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[BOINC] [生命科学类] Rosetta@home

发表于 2006-2-16 09:14:47 | 显示全部楼层

February 15, 2006

Volunteers needed!!

We are seeking volunteers for our new alpha test project, RALPH (http://ralph.bakerlab.org).

There are a number of recent improvements to the rosetta application but we need volunteers to speed up the process of testing to make the updated application available for production as soon as possible.

If you are interested in helping to improve Rosetta@home and can spare a few extra cycles for testing, please join RALPH@home.



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发表于 2006-2-17 21:46:15 | 显示全部楼层

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发表于 2006-2-18 11:06:16 | 显示全部楼层

February 17, 2006

Outage Notice: The project will be down starting today at 3pm PST for maintenance. The server should be back online later in the evening.


We will be updating the rosetta application today. There are a number of new features:


Work units will have a default cpu run time of 8 hours, and users will have the option to change the cpu run time as a project specific preference. The length of work units will no longer depend on the number of predicted structures. This option was added to allow participants to reduce bandwidth usage per work unit and maintain consistent run times.


Users will also have the option to change the frame rate and cpu use for graphics.
A new graphics version will be available for Mac OSX users.



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发表于 2006-2-18 13:29:40 | 显示全部楼层

[分享] Rosetta@home 科学新闻


January 25, 2006

I will use this space to give biweekly updates on recent results and the work units planned for upcoming weeks.


Today I will begin by summarizing some of the main results of the last few weeks.


More computing power can significantly improve results. This is illustrated by the 1ogw case. For one of the work unit types (NO_SIM_ANNEAL_BARCODE_30) we ran 60,000 independent jobs, for a total of 600,000 structures. If we take the lowest energy ten structures, the median rmsd is 2.86. If we instead take the lowest energy ten structures just from the first 18,000 jobs, the median rmsd is 4.49. So with more sampling, we are able to land more explorers closer to the global minimum, and get more accurate results.


Allowing additional flexibility in the chain can significantly improve results (this was the "breakthrough" I described several months ago). In the "NO_VARY_OMEGA" runs, we went back to the pre breakthrough less flexible chain, and the results were consistently worse. For example, in the 1ogw case, the median rmsd of the low energy structures increased to 4.50. For 1r69, the median rmsd of the low energy structures increased from 1.29 to 2.80.


The computationally less expensive NO_SIM_ANNEAL methods were no worse in locating low energy low rmsd structures than the SIM_ANNEAL runs. This is good news, as we can carry out many more of the NO_SIM_ANNEAL searches and so do more searching for the same amount of CPU time.


As Paul Buck anticipated, most of the remaining alternative methods we tested were roughly equivalent (except for the NO_VARY_OMEGA). One way of looking at this is that given the huge space we have to search, all that matters is how many independent explorers are sent out to search, not the details of the instructions each are given about where to search.

正如Paul Buck期望的,其它大部分我们测试过的方法大体上效果都差不多(除了“NO_VARY_OMEGA”)。也可以这样看,对于我们要搜寻的巨大空间,重要的是有多少探索者被送出去搜寻,具体我们怎么指导探索者去搜寻反而并不那么重要。

Excitingly, for many of the proteins, the lowest energy structures are very close (less than 3.0A rmsd) from the true structure. For example, in the NO_SIM_ANNEAL_BARCODE_30 the rmsds of the lowest energy structures are


1dtj: 1.93
1dcj: 2.72
1ogw: 2.65
2reb: 1.46
1r69: 1.79
1di2: 1.40

These results are a significant improvement over anything that has been done before. If we are able to do this consistently for proteins in this size range, it will be a major scientific breakthrough.


Our next step will be to test out the computationally efficient NO_SIM_ANNEAL_BARCODE_30 method on 25 new proteins we haven't done calculations on yet. You will see the new proteins on your screen saver by early next week. The "BARCODE_30" means that for every 30 amino acid residue segment in the protein, a random choice as to the value of the angles for one residue are randomly picked at the beginning of the run. This directs different runs to explore different regions of the space, and is more or less equivalent to directing different explorers to different lattitudes and longitudes.


You will also see more "PRODUCTION_AB_INITIO" runs in the next few weeks. In these runs we are testing the first low resolution part of the search. We will lower the number of trajectories per work unit to avoid the max_cpu_time problem. I think we have largely solved this problem now by going to shorter work units and doubling the max_cpu_time limit.


There will also be tests of calculations for some of the other projects described in the introduction section of the web site. We hope to get the vaccine design calculations running on BOINC in the near future. With regard to the message board posts, we aren't yet doing any work on diabetes or MS specifically, but if we can generate accurate structures of proteins involved in these diseases using the methods you are helping us to develop, it will contribute to efforts to develop therapies.


Thank you again for all of your wonderful contributions!


