Moving to Beta D@H


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Profile Michela
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Message 4246 - Posted 12 Aug 2008 14:03:08 UTC

This is the first message of a thread that aims to keep you updated on our steps we are taking to move D@H to Beta.

Today we will distribute a new charmm (6.13) for Windows and Linux with screensaver.

We are also updating public and private keys. This is a little bit more painful because will require you to detach and reattach. Hopefully we will not renew the keys again in the next future. The reason why we update the keys is security. An e-mail will be sent to all volunteers with this message.

If the transition to new keys and new executables will be successful, we will start the distribution of a new molecular complex in one week.

We are working to extend the webpage to include the top docking conformations and users providing those conformations.

The relocation to Beta is planed for the end of August. For that time, we will remove the code invitation for the generation of new accounts.

Michela




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Message 4254 - Posted 12 Aug 2008 21:39:23 UTC
Last modified: 13 Aug 2008 0:38:13 UTC

Next update for you all:

1. It seems that sometime several de- and re-attachments are needed.

2. We are monitoring a validation issue occurred today. We made some changes to the server and starting from wu=12108 the issues should be solved (of course if we have correctly fixed the problem). We are monitoring the system and will keep you posted.

3. We would like to know whether the screensaver works fine for both Linux and Windows boxes. We were successful in testing it so far. Only when Linux runs on top of a virtual machine, the screensaver seems not to work. If it is Windows running in a virtual machine, the screensaver works fine on our testing platform.

Michela
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Message 4267 - Posted 13 Aug 2008 20:50:22 UTC

Hi All,

We have a couple of news for you:

1.- We are distributing a new complex (1hvj) it is the same protein but a different ligand.

2.- We have now the section to show the best docking results. The url is http://docking.cis.udel.edu/ourresults.php . We will also include soon the user who provided that best result. The molecules are displayed by an applet, so you need to have the applets enabled in your browser.

Thank you

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Message 4285 - Posted 19 Aug 2008 2:25:15 UTC

We improved the graphics part: the two graphs with energy and rmsd have been improved and starting from charmm34 6.15 they show the evolution of the two values as the simulation evolves.

Michela
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Message 4290 - Posted 21 Aug 2008 1:58:21 UTC

We are getting closer and closer to the beta.

Something to keep you busy in the meanwhile: take a close look at our targets by scrolling to the bottom of the main D@H webpage and clicking on the target icons!

Michela
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Message 4292 - Posted 26 Aug 2008 20:52:09 UTC

I am most anxious for this, so I might turn my dogs loose.

This is a VERY high value project for me and I will be delighted for it to really take off.

mike

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Message 4312 - Posted 30 Aug 2008 12:28:36 UTC - in response to Message ID 4246 .

The relocation to Beta is planed for the end of August. For that time, we will remove the code invitation for the generation of new accounts.

"End of August" seems to be quite near, at least if it was really 2008 you were talking about ;)

I definitely don't want to rush you, but is there a new estimate when it will really happen?
And what are the final obstacles that prevented the move 'til now?
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Message 4314 - Posted 2 Sep 2008 0:01:01 UTC - in response to Message ID 4312 .


"End of August" seems to be quite near, at least if it was really 2008 you were talking about ;)

I definitely don't want to rush you, but is there a new estimate when it will really happen?
And what are the final obstacles that prevented the move 'til now?


Well now is September, but we definitely meant August 2008. Maybe this week we will have the mayor upgrade. We are working hard to overcome the last obstacles:

  • Collection and storage of a really large number of results, which will be larger once we move to Beta
  • Testing of the graphs and a more robust application. This is basically done with all your help
  • Divulgation of the science: a more effective way to communicate to all of our volunteers what we are doing. This point includes the section to show you the docking results, as well as a new section with the glossary of the project and a new newsletter.



We know that you are donating cycles to this project because you want to advance science, but also because you want to learn what is behind. We only hope to be effective reaching this point.

