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Yifan Song
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Message 62652 - Posted 30 Jul 2009 19:59:02 UTC
Last modified: 30 Jul 2009 20:57:43 UTC

This version should solve the slowing down, and instant quitting problems.

New protocol added for predictions of changes in protein stability by mutations.

-----
DEK posted an explanation on what caused all the trouble in the last week:
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=5011&nowrap=true#62640

Here are some more details on what was done so far:
1. The signature problem that initially causes massive network traffic was solved on Monday.
2. The slowing down of the program was caused by two large changes in the code. One of the changes is to allow rosetta to model large, symmetric molecules (oligomers http://en.wikipedia.org/wiki/Oligomer). And the other is to allow modeling atomic interactions with higher definition. The bug introduced in the first change was fixed. And the second change is temporarily reversed until further evaluation of the computation cost.

Now unfortunately, due to the signature error and the update of the program, the web server will be extremely busy for the next few days. So downloading/uploading errors are still expected.

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Message 62653 - Posted 30 Jul 2009 20:30:26 UTC - in response to Message ID 62652.
Last modified: 30 Jul 2009 20:31:55 UTC

This version should solve the slowing down, and instant quitting problems.

New protocol added for predictions of changes in protein stability by mutations.


NVM. Answered my own question.
____________

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Message 62659 - Posted 30 Jul 2009 21:37:15 UTC

Part of my log today:

2009-07-30 23:31:43 rosetta@home Started download of boinc_rb1_1ubi.pdb
2009-07-30 23:32:05 Project communication failed: attempting access to reference site
2009-07-30 23:32:05 rosetta@home Temporarily failed download of boinc_rb1_1ubi.pdb: connect() failed
2009-07-30 23:32:05 rosetta@home Backing off 1 min 0 sec on download of boinc_rb1_1ubi.pdb
2009-07-30 23:32:06 Internet access OK - project servers may be temporarily down.
2009-07-30 23:32:13 Project communication failed: attempting access to reference site
2009-07-30 23:32:13 rosetta@home Temporarily failed download of boinc_rb1_1tza.pdb: HTTP error
2009-07-30 23:32:15 Internet access OK - project servers may be temporarily down.
2009-07-30 23:32:15 rosetta@home [error] File boinc_rb1_1tza.pdb has wrong size: expected 84240, got 0
2009-07-30 23:32:15 rosetta@home Started download of boinc_rb1_1tza.pdb
2009-07-30 23:32:36 Project communication failed: attempting access to reference site
2009-07-30 23:32:36 rosetta@home Temporarily failed download of boinc_rb1_1tza.pdb: connect() failed
2009-07-30 23:32:37 Internet access OK - project servers may be temporarily down.
2009-07-30 23:32:37 rosetta@home [error] File boinc_rb1_1tza.pdb has wrong size: expected 84240, got 0
2009-07-30 23:32:37 rosetta@home Started download of boinc_rb1_1tza.pdb
2009-07-30 23:32:59 Project communication failed: attempting access to reference site
2009-07-30 23:32:59 rosetta@home Temporarily failed download of boinc_rb1_1tza.pdb: connect() failed
2009-07-30 23:32:59 rosetta@home Backing off 1 min 30 sec on download of boinc_rb1_1tza.pdb
2009-07-30 23:33:00 Internet access OK - project servers may be temporarily down.
2009-07-30 23:33:06 rosetta@home [error] File boinc_rb1_1ubi.pdb has wrong size: expected 45603, got 0
2009-07-30 23:33:06 rosetta@home Started download of boinc_rb1_1ubi.pdb
2009-07-30 23:33:27 Project communication failed: attempting access to reference site
2009-07-30 23:33:27 rosetta@home Temporarily failed download of boinc_rb1_1ubi.pdb: connect() failed
2009-07-30 23:33:28 Internet access OK - project servers may be temporarily down.
2009-07-30 23:33:28 rosetta@home [error] File boinc_rb1_1ubi.pdb has wrong size: expected 45603, got 0
2009-07-30 23:33:28 rosetta@home Started download of boinc_rb1_1ubi.pdb
2009-07-30 23:33:50 Project communication failed: attempting access to reference site
2009-07-30 23:33:50 rosetta@home Temporarily failed download of boinc_rb1_1ubi.pdb: connect() failed
2009-07-30 23:33:51 Internet access OK - project servers may be temporarily down.
2009-07-30 23:33:51 rosetta@home [error] File boinc_rb1_1ubi.pdb has wrong size: expected 45603, got 0
2009-07-30 23:33:51 rosetta@home Started download of boinc_rb1_1ubi.pdb
2009-07-30 23:34:14 Project communication failed: attempting access to reference site
2009-07-30 23:34:14 rosetta@home Temporarily failed download of boinc_rb1_1ubi.pdb: connect() failed
2009-07-30 23:34:15 Internet access OK - project servers may be temporarily down.
2009-07-30 23:34:15 rosetta@home [error] File boinc_rb1_1ubi.pdb has wrong size: expected 45603, got 0
2009-07-30 23:34:15 rosetta@home Started download of boinc_rb1_1ubi.pdb
2009-07-30 23:34:30 rosetta@home [error] File boinc_rb1_1tza.pdb has wrong size: expected 84240, got 0

Yifan Song
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Message 62660 - Posted 30 Jul 2009 21:50:49 UTC

all services were temporarily shut down to add more web servers.

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Message 62669 - Posted 31 Jul 2009 3:10:02 UTC

Any chance that the "MINIROSETTA ..WINDOWS_INTELx86.exe" will be code signed in the future? Everyone I get is stopped by my Kaspersky software as a possible threat.

I have not found a place in Kaspersky to give it a wild card okey-dokey.


____________

Luciano Bastianello

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Message 62672 - Posted 31 Jul 2009 7:34:45 UTC

minirosetta_1.90_windows_x86_64.exe
My Windows Vista 64 + kasperksy internet security refuse and abort execution, minirosetta bad signature.
____________

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Message 62674 - Posted 31 Jul 2009 7:55:37 UTC
Last modified: 31 Jul 2009 7:56:21 UTC

good news on Linux (32 bits): 1.90 crunch smootly now & download speed is normal with some latence to catch the server, but it's on the good way.

