Minirosetta 1.90 and 1.91

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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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Profile Chilean
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Message 62653 - Posted: 30 Jul 2009, 20:30:26 UTC - in response to Message 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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alterfenix

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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
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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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Profile MacroAlan

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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.


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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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gerlik

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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
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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 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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Yifan Song
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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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Profile David E K
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Message 62686 - Posted: 31 Jul 2009, 19:09:24 UTC - in response to Message 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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Rich

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

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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
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Yifan Song
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Message 62703 - Posted: 1 Aug 2009, 20:27:42 UTC - in response to Message 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 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 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.
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Sid Celery

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

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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

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Message boards : Number crunching : Minirosetta 1.90 and 1.91



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