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Message 4319 - Posted 3 Sep 2008 15:41:42 UTC - in response to Message ID 4314 .



* Divulgation of the science: a more effective way to communicate to all of our volunteers what we are doing. This point includes the section to show you the docking results, as well as a new section with the glossary of the project and a new newsletter.
[/list]

We know that you are donating cycles to this project because you want to advance science, but also because you want to learn what is behind. We only hope to be effective reaching this point.

That is great! I love learning the science behind the projects I support! I just signed up for this project.

Saw this on your site:

"Extend knowledge with respect to protein-ligand complexes and make this knowledge accessible to the scientific community via cyber-infrastructures"

What does this mean, that you will not be submitting papers to peer-reviewed scientific journals, but will create a data base of our results that other scientists can access? Not sure...

Thanks for the clarification!

Regards,
Bob P.
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Message 4320 - Posted 3 Sep 2008 16:15:10 UTC - in response to Message ID 4319 .
Last modified: 3 Sep 2008 16:17:06 UTC


That is great! I love learning the science behind the projects I support! I just signed up for this project.

Saw this on your site:

"Extend knowledge with respect to protein-ligand complexes and make this knowledge accessible to the scientific community via cyber-infrastructures"

What does this mean, that you will not be submitting papers to peer-reviewed scientific journals, but will create a data base of our results that other scientists can access? Not sure...

Thanks for the clarification!

Regards,
Bob P.


No, of course we are sending our results first to peer-reviewed scientific journals/conferences, but after that we will make them available, so that the scientific community in general can benefit from them, and also can validate (or contradict) our findings. That's how science advances.

Thank you for joining us [ :) ]
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Message 4321 - Posted 3 Sep 2008 16:30:06 UTC - in response to Message ID 4320 .
Last modified: 3 Sep 2008 16:36:02 UTC

No, of course we are sending our results first to peer-reviewed scientific journals/conferences, but after that we will make them available, so that the scientific community in general can benefit from them, and also can validate (or contradict) our findings. That's how science advances.

Thank you for joining us [ :) ]

Thank you! It is always nice to see links to published papers/conferences on a project site! And the main BOINC site has been publicizing links to scientific publications of BOINC-based projects.

All of which is really great! Looking forward to seeing work from DAH, at some point in the future! :)

Thanks again.

Regards,
Bob P.
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Message 4326 - Posted 4 Sep 2008 19:03:06 UTC
Last modified: 4 Sep 2008 19:03:34 UTC

Hi All,

We changed the code sign keys about one month ago, but we still getting messages of "received old code sign key" for many users.

Please, if you haven't done it yet (in the last month), you need to detach-attach the project to receive the new key and be able to receive new workunits.

Thank you for your cooperation

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Message 4353 - Posted 9 Sep 2008 7:59:26 UTC - in response to Message ID 4326 .

Please, if you haven't done it yet (in the last month), you need to detach-attach the project to receive the new key and be able to receive new workunits.


Is a project 'reset' sufficient or does it have to be a full blown detach/attach? I did a reset a while back (and haven't seen any messages) but thought I'd best check! :?
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Message 4356 - Posted 9 Sep 2008 12:44:29 UTC

If you have been able to download new work, then you don't need to detach and attach, in your case it might have been sufficient the reset.

Only in the case of hosts that have not been able to download successfully new work is necessary the reattaching to the project, they usually will have a message related to the code sign

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Message 4357 - Posted 9 Sep 2008 16:53:31 UTC
Last modified: 9 Sep 2008 16:55:28 UTC

Beta is looking great! I attached for the first time in the normal way, got and completed work, checkpoints worked, and got credit. XML stats work both for the project in showing an increase in participants and individually in showing my credits on my signature. Great to finally be a part of docking!
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Message 4358 - Posted 9 Sep 2008 17:52:31 UTC - in response to Message ID 4356 .

Joined this project today, attached 5 hosts, got work, crunched without problems, credit granted. Trouble-free. If only all projects were this simple to join! :)

Al.