Thanks admin
____________

soundtek

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Message 62678 - Posted 31 Jul 2009 11:18:01 UTC

My Kaspersky Internet security is doing the same on ALL my machines. If it cannot be signed or a wildcard fix done soon. I will have to remove rosetta from my project list, which I do not want to have to do. I have been doing them for quite a while, but it is a pain having to go to each machine and add move each to Low Restricted everytime the version changes.
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Message 62684 - Posted 31 Jul 2009 18:45:20 UTC - in response to Message ID 62678.

My Kaspersky Internet security is doing the same on ALL my machines. If it cannot be signed or a wildcard fix done soon. I will have to remove rosetta from my project list, which I do not want to have to do. I have been doing them for quite a while, but it is a pain having to go to each machine and add move each to Low Restricted everytime the version changes.


In the case of Rosetta, what Kaspersky need to provide is the ability to say "Don't bother checking for a signature on files that match this wildcard."

The purpose of signatures is twofold:

1. If a file shows up with a virus and a valid signature, you now know where the virus came from.

2. If a file shows up with an invalid signature, it has been tampered with, and therefore should be rejected.

Case 2 is the far more common scenario, and is the main reason why Kaspersky is unwilling to let Rosetta run. It has no signature, and therefore there's no way to determine if it's been tampered with.

That said, in the case of Rosetta the likelihood of tampering is zero, since BOINC itself verifies that the file saved to your disk is what was sent from the server, plus the fact that you always download directly from the project website.

What should be done is to contact Kaspersky and ask them to add this feature. ESET's NOD32 has a very similar feature, which has proven very useful at times.

____________

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Message 62685 - Posted 31 Jul 2009 18:55:04 UTC

The good news is that 1.90 seems to be stable so far. The network traffic is still heavy, but a lot better than yesterday.

As for Kaspersky, DK contacted the vendor a while ago and it went no where. Maybe it's time to try again.

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Message 62686 - Posted 31 Jul 2009 19:09:24 UTC - in response to Message ID 62685.

The good news is that 1.90 seems to be stable so far. The network traffic is still heavy, but a lot better than yesterday.

As for Kaspersky, DK contacted the vendor a while ago and it went no where. Maybe it's time to try again.



I didn't contact that vendor but did try to contact ESET a while back. Nothing happened though.

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Message 62688 - Posted 31 Jul 2009 20:18:00 UTC - in response to Message ID 62684.

Can't it be configured to ignore the download directory?

My Kaspersky Internet security is doing the same on ALL my machines. If it cannot be signed or a wildcard fix done soon. I will have to remove rosetta from my project list, which I do not want to have to do. I have been doing them for quite a while, but it is a pain having to go to each machine and add move each to Low Restricted everytime the version changes.


In the case of Rosetta, what Kaspersky need to provide is the ability to say "Don't bother checking for a signature on files that match this wildcard."

The purpose of signatures is twofold:

1. If a file shows up with a virus and a valid signature, you now know where the virus came from.

2. If a file shows up with an invalid signature, it has been tampered with, and therefore should be rejected.

Case 2 is the far more common scenario, and is the main reason why Kaspersky is unwilling to let Rosetta run. It has no signature, and therefore there's no way to determine if it's been tampered with.

That said, in the case of Rosetta the likelihood of tampering is zero, since BOINC itself verifies that the file saved to your disk is what was sent from the server, plus the fact that you always download directly from the project website.

What should be done is to contact Kaspersky and ask them to add this feature. ESET's NOD32 has a very similar feature, which has proven very useful at times.

AMD_is_logical

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Message 62702 - Posted 1 Aug 2009 19:43:04 UTC

I got a few errors on lr5_combine_mods_run01_rlbn WUs.

http://boinc.bakerlab.org/rosetta/result.php?resultid=269713462
http://boinc.bakerlab.org/rosetta/result.php?resultid=269758962
http://boinc.bakerlab.org/rosetta/result.php?resultid=269787057
http://boinc.bakerlab.org/rosetta/result.php?resultid=269811876

They end after about 10 seconds with the error:

Native pose needed for OptionKeys::relax::constrain_relax_to_native_coords
ERROR:: Exit from: src/protocols/relax/ClassicRelax.cc line: 544
BOINC:: Error reading and gzipping output datafile: default.out

Yifan Song
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Message 62703 - Posted 1 Aug 2009 20:27:42 UTC - in response to Message ID 62702.

Thanks! There was a change in that flag and I missed it. That work unit is disabled.

I got a few errors on lr5_combine_mods_run01_rlbn WUs.

http://boinc.bakerlab.org/rosetta/result.php?resultid=269713462
http://boinc.bakerlab.org/rosetta/result.php?resultid=269758962
http://boinc.bakerlab.org/rosetta/result.php?resultid=269787057
http://boinc.bakerlab.org/rosetta/result.php?resultid=269811876

They end after about 10 seconds with the error:

Native pose needed for OptionKeys::relax::constrain_relax_to_native_coords
ERROR:: Exit from: src/protocols/relax/ClassicRelax.cc line: 544
BOINC:: Error reading and gzipping output datafile: default.out

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Message 62709 - Posted 2 Aug 2009 1:59:35 UTC - in response to Message ID 62685.
Last modified: 2 Aug 2009 2:02:54 UTC

The good news is that 1.90 seems to be stable so far. The network traffic is still heavy, but a lot better than yesterday.


Agreed - I'm now on 1.90 except for a single 1.88 task at about 75% complete. Everything is running smoothly.


As for Kaspersky, DK contacted the vendor a while ago and it went no where. Maybe it's time to try again.


The other option would be to sign the executable. Depending on the available budget, there are several vendors selling code signing certificates - prices appear to be in the $150 to 200 to 250 per year, with Verisign coming in a little high in the $400 to $500 range.

