Posts by Craig Dickinson

1) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 77487)
Posted 19 Sep 2014 by Craig Dickinson
Post:
Can I ask, do you use Norton 360 too? I've always suspected it's something to do with that, but can't quite put my finger on it.

I haven't used Norton for over 15 years because it was a regular cause of app crashes and system hangs. I use AVG & Comodo and set each projects exe files (some projects run multiple versions of analysis programs) as allowed applications so they have un-restricted access.

That's fine. I think we can exclude the AVFirewall being the cause then - that's all I was getting at, as I thought it might be some kind of false positive.

On the flipside, I was getting this on both desktop and laptop to a greater or lesser degree. Now I'm on my travels again and the moment I started my laptop, the 5 stalled uploads cleared and new files came down without error.

For what it's worth, the desktop is wired into cable broadband, while the laptop cleared itself once connected to analogue broadband (BT in England but not BT Infinity).

Does this provide me any clues? I don't know. I'm not in a position to reboot the cable router until the weekend when I return, though it's worth noting that only Rosetta is affected. WCG & Simap go through without any errors.

Definitely weird...

I've rebooted the router then the PC and there is no change in behaviour of this project. I also run Einstein, Seti & Virtual LHC projects all of those exchange WU's without any problems.

I've done the same in the past and it's made no difference, but lo and behold, 6 hours ago everything cleared up for me. No reason it went wrong 5 days before. No reason it sorted itself out.

Still as confused as ever. No advice I can give to help anyone else in the same situation...


Put the PC on this morning and waiting WU's uploaded and 2 new WU's downloaded and currently running and have since downloaded a third WU. Guess someone somewhere flicked a switch or something.
2) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 77485)
Posted 18 Sep 2014 by Craig Dickinson
Post:
Can I ask, do you use Norton 360 too? I've always suspected it's something to do with that, but can't quite put my finger on it.

I haven't used Norton for over 15 years because it was a regular cause of app crashes and system hangs. I use AVG & Comodo and set each projects exe files (some projects run multiple versions of analysis programs) as allowed applications so they have un-restricted access.

That's fine. I think we can exclude the AVFirewall being the cause then - that's all I was getting at, as I thought it might be some kind of false positive.

On the flipside, I was getting this on both desktop and laptop to a greater or lesser degree. Now I'm on my travels again and the moment I started my laptop, the 5 stalled uploads cleared and new files came down without error.

For what it's worth, the desktop is wired into cable broadband, while the laptop cleared itself once connected to analogue broadband (BT in England but not BT Infinity).

Does this provide me any clues? I don't know. I'm not in a position to reboot the cable router until the weekend when I return, though it's worth noting that only Rosetta is affected. WCG & Simap go through without any errors.

Definitely weird...


I've rebooted the router then the PC and there is no change in behaviour of this project. I also run Einstein, Seti & Virtual LHC projects all of those exchange WU's without any problems.
3) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 77473)
Posted 17 Sep 2014 by Craig Dickinson
Post:
I am having upload and download failures for this project and no issues with my other 3 projects. Latest failure details:-

