12/01/2008 01:11 PM 66 core_2ESHA_14_noloop_loops.txt
12/01/2008 01:11 PM 89 core_1YYVA_9_noloop_loops.txt
12/01/2008 01:11 PM 89 core_1YYVA_7_noloop_loops.txt
12/01/2008 01:11 PM 66 core_2FSWA_7_noloop_loops.txt
12/01/2008 01:11 PM 43 core_2FRHA_10_noloop_loops.txt
12/01/2008 01:11 PM 89 core_1YYVA_5_noloop_loops.txt
12/01/2008 01:11 PM 89 core_1YYVA_10_noloop_loops.txt
12/01/2008 01:11 PM 66 core_1XMAA_17_noloop_loops.txt
12/01/2008 01:11 PM 66 core_1XMAA_15_noloop_loops.txt
12/01/2008 01:11 PM 66 core_1XMAA_14_noloop_loops.txt
12/01/2008 01:11 PM 89 core_1XMAA_10_noloop_loops.txt
12/01/2008 01:11 PM 43 core_1UB9A_8_noloop_loops.txt
12/01/2008 01:11 PM 43 core_1UB9A_6_noloop_loops.txt
12/01/2008 01:11 PM 66 core_2F2EA_2_noloop_loops.txt
12/01/2008 01:11 PM 66 core_2FSWA_5_noloop_loops.txt
12/01/2008 01:11 PM 66 core_2F2EA_4_noloop_loops.txt
12/01/2008 01:11 PM 89 core_2FSWA_3_noloop_loops.txt
12/01/2008 01:11 PM 43 core_2FSWA_2_noloop_loops.txt
12/01/2008 01:11 PM 89 core_2F2EA_7_noloop_loops.txt
12/01/2008 01:11 PM 66 core_2FSWA_13_noloop_loops.txt
12/01/2008 01:11 PM 66 core_2F2EA_9_noloop_loops.txt
12/01/2008 01:11 PM 66 core_2FSWA_10_noloop_loops.txt
12/01/2008 01:11 PM 89 core_2FRHA_3_noloop_loops.txt
12/01/2008 01:11 PM 66 core_2FSWA_8_noloop_loops.txt
12/01/2008 01:11 PM 66 core_2F2EA_6_noloop_loops.txt
12/01/2008 01:11 PM 89 core_1YYVA_6_noloop_loops.txt
12/01/2008 01:12 PM 89 core_2FSWA_6_noloop_loops.txt
12/01/2008 01:12 PM 43 core_2FSWA_4_noloop_loops.txt
12/01/2008 01:12 PM 66 core_2FSWA_1_noloop_loops.txt
12/01/2008 01:12 PM 43 core_2FSWA_11_noloop_loops.txt
12/01/2008 01:12 PM 66 core_2F2EA_8_noloop_loops.txt
12/01/2008 01:12 PM 66 core_2F2EA_5_noloop_loops.txt
12/01/2008 01:12 PM 43 core_2F2EA_15_noloop_loops.txt
12/01/2008 01:12 PM 66 core_2F2EA_12_noloop_loops.txt
12/01/2008 01:12 PM 89 core_2F2EA_10_noloop_loops.txt
12/01/2008 01:12 PM 89 core_1YYVA_8_noloop_loops.txt
12/01/2008 01:12 PM 89 core_1YYVA_3_noloop_loops.txt
12/01/2008 01:12 PM 89 core_1YYVA_14_noloop_loops.txt
12/01/2008 01:12 PM 89 core_1YYVA_12_noloop_loops.txt
12/01/2008 01:12 PM 66 core_1XMAA_16_noloop_loops.txt
12/01/2008 01:12 PM 89 core_1XMAA_13_noloop_loops.txt
12/01/2008 01:12 PM 66 core_1XMAA_11_noloop_loops.txt
12/01/2008 01:12 PM 43 core_1UB9A_5_noloop_loops.txt
12/01/2008 01:12 PM 43 core_1UB9A_2_noloop_loops.txt
12/01/2008 01:12 PM 43 core_1UB9A_13_noloop_loops.txt
12/01/2008 01:12 PM 66 core_2FSWA_9_noloop_loops.txt
12/01/2008 01:12 PM 43 core_1UB9A_10_noloop_loops.txt
01/14/2009 11:51 PM 3,618 good_template_config_file.txt
01/14/2009 11:51 PM 0 1
01/26/2009 12:44 AM 114 graphics_app
01/26/2009 12:44 AM 105 minirosetta_1.53_windows_intelx86.exe
01/26/2009 12:44 AM 81 Helvetica.txf
01/26/2009 12:44 AM 4,165 init_data.xml
01/26/2009 12:44 AM 136 test_cc_1_8_nocst4.foldcst_chunk_general.t327_.mtyka.boinc_files.zip
01/26/2009 12:44 AM 101 minirosetta_database.zip
01/26/2009 12:44 AM 130 default.out.gz
01/26/2009 12:44 AM 132 test_cc_1_8_nocst4.foldcst_chunk_general.t327_.mtyka.flags.boinc
01/26/2009 12:44 AM 0 boinc_lockfile
01/26/2009 12:44 AM <DIR> minirosetta_database
01/26/2009 12:44 AM 3 boinc_init_count.txt
01/26/2009 12:59 AM 12,359 chk_S_1UB9A_2_00000001_ClassicAbinitio___lc_1.out
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01/26/2009 01:09 AM 12,680 chk_S_1UB9A_2_00000002_ClassicAbinitio___lc_1.out