MSDN article that covers signing executables.

Ignore the under $70 price on Comodo's page, that appears to be a bait and switch. I could not find a way to buy from them at that price when I hit the "Visit our store" link.
____________

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Message 62712 - Posted 2 Aug 2009 7:30:33 UTC - in response to Message ID 62709.


As for Kaspersky, DK contacted the vendor a while ago and it went no where. Maybe it's time to try again.


The other option would be to sign the executable. Depending on the available budget, there are several vendors selling code signing certificates - prices appear to be in the $150 to 200 to 250 per year, with Verisign coming in a little high in the $400 to $500 range.

MSDN article that covers signing executables.

Ignore the under $70 price on Comodo's page, that appears to be a bait and switch. I could not find a way to buy from them at that price when I hit the "Visit our store" link.


Never Mind. I just saw in another thread that there are the necessary files for generating signatures, just that the process had a hiccup.

____________

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Message 62714 - Posted 2 Aug 2009 9:06:10 UTC
Last modified: 2 Aug 2009 9:08:16 UTC

Just saw these messages in the BOINC manager, but looking at the results here, the tasks completed ok and the files were generated.

So just a FYI on something weird going on in these tasks:
lr13_seq_score12_F_rlbd_2acy_IGNORE_THE_REST_DECOY_14592_3021_1
lr13_seq_score12_F_rlbd_1bmg_IGNORE_THE_REST_DECOY_14592_3375_1

They reported in as OK later on in the day.


8/2/2009 2:27:10 AM|rosetta@home|Task lr13_seq_score12_F_rlbd_2acy_IGNORE_THE_REST_DECOY_14592_3021_1 exited with zero status but no 'finished' file
8/2/2009 2:27:10 AM|rosetta@home|If this happens repeatedly you may need to reset the project.
8/2/2009 2:27:10 AM|rosetta@home|Task lr13_seq_score12_F_rlbd_1bmg_IGNORE_THE_REST_DECOY_14592_3375_1 exited with zero status but no 'finished' file
8/2/2009 2:27:10 AM|rosetta@home|If this happens repeatedly you may need to reset the project.

Sid Celery

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Message 62717 - Posted 2 Aug 2009 13:19:19 UTC - in response to Message ID 62688.

Can't it be configured to ignore the download directory?
My Kaspersky Internet security is doing the same on ALL my machines. If it cannot be signed or a wildcard fix done soon. I will have to remove rosetta from my project list, which I do not want to have to do. I have been doing them for quite a while, but it is a pain having to go to each machine and add move each to Low Restricted everytime the version changes.

It should be able to and it's the right way to go. This is a user option and little to do with Rosetta or Kaspersky. I understand it's still happening with Norton Internet Security 2009 (but not with my Norton 360).

The (unnecessary) procedure in N360 under Vista64 is as follows - I'm sure there's an equivalent in Kaspersky as it's also a very reputable AV program:

- Click "Settings" at the top of the main page, then click Antivirus for its detailed settings.
- Under the "Scans and Risks" tab go down to "Exclusions\Low Risks" and against "Scan Exclusions" click "Configure [+]".
- Under "Scan Exclusions" Click the "Add" button, and with the "Include subfolders" option checked, click the Browse button.
- Under Vista64 navigate to the C:\Program Files\BOINC and single- (not double-) click it before pressing Ok. The directory will be excluded from scans.
- Under Vista64 do the same for C:\ProgramData\BOINC directory. Apply and Ok as necessary.
- Use the appropriate directories for your OS.
____________

svincent

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Message 62719 - Posted 2 Aug 2009 13:46:24 UTC

269810769 failed on Mac in a way similar to some reported above

Watchdog active.
Native pose needed for OptionKeys::relax::constrain_relax_to_native_coords
ERROR:: Exit from: src/protocols/relax/ClassicRelax.cc line: 544
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

____________

Sid Celery

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Message 62720 - Posted 2 Aug 2009 13:49:27 UTC
Last modified: 2 Aug 2009 13:51:15 UTC

A couple of errors showing the same issue:

ERROR: Option matching -in:detect_disulfides not found in command line top-level context

lr8_seq_score12_noss_rlbn_1opd_IGNORE_THE_REST_NATIVE_NOCON_14249_3_1
lr8_seq_score12_noss_rlbn_1kpe_IGNORE_THE_REST_NATIVE_14249_11_2

Server state Over
Outcome Client error
Client state Compute error
CPU time 0

stderr out <core_client_version>6.6.36</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
[2009- 8- 1 19:21:23:] :: BOINC:: Initializing ... ok.
[2009- 8- 1 19:21:23:] :: 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..
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize() End reached
ERROR: Option matching -in:detect_disulfides not found in command line top-level context

</stderr_txt>
]]>


Validate state Invalid
Claimed credit 0
Granted credit 0
application version 1.90

____________

j2satx

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Message 62721 - Posted 2 Aug 2009 14:19:49 UTC - in response to Message ID 62703.

Thanks! There was a change in that flag and I missed it. That work unit is disabled.

I got a few errors on lr5_combine_mods_run01_rlbn WUs.

http://boinc.bakerlab.org/rosetta/result.php?resultid=269713462
http://boinc.bakerlab.org/rosetta/result.php?resultid=269758962
http://boinc.bakerlab.org/rosetta/result.php?resultid=269787057
http://boinc.bakerlab.org/rosetta/result.php?resultid=269811876

They end after about 10 seconds with the error:

Native pose needed for OptionKeys::relax::constrain_relax_to_native_coords
ERROR:: Exit from: src/protocols/relax/ClassicRelax.cc line: 544
BOINC:: Error reading and gzipping output datafile: default.out



Is this one of the WUs tested on Ralph?

Mel

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Message 62725 - Posted 2 Aug 2009 17:35:32 UTC - in response to Message ID 62652.

This version should solve the slowing down, and instant quitting problems.