15/09/2014 23:46:23 | rosetta@home | Started upload of rb_09_13_50527_95885__t000__0_C1_SAVE_ALL_OUT_IGNORE_THE_REST_208662_1937_0_0
15/09/2014 23:46:25 | rosetta@home | Temporarily failed upload of rb_09_13_50527_95885__t000__0_C1_SAVE_ALL_OUT_IGNORE_THE_REST_208662_1937_0_0: transient upload error
15/09/2014 23:46:25 | rosetta@home | Backing off 05:08:00 on upload of rb_09_13_50527_95885__t000__0_C1_SAVE_ALL_OUT_IGNORE_THE_REST_208662_1937_0_0
15/09/2014 23:46:29 | rosetta@home | work fetch resumed by user
15/09/2014 23:46:30 | rosetta@home | update requested by user
15/09/2014 23:46:34 | rosetta@home | Sending scheduler request: Requested by user.
15/09/2014 23:46:34 | rosetta@home | Requesting new tasks for CPU and ATI
15/09/2014 23:46:36 | rosetta@home | Scheduler request completed: got 2 new tasks
15/09/2014 23:46:39 | rosetta@home | Started download of fold_and_dock_zibochen.22.7filled_1.res.xmlfilled_data.zip
15/09/2014 23:46:39 | rosetta@home | Started download of zibochen.22.7filled_1.res.xmlfilled_fold_and_dock_flags
15/09/2014 23:46:40 | rosetta@home | Incomplete read of 1844.000000 < 5KB for fold_and_dock_zibochen.22.7filled_1.res.xmlfilled_data.zip - truncating
15/09/2014 23:46:40 | rosetta@home | Incomplete read of 1844.000000 < 5KB for zibochen.22.7filled_1.res.xmlfilled_fold_and_dock_flags - truncating
15/09/2014 23:46:40 | rosetta@home | Finished download of fold_and_dock_zibochen.22.7filled_1.res.xmlfilled_data.zip
15/09/2014 23:46:40 | rosetta@home | Finished download of zibochen.22.7filled_1.res.xmlfilled_fold_and_dock_flags
15/09/2014 23:46:40 | rosetta@home | Started download of fold_and_dock_zibochen.6.2.75_1_0001_4_0001_fine5_data.zip
15/09/2014 23:46:40 | rosetta@home | Started download of zibochen.6.2.75_1_0001_4_0001_fine5_fold_and_dock_flags
15/09/2014 23:46:40 | rosetta@home | [error] File fold_and_dock_zibochen.22.7filled_1.res.xmlfilled_data.zip has wrong size: expected 3031540, got 0
15/09/2014 23:46:40 | rosetta@home | [error] Checksum or signature error for fold_and_dock_zibochen.22.7filled_1.res.xmlfilled_data.zip
15/09/2014 23:46:40 | rosetta@home | [error] File zibochen.22.7filled_1.res.xmlfilled_fold_and_dock_flags has wrong size: expected 625, got 0
15/09/2014 23:46:40 | rosetta@home | [error] Checksum or signature error for zibochen.22.7filled_1.res.xmlfilled_fold_and_dock_flags
15/09/2014 23:46:41 | rosetta@home | Incomplete read of 1844.000000 < 5KB for fold_and_dock_zibochen.6.2.75_1_0001_4_0001_fine5_data.zip - truncating
15/09/2014 23:46:41 | rosetta@home | Incomplete read of 1844.000000 < 5KB for zibochen.6.2.75_1_0001_4_0001_fine5_fold_and_dock_flags - truncating
15/09/2014 23:46:41 | rosetta@home | Finished download of fold_and_dock_zibochen.6.2.75_1_0001_4_0001_fine5_data.zip
15/09/2014 23:46:41 | rosetta@home | Finished download of zibochen.6.2.75_1_0001_4_0001_fine5_fold_and_dock_flags
15/09/2014 23:46:41 | rosetta@home | [error] File fold_and_dock_zibochen.6.2.75_1_0001_4_0001_fine5_data.zip has wrong size: expected 3085359, got 0
15/09/2014 23:46:41 | rosetta@home | [error] Checksum or signature error for fold_and_dock_zibochen.6.2.75_1_0001_4_0001_fine5_data.zip
15/09/2014 23:46:41 | rosetta@home | [error] File zibochen.6.2.75_1_0001_4_0001_fine5_fold_and_dock_flags has wrong size: expected 625, got 0
15/09/2014 23:46:41 | rosetta@home | [error] Checksum or signature error for zibochen.6.2.75_1_0001_4_0001_fine5_fold_and_dock_flags