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01/26/2009 01:09 AM 8,630 chk_S_1UB9A_2_00000002_ClassicAbinitio___lc_2.rng.state.gz
01/26/2009 01:09 AM 12,365 chk_S_1UB9A_2_00000002_ClassicAbinitio___lc_2.out
01/26/2009 01:18 AM 8,691 chk_S_1UB9A_2_00000003_ClassicAbinitio___lc_1.rng.state.gz
01/26/2009 01:18 AM 12,365 chk_S_1UB9A_2_00000003_ClassicAbinitio___lc_1.out
01/26/2009 01:29 AM 8,632 chk_S_1UB9A_2_00000004_ClassicAbinitio___lc_1.rng.state.gz
01/26/2009 01:29 AM 12,365 chk_S_1UB9A_2_00000004_ClassicAbinitio___lc_1.out
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01/26/2009 01:38 AM 12,682 chk_S_1UB9A_2_00000005_ClassicAbinitio___lc_1.out
01/26/2009 01:38 AM 12,365 chk_S_1UB9A_2_00000005_ClassicAbinitio___lc_2.out
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01/26/2009 02:47 AM 8,647 chk_S_1UB9A_2_00000006_ClassicAbinitio___lc_1.rng.state.gz
01/26/2009 02:47 AM 12,680 chk_S_1UB9A_2_00000006_ClassicAbinitio___lc_1.out
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01/26/2009 02:47 AM 12,365 chk_S_1UB9A_2_00000006_ClassicAbinitio___lc_2.out
01/26/2009 03:59 AM 12,680 chk_S_1UB9A_2_00000007_ClassicAbinitio___lc_1.out
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01/26/2009 03:59 AM 12,365 chk_S_1UB9A_2_00000007_ClassicAbinitio___lc_2.out
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01/26/2009 04:12 AM 8,740 chk_S_1UB9A_2_00000008_ClassicAbinitio___lc_1.rng.state.gz
01/26/2009 04:12 AM 12,680 chk_S_1UB9A_2_00000008_ClassicAbinitio___lc_1.out
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01/26/2009 04:12 AM 12,365 chk_S_1UB9A_2_00000008_ClassicAbinitio___lc_2.out
01/26/2009 04:21 AM 8,701 chk_S_1UB9A_2_00000009_ClassicAbinitio___lc_1.rng.state.gz
01/26/2009 04:21 AM 12,365 chk_S_1UB9A_2_00000009_ClassicAbinitio___lc_1.out
01/26/2009 04:34 AM 8,702 chk_S_1UB9A_2_00000010_ClassicAbinitio___lc_1.rng.state.gz
01/26/2009 04:34 AM 12,680 chk_S_1UB9A_2_00000010_ClassicAbinitio___lc_1.out
01/26/2009 04:34 AM 12,365 chk_S_1UB9A_2_00000010_ClassicAbinitio___lc_2.out
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01/26/2009 04:43 AM 12,365 chk_S_1UB9A_2_00000011_ClassicAbinitio___lc_1.out
01/26/2009 04:43 AM 8,738 chk_S_1UB9A_2_00000011_ClassicAbinitio___lc_1.rng.state.gz
01/26/2009 04:51 AM 8,657 chk_S_1UB9A_2_00000012_ClassicAbinitio___lc_1.rng.state.gz
01/26/2009 04:51 AM 12,365 chk_S_1UB9A_2_00000012_ClassicAbinitio___lc_1.out
01/26/2009 05:00 AM 8,719 chk_S_1UB9A_2_00000013_ClassicAbinitio___lc_1.rng.state.gz
01/26/2009 05:00 AM 12,365 chk_S_1UB9A_2_00000013_ClassicAbinitio___lc_1.out
01/26/2009 05:08 AM 22,784 chk_S_1UB9A_2_00000001_Abrelax__rg_state_fa.out
01/26/2009 05:08 AM 8,687 chk_S_1UB9A_2_00000001_Abrelax__rg_state_fa.rng.state.gz
01/26/2009 05:08 AM 8,759 chk_S_1UB9A_2_00000001_Abrelax__fastrelax_fa.rng.state.gz
01/26/2009 05:08 AM 23,193 chk_S_1UB9A_2_00000001_Abrelax__fastrelax_fa.out
01/26/2009 05:08 AM 8,759 chk_S_1UB9A_2_00000002_Abrelax__rg_state_fa.rng.state.gz
01/26/2009 05:08 AM 22,790 chk_S_1UB9A_2_00000002_Abrelax__rg_state_fa.out
01/26/2009 05:08 AM 8,676 chk_S_1UB9A_2_00000002_Abrelax__fastrelax_fa.rng.state.gz
01/26/2009 05:08 AM 23,178 chk_S_1UB9A_2_00000002_Abrelax__fastrelax_fa.out
01/26/2009 05:08 AM 8,676 chk_S_1UB9A_2_00000003_Abrelax__rg_state_fa.rng.state.gz
01/26/2009 05:08 AM 22,790 chk_S_1UB9A_2_00000003_Abrelax__rg_state_fa.out