New protocol added for predictions of changes in protein stability by mutations.

-----
DEK posted an explanation on what caused all the trouble in the last week:
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=5011&nowrap=true#62640

Here are some more details on what was done so far:
1. The signature problem that initially causes massive network traffic was solved on Monday.
2. The slowing down of the program was caused by two large changes in the code. One of the changes is to allow rosetta to model large, symmetric molecules (oligomers http://en.wikipedia.org/wiki/Oligomer). And the other is to allow modeling atomic interactions with higher definition. The bug introduced in the first change was fixed. And the second change is temporarily reversed until further evaluation of the computation cost.

Now unfortunately, due to the signature error and the update of the program, the web server will be extremely busy for the next few days. So downloading/uploading errors are still expected.


____________

Mel

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Message 62726 - Posted 2 Aug 2009 17:41:53 UTC

I can no longer run Rosetta as none of my 4 machines will load minirosetta-database-rev31588.zip. This all started on the 30th of July. I have been running Rosetta since 2006 and this is the first time for this problem, however, it will run using version 5-10-45 ONLY. Is there a fix for this or do I just have to run the old version ??????????????
____________

Path7

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Message 62727 - Posted 2 Aug 2009 18:57:32 UTC - in response to Message ID 62726.

I can no longer run Rosetta as none of my 4 machines will load minirosetta-database-rev31588.zip. This all started on the 30th of July. I have been running Rosetta since 2006 and this is the first time for this problem, however, it will run using version 5-10-45 ONLY. Is there a fix for this or do I just have to run the old version ??????????????

Hello Mel,
Had the same problems:
2-8-2009 19:50:27|rosetta@home|[error] Signature verification failed for minirosetta_database_rev31588.zip
2-8-2009 19:50:27|rosetta@home|[error] Checksum or signature error for minirosetta_database_rev31588.zip
This is on a Vista laptop & BOINC 5.10.45.
I tried often to download a new WU without success.
Yet i decided to reset the project and now the download proceeded successfully.
I'm not sure whether I was just lucky or the reset did the trick.

Good luck,
Path7.

Sid Celery

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Message 62728 - Posted 2 Aug 2009 19:19:29 UTC - in response to Message ID 62726.
Last modified: 2 Aug 2009 19:24:44 UTC

I can no longer run Rosetta as none of my 4 machines will load minirosetta-database-rev31588.zip. This all started on the 30th of July. I have been running Rosetta since 2006 and this is the first time for this problem, however, it will run using version 5-10-45 ONLY. Is there a fix for this or do I just have to run the old version ??????????????

I wasn't aware this was happening any more.

Looking at your computers:
Computer ID 1116016 has failed downloading this file using Boinc 6.2.14
Computer ID 1116076 looks ok using Boinc 5.10.45 except for those WUs reporting errors as above:
Native pose needed for OptionKeys::relax::constrain_relax_to_native_coords
ERROR:: Exit from: src/protocols/relax/ClassicRelax.cc line: 544
BOINC:: Error reading and gzipping output datafile: default.out

And
ERROR: Option matching -in:detect_disulfides not found in command line top-level context

Computer ID 1116054 has downloaded 56 files but hasn't reported anything back yet.
Computer ID 1114788 has downloaded 1 file but hasn't reported anything back yet (running XP Pro SP2 - others all run SP3).

On the machines that don't work let your failed jobs return, upgrade to 6.4.7 which seems to be the most stable released version and try again. If they don't you may have to go to 5.10.45. There don't seem to be many\differences between your machines, so it is odd that some work and some don't.

EDIT: Also, why do you use just a 1 hour run-time? Seems like an awful lot of to-ing a fro-ing when you could get much the same results with less impact on the servers here. Is it an indication of previous problems?
____________

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Message 62735 - Posted 3 Aug 2009 4:16:38 UTC - in response to Message ID 62727.
Last modified: 3 Aug 2009 4:27:16 UTC

I can no longer run Rosetta as none of my 4 machines will load minirosetta-database-rev31588.zip. This all started on the 30th of July. I have been running Rosetta since 2006 and this is the first time for this problem, however, it will run using version 5-10-45 ONLY. Is there a fix for this or do I just have to run the old version ??????????????

Hello Mel,
Had the same problems:
2-8-2009 19:50:27|rosetta@home|[error] Signature verification failed for minirosetta_database_rev31588.zip
2-8-2009 19:50:27|rosetta@home|[error] Checksum or signature error for minirosetta_database_rev31588.zip
This is on a Vista laptop & BOINC 5.10.45.
I tried often to download a new WU without success.
Yet i decided to reset the project and now the download proceeded successfully.
I'm not sure whether I was just lucky or the reset did the trick.

Good luck,
Path7.


I just change another computer in my home for more than a month, because the previous one can not turn on due to the problem of the mainboard. My current computer also has such problems, too! Its CPU is Pemtium 4 3.06GHz with hyper threading, and its RAM is 1GB DDR2 SDRAM. The OS is Windows XP SP3, and the BOINC manager version is 6.6.36. Today when my computer downloaded 2 minirosetta version 1.90 workunits (Task ID 270050079 and 270139479), then the BOINC manager also showed download error message like you previously mentioned. And the message of task details is in the following:

<core_client_version>6.6.36</core_client_version>
<![CDATA[
<message>
app_version download error: couldn't get input files:
<file_xfer_error>
<file_name>minirosetta_database_rev31588.zip</file_name>
<error_code>-120</error_code>
<error_message>signature verification failed</error_message>
</file_xfer_error>

</message>
]]>

I have reset the Rosetta@home project with BOINC manager in this compter, but such error still happened. So at last I decided to abort both workunits and let my computer not download and run Rosetta@home workunits for a while until this problem can be completely solved.
____________


P . P . L .
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Message 62737 - Posted 3 Aug 2009 4:45:14 UTC

Hi.

Not really an error i guess but has the limit of 99 been taken off tasks

because i saw this on one of mine.