Just dropping in. I've had exactly the same just now.
16/09/2014 03:14:02 | rosetta@home | Reporting 4 completed tasks
16/09/2014 03:14:02 | rosetta@home | Requesting new tasks for CPU
16/09/2014 03:14:04 | rosetta@home | Scheduler request completed: got 3 new tasks
16/09/2014 03:14:06 | rosetta@home | Started download of fold_and_dock_zibochen.7.2filled_1.res.xmlfilled_data.zip
16/09/2014 03:14:06 | rosetta@home | Started download of zibochen.7.2filled_1.res.xmlfilled_fold_and_dock_flags
16/09/2014 03:14:08 | rosetta@home | Incomplete read of 1844.000000 < 5KB for fold_and_dock_zibochen.7.2filled_1.res.xmlfilled_data.zip - truncating
16/09/2014 03:14:08 | rosetta@home | Incomplete read of 1844.000000 < 5KB for zibochen.7.2filled_1.res.xmlfilled_fold_and_dock_flags - truncating
16/09/2014 03:14:08 | rosetta@home | Finished download of fold_and_dock_zibochen.7.2filled_1.res.xmlfilled_data.zip
16/09/2014 03:14:08 | rosetta@home | Finished download of zibochen.7.2filled_1.res.xmlfilled_fold_and_dock_flags
16/09/2014 03:14:08 | rosetta@home | Started download of 1408310_Exp02-027c_cavity_fold_03_04024_059_TYR_0005_fragments_data.zip
16/09/2014 03:14:08 | rosetta@home | Started download of 1408312_Exp02-027c_cavity_fold_04_56009_051_MET_0001_fragments_data.zip
16/09/2014 03:14:08 | rosetta@home | [error] File fold_and_dock_zibochen.7.2filled_1.res.xmlfilled_data.zip has wrong size: expected 3077245, got 0
16/09/2014 03:14:08 | rosetta@home | [error] Checksum or signature error for fold_and_dock_zibochen.7.2filled_1.res.xmlfilled_data.zip
16/09/2014 03:14:08 | rosetta@home | [error] File zibochen.7.2filled_1.res.xmlfilled_fold_and_dock_flags has wrong size: expected 625, got 0
16/09/2014 03:14:08 | rosetta@home | [error] Checksum or signature error for zibochen.7.2filled_1.res.xmlfilled_fold_and_dock_flags
16/09/2014 03:14:09 | rosetta@home | Incomplete read of 1844.000000 < 5KB for 1408310_Exp02-027c_cavity_fold_03_04024_059_TYR_0005_fragments_data.zip - truncating
16/09/2014 03:14:09 | rosetta@home | Incomplete read of 1844.000000 < 5KB for 1408312_Exp02-027c_cavity_fold_04_56009_051_MET_0001_fragments_data.zip - truncating
16/09/2014 03:14:09 | rosetta@home | Finished download of 1408310_Exp02-027c_cavity_fold_03_04024_059_TYR_0005_fragments_data.zip
16/09/2014 03:14:09 | rosetta@home | Finished download of 1408312_Exp02-027c_cavity_fold_04_56009_051_MET_0001_fragments_data.zip
16/09/2014 03:14:09 | rosetta@home | [error] File 1408310_Exp02-027c_cavity_fold_03_04024_059_TYR_0005_fragments_data.zip has wrong size: expected 3006865, got 0
16/09/2014 03:14:09 | rosetta@home | [error] Checksum or signature error for 1408310_Exp02-027c_cavity_fold_03_04024_059_TYR_0005_fragments_data.zip
16/09/2014 03:14:09 | rosetta@home | [error] File 1408312_Exp02-027c_cavity_fold_04_56009_051_MET_0001_fragments_data.zip has wrong size: expected 3036072, got 0
16/09/2014 03:14:09 | rosetta@home | [error] Checksum or signature error for 1408312_Exp02-027c_cavity_fold_04_56009_051_MET_0001_fragments_data.zip

Can I ask, do you use Norton 360 too? I've always suspected it's something to do with that, but can't quite put my finger on it.


I haven't used Norton for over 15 years because it was a regular cause of app crashes and system hangs. I use AVG & Comodo and set each projects exe files (some projects run multiple versions of analysis programs) as allowed applications so they have un-restricted access.
4) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 77465)
Posted 15 Sep 2014 by Craig Dickinson
Post:
I am having upload and download failures for this project and no issues with my other 3 projects. Latest failure details:-