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Message 4367 - Posted 20 Sep 2008 5:25:04 UTC

Looks like the move to Beta was too successful as we have run out of work.

The Servers are dry. I am unable to download any more work.
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Message 4368 - Posted 20 Sep 2008 13:26:56 UTC - in response to Message ID 4367 .

Well moving to Beta is going fine, most of the issues have been solved and we got about 1000 volunteers. But this specific case was an error with the work generator. It's back now, I'll keep watching during the day to make sure it doesn't die again.

Thank you Conan, have a great weekend

P.S. Now you should be able to get more work

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Message 4369 - Posted 20 Sep 2008 14:15:08 UTC - in response to Message ID 4368 .

Well moving to Beta is going fine, most of the issues have been solved and we got about 1000 volunteers. But this specific case was an error with the work generator. It's back now, I'll keep watching during the day to make sure it doesn't die again.

Thank you Conan, have a great weekend

P.S. Now you should be able to get more work


Thank You for taking time during your weekend to correct the problem.

mike
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Message 4371 - Posted 21 Sep 2008 0:50:43 UTC - in response to Message ID 4368 .

Well moving to Beta is going fine, most of the issues have been solved and we got about 1000 volunteers. But this specific case was an error with the work generator. It's back now, I'll keep watching during the day to make sure it doesn't die again.

Thank you Conan, have a great weekend

P.S. Now you should be able to get more work


Thanks Trilce,

Unfortunately there is still have a problem.
All my work is now going to Pending.
It still shows No Work available on the Server status page with a growing amount waiting for deletion.

Catch'a later, Conan.
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Message 4372 - Posted 21 Sep 2008 7:55:41 UTC

Hi all,

Just joined this project, but ....