======================================================
DONE :: 109 starting structures 14284.6 cpu seconds
This process generated 109 decoys from 109 attempts
======================================================


____________


TimL

Joined: Sep 16 06
Posts: 14
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Credit: 8,734,759
RAC: 8,043
Message 62739 - Posted 3 Aug 2009 9:55:21 UTC

looprebuild_t374_nat_rlx_A_12863_3605_1 failed with error
ERROR: Option matching -in:detect_disulfides not found in command line top-level context


____________

Greg_BE Profile
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Message 62741 - Posted 3 Aug 2009 12:09:07 UTC

6 failed tasks with all the same error message

Native pose needed for OptionKeys::relax::constrain_relax_to_native_coords
ERROR:: Exit from: ..\..\src\protocols\relax\ClassicRelax.cc line: 544
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


lr5_combine_mods_run01_rlbn_1tit_IGNORE_THE_REST_NATIVE_14608_97_0
lr5_combine_mods_run01_rlbn_1tul_IGNORE_THE_REST_NATIVE_14608_97_0
lr5_combine_mods_run01_rlbn_1ubi_IGNORE_THE_REST_NATIVE_14608_97_0
lr5_combine_mods_run01_rlbn_1ugh_IGNORE_THE_REST_NATIVE_14608_97_0
lr5_combine_mods_run01_rlbn_1unp_IGNORE_THE_REST_NATIVE_14608_97_0
lr5_combine_mods_run01_rlbn_1unr_IGNORE_THE_REST_NATIVE_14608_97_0

Sid Celery

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Message 62745 - Posted 3 Aug 2009 15:04:06 UTC
Last modified: 3 Aug 2009 15:06:41 UTC

More of the same:

Incorrect function. (0x1) - exit code 1 (0x1)
lr5_combine_mods_run01_rlbn_1ttz_IGNORE_THE_REST_NATIVE_14608_21_1

Native pose needed for OptionKeys::relax::constrain_relax_to_native_coords
ERROR:: Exit from: ..\..\src\protocols\relax\ClassicRelax.cc line: 544
BOINC:: Error reading and gzipping output datafile: default.out
lr5_combine_mods_run01_rlbn_1ew4_IGNORE_THE_REST_NATIVE_14608_26_0
lr5_combine_mods_run01_rlbn_2ci2_IGNORE_THE_REST_NATIVE_14608_42_1
lr5_combine_mods_run01_rlbn_2hl7_IGNORE_THE_REST_NATIVE_14608_141_0

Is there a range of WUs we can abort before they even start?
A pattern's forming but I don't want to assume anything.
____________

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Message 62756 - Posted 3 Aug 2009 22:22:25 UTC - in response to Message ID 62741.

Make that 7 now: lr5_combine_mods_run01_rlbn_1pxu_IGNORE_THE_REST_NATIVE_14608_4_1

Run time is between 0-10 seconds on these errors.
Someone please check what is going on, your killing my RAC.


6 failed tasks with all the same error message

Native pose needed for OptionKeys::relax::constrain_relax_to_native_coords
ERROR:: Exit from: ..\..\src\protocols\relax\ClassicRelax.cc line: 544
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


lr5_combine_mods_run01_rlbn_1tit_IGNORE_THE_REST_NATIVE_14608_97_0
lr5_combine_mods_run01_rlbn_1tul_IGNORE_THE_REST_NATIVE_14608_97_0
lr5_combine_mods_run01_rlbn_1ubi_IGNORE_THE_REST_NATIVE_14608_97_0
lr5_combine_mods_run01_rlbn_1ugh_IGNORE_THE_REST_NATIVE_14608_97_0
lr5_combine_mods_run01_rlbn_1unp_IGNORE_THE_REST_NATIVE_14608_97_0
lr5_combine_mods_run01_rlbn_1unr_IGNORE_THE_REST_NATIVE_14608_97_0

Sid Celery

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Message 62760 - Posted 4 Aug 2009 6:40:23 UTC - in response to Message ID 62756.

Run time is between 0-10 seconds on these errors.
Someone please check what is going on, your killing my RAC.

How can they be killing your RAC if they only run 10 seconds each?

Granted credit is definitely low compared to claimed credit in the current batches of WUs but the failing jobs have nothing to do with that.
____________

Rabenherz85

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Message 62761 - Posted 4 Aug 2009 7:28:14 UTC

Here are 4 CPU`s waiting for work...but Rosetta doesn't download anything and just requests Tasks for GPU ?

Greg_BE Profile
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Message 62766 - Posted 4 Aug 2009 17:14:59 UTC - in response to Message ID 62760.
Last modified: 4 Aug 2009 17:16:49 UTC

Run time is between 0-10 seconds on these errors.
Someone please check what is going on, your killing my RAC.

How can they be killing your RAC if they only run 10 seconds each?

Granted credit is definitely low compared to claimed credit in the current batches of WUs but the failing jobs have nothing to do with that.



Well in general the RAC was diving like a dive bomber, but now I see it it going the other way. Going up like a rocket. So must have been all this server trouble and who knows what else that was causing it to drop so bad. From the graph it looks like it has climbed 40 points in the last 3 days. So never mind my statement there about killed RAC. Also looks like I finally got out of that bad batch of tasks.

TimL

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Message 62767 - Posted 4 Aug 2009 20:30:12 UTC

lr5_combine_mods_run01_rlbn_1wdv_IGNORE_THE_REST_NATIVE_14608_112_1 failed with:

ERROR:: Exit from: ..\..\src\protocols\relax\ClassicRelax.cc line: 544
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

____________

Greg_BE Profile
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Message 62769 - Posted 4 Aug 2009 21:11:10 UTC - in response to Message ID 62767.
Last modified: 4 Aug 2009 21:13:45 UTC

oops..duplicate to the one above.