01/26/2009 05:08 AM 23,185 chk_S_1UB9A_2_00000003_Abrelax__fastrelax_fa.out
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01/26/2009 05:08 AM 22,790 chk_S_1UB9A_2_00000004_Abrelax__rg_state_fa.out
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01/26/2009 05:08 AM 8,632 chk_S_1UB9A_2_00000004_Abrelax__fastrelax_fa.rng.state.gz
01/26/2009 05:08 AM 23,192 chk_S_1UB9A_2_00000004_Abrelax__fastrelax_fa.out
01/26/2009 05:08 AM 22,790 chk_S_1UB9A_2_00000005_Abrelax__rg_state_fa.out
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01/26/2009 05:08 AM 8,696 chk_S_1UB9A_2_00000005_Abrelax__fastrelax_fa.rng.state.gz
01/26/2009 05:08 AM 23,185 chk_S_1UB9A_2_00000005_Abrelax__fastrelax_fa.out
01/26/2009 05:08 AM 22,790 chk_S_1UB9A_2_00000006_Abrelax__rg_state_fa.out
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01/26/2009 05:08 AM 23,192 chk_S_1UB9A_2_00000006_Abrelax__fastrelax_fa.out
01/26/2009 05:08 AM 8,709 chk_S_1UB9A_2_00000006_Abrelax__fastrelax_fa.rng.state.gz
01/26/2009 05:08 AM 8,709 chk_S_1UB9A_2_00000007_Abrelax__rg_state_fa.rng.state.gz
01/26/2009 05:08 AM 22,790 chk_S_1UB9A_2_00000007_Abrelax__rg_state_fa.out
01/26/2009 05:08 AM 23,185 chk_S_1UB9A_2_00000007_Abrelax__fastrelax_fa.out
01/26/2009 05:08 AM 8,704 chk_S_1UB9A_2_00000007_Abrelax__fastrelax_fa.rng.state.gz
01/26/2009 05:08 AM 22,790 chk_S_1UB9A_2_00000008_Abrelax__rg_state_fa.out
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01/26/2009 05:08 AM 8,689 chk_S_1UB9A_2_00000009_Abrelax__rg_state_fa.rng.state.gz
01/26/2009 05:08 AM 22,790 chk_S_1UB9A_2_00000009_Abrelax__rg_state_fa.out
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01/26/2009 05:08 AM 22,790 chk_S_1UB9A_2_00000010_Abrelax__rg_state_fa.out
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01/26/2009 05:08 AM 8,767 chk_S_1UB9A_2_00000010_Abrelax__fastrelax_fa.rng.state.gz
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01/26/2009 05:08 AM 23,192 chk_S_1UB9A_2_00000012_Abrelax__fastrelax_fa.out
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01/26/2009 05:08 AM 8,689 chk_S_1UB9A_2_00000013_Abrelax__fastrelax_fa.rng.state.gz
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01/26/2009 05:50 AM 12,365 chk_S_1UB9A_2_00000017_ClassicAbinitio___lc_1.out
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01/26/2009 07:24 AM 12,680 chk_S_1UB9A_2_00000020_ClassicAbinitio___lc_1.out
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01/26/2009 07:24 AM 12,365 chk_S_1UB9A_2_00000020_ClassicAbinitio___lc_2.out
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01/26/2009 08:56 AM 7,811 chk_S_1UB9A_2_00000036_ClassicAbinitio___lc_2.rng.state.gz
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01/26/2009 08:57 AM 22,790 chk_S_1UB9A_2_00000016_Abrelax__rg_state_fa.out
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01/26/2009 05:36 PM 8,696 chk_S_1UB9A_2_00000102_ClassicAbinitio___lc_3.rng.state.gz
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01/26/2009 05:43 PM 81,786 score.fsc
01/26/2009 05:43 PM 2,225,351 default.out
01/26/2009 05:43 PM 8,688 rng.state.gz
01/26/2009 05:43 PM 3 boinc_checkpoint_count.txt
01/26/2009 05:43 PM 10,423 jumps_pre.log
01/26/2009 05:43 PM 5,969 stderr.txt
01/26/2009 05:47 PM 658 stderrgfx.txt
01/26/2009 05:48 PM 8,639 chk_S_1UB9A_2_00000104_ClassicAbinitio___lc_1.rng.state.gz