15/09/2014 23:46:23 | rosetta@home | Started upload of rb_09_13_50527_95885__t000__0_C1_SAVE_ALL_OUT_IGNORE_THE_REST_208662_1937_0_0
15/09/2014 23:46:25 | rosetta@home | Temporarily failed upload of rb_09_13_50527_95885__t000__0_C1_SAVE_ALL_OUT_IGNORE_THE_REST_208662_1937_0_0: transient upload error
15/09/2014 23:46:25 | rosetta@home | Backing off 05:08:00 on upload of rb_09_13_50527_95885__t000__0_C1_SAVE_ALL_OUT_IGNORE_THE_REST_208662_1937_0_0
15/09/2014 23:46:29 | rosetta@home | work fetch resumed by user
15/09/2014 23:46:30 | rosetta@home | update requested by user
15/09/2014 23:46:34 | rosetta@home | Sending scheduler request: Requested by user.
15/09/2014 23:46:34 | rosetta@home | Requesting new tasks for CPU and ATI
15/09/2014 23:46:36 | rosetta@home | Scheduler request completed: got 2 new tasks
15/09/2014 23:46:39 | rosetta@home | Started download of fold_and_dock_zibochen.22.7filled_1.res.xmlfilled_data.zip
15/09/2014 23:46:39 | rosetta@home | Started download of zibochen.22.7filled_1.res.xmlfilled_fold_and_dock_flags
15/09/2014 23:46:40 | rosetta@home | Incomplete read of 1844.000000 < 5KB for fold_and_dock_zibochen.22.7filled_1.res.xmlfilled_data.zip - truncating
15/09/2014 23:46:40 | rosetta@home | Incomplete read of 1844.000000 < 5KB for zibochen.22.7filled_1.res.xmlfilled_fold_and_dock_flags - truncating
15/09/2014 23:46:40 | rosetta@home | Finished download of fold_and_dock_zibochen.22.7filled_1.res.xmlfilled_data.zip
15/09/2014 23:46:40 | rosetta@home | Finished download of zibochen.22.7filled_1.res.xmlfilled_fold_and_dock_flags
15/09/2014 23:46:40 | rosetta@home | Started download of fold_and_dock_zibochen.6.2.75_1_0001_4_0001_fine5_data.zip
15/09/2014 23:46:40 | rosetta@home | Started download of zibochen.6.2.75_1_0001_4_0001_fine5_fold_and_dock_flags
15/09/2014 23:46:40 | rosetta@home | [error] File fold_and_dock_zibochen.22.7filled_1.res.xmlfilled_data.zip has wrong size: expected 3031540, got 0
15/09/2014 23:46:40 | rosetta@home | [error] Checksum or signature error for fold_and_dock_zibochen.22.7filled_1.res.xmlfilled_data.zip
15/09/2014 23:46:40 | rosetta@home | [error] File zibochen.22.7filled_1.res.xmlfilled_fold_and_dock_flags has wrong size: expected 625, got 0
15/09/2014 23:46:40 | rosetta@home | [error] Checksum or signature error for zibochen.22.7filled_1.res.xmlfilled_fold_and_dock_flags
15/09/2014 23:46:41 | rosetta@home | Incomplete read of 1844.000000 < 5KB for fold_and_dock_zibochen.6.2.75_1_0001_4_0001_fine5_data.zip - truncating
15/09/2014 23:46:41 | rosetta@home | Incomplete read of 1844.000000 < 5KB for zibochen.6.2.75_1_0001_4_0001_fine5_fold_and_dock_flags - truncating
15/09/2014 23:46:41 | rosetta@home | Finished download of fold_and_dock_zibochen.6.2.75_1_0001_4_0001_fine5_data.zip
15/09/2014 23:46:41 | rosetta@home | Finished download of zibochen.6.2.75_1_0001_4_0001_fine5_fold_and_dock_flags
15/09/2014 23:46:41 | rosetta@home | [error] File fold_and_dock_zibochen.6.2.75_1_0001_4_0001_fine5_data.zip has wrong size: expected 3085359, got 0
15/09/2014 23:46:41 | rosetta@home | [error] Checksum or signature error for fold_and_dock_zibochen.6.2.75_1_0001_4_0001_fine5_data.zip
15/09/2014 23:46:41 | rosetta@home | [error] File zibochen.6.2.75_1_0001_4_0001_fine5_fold_and_dock_flags has wrong size: expected 625, got 0
15/09/2014 23:46:41 | rosetta@home | [error] Checksum or signature error for zibochen.6.2.75_1_0001_4_0001_fine5_fold_and_dock_flags
5) Message boards : Number crunching : minirosetta 2.05 (Message 65338)
Posted 15 Feb 2010 by Craig Dickinson
Post:

I have the wireshark trace from the re-attaching of the Rosetta project to the Boinc client showing the original download failure of the graphics file and the first 2 attempts to resume the download of the graphics file. Once again all other Rosetta files and the first work unit have sucessfully downloaded.

Where do you want me to send the wireshark trace report.


Craig and I arranged exchange of the trace via PMs... Craig, I've reviewed the trace and it seems the BOINC client is requesting a partial transfer from the next server in Rosetta's cluster, just as expected. But your machine never acknowledges receipt of any of the packets. And so the 3rd and 4th try are asking for the same point in the file that the second did. Plenty of time elapses, and the frame is resend about 10 times. But never acknowledged. Eventually the connection is closed.

The only times I've seen such fundamental things not work properly is when (bear with me :) there is a fundamental problem. Some examples from my past... bad ethernet port in the hub. Bad cable. But most commonly there's a router between the client and the server that's in need of a code refresh. That, or perhaps Win7 itself or the driver for your LAN adapter need an update. Because it sounds like it is happening so consistently at the same point, I tend to think there is a code problem here, because a hardware problem like a bad cable or port would probably be more intermittent.

