Minirosetta 1.98

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Yifan Song
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Message 63690 - Posted: 15 Oct 2009, 0:31:55 UTC

A few more command line level options are added.
Report bugs here.
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Message 63694 - Posted: 15 Oct 2009, 3:03:29 UTC

What do these \"options\" mean exactly?
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Yifan Song
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Message 63695 - Posted: 15 Oct 2009, 7:13:11 UTC - in response to Message 63694.  
Last modified: 15 Oct 2009, 7:15:58 UTC

As David described in his journal (http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177&nowrap=true#63383), we are working on improving energy functions. Currently, a lot of parameters are either defined in the code or in minirosetta_database. The new options allow us to test different energy functions from command line.
One example of what we plan to test in the coming weeks is a hydrogen bond potential with sharper distance and angular dependence. As many of you know, hydrogen bond plays an important role in drug design, as well as in protein/DNA interface design for gene therapy. However the exact form and magnitude of hydrogen bond is still underdetermined. Now from command line we can change the shape of hydrogen bond potential, and test whether they agree with the experimental data we\'ve collected.

What do these \"options\" mean exactly?
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Mod.Sense
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Message 63700 - Posted: 15 Oct 2009, 15:48:07 UTC

The \"command line\" is what drives each task to get it started on your machine at home. Just like Linux/Unix or DOS commands, BOINC applications are started with a number of options that direct them on how to run. So it is easily changed, without changing the program. And also easy to create several tasks with the same protein and starting point, and see if the command line adjustments make a demonstrable difference in the outcome.
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Michael G.R.

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Message 63703 - Posted: 15 Oct 2009, 16:26:32 UTC

Thank you Yifan.
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AMD_is_logical

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Message 63708 - Posted: 16 Oct 2009, 2:27:52 UTC

I\'m getting some errors with lr8_score12_run03_rlbd WUs. They exit after a few seconds with the message:

ERROR: Illegal attempt to score with non-identical atom set between pose and etable
ERROR:: Exit from: src/core/scoring/etable/EtableEnergy.cc line: 72
BOINC:: Error reading and gzipping output datafile: default.out

Here\'s a few examples:
http://boinc.bakerlab.org/rosetta/result.php?resultid=288322249
http://boinc.bakerlab.org/rosetta/result.php?resultid=288322220
http://boinc.bakerlab.org/rosetta/result.php?resultid=288263880
http://boinc.bakerlab.org/rosetta/result.php?resultid=288239633
http://boinc.bakerlab.org/rosetta/result.php?resultid=288212752
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P . P . L .

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Message 63709 - Posted: 16 Oct 2009, 4:43:29 UTC

Same error here by the look of it.

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=263115946

Fri 16 Oct 2009 15:22:49 EST|rosetta@home|Output file lr8_score12_run03_rlbd_1py9_IGNORE_THE_REST_DECOY_14712_976_1_0 for task absent

ERROR: Illegal attempt to score with non-identical atom set between pose and etable
ERROR:: Exit from: src/core/scoring/etable/EtableEnergy.cc line: 72
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

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googloo
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Message 63712 - Posted: 16 Oct 2009, 12:08:08 UTC

How many times must I ask that you post new versions to the Rosetta Application Version Release Log?

If you do that, those of us subscribed to that thread will get an email and be able to adjust our firewalls BEFORE there are problems.
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MarcoA

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Message 63713 - Posted: 16 Oct 2009, 13:03:40 UTC

same as with AMD_is_logical:
http://boinc.bakerlab.org/rosetta/result.php?resultid=288316563:

ERROR: Illegal attempt to score with non-identical atom set between pose and etable
ERROR:: Exit from: src/core/scoring/etable/EtableEnergy.cc line: 72

at least it took only 6s of CPU-Time.
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Snags

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Message 63715 - Posted: 16 Oct 2009, 14:24:08 UTC

symm_lr8_seq_score12_ss_1.7_rlbd_1lou_IGNORE_THE_REST_DECOY_14923_2775

Exception:
failure to read decoy F_00023_0001585_0 from silent-file lr8_1lou.out

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svincent

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Message 63716 - Posted: 16 Oct 2009, 16:57:40 UTC

Task 288375137 (symm_lr8_seq_score12_ss_1.7_rlbd_1h75_IGNORE_THE_REST_DECOY_14923_2689_0) failed on Mac OS X 10.6

ERROR: !core::conformation::symmetry::is_symmetric( pose )
ERROR:: Exit from: src/core/optimization/AtomTreeMinimizer.cc line: 55
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>
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Yifan Song
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Message 63718 - Posted: 16 Oct 2009, 20:33:24 UTC

Hmm, I can\'t figure out right away where these errors could be from. They are rather old work units which has been running ok. The same type of jobs also passed the alpha test on ralph for v1.98. I\'ll do some more tests over the weekend.
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Stephenish

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Message 63721 - Posted: 16 Oct 2009, 22:21:39 UTC
Last modified: 16 Oct 2009, 23:00:35 UTC

I had two WUs fail earlier also.

