Changes in WUs and tasks

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Message 1907 - Posted: 4 Dec 2009, 10:16:16 UTC

Here will be posted the changes which are under preparation and expected to be implemented in computational tasks.
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Message 1908 - Posted: 4 Dec 2009, 16:49:14 UTC - in response to Message 1907.  

Currently we are now running continues workflow of short mdrun workunits. I am keeping an eye on these because they will be going to all hosts on our project. Already I have observe some errors on Windows 7 64-bit and I am hoping to get some insight on the cause.
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Message 1909 - Posted: 4 Dec 2009, 16:58:56 UTC - in response to Message 1908.  

Ok I read about the error message in question.

-185 (0xffffffffffffff47) ERR_RESULT_START

[boincadm@vps boinc]$ grep -r ERR_RESULT_START lib
lib/.svn/text-base/error_numbers.h.svn-base:#define ERR_RESULT_START -185
lib/.svn/text-base/str_util.cpp.svn-base: case ERR_RESULT_START: return "result start failed";
lib/str_util.cpp: case ERR_RESULT_START: return "result start failed";
lib/error_numbers.h:#define ERR_RESULT_START -185

So this means that it failed to start, but it does not tell us why. Sometimes I have problems starting an app if the permissions are not properly on the applicaiton files. That means when they client downloads the application files, they do not have permission to execute. It could be another issue. To check, I will update the application version with the modified permissions.
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Message 1910 - Posted: 4 Dec 2009, 18:25:35 UTC - in response to Message 1909.  
Last modified: 4 Dec 2009, 18:26:43 UTC

Currently we have 3 ways of generating work and they are all represent different point of our workflow

1st we run a perl script that generates autodock workunits which returns most likely sites of binding for a ligand

2nd we have a perl script sorting through the scores and then generating an initial docking simulaton, by starting another time interval at the point we finished the previous.

e.g.
nsteps_5000_int_0_-_500_autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000336_ts_1259844582800274000_1259946062147284000.7z


nsteps = total number of steps for simulation
int = the current intervals of our simulation that the workunit is running. Units are timesteps. For our simulations we use 2 femto second timesteps

ga_run = tells us how many genetic algorithm runs were used to optimize this docking simulation
bt = biotarget, whatever protein molecule we have complexed
lig = ligand molecule complexed with the protein
ts = timestep when the workunit was generated...1st timestep for autodock second for mdrun

3rd type of workunit generation is extension. We extend the length of our mdrun simulations

When you see an interval of 500 steps. That tells you they are very short simulations. Depending on your hardware they could run between 2 - 8 minutes. When we feel comfortable we will extend the length.
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Message 1911 - Posted: 4 Dec 2009, 18:32:05 UTC - in response to Message 1910.  
Last modified: 4 Dec 2009, 18:32:14 UTC

A new change, since Windows is perfoming well now. Let's see how our linux platforms behave

This is the success rate on current Windows mdrun application
724 Windows 49 97.9592%
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Message 1913 - Posted: 4 Dec 2009, 20:42:27 UTC - in response to Message 1911.  

new update on the linux platform of mdrun. It was missing an application file that was registered. Caused a download error
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Message 1920 - Posted: 5 Dec 2009, 21:36:35 UTC - in response to Message 1913.  

We have to update our application again. We have a problem with the progress bar getting disabled when we run workunits. This new code modification will affect all windows platforms. I have not seen the error with too much output on other platforms. If it is required we will update the other platforms. So updating to 725 now
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Message 1921 - Posted: 5 Dec 2009, 22:52:13 UTC - in response to Message 1920.  

this code modification did not resolve the issue. still too much memory is used by the verbose flags. I will try another modification.
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Message 1922 - Posted: 5 Dec 2009, 23:51:44 UTC - in response to Message 1921.  

We are at version 727 now. Testing to see if the progress will work with verbose flag and that the output will not crash any computers.
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Message 1923 - Posted: 6 Dec 2009, 0:30:53 UTC - in response to Message 1922.  

so right now I don't have any autodock running. I will try updating one more time before reverting back to our standard version.
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Message 1925 - Posted: 6 Dec 2009, 14:27:46 UTC - in response to Message 1923.  

despite all my efforts, it still only provides progress bar tracking when we use the verbose mode. But when we use verbose mode it makes the runs unstable. I am going to see if there are any other function used when the verbose flag is called.
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Message 1927 - Posted: 6 Dec 2009, 16:49:29 UTC - in response to Message 1925.  

I am reverting back to the older version. I will generate some intial runs using a longer minimization. You can read a little about the LINCS warnings here

http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
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Message 1930 - Posted: 8 Dec 2009, 11:33:34 UTC - in response to Message 1927.  

I noticed the 7za was failing on several occasions so I updated us to windows version 730
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Message 1931 - Posted: 8 Dec 2009, 18:05:42 UTC - in response to Message 1930.  

updating the dll for this 7za. If this keeps failing, I have to switch to zip archives
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Message 1932 - Posted: 9 Dec 2009, 2:20:16 UTC - in response to Message 1931.  

Instead of replacing all the 7za what we will be doing is using zip format with the 7za. It will be much easier this way.
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Message 1953 - Posted: 11 Dec 2009, 11:47:40 UTC - in response to Message 1932.  

I tried to get better results using normal zip format. It did not work better.
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Message 2082 - Posted: 6 Jan 2010, 2:10:23 UTC - in response to Message 1953.  

I'm updating the app version again because we need to make some additional changes...version of MGLTools was not updated yet. It has to have some additional changes to the scripts we need to add.
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Message 2217 - Posted: 6 Feb 2010, 0:42:08 UTC - in response to Message 2082.  

This weekend I'll be focusing on these issues with checkpointing on mdrun. I will test how we can get checkpointing to work properly. Initially I thought our checkpointing was working because I had it suspended and I restart, it returns to where it was left off. I exit the manager, restart the manager it works. But as some of you have informed me and later I tested, it does not return to the same state when we terminate all boinc process such as tray. This is because the state is getting stored into memory, its not ready the state when it restarts.

mdrun has checkpointing files, I have to test this more...
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Message 2218 - Posted: 6 Feb 2010, 16:19:55 UTC - in response to Message 2217.  

I'm making some progress on the checkpointing and hope to have this issue resolved in a few hours if I don't lost wondering in the snow outside.
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Message 2220 - Posted: 6 Feb 2010, 17:43:33 UTC - in response to Message 2218.  

I'm making some progress on the checkpointing and hope to have this issue resolved in a few hours if I don't lost wondering in the snow outside.


how much snow you end up with from yesterday.?

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Message boards : Number crunching : Changes in WUs and tasks


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