Minirosetta 3.54

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Profile [VENETO] boboviz

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Message 78178 - Posted: 3 May 2015, 18:17:03 UTC

732848733

ERROR: Can\'t create a polymer bond after residue 239 due to incompatible type: ALA_p:CtermProteinFull
ERROR:: Exit from: ..\\..\\..\\src\\core\\conformation\\Conformation.cc line: 643
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Message 78218 - Posted: 19 May 2015, 6:10:20 UTC
Last modified: 19 May 2015, 6:12:03 UTC

Hello

I recently installed Debian Jessie 64-bit on an Intel i7 box with just the basic system tools, Samba and the Boinc-client. This is command-line only - done as a file-server install so no GUI. I am getting a LOT of compute errors - below is just the one page:

735265145 666160586 17 May 2015 17:36:01 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.55 0.05 ---
735264415 666159908 17 May 2015 17:27:45 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 2.22 0.02 ---
735264319 666159812 17 May 2015 17:31:53 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 3.01 0.03 ---
735263156 666158694 17 May 2015 17:23:33 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 3.76 0.04 ---
735262945 666158497 17 May 2015 17:19:23 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 2.00 0.02 ---
735262179 666157804 17 May 2015 17:11:07 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 1.01 0.01 ---
735261760 666157386 17 May 2015 17:15:14 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.65 0.05 ---
735261098 666156741 17 May 2015 17:06:59 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.92 0.06 ---
735260316 666156003 17 May 2015 17:02:50 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.76 0.05 ---
735259902 666155598 17 May 2015 16:58:42 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.63 0.05 ---
735259688 666155396 17 May 2015 16:54:34 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.88 0.05 ---
735258808 666154613 17 May 2015 16:50:26 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 3.82 0.04 ---
735258672 666154477 17 May 2015 16:46:18 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 0.80 0.01 ---
735258071 666153955 17 May 2015 16:42:09 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.44 0.05 ---
735257419 666153326 17 May 2015 16:38:00 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 1.53 0.02 ---
735257050 666153003 17 May 2015 16:33:51 UTC 17 May 2015 22:19:26 UTC Over Client error Downloading 0.00 0.00 ---
735256597 666152571 17 May 2015 16:29:44 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 5.52 0.06 ---
735255994 666152024 17 May 2015 16:21:29 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 0.00 0.00 ---
735255589 666151620 17 May 2015 16:25:36 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.61 0.05 ---

Please let me know if I need to provide any other info ?

Thanks
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Message 78221 - Posted: 20 May 2015, 1:18:09 UTC - in response to Message 78218.  

Hello

I recently installed Debian Jessie 64-bit on an Intel i7 box with just the basic system tools, Samba and the Boinc-client. This is command-line only - done as a file-server install so no GUI. I am getting a LOT of compute errors - below is just the one page:

735265145 666160586 17 May 2015 17:36:01 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.55 0.05 ---
735264415 666159908 17 May 2015 17:27:45 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 2.22 0.02 ---
735264319 666159812 17 May 2015 17:31:53 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 3.01 0.03 ---
735263156 666158694 17 May 2015 17:23:33 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 3.76 0.04 ---
735262945 666158497 17 May 2015 17:19:23 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 2.00 0.02 ---
735262179 666157804 17 May 2015 17:11:07 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 1.01 0.01 ---
735261760 666157386 17 May 2015 17:15:14 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.65 0.05 ---
735261098 666156741 17 May 2015 17:06:59 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.92 0.06 ---
735260316 666156003 17 May 2015 17:02:50 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.76 0.05 ---
735259902 666155598 17 May 2015 16:58:42 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.63 0.05 ---
735259688 666155396 17 May 2015 16:54:34 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.88 0.05 ---
735258808 666154613 17 May 2015 16:50:26 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 3.82 0.04 ---
735258672 666154477 17 May 2015 16:46:18 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 0.80 0.01 ---
735258071 666153955 17 May 2015 16:42:09 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.44 0.05 ---
735257419 666153326 17 May 2015 16:38:00 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 1.53 0.02 ---
735257050 666153003 17 May 2015 16:33:51 UTC 17 May 2015 22:19:26 UTC Over Client error Downloading 0.00 0.00 ---
735256597 666152571 17 May 2015 16:29:44 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 5.52 0.06 ---
735255994 666152024 17 May 2015 16:21:29 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 0.00 0.00 ---
735255589 666151620 17 May 2015 16:25:36 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.61 0.05 ---

Please let me know if I need to provide any other info ?

