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Vecchio 14-01-2006, 00.29.01   #61
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Due nuovi messaggi datati 10 gennaio...
Quota:
Dear Members,

Sorry for the late status, but I wanted to finish a test before posting:

New Cancer Data - I have been running some tests on an internal system and believe that I have some good news. It appears from my testing that everything is working as expected. There was a false alarm last week when I reported that we were ready to send results to our Oxford contact. Upon further investigation it was seen that there were some missing output files. This problem has been resolved internally so I am ready to grab the results from the new test job that has been running on Grid.org to see if the results are the same.

I will need to run the result aggregation script which is always run after a job is complete. An effect of running the script is that the workunits will all be marked complete and dispatching will stop. This may result in a lost workunit result or two. I will re-enable the job as soon as the result script completes so there will be minimum outage.

Lost Workunits - There have been some complaints of lost workunits with the new data. Since we have many results for each workunit, this is not a problem with the new cancer data per se. We will keep investigating this issue until we understand what is happening.
_________________
Robby Brewer
Senior Support Engineer
United Devices
Quota:
I have sent the results from our small test job to our Oxford contact. We will now have to wait to see what they say. As soon as I get confirmation, I can upload all of the new data. Note that we know that there is a problem with the format of the data. I had to manually convert the data in order to run our test. I am asking our contact to provide us with the correct format so that we know the input data is valid from their point of view.
_________________
Robby Brewer
Senior Support Engineer
United Devices
___________________________________

Crunching for WCG , Rosetta and PrimeGrid on BOINC
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Vecchio 17-01-2006, 17.49.20   #62
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Nuov comunicazione ufficiale datata 16 gennaio
Quota:
Dear Members,

Not a lot to mention this week:

New Cancer Data - The results from the current job have been sent to our Oxford contact. We must now wait for the results to be verified. Note that there is already one issue. Oxford is requesting an additional tag Molecule_ID be added to the input data. Hopefully this is something they will be able to deliver. As soon as I hear back, I will post.

Lost Workunits - One of our 3 servers that handle dispatch and result retrieval was not working properly. I do not see how that would cause workunits to be lost, but I guess it is possible. That server has been fixed and is working properly now. Let's keep an eye on the workunits and see if this has a positive affect on those experiencing the problem.
_________________
Robby Brewer
Senior Support Engineer
United Devices
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Vecchio 27-01-2006, 21.13.51   #63
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Nuova comunicazione del 26 gennaio
Quota:
Dear Members,

I apologize for not posting a status on Monday, but we are having a company conference this week which is consuming most of my time. The status of the new cancer data is the topic everyone is interested in so here is a very quick status.

I have a conference call with our Oxford contact tomorrow morning to discuss the new data and the results I sent a couple of weeks ago. After the call, I hope to have much more information to share. I know there is frustration about not having all of the new data loaded for members to work on. Since Oxford is the one that will ultimately be using the results, I have had to wait for them to respond as to the validity of the results. That is out of my control.

Regardless of what Oxford has to say, I will load some more of the new data next week. If the data must be recrunched later, so be it. I was trying to minimize the amount of data that must be reworked to cut down on the complaints about wasted time later. Since there are already complaints about time wasted crunching the same workunits, I guess it does not matter.

Please understand that having the data validated by Oxford is the bottleneck here and that United Devices is ready to upload all the new data as soon as the results are confirmed.
_________________
Robby Brewer
Senior Support Engineer
United Devices
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Crunching for WCG , Rosetta and PrimeGrid on BOINC
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Vecchio 31-01-2006, 14.46.22   #64
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Comunicazione del 30 gennaio
Quota:
Dear Members,

Here is the weekly status:

New Cancer Data - I had a conference call with our Oxford contact on Friday. There is an additional field they would like in the results so they have sent a sample data file containing this information. I will be uploading this later today or tomorrow. Hopefully this will produce the results they are expecting and we will be able to make all of the new data available for members later this week or next.

Rosetta - The current batch has been processed and we will be making a new batch available later this week. As always, there will be a two week period for any outstanding workunits to be credited.

Team Stats - For some reason these are missing for the 26th. The stats job will be rerun shortly to pick up this day.