The only other thing I can think of to try is that the downloads started out looking good, so after that first one gets most of the file and fails, shutdown BOINC, and shutdown the LAN adapter ("disable"), reenable the adapter, and fire up BOINC again. Now the retry will occur with a fresh start on the adapter and perhaps get you over the hump. But ultimately, that is just a work around. I think the true fix is going to be drivers, Win7, or router/firewall code updates. You might also try disabling the IPv6 support on the adapter.

Is anyone aware of any specific TCP fixes for Win7?

Notes to self (cuz this little scrap of paper is sure to disappear as soon as anyone askes me anything else about it!): client starts on srv1, retries occur to srv5, srv6, and srv3. Local ports used are 51221, 51229, 51235, 51241. These make good filters, such as: tcp.port == 51235 in the Wireshark display.



I am using a router so re-loaded the firmware as suggested and this has fixed the problem. Didn't think about the router being the cause as I would have expected that to have caused problems with other BOINC project updates or other software auto updaters.
6) Message boards : Number crunching : minirosetta 2.05 (Message 65264)
Posted 10 Feb 2010 by Craig Dickinson
Post:

It does not show which server it is connecting to, I tried the url you provided and srv3 as well. Both of these download at 136KB/sec consistently until the download hits 4.57MB then the transfer rate drops to 0KB/sec and after 5 minutes or so it times out the connection.


...even so, the reaction on the client should be to see that it did not receive the entire length of the file, and then try a second request for just the remainder of the file (this is done with an HTTP range header).

I just tried the link from home and it worked fine for me 5.1MB. So that would explain why others are not seeing the same.

Is it possible your ISP is limiting the time of each connection or something? Even so, I'm still puzzled why it doesn't sound like it is doing a retry from where it left off. What is the reaction on the client after the connection gets the 4.57M and then times out?? It should schedule a retry on the file until it gets it. And the retry should pick up where the first attempt left off at the 4.57M. You should see this in the advanced view, in the transfers tab.

Perhaps there is something up with Win7? I'd be curious to have a look at a Wireshark trace if you would take the time to gather one.




I have the wireshark trace from the re-attaching of the Rosetta project to the Boinc client showing the original download failure of the graphics file and the first 2 attempts to resume the download of the graphics file. Once again all other Rosetta files and the first work unit have sucessfully downloaded.

Where do you want me to send the wireshark trace report.
7) Message boards : Number crunching : minirosetta 2.05 (Message 65251)
Posted 9 Feb 2010 by Craig Dickinson
Post:
Anyone else seeing the following consistent error:-

File - minirosetta_graphics_1.92_windows_x86_64.exe stops downloading at 4.57/5.10 MB

Message section is showing this as a HTTP error followed by Internet access OK - project servers may temporarily be down.

I have reset the project (more than once) also detached and waited until next PC boot to re-attach. All this had no impact and its been doing this for several days now. So I am unable to process any work units as the applications hasn't finished downloading.

Running on Boinc 6.10.18 for Windows 64Bit on Windows 7, AMD 64Bit Dual Core, 4GB RAM

I am also running Seti@Home and this is running error free in both the standard and astropulse projects.


It should recover the transfer from where it left off and get the rest of the file. But it seems it must have a hiccup along the way. Are you using a cacheing proxy server or something?

Sounds like you've enabled the http tracing. Which Rosetta server does it say it is trying to get the file from? It should actually cycle through all of them as it does the retries. This should confuse a proxy enough that it would start fresh.

You could always download it with your browser and drop it in the rosetta project directory. Here is one of the direct URLs:
http://srv4.bakerlab.org/download/minirosetta_graphics_1.92_windows_x86_64.exe


It does not show which server it is connecting to, I tried the url you provided and srv3 as well. Both of these download at 136KB/sec consistently until the download hits 4.57MB then the transfer rate drops to 0KB/sec and after 5 minutes or so it times out the connection.
8) Message boards : Number crunching : minirosetta 2.05 (Message 65239)
Posted 8 Feb 2010 by Craig Dickinson
Post:
Anyone else seeing the following consistent error:-

File - minirosetta_graphics_1.92_windows_x86_64.exe stops downloading at 4.57/5.10 MB

Message section is showing this as a HTTP error followed by Internet access OK - project servers may temporarily be down.

I have reset the project (more than once) also detached and waited until next PC boot to re-attach. All this had no impact and its been doing this for several days now. So I am unable to process any work units as the applications hasn't finished downloading.

Running on Boinc 6.10.18 for Windows 64Bit on Windows 7, AMD 64Bit Dual Core, 4GB RAM

I am also running Seti@Home and this is running error free in both the standard and astropulse projects.






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