Thanks


Just took a look at one of your error\'d workunits:
Unpacking WU data ...
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/fold_and_dock_foldit_2000569_s003_data.zip
./00001.200.3mers: write error (disk full?). Continue? (y/n/^C)
warning: ./00001.200.3mers is probably truncated
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...

ERROR: Cannot open PDB file \"multimer.pdb\"

... from what I can see either your disk is full, not enough space is available/allocated in your boinc setup, or there\'s some other type of filesystem issue.

Wish I could be more help, but hopefully this points you in the right direction. PS - these aren\'t issues with the workunits themselves as your error\'d WUs are being re-run successfully on other clients.

On the good side, I do see that your latest work unit did not error out so maybe you fixed the issue?
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Message 78222 - Posted: 20 May 2015, 9:04:31 UTC - in response to Message 78221.  

Hello

I recently installed Debian Jessie 64-bit on an Intel i7 box with just the basic system tools, Samba and the Boinc-client. This is command-line only - done as a file-server install so no GUI. I am getting a LOT of compute errors - below is just the one page:

735265145 666160586 17 May 2015 17:36:01 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.55 0.05 ---
735264415 666159908 17 May 2015 17:27:45 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 2.22 0.02 ---
735264319 666159812 17 May 2015 17:31:53 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 3.01 0.03 ---
735263156 666158694 17 May 2015 17:23:33 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 3.76 0.04 ---
735262945 666158497 17 May 2015 17:19:23 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 2.00 0.02 ---
735262179 666157804 17 May 2015 17:11:07 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 1.01 0.01 ---
735261760 666157386 17 May 2015 17:15:14 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.65 0.05 ---
735261098 666156741 17 May 2015 17:06:59 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.92 0.06 ---
735260316 666156003 17 May 2015 17:02:50 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.76 0.05 ---
735259902 666155598 17 May 2015 16:58:42 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.63 0.05 ---
735259688 666155396 17 May 2015 16:54:34 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.88 0.05 ---
735258808 666154613 17 May 2015 16:50:26 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 3.82 0.04 ---
735258672 666154477 17 May 2015 16:46:18 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 0.80 0.01 ---
735258071 666153955 17 May 2015 16:42:09 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.44 0.05 ---
735257419 666153326 17 May 2015 16:38:00 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 1.53 0.02 ---
735257050 666153003 17 May 2015 16:33:51 UTC 17 May 2015 22:19:26 UTC Over Client error Downloading 0.00 0.00 ---
735256597 666152571 17 May 2015 16:29:44 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 5.52 0.06 ---
735255994 666152024 17 May 2015 16:21:29 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 0.00 0.00 ---
735255589 666151620 17 May 2015 16:25:36 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.61 0.05 ---

Please let me know if I need to provide any other info ?

Thanks


Just took a look at one of your error\'d workunits:
Unpacking WU data ...
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/fold_and_dock_foldit_2000569_s003_data.zip
./00001.200.3mers: write error (disk full?). Continue? (y/n/^C)
warning: ./00001.200.3mers is probably truncated
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...

ERROR: Cannot open PDB file \"multimer.pdb\"

... from what I can see either your disk is full, not enough space is available/allocated in your boinc setup, or there\'s some other type of filesystem issue.

Wish I could be more help, but hopefully this points you in the right direction. PS - these aren\'t issues with the workunits themselves as your error\'d WUs are being re-run successfully on other clients.

On the good side, I do see that your latest work unit did not error out so maybe you fixed the issue?