Thanks to everyone for their contribution.
_________________
Robby Brewer
Senior Support Engineer
United Devices
___________________________________

Crunching for WCG , Rosetta and PrimeGrid on BOINC
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Vecchio 02-02-2006, 22.57.18   #65
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Ottime notizie in una comunicazione di oggi
Quota:
Dear Members,

I have just uploaded a portion of the latest data I received from Oxford. My internal tests looked good as far as the workunits being able to be processed. We will let this job run for a while before shipping the results back to Oxford for verification. Note that the previous cancer job is still running as well, so it is up to the dispatcher as to whether you get one of the new workunits or not. As soon as I see a few successful results, I will stop the previous job from dispatching so everyone will be crunching the new data.
_________________
Robby Brewer
Senior Support Engineer
United Devices
___________________________________

Crunching for WCG , Rosetta and PrimeGrid on BOINC
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Vecchio 06-02-2006, 21.05.29   #66
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hanno confermato le buone notizie, sono pronti a mettere sotto scaccolo tutte le nuove proteine del progetto contro il cancro
Quota:
Dear Members,

I have received confirmation from our Oxford contact that the sample result data from the latest cancer job looks good. This means that we are ready to start crunching all of the new data. The new data will be uploaded in pieces (jobs) just like we have been doing with Rosetta. When a job has completed, I will allow at least a week for any outstanding results to be uploaded by members.

This is great news for all of us. Thank you for your continued patience and contribution.
_________________
Robby Brewer
Senior Support Engineer
United Devices
___________________________________

Crunching for WCG , Rosetta and PrimeGrid on BOINC
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Vecchio 12-02-2006, 18.56.42   #67
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Nuova comunicazione del 10 febbraio
Quota:
Dear Members,

We have finished processing the current Rosetta job. A new one will be uploaded tonight. Some members may have experienced a "Cannot connect" message due to this. Until the new job is active, I have reset the current one to continue to dispatch to prevent these messages.

Thank you for your contribution.
_________________
Robby Brewer
Senior Support Engineer
United Devices
___________________________________

Crunching for WCG , Rosetta and PrimeGrid on BOINC
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Vecchio 13-02-2006, 17.09.26   #68
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Comunicazione riguardante i problemi di collegamento dovuti alle caccole dello Humen Proteome Folding
Quota:
Dear Members,

We are currently experiencing an issue with agents not being able to connect to the UD servers. This is due to the huge amounts of results we have received for Ligandfit (as well as Rosetta). Since we have been looking into an issue with aborted WUs on the Ligandfit job, I have not been running the result rollup script. This is the process that consolidates the results and then allows us to delete all of the temporary files.

Since we have valid results for all of the current Cancer WUs, I will go ahead and run the rollup script. As soon as that finishes processing, we will be able to delete the temporary result files and dispatching will resume. I will upload a new chunk of cancer data later today.
_________________
Robby Brewer
Senior Support Engineer
United Devices
___________________________________

Crunching for WCG , Rosetta and PrimeGrid on BOINC
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Vecchio 19-02-2006, 14.17.08   #69
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Nuovo batch di caccole sul cancro immesse nel sistema
Quota:
Dear Members,

I have uploaded another batch of cancer data. The last job will remain active for a few days to give members time to receive credit for any outstanding workunits. Since these new workunits are processing so quickly, I do not think we need to wait a whole week.

Thank you for your contribution.
_________________
Robby Brewer
Senior Support Engineer
United Devices
___________________________________

Crunching for WCG , Rosetta and PrimeGrid on BOINC
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Vecchio 21-02-2006, 11.51.46   #70
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Aggiornamento da Grid.org del 20/2
Quota:
Dear Members,

Here is the weekly status:

Cancer Data - We continue to have an issue with occassional aborts that is still under investigation. As I mentioned in the Member to Member Support thread, this issue has been identified as a problem with the Ligandfit application itself crashing. This has nothing to do with the UD servers dropping results or not giving due credit. The Ligandfit application has not changed in a very long time, prior to the last batch of cancer data that received no complaints. This would point to something with the new data that is causing Ligandfit to be unstable.

Note that we are receiving successful results from each and every workunit so there are not "bad workunits" that will always fail. Some members have stated that retrying a workunit that just aborted will result in a successful completion.

Although a bit frustrating because of lost points, know that we are getting successful results that can be returned to Oxford to assist in the search for the cure for cancer which is the ultimate objective of this project.
_________________
Robby Brewer
Senior Support Engineer
United Devices
___________________________________

Crunching for WCG , Rosetta and PrimeGrid on BOINC
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Vecchio 01-03-2006, 14.20.52   #71
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Aggiornamento da Grid.org del 27/2
Quota:
Dear Members,

Here is the weekly status of Grid.org.