2008-9-21 15:00:26|Docking@Home|Sending scheduler request: To fetch work. Requesting 34560 seconds of work, reporting 2 completed tasks
2008-9-21 15:00:31|Docking@Home|Scheduler request succeeded: got 2 new tasks
2008-9-21 15:00:35|Docking@Home|[error] Checksum or signature error for grid_probes.rtf
2008-9-21 15:00:35|Docking@Home|[error] Checksum or signature error for lpdb_amino.rtf
2008-9-21 15:00:37|Docking@Home|[error] Checksum or signature error for lpdb.prm
2008-9-21 15:00:37|Docking@Home|[error] Checksum or signature error for lpdb_probes.prm
2008-9-21 15:00:40|Docking@Home|[error] Checksum or signature error for logo.jpg
2008-9-21 15:00:40|Docking@Home|[error] Checksum or signature error for minus.jpg
2008-9-21 15:00:41|Docking@Home|[error] Checksum or signature error for plus.jpg
2008-9-21 15:00:41|Docking@Home|[error] Checksum or signature error for rotate_left.jpg
2008-9-21 15:00:42|Docking@Home|[error] Checksum or signature error for rotate_right.jpg
2008-9-21 15:00:42|Docking@Home|[error] Checksum or signature error for helvetica.txf
2008-9-21 15:01:42|Docking@Home|Sending scheduler request: To fetch work. Requesting 34560 seconds of work, reporting 2 completed tasks
2008-9-21 15:01:47|Docking@Home|Scheduler request succeeded: got 2 new tasks
2008-9-21 15:01:51|Docking@Home|[error] Checksum or signature error for grid_probes.rtf
2008-9-21 15:01:51|Docking@Home|[error] Checksum or signature error for lpdb_amino.rtf
2008-9-21 15:01:53|Docking@Home|[error] Checksum or signature error for lpdb.prm
2008-9-21 15:01:53|Docking@Home|[error] Checksum or signature error for lpdb_probes.prm
2008-9-21 15:01:55|Docking@Home|[error] Checksum or signature error for logo.jpg
2008-9-21 15:01:55|Docking@Home|[error] Checksum or signature error for minus.jpg
2008-9-21 15:01:57|Docking@Home|[error] Checksum or signature error for plus.jpg
2008-9-21 15:01:57|Docking@Home|[error] Checksum or signature error for rotate_left.jpg
2008-9-21 15:01:59|Docking@Home|[error] Checksum or signature error for rotate_right.jpg
2008-9-21 15:01:59|Docking@Home|[error] Checksum or signature error for helvetica.txf
2008-9-21 15:02:07|Docking@Home|Resetting project
2008-9-21 15:02:53|Docking@Home|Sending scheduler request: To fetch work. Requesting 8537 seconds of work, reporting 0 completed tasks
2008-9-21 15:02:58|Docking@Home|Scheduler request succeeded: got 1 new tasks
2008-9-21 15:03:13|Docking@Home|Sending scheduler request: To fetch work. Requesting 13208 seconds of work, reporting 0 completed tasks
2008-9-21 15:03:18|Docking@Home|Scheduler request succeeded: got 1 new tasks
2008-9-21 15:04:13|Docking@Home|[error] Checksum or signature error for grid_probes.rtf
2008-9-21 15:04:14|Docking@Home|[error] Checksum or signature error for lpdb_amino.rtf
2008-9-21 15:04:15|Docking@Home|[error] Checksum or signature error for lpdb.prm
2008-9-21 15:04:16|Docking@Home|[error] Checksum or signature error for lpdb_probes.prm
2008-9-21 15:04:17|Docking@Home|[error] Checksum or signature error for logo.jpg
2008-9-21 15:04:18|Docking@Home|[error] Checksum or signature error for minus.jpg
2008-9-21 15:04:19|Docking@Home|[error] Checksum or signature error for plus.jpg
2008-9-21 15:04:20|Docking@Home|[error] Checksum or signature error for rotate_left.jpg
2008-9-21 15:04:21|Docking@Home|[error] Checksum or signature error for rotate_right.jpg
2008-9-21 15:04:23|Docking@Home|[error] Checksum or signature error for helvetica.txf
2008-9-21 15:42:23|Docking@Home|Sending scheduler request: To fetch work. Requesting 34560 seconds of work, reporting 2 completed tasks
2008-9-21 15:42:28|Docking@Home|Scheduler request succeeded: got 2 new tasks
2008-9-21 15:42:31|Docking@Home|[error] Checksum or signature error for grid_probes.rtf
2008-9-21 15:42:31|Docking@Home|[error] Checksum or signature error for lpdb_amino.rtf
2008-9-21 15:42:32|Docking@Home|[error] Checksum or signature error for lpdb.prm
2008-9-21 15:42:32|Docking@Home|[error] Checksum or signature error for lpdb_probes.prm
2008-9-21 15:42:34|Docking@Home|[error] Checksum or signature error for logo.jpg
2008-9-21 15:42:34|Docking@Home|[error] Checksum or signature error for minus.jpg
2008-9-21 15:42:35|Docking@Home|[error] Checksum or signature error for plus.jpg
2008-9-21 15:42:35|Docking@Home|[error] Checksum or signature error for rotate_left.jpg
2008-9-21 15:42:37|Docking@Home|[error] Checksum or signature error for rotate_right.jpg
2008-9-21 15:42:37|Docking@Home|[error] Checksum or signature error for helvetica.txf


Only charmm34_6.15_windows_intelx86, charmm34_6.15_graphics_windows_intelx86,1d4h_****.inp have been downloaded successfully.

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Message 4374 - Posted 21 Sep 2008 9:21:25 UTC - in response to Message ID 4371 .
Last modified: 21 Sep 2008 9:22:06 UTC

Well moving to Beta is going fine, most of the issues have been solved and we got about 1000 volunteers. But this specific case was an error with the work generator. It's back now, I'll keep watching during the day to make sure it doesn't die again.

Thank you Conan, have a great weekend

P.S. Now you should be able to get more work


Thanks Trilce,

Unfortunately there is still have a problem.
All my work is now going to Pending.
It still shows No Work available on the Server status page with a growing amount waiting for deletion.