Hello Timo

Thanks for that suggestion - I have just finished re-installing Debian Jessie again - but this time I have allocated 100 GB for the system - in the first install I took the default suggested partition sizes (where /, var, tmp and home are all separate) - which included 9 GB for system - which would have been fine for a normal server, but possibly not when Boinc is included...

Rosetta has been re-attached. Here\'s hoping this runs flawlessly ! :)

Thank you

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Message 78223 - Posted: 21 May 2015, 6:33:22 UTC - in response to Message 78222.  

Hello

I recently installed Debian Jessie 64-bit on an Intel i7 box with just the basic system tools, Samba and the Boinc-client. This is command-line only - done as a file-server install so no GUI. I am getting a LOT of compute errors - below is just the one page:

735265145 666160586 17 May 2015 17:36:01 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.55 0.05 ---
735264415 666159908 17 May 2015 17:27:45 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 2.22 0.02 ---
735264319 666159812 17 May 2015 17:31:53 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 3.01 0.03 ---
735263156 666158694 17 May 2015 17:23:33 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 3.76 0.04 ---
735262945 666158497 17 May 2015 17:19:23 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 2.00 0.02 ---
735262179 666157804 17 May 2015 17:11:07 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 1.01 0.01 ---
735261760 666157386 17 May 2015 17:15:14 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.65 0.05 ---
735261098 666156741 17 May 2015 17:06:59 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.92 0.06 ---
735260316 666156003 17 May 2015 17:02:50 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.76 0.05 ---
735259902 666155598 17 May 2015 16:58:42 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.63 0.05 ---
735259688 666155396 17 May 2015 16:54:34 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.88 0.05 ---
735258808 666154613 17 May 2015 16:50:26 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 3.82 0.04 ---
735258672 666154477 17 May 2015 16:46:18 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 0.80 0.01 ---
735258071 666153955 17 May 2015 16:42:09 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.44 0.05 ---
735257419 666153326 17 May 2015 16:38:00 UTC 17 May 2015 22:37:37 UTC Over Client error Compute error 1.53 0.02 ---
735257050 666153003 17 May 2015 16:33:51 UTC 17 May 2015 22:19:26 UTC Over Client error Downloading 0.00 0.00 ---
735256597 666152571 17 May 2015 16:29:44 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 5.52 0.06 ---
735255994 666152024 17 May 2015 16:21:29 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 0.00 0.00 ---
735255589 666151620 17 May 2015 16:25:36 UTC 17 May 2015 22:19:26 UTC Over Client error Compute error 4.61 0.05 ---

Please let me know if I need to provide any other info ?

Thanks


Just took a look at one of your error\'d workunits:
Unpacking WU data ...
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/fold_and_dock_foldit_2000569_s003_data.zip
./00001.200.3mers: write error (disk full?). Continue? (y/n/^C)
warning: ./00001.200.3mers is probably truncated
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...

ERROR: Cannot open PDB file \"multimer.pdb\"

... from what I can see either your disk is full, not enough space is available/allocated in your boinc setup, or there\'s some other type of filesystem issue.

Wish I could be more help, but hopefully this points you in the right direction. PS - these aren\'t issues with the workunits themselves as your error\'d WUs are being re-run successfully on other clients.

On the good side, I do see that your latest work unit did not error out so maybe you fixed the issue?


Hello Timo

Thanks for that suggestion - I have just finished re-installing Debian Jessie again - but this time I have allocated 100 GB for the system - in the first install I took the default suggested partition sizes (where /, var, tmp and home are all separate) - which included 9 GB for system - which would have been fine for a normal server, but possibly not when Boinc is included...

Rosetta has been re-attached. Here\'s hoping this runs flawlessly ! :)

Thank you


Hello Timo

An update: so far the work units seem to be succeeding - barring one that happened around the time that my UPS ran out of power and the server went down...

Thank you

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Message 78224 - Posted: 21 May 2015, 13:34:33 UTC - in response to Message 78223.  


Hello Timo

An update: so far the work units seem to be succeeding - barring one that happened around the time that my UPS ran out of power and the server went down...

Thank you


Glad to hear that it\'s working. Happy crunching sir! XD
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