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01/26/2009 05:48 PM 13,158 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_1.out
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01/26/2009 05:48 PM 8,826 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_2.rng.state.gz
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01/26/2009 05:48 PM 13,994 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_3_iter1_3.out
01/26/2009 05:48 PM 8,699 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_3_iter1_4.rng.state.gz
01/26/2009 05:48 PM 13,994 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_3_iter1_4.out
01/26/2009 05:48 PM 13,994 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_3_iter1_5.out
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01/26/2009 05:48 PM 13,994 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_3_iter1_6.out
01/26/2009 05:48 PM 8,659 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_3_iter1_6.rng.state.gz
01/26/2009 05:48 PM 14,102 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_3_iter1_7.out
01/26/2009 05:48 PM 8,632 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_3_iter1_7.rng.state.gz
01/26/2009 05:48 PM 8,655 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_3_iter1_8.rng.state.gz
01/26/2009 05:48 PM 14,102 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_3_iter1_8.out
01/26/2009 05:48 PM 8,591 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_3_iter1_9.rng.state.gz
01/26/2009 05:48 PM 14,210 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_3_iter1_9.out
01/26/2009 05:48 PM 8,674 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_3_iter1_10.rng.state.gz
01/26/2009 05:48 PM 14,289 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage_3_iter1_10.out
01/26/2009 05:48 PM 8,715 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage4_kk_1.rng.state.gz
01/26/2009 05:48 PM 13,938 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage4_kk_1.out
01/26/2009 05:48 PM 13,938 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage4_kk_2.out
01/26/2009 05:48 PM 8,619 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage4_kk_2.rng.state.gz
01/26/2009 05:48 PM 8,640 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage4_kk_3.rng.state.gz
01/26/2009 05:48 PM <DIR> ..
01/26/2009 05:48 PM 13,938 chk_S_1UB9A_2_00000105_ClassicAbinitio__stage4_kk_3.out
01/26/2009 05:48 PM <DIR> .
01/26/2009 05:48 PM 10,423 jumps.log
01/26/2009 05:49 PM 60,626 stdout.txt


Perhaps you could offer advice on how to look for any checkpointing problems. It seems it is either writing checkpoints more then it should... sometimes. Or, that it's got some models that complete in less then a minute and others that run for some time.

If you could tell us more about the naming used on these files, I guess that would clear up some of my doubts on what I'm looking at, and for.

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I was starting to think that must be what was occuring. And also was thinking that once the model was completed, that these temp files should be deletable. So, great minds think alike I guess... and so do we!

Glad the info. came of some good use.

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Its not suuuuuper urgent...

Agreed. The only ill effect should be slightly higher disk space usage. Even then, it should still be within the normal range.

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