I think these two made computation errors:

10/16/2009 4:37:11 PM rosetta@home Output file denovo_design_rossmann2x3_flxbb_SAVE_ALL_OUT_r2x3_001_rbd_h15_001_0001.10_0001_15195_294_0_0 for task denovo_design_rossmann2x3_flxbb_SAVE_ALL_OUT_r2x3_001_rbd_h15_001_0001.10_0001_15195_294_0 absent

10/16/2009 12:57:47 PM rosetta@home Output file lr8_A_seq_score12_shake_ss1.7_rlbd_2apb_IGNORE_THE_REST_DECOY_14949_3396_0_0 for task lr8_A_seq_score12_shake_ss1.7_rlbd_2apb_IGNORE_THE_REST_DECOY_14949_3396_0 absent

And these two definitely had issues (computation errors):

10/16/2009 5:38:05 PM rosetta@home Output file mega_lr8_seq_score12_rlbd_1srr_IGNORE_THE_REST_DECOY_15198_4_0_0 for task mega_lr8_seq_score12_rlbd_1srr_IGNORE_THE_REST_DECOY_15198_4_0 absent

10/16/2009 5:38:10 PM rosetta@home Output file lr5_dun08_it01_A_rlbd_1gvp_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_15193_176_0_0 for task lr5_dun08_it01_A_rlbd_1gvp_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_15193_176_0 absent

I seem to be getting bad WUs back to back. Only on my Pentium D 3.2GHz machine, though.
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Profile Jerry Goggin

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Message 63724 - Posted: 17 Oct 2009, 2:12:47 UTC

This task appears to have hung

10/16/2009 10:02:03 PM rosetta@home task denovo_design_rossmann2x3_flxbb_SAVE_ALL_OUT_r2x3_001_rbd_h15_001_0001.82_0001_15195_60_0 suspended by user

so I am going to abort it. Task properties indicate the State \"Waiting for memory\" whatever that means. There is plenty of memory available. I can resume it, but it simply does not run.

10/16/2009 10:08:35 PM rosetta@home task denovo_design_rossmann2x3_flxbb_SAVE_ALL_OUT_r2x3_001_rbd_h15_001_0001.82_0001_15195_60_0 resumed by user

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Message 63726 - Posted: 17 Oct 2009, 3:12:25 UTC

Jerry, BOINC allows you to control the amount of memory used by BOINC. Check your settings to see what % of memory you allow when computer is in use, and when idle. Often more memory is allowed when idle, and so BOINC is waiting either for another task to complete, or for the machine to go idle again to resume work on the task.

So, what you are seeing is normal, not \"hung\".
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Profile Jerry Goggin

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Message 63727 - Posted: 17 Oct 2009, 12:07:57 UTC - in response to Message 63726.  

I understand what you are saying, but think something else was going on. Based on my settings and running processes, task manager indicated over 500MB free physical memory available and considerably more swap space. Settings allow 50% when computer in use and 100% when computer idle, and Rosetta has had no problems during the years I\'ve been running it. Thing I noticed was that Rosetta had disappeared from the process list -- it wasn\'t waiting for anything, it was gone.

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Message 63729 - Posted: 17 Oct 2009, 15:58:37 UTC

The amount free is not relevant. The total size times 50% when in use, and then how many CPUs do you have?

It sounds like what you are seeing is that Rosetta often takes more memory to run then it used to, and they increased the recommended minimum system memory in the past year as well to reflect this.

I see you have 1 Windows machine, with 1 CPU and 768MB of memory. So 50% of that is less then the 512MB recommended. But when your machine goes idle and you allow 100%, the task is probably running. As soon as you use the machine to try and see it, computer is in use and it must be suspended.

With such settings, be sure you check the box to keep tasks in memory while suspended to avoid losing work everytime you sit down to use your computer and more memory is required.

If BOINC just got started, and knows that the task was using 200MB when it was last running, and does not presently have 200MB to devote to it, then it may not start the task on the task list until sufficient memory is available.

Also, your original post said the task was waiting for memory, but the message you copied said that you (the user) had suspended it. Perhaps that was as you were preparing to abort it?

Anyway, next time, note the task name and check back in a day and see if it is still \"hung\". It should work it\'s way through normally without any intervention.
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AMD_is_logical

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Message 63731 - Posted: 17 Oct 2009, 19:09:38 UTC

I\'m getting some errors with symm_lr8_seq_score12_ss_1.7_rlbd WUs.

ERROR: !core::conformation::symmetry::is_symmetric( pose )
ERROR:: Exit from: src/core/optimization/AtomTreeMinimizer.cc line: 55
BOINC:: Error reading and gzipping output datafile: default.out

http://boinc.bakerlab.org/rosetta/result.php?resultid=288650449
http://boinc.bakerlab.org/rosetta/result.php?resultid=288656157
http://boinc.bakerlab.org/rosetta/result.php?resultid=288660509
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Profile Jerry Goggin

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Message 63732 - Posted: 17 Oct 2009, 23:21:43 UTC - in response to Message 63729.  

Really appreciate the prompt feedback. The box to \"keep tasks in memory while suspended\" was not checked, so that got changed. This is a very old computer which needs replacing soon. Going from Win2K to Windows 7 will be interesting, I\'m sure.
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Evan

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Message 63736 - Posted: 18 Oct 2009, 9:43:35 UTC

Second chance for this one also proved a failure:

lr8_A_seq_score12_shake_ss1.7_rlbd_1c8c_IGNORE_THE_REST_DECOY_14949_2196

Repeated lines in the stderr txt point to this error

Exception:
failure to read decoy F_00018_0004416_0_0001 from silent-file lr8_shake_1c8c.out
[2009-10-17 20:10:35:] :: BOINC:: Initializing ... ok.

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