Catch'a later, Conan.


At the present, I have no work pending and there is work available per the server status page[not a lot but work].

mike
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Message 4377 - Posted 21 Sep 2008 11:52:13 UTC - in response to Message ID 4374 .
Last modified: 21 Sep 2008 11:52:55 UTC

Well moving to Beta is going fine, most of the issues have been solved and we got about 1000 volunteers. But this specific case was an error with the work generator. It's back now, I'll keep watching during the day to make sure it doesn't die again.

Thank you Conan, have a great weekend

P.S. Now you should be able to get more work


Thanks Trilce,

Unfortunately there is still have a problem.
All my work is now going to Pending.
It still shows No Work available on the Server status page with a growing amount waiting for deletion.

Catch'a later, Conan.


At the present, I have no work pending and there is work available per the server status page[not a lot but work].

mike


G'Day Mike,
Yes mine have now all been granted credit and I have received some new work.

Conan.
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Message 4379 - Posted 21 Sep 2008 19:09:55 UTC - in response to Message ID 4377 .

Dear All,

we have some issues with the download partition on the server. We are working on this right now. We will keep you posted.

Michela
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Message 4380 - Posted 21 Sep 2008 19:21:16 UTC - in response to Message ID 4379 .

Dear All,

we have some issues with the download partition on the server. We are working on this right now. We will keep you posted.

Michela



Thank You, Michela

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Message 4381 - Posted 21 Sep 2008 20:41:07 UTC

Should work be taking 4+ hours? Nothing I have done so far has exceeded two hours and most have been right around 1 hour on 2.4-2.5 ghz quads. I now have a number of work units reporting over 4 hours cpu time.

Are these normal or a symptom of the server issues?

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Message 4385 - Posted 21 Sep 2008 21:35:07 UTC - in response to Message ID 4381 .

Should work be taking 4+ hours? Nothing I have done so far has exceeded two hours and most have been right around 1 hour on 2.4-2.5 ghz quads. I now have a number of work units reporting over 4 hours cpu time.

Are these normal or a symptom of the server issues?


What is the work-unit name?

Michela


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Message 4390 - Posted 21 Sep 2008 23:36:10 UTC
Last modified: 21 Sep 2008 23:37:54 UTC

Ahh, you have a 5 hr limit. They errored out.

http://docking.cis.udel.edu/workunit.php?wuid=274305
http://docking.cis.udel.edu/workunit.php?wuid=274303
http://docking.cis.udel.edu/workunit.php?wuid=273902
http://docking.cis.udel.edu/workunit.php?wuid=273791
http://docking.cis.udel.edu/workunit.php?wuid=274224

I have a bunch still running, but as long as they abort in reasonable time I won't worry too much ... as long as there aren't too many of them.

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Message 4397 - Posted 22 Sep 2008 12:44:52 UTC - in response to Message ID 4390 .

The project is stable and therefore we moved to beta. We have still one major thing that is currently challenging us:

charmm seems to randomly generate this error: -177 (0xffffffffffffff4f) ERR_RSC_LIMIT_EXCEEDED

For some complexes this is more frequent than for others. We are having a hard time to reproduce the error and therefore find a solution. We are working on this and we keep you posted!

Michela

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Message 4398 - Posted 22 Sep 2008 14:06:14 UTC - in response to Message ID 4397 .

charmm seems to randomly generate this error: -177 (0xffffffffffffff4f) ERR_RSC_LIMIT_EXCEEDED

A resources usage, such as disk space or CPU time, has been exceeded. Typically, exceeding the CPU time is more common, as it's often underestimated.

In my anecdotal experience it's more often underestimated in Linux because this OS, unlike Windows, runs BOINC processes (or any other nice process) at the lowest CPU speed (see this ), whereas it seems to be common that projects use Windows runs to estimate the CPU time limit for WUs.

HTH

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Message 4449 - Posted 1 Oct 2008 0:15:55 UTC

On a good note for my systems, The project wu seem to be working on all os types.