Outage: There was a temporary outage over the weekend that caused connectivity problems with Grid.org servers. This was caused by a router failure in our datacenter and was unanticipated. The problem has since been rectified and everything should be functioning normally.

Cancer data: I have uploaded a new chunk of data and have sent the last result set to Oxford for analysis. Some members have noticed that this batch produces an awful lot of hits. I am asking if this is to be expected and if this could in any way be related to the occassional workunit aborts that some members are seeing.

Thank you for your contribution.
_________________
Robby Brewer
Senior Support Engineer
United Devices
___________________________________

Crunching for WCG , Rosetta and PrimeGrid on BOINC
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Vecchio 01-03-2006, 17.04.04   #72
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(Y)

Grazie Pup
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già Cruncher for WinTricks.it Italian Team
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Vecchio 08-03-2006, 00.00.20   #73
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Comunicazione del 6 marzo
Quota:
Dear Members,

Here is the weekly Grid.org status. Things are relatively quiet although we still have a few outstanding issues.

Cancer data - I have not heard back from our Oxford contact regarding the last batch of results I sent. This was an attempt to have them validate the many hits we are seeing on some of these workunits. It seems suspicious to me, but I am not well versed in computational chemistry and cannot speak to this. It will be up to Oxford, who provided the data, to determine if the results are valid for their research. Until then we will just keep crunching away at the new data.

There is still the issue of Ligandfit crashing. Although I do not know why, it appears that there is something about the new data that causes Ligandfit to get in a bad state. I have also mentioned this to our Oxford contact and hope that he may be able to shed some light on this issue. Perhaps the many hits or complexity of the new data is the contributing factor.

As always, thank you for your contribution.
_________________
Robby Brewer
Senior Support Engineer
United Devices
___________________________________

Crunching for WCG , Rosetta and PrimeGrid on BOINC
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Vecchio 09-03-2006, 09.23.54   #74
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Nuova comunicazione del 8/3
Quota:
Dear Members,

I have received a response from our Oxford contact regarding some of the issues we have seen with the new cancer data.

High number of hits - It was stated that a determination could not be made at this stage as to whether the data was generating too many hits or not. After we process all of the data and send it back, they will apply a cutoff criteria in order to isolate the best hits. It may be that once the data is analyzed, they will suggest a change to the Ligandfit input parameters and a rerun of the data. Remember, research implies trial and error.

Aborts - While nothing specific was identified yet, they stated that is was possible for the data to cause Ligandfit to error out. It was mentioned that some of the datas are not discrete organic molecules which may be different that data that was processed in the past. It may be that under certain circumstances this data causes Ligandfit to abort, although we have seen that a replay of the data usually produces a good result so we are not talking about a bad WU per se. They also stated that in the future they will filter out anything that they think may cause an issue. Bottom line is this issue remains elusive and we do not have the answer yet.
_________________
Robby Brewer
Senior Support Engineer
United Devices
___________________________________

Crunching for WCG , Rosetta and PrimeGrid on BOINC
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Vecchio 16-03-2006, 19.17.10   #75
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Messaggio del 13 marzo...
Quota:
Dear Members,

Here is the weekly status for Grid.org.

Cancer job - As you probably noticed, we had a small outage last week due to the amount of results being returned for the new cancer jobs. These WUs are running within a few hours each probably due to the (non) complexity of the new protein. This translates to lots of disk space being used up very quickly. Due to this, I will need to roll up the results of these jobs much faster than pervious ones in order to keep below maximum disk space. Here is what I propose:

On Wednesdays I will submit a new cancer job. Once it has been activated, I will run the roll up script which should only affect the previous job. The roll up script will mark the previous job inactive as part of its processing. Once the roll up script has finished, I will reset the job to be active. This will allow outstanding results to be credited.

On Fridays, I will delete the older job that has already had the results rolled up so any outstanding workunits will not be credited. You would have had 2 days to return your results which should be plenty considering the WUs complete within hours.

There may be a small window while the results are being rolled up to where newly returned results will be rejected. This would be due to the job being temporarily marked as inactive. Unfortunately, I see no way around this. The impact should be very minimal. If you are that concerned about a lost workunit, shutdown your agent on wednesdays until I post that the job has been reactivated.

Thank you for your contribution.
_________________
Robby Brewer
Senior Support Engineer
United Devices
___________________________________

Crunching for WCG , Rosetta and PrimeGrid on BOINC
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