Greg_BE Profile
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Message 62770 - Posted 4 Aug 2009 21:12:39 UTC - in response to Message ID 62767.

lr5_combine_mods_run01_rlbn_1wdv_IGNORE_THE_REST_NATIVE_14608_112_1 failed with:

ERROR:: Exit from: ..\..\src\protocols\relax\ClassicRelax.cc line: 544
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish



Tim, watch out on those run01 tasks.
I had that same error in most if not all of them.
They will die within 10 secs. if that error shows up.
Will you list the ones that die here? It would be nice to see how many bugged out on your system.

Sid Celery

Joined: Feb 11 08
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Message 62771 - Posted 4 Aug 2009 21:30:11 UTC - in response to Message ID 62770.

Tim, watch out on those run01 tasks.
I had that same error in most if not all of them.
They will die within 10 secs. if that error shows up.
Will you list the ones that die here? It would be nice to see how many bugged out on your system.

Not quite true.

The ones that start "lr5_combine_mods_run01_rlbn_" have been problematic but
I'm currently running one starting "lr5_combine_mods_run01_rlbd_" and it's going just fine.
____________

Greg_BE Profile
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Message 62772 - Posted 5 Aug 2009 1:25:09 UTC - in response to Message ID 62771.

Tim, watch out on those run01 tasks.
I had that same error in most if not all of them.
They will die within 10 secs. if that error shows up.
Will you list the ones that die here? It would be nice to see how many bugged out on your system.

Not quite true.

The ones that start "lr5_combine_mods_run01_rlbn_" have been problematic but
I'm currently running one starting "lr5_combine_mods_run01_rlbd_" and it's going just fine.


thanks for the clarification.

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Message 62773 - Posted 5 Aug 2009 3:41:43 UTC

Agreed - I had this guy error out on one of my boxes:

resultid 269800139

Name matches the format noted by Sid, error matches the one posted by Tim.
____________

NightmareXX

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Message 62781 - Posted 5 Aug 2009 16:52:59 UTC - in response to Message ID 62773.

05/08/2009 17:06:15|rosetta@home|Started download of boinc_rb1_1aiu.pdb
05/08/2009 17:06:17|rosetta@home|Finished download of boinc_rb1_1aiu.pdb
05/08/2009 17:06:17|rosetta@home|Started download of lr8_1aiu.out.zip
05/08/2009 17:06:45|rosetta@home|Finished download of minirosetta_database_rev31588.zip
05/08/2009 17:06:45|rosetta@home|Started download of boinc_rb1_1acf.pdb
05/08/2009 17:06:45|rosetta@home|[error] Signature verification failed for minirosetta_database_rev31588.zip
05/08/2009 17:06:45|rosetta@home|[error] Checksum or signature error for minirosetta_database_rev31588.zip



How do I fix these errors? :(

http://boinc.bakerlab.org/rosetta/results.php?hostid=986605&offset=20
____________

Murasaki
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Message 62782 - Posted 5 Aug 2009 17:57:56 UTC - in response to Message ID 62781.
Last modified: 5 Aug 2009 17:59:16 UTC


How do I fix these errors? :(

http://boinc.bakerlab.org/rosetta/results.php?hostid=986605&offset=20


Try installing a more recent version of BOINC. Version 6.4.7 is said to be quite stable (Version 6.4.5 has been working well for me since I installed it so I am sticking with that for now).

Check the logs of your firewall and anti-virus software to see if either have been blocking files from downloading.
____________

NightmareXX

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Credit: 1,885,318
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Message 62784 - Posted 5 Aug 2009 22:17:32 UTC - in response to Message ID 62782.


How do I fix these errors? :(

http://boinc.bakerlab.org/rosetta/results.php?hostid=986605&offset=20


Try installing a more recent version of BOINC. Version 6.4.7 is said to be quite stable (Version 6.4.5 has been working well for me since I installed it so I am sticking with that for now).

Check the logs of your firewall and anti-virus software to see if either have been blocking files from downloading.

I don't have a firewall or AV on my server and no, it doesn't have any virii either. I've updated to the latest version of BOINC but no luck, still the same problem.
____________

amgthis

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Message 62785 - Posted 5 Aug 2009 22:39:31 UTC

Anyone else having trouble with these w/u's bombing out after only 20 seconds or so? More output file absent errors?

05-Aug-2009 12:16:20 [rosetta@home] Starting task lr5_combine_mods_run01_rlbn_1enh_IGNORE_THE_REST_NATIVE_14608_23_0 using minirosetta version 190
05-Aug-2009 12:16:42 [rosetta@home] Computation for task lr5_combine_mods_run01_rlbn_1enh_IGNORE_THE_REST_NATIVE_14608_23_0 finished
05-Aug-2009 12:16:42 [rosetta@home] Output file RE_THE_REST_lr5_combine_mods_run01_rlbn_1enh_IGNONATIVE_14608_23_0_0 for task lr5_combine_mods_run01_rlbn_1enh_IGNORE_THE_REST_NATIVE_14608_23_0 absent

____________

P . P . L .
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Message 62786 - Posted 5 Aug 2009 22:53:52 UTC - in response to Message ID 62781.

05/08/2009 17:06:15|rosetta@home|Started download of boinc_rb1_1aiu.pdb
05/08/2009 17:06:17|rosetta@home|Finished download of boinc_rb1_1aiu.pdb
05/08/2009 17:06:17|rosetta@home|Started download of lr8_1aiu.out.zip
05/08/2009 17:06:45|rosetta@home|Finished download of minirosetta_database_rev31588.zip
05/08/2009 17:06:45|rosetta@home|Started download of boinc_rb1_1acf.pdb
05/08/2009 17:06:45|rosetta@home|[error] Signature verification failed for minirosetta_database_rev31588.zip
05/08/2009 17:06:45|rosetta@home|[error] Checksum or signature error for minirosetta_database_rev31588.zip



How do I fix these errors? :(

http://boinc.bakerlab.org/rosetta/results.php?hostid=986605&offset=20


You could try to reset project if you have not tried already, could not hurt!

____________


m

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Posts: 7
ID: 313928
Credit: 308,471
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Message 62787 - Posted 6 Aug 2009 0:22:00 UTC - in response to Message ID 62786.