The only down side is that the credits seem a little low compared to most other projects that I run....

Other than that life is good...Cheers....
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Message 4525 - Posted 26 Oct 2008 0:10:21 UTC

Howdy,

My BIONC Manager continues to list my account as "Valued Customer" rather than as I am registered (David A Ort). Can this be adjusted or should I re-gister or ???. Thanks for you help.

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Message 4633 - Posted 1 Dec 2008 19:09:48 UTC

Please expect many short workunits, we are trying to distribute trypsin again, but these complexes tend to have energy violations, which result in shorter workunits. Sorry for the inconvenience

Message boards : Number crunching : Moving to Beta D@H

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      ["db_conn"]=>
      resource(132) of type (mysql link persistent)
      ["db_name"]=>
      string(7) "docking"
    }
    ["type"]=>
    string(2) "->"
    ["args"]=>
    array(1) {
      [0]=>
      &string(51) "update DBNAME.thread set views=views+1 where id=323"
    }
  }
  [1]=>
  array(7) {
    ["file"]=>
    string(48) "/boinc/projects/docking/html_v2/inc/forum_db.inc"
    ["line"]=>
    int(60)
    ["function"]=>
    string(6) "update"
    ["class"]=>
    string(6) "DbConn"
    ["object"]=>
    object(DbConn)#38 (2) {
      ["db_conn"]=>
      resource(132) of type (mysql link persistent)
      ["db_name"]=>
      string(7) "docking"
    }
    ["type"]=>
    string(2) "->"
    ["args"]=>
    array(3) {
      [0]=>
      object(BoincThread)#3 (16) {
        ["id"]=>
        string(3) "323"
        ["forum"]=>
        string(1) "2"
        ["owner"]=>
        string(2) "10"
        ["status"]=>
        string(1) "0"
        ["title"]=>
        string(18) "Moving to Beta D@H"
        ["timestamp"]=>
        string(10) "1228158588"
        ["views"]=>
        string(4) "7929"
        ["replies"]=>
        string(2) "32"
        ["activity"]=>
        string(18) "8.874431353341e-97"
        ["sufferers"]=>
        string(1) "0"
        ["score"]=>
        string(1) "0"
        ["votes"]=>
        string(1) "0"
        ["create_time"]=>
        string(10) "1218549788"
        ["hidden"]=>
        string(1) "0"
        ["sticky"]=>
        string(1) "0"
        ["locked"]=>
        string(1) "0"
      }
      [1]=>
      &string(6) "thread"
      [2]=>
      &string(13) "views=views+1"
    }
  }
  [2]=>
  array(7) {
    ["file"]=>
    string(63) "/boinc/projects/docking/html_v2/user/community/forum/thread.php"
    ["line"]=>
    int(184)
    ["function"]=>
    string(6) "update"
    ["class"]=>
    string(11) "BoincThread"
    ["object"]=>
    object(BoincThread)#3 (16) {
      ["id"]=>
      string(3) "323"
      ["forum"]=>
      string(1) "2"
      ["owner"]=>
      string(2) "10"
      ["status"]=>
      string(1) "0"
      ["title"]=>
      string(18) "Moving to Beta D@H"
      ["timestamp"]=>
      string(10) "1228158588"
      ["views"]=>
      string(4) "7929"
      ["replies"]=>
      string(2) "32"
      ["activity"]=>
      string(18) "8.874431353341e-97"
      ["sufferers"]=>
      string(1) "0"
      ["score"]=>
      string(1) "0"
      ["votes"]=>
      string(1) "0"
      ["create_time"]=>
      string(10) "1218549788"
      ["hidden"]=>
      string(1) "0"
      ["sticky"]=>
      string(1) "0"
      ["locked"]=>
      string(1) "0"
    }
    ["type"]=>
    string(2) "->"
    ["args"]=>
    array(1) {
      [0]=>
      &string(13) "views=views+1"
    }
  }
}
query: update docking.thread set views=views+1 where id=323