05/08/2009 17:06:15|rosetta@home|Started download of boinc_rb1_1aiu.pdb
05/08/2009 17:06:17|rosetta@home|Finished download of boinc_rb1_1aiu.pdb
05/08/2009 17:06:17|rosetta@home|Started download of lr8_1aiu.out.zip
05/08/2009 17:06:45|rosetta@home|Finished download of minirosetta_database_rev31588.zip
05/08/2009 17:06:45|rosetta@home|Started download of boinc_rb1_1acf.pdb
05/08/2009 17:06:45|rosetta@home|[error] Signature verification failed for minirosetta_database_rev31588.zip
05/08/2009 17:06:45|rosetta@home|[error] Checksum or signature error for minirosetta_database_rev31588.zip



How do I fix these errors? :(

http://boinc.bakerlab.org/rosetta/results.php?hostid=986605&offset=20


You could try to reset project if you have not tried already, could not hurt!


I have just added Rosetta to the list on two boxes, one Windoze, one Linux and have this error on both. The project hasn't even started, not much to reset. Running BOINC 5.10.45

Sid Celery

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Posts: 806
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Credit: 9,805,706
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Message 62789 - Posted 6 Aug 2009 1:21:14 UTC - in response to Message ID 62772.

The ones that start "lr5_combine_mods_run01_rlbn_" have been problematic but
I'm currently running one starting "lr5_combine_mods_run01_rlbd_" and it's going just fine.

Thanks for the clarification.

It's the pattern I was thinking about earlier.

Yifan seems to have spotted it up the thread (1st August) and dealt with it already, but it looks like we all had some in our buffers, working their way out of the system. At least, seeing as they only ran a few seconds, it didn't affect any of us much. However:

05/08/2009 17:06:45|rosetta@home|[error] Signature verification failed for minirosetta_database_rev31588.zip
05/08/2009 17:06:45|rosetta@home|[error] Checksum or signature error for minirosetta_database_rev31588.zip


A few people seem to be still getting this (I certainly don't since the server issues got solved). I have no idea why it's occurring but someone at TPTB should see if they can spot what the issue is.
____________

m

Joined: May 2 09
Posts: 7
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Message 62810 - Posted 6 Aug 2009 23:19:02 UTC - in response to Message ID 62789.


05/08/2009 17:06:45|rosetta@home|[error] Signature verification failed for minirosetta_database_rev31588.zip
05/08/2009 17:06:45|rosetta@home|[error] Checksum or signature error for minirosetta_database_rev31588.zip


A few people seem to be still getting this (I certainly don't since the server issues got solved). I have no idea why it's occurring but someone at TPTB should see if they can spot what the issue is.[/quote]

Minirosetta 1.91 comes with database xxx_rev31589.zip and this downloads OK. So, namy thanks to TPTB.

P . P . L .
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Message 62813 - Posted 7 Aug 2009 2:51:41 UTC

Hi.

I've got another that went past 99, anyone?

mini 1.90.

======================================================
DONE :: 125 starting structures 14234.5 cpu seconds
This process generated 125 decoys from 125 attempts
======================================================

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish

____________


Luciano Bastianello

Joined: Sep 9 06
Posts: 4
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Credit: 269,064
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Message 62816 - Posted 7 Aug 2009 8:08:59 UTC

My kaspersky internet security still block 1.91 application.
____________

Speedy
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Message 62832 - Posted 8 Aug 2009 10:19:49 UTC

Short running task My time pref is 6 hours task ran for 3.11 hours 33 decoys from 33 attempt's. Is this normal?
____________
Have a crunching good day!!

Marcus Hartsfield
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Message 62835 - Posted 8 Aug 2009 13:04:01 UTC

I am not geting any work. Why is that?


Sat Aug 8 04:57:31 2009 Starting BOINC client version 6.6.20 for powerpc-apple-darwin
Sat Aug 8 04:57:31 2009 log flags: task, file_xfer, sched_ops
Sat Aug 8 04:57:31 2009 Libraries: libcurl/7.19.4 OpenSSL/0.9.7l zlib/1.2.3 c-ares/1.6.0
Sat Aug 8 04:57:31 2009 Data directory: /Library/Application Support/BOINC Data
Sat Aug 8 04:57:31 2009 Processor: 1 Power Macintosh Power Macintosh [Power Macintosh Model PowerMac4,5] [AltiVec]
Sat Aug 8 04:57:31 2009 Processor features:
Sat Aug 8 04:57:31 2009 OS: Darwin: 8.11.0
Sat Aug 8 04:57:31 2009 Memory: 512.00 MB physical, 26.06 GB virtual
Sat Aug 8 04:57:31 2009 Disk: 111.65 GB total, 25.81 GB free
Sat Aug 8 04:57:31 2009 Local time is UTC -7 hours
Sat Aug 8 04:57:31 2009 Can't load library libcudart
Sat Aug 8 04:57:31 2009 No coprocessors
Sat Aug 8 04:57:31 2009 Not using a proxy
Sat Aug 8 04:57:31 2009 rosetta@home URL: http://boinc.bakerlab.org/rosetta/; Computer ID: 1122167; location: (none); project prefs: default
Sat Aug 8 04:57:31 2009 SETI@home URL: http://setiathome.berkeley.edu/; Computer ID: 4884798; location: (none); project prefs: default
Sat Aug 8 04:57:31 2009 No general preferences found - using BOINC defaults
Sat Aug 8 04:57:31 2009 Reading preferences override file
Sat Aug 8 04:57:31 2009 Preferences limit memory usage when active to 256.00MB
Sat Aug 8 04:57:31 2009 Preferences limit memory usage when idle to 460.80MB
Sat Aug 8 04:57:31 2009 Preferences limit disk usage to 10.00GB
Sat Aug 8 04:57:32 2009 SETI@home Restarting task 18fe09ab.18567.10706.16.10.48_0 using setiathome_enhanced version 603
Sat Aug 8 05:56:44 2009 rosetta@home Sending scheduler request: Requested by user.
Sat Aug 8 05:56:44 2009 rosetta@home Requesting new tasks
Sat Aug 8 05:56:49 2009 rosetta@home Scheduler request completed: got 0 new tasks
Sat Aug 8 05:56:49 2009 rosetta@home Message from server: No work sent
Sat Aug 8 05:56:49 2009 rosetta@home Message from server: (there was work for other platforms)
Sat Aug 8 05:59:06 2009 rosetta@home Sending scheduler request: Requested by user.
Sat Aug 8 05:59:06 2009 rosetta@home Requesting new tasks
Sat Aug 8 05:59:11 2009 rosetta@home Scheduler request completed: got 0 new tasks
Sat Aug 8 06:03:18 2009 rosetta@home Sending scheduler request: To fetch work.
Sat Aug 8 06:03:18 2009 rosetta@home Requesting new tasks
Sat Aug 8 06:03:23 2009 rosetta@home Scheduler request completed: got 0 new tasks
Sat Aug 8 06:03:23 2009 rosetta@home Message from server: No work sent
Sat Aug 8 06:03:23 2009 rosetta@home Message from server: (there was work for other platforms)
Sat Aug 8 06:03:43 2009 rosetta@home Resetting project
Sat Aug 8 06:03:48 2009 rosetta@home Sending scheduler request: To fetch work.
Sat Aug 8 06:03:48 2009 rosetta@home Requesting new tasks
Sat Aug 8 06:03:53 2009 rosetta@home Scheduler request completed: got 0 new tasks
Sat Aug 8 06:03:53 2009 rosetta@home Message from server: Not sending work - last request too recent: 31 sec

____________
K. Marcus Hartsfield, M.A., MFT
415.286.3298

Murasaki
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Message 62836 - Posted 8 Aug 2009 13:33:19 UTC - in response to Message ID 62835.

I am not geting any work. Why is that?

...
...

Sat Aug 8 06:03:23 2009 rosetta@home Message from server: (there was work for other platforms)


Your computer is described as a "Power Macintosh". Does that mean it uses a PPC processor?

Due to the decline in the number of PPC computers, the Rosetta team have decided not to support the PPC processor any longer; the number of computers contributing with PPC does not justify the effort of maintaining PPC compatible code. The project team have instead focussed their limited resources on supporting the Intel processors that are used in new Macintosh computers.

Some users report picking up a PPC compatible task once every few months, but they are rare and probably getting rarer.
____________

Mod.Sense
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Message 62838 - Posted 8 Aug 2009 15:33:38 UTC

Rosetta has several active application versions. So it is not entirely true to say PPC is no longer supported. However, it is only supported by specific application versions. And at any given point in time, there may or may not be work available for a version that runs on PPC.

So, it would be more correct to say the reason is that no WUs were immediately available for PPC. And that Rosetta only expects to have PPC work available periodically.
____________
Rosetta Moderator: Mod.Sense

googloo
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Message 62839 - Posted 8 Aug 2009 16:07:22 UTC

Version 1.91 is still not posted to Rosetta Application Version Release Log.

AMD_is_logical

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Message 62870 - Posted 11 Aug 2009 0:55:50 UTC

I've had a few looprebuild_t374 WUs exit in zero time with the message:

ERROR: Option matching -in:detect_disulfides not found in command line top-level context

http://boinc.bakerlab.org/rosetta/result.php?resultid=272007811
http://boinc.bakerlab.org/rosetta/result.php?resultid=271996598
http://boinc.bakerlab.org/rosetta/result.php?resultid=271963149

Sid Celery

Joined: Feb 11 08
Posts: 806
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Message 62874 - Posted 11 Aug 2009 3:09:21 UTC - in response to Message ID 62870.

I've had a few looprebuild_t374 WUs exit in zero time with the message:

ERROR: Option matching -in:detect_disulfides not found in command line top-level context

Same here, but just one in the last few days:

looprebuild_t374_S_00005_0000006_05.pdb_t374_.set4.loopfile_12864_3785_1
____________

P . P . L .
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Message 62922 - Posted 13 Aug 2009 22:12:46 UTC

This one had a interesting problem, did not get much credit either.

Looks like it only counted the last two!

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=248458028

lr8_A_seq_score12_ss2.5_rlbd_1bk2_IGNORE_THE_REST_DECOY_14618_763_0

======================================================
DONE :: 72 starting structures 14227.5 cpu seconds
This process generated 72 decoys from 72 attempts
======================================================

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish

# cpu_run_time_pref: 14400
Fullatom mode ..
======================================================
DONE :: 2 starting structures 14586 cpu seconds
This process generated 2 decoys from 2 attempts
======================================================

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish

</stderr_txt>

____________


gazzawazza

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Message 62936 - Posted 15 Aug 2009 11:45:32 UTC

hi all.

Sorry to say this but I'm still getting the odd "...exited with zero status but no 'finished' file" issue:

272737041

272128367

I've no idea whether this is Rosetta related or to do with my BOINC client (6.6.36) but it doesn't appear to happen with any of the other projects I'm crunching.


Regards,

Gary

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Message 62945 - Posted 16 Aug 2009 11:31:25 UTC

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=246770259

Mod.Sense
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Message 62947 - Posted 16 Aug 2009 15:09:14 UTC

Rochester, the WU you linked shows you past the expiration date. I take it this was a "ghost" that you didn't see on your machine? It was originally sent Aug 5th, so that was when servers were under extreme loads and timing out and this is the likely underlying cause.
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Message 62949 - Posted 16 Aug 2009 21:32:55 UTC - in response to Message ID 62947.

Rochester, the WU you linked shows you past the expiration date. I take it this was a "ghost" that you didn't see on your machine? It was originally sent Aug 5th, so that was when servers were under extreme loads and timing out and this is the likely underlying cause.


ok thanks

Message boards : Number crunching : Minirosetta 1.90 and 1.91


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