David Baker

[ Last edited by Youth on 2006-2-18 at 22:51 ]


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发表于 2006-2-18 13:31:16 | 显示全部楼层
去年底David Baker发布在论坛里的一篇帖子,也是类似内容的:


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发表于 2006-2-18 14:35:36 | 显示全部楼层

February 17, 2006

Work is flowing again. Today we upgraded our database server. Unfortunately, we will be delaying the application update for a day or two to work out a few minor issues. See Technical News for details.



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发表于 2006-2-18 18:20:16 | 显示全部楼层
2006-2-18 17:16:30|rosetta@home|Sending scheduler request to http://boinc.bakerlab.org/rosetta_cgi/cgi
2006-2-18 17:16:30|rosetta@home|Reason: To fetch work
2006-2-18 17:16:30|rosetta@home|Requesting 196796 seconds of new work
2006-2-18 17:16:40|rosetta@home|Scheduler request to http://boinc.bakerlab.org/rosetta_cgi/cgi succeeded
2006-2-18 17:16:41|rosetta@home|Message from server: Server can't open database
2006-2-18 17:16:41|rosetta@home|Project is down



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发表于 2006-2-18 22:46:38 | 显示全部楼层

[分享] Rosetta@home 技术新闻


November 27, 2005
Welcome to our new technical news bulletin.

Today, we backed up our database and reconfigured the database server to match Seti@home's configuration. We'd like to thank Bob Bankay, Seti@home's database administrator, and David Hammer at Einstein@home for providing useful advice and copies of their my.cnf files. Soon, we will be testing database replication on two test servers (64 bit dual Opterons w/ 8 GB RAM) set up by Keith, and if the tests look good, they will be used for production. The benefits of using replication (as stated in the MySQL documentation) are 1) server robustness (if the master server goes down another can be used as a backup), 2) load balancing for non-updating queries, and 3) server maintenance (such as database backups) without disruptions.


今天我们按照SETI项目的配置对我们的数据库进行了备份和重新配置。感谢SETI项目的数据库管理员Bob Bankay和Einstein项目的David Hammer提供了有用的建议和他们的my.cnf文件的复件。很快我们将在由Keith搭建的两台测试服务器(64位双皓龙,8G内存)上测试数据库复制。如果测试结果良好,将正式使用。使用数据库复制的好处(请参考MySQL的文档)有:增强服务器的健壮性(主服务器停机时可以使用备用服务器),对非更新的查询类型的负载均衡,不中断的服务器维护(比如数据库备份)。

December 12, 2005
Our work unit feeder is having a tough time keeping up with all the client requests for work. A short term fix (as has been done before), is to optimize the database tables. We will be doing this later today at 3pm and also backing up the database. As stated before, we are going to expand our servers soon to deal with this issue.


December 20, 2005
Last evening we released updated versions of the rosetta application for all three platforms. The updates include changes to, again, increase diversity in the searches. For those familiar with Rosetta, the protocol can now use larger protein fragment libraries and run more cycles. There were also minor changes to the graphics to allow rotation of the native structure.

Additionally, a bug was found and fixed by Bin, a post doc in our lab, that may have been causing the "1%" continual loop. This bug would occur very infrequently in specific circumstances. We do not know for sure yet if this is the only "1%" bug.

We also put our new work unit batch submission system into production. Unfortunately, a batch of work units using this system was not set up correctly. Work units from this batch have names starting with "DEFAULT_xxxxx_205_" where xxxxx are the protein code and chain id. 205 is the batch id.

IF YOU ARE RUNNING ONE OF THESE WORK UNITS, PLEASE ABORT IT. Batch 206 and greater are okay, and should not be aborted.

The work units in batch 205 were set up to predict 1000 structures instead of 10, so they will all reach the run time limit of 12-16 hours before finishing and will eventually error out. WE WILL GRANT CREDIT TO PEOPLE WHO HAVE RUN AND ABORTED THESE WORK UNITS.

Another problem has been identified with some new work units which is causing a 0xc0000005 UNHANDLED EXCEPTION error. This is a weird bug that appears to be dependent on the random number seed and we are currently looking into its cause. A short-term fix of using the computer clock to generate the seed (as has been done in previous runs) is in place.

In an effort to prevent errors like this in the future, we will set up a local test boinc server and do quality control after the holidays.






另外一个引发“0xc0000005 UNHANDLED EXCEPTION”错误的问题也已被确定。这个奇怪的臭虫似乎依赖于随机数种子,我们正在试图找出其原因。一个临时的修复已经准备好了,它将使用计算机时钟来产生这个种子。



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发表于 2006-2-18 22:59:16 | 显示全部楼层


January 6, 2006
Today, we are going to back up the database and optimize tables for general maintenance starting at 3pm PST. We are also going to replace the data fileserver with one that is more robust. Our initial fileserver used a logical volume consisting of 5 146GB Ultra3 SCSI drives, w/o redundancy. One of the disks has developed a problem putting the logical volume in peril. As a replacement we've built a new fileserver from a dual 2.8GHz XEON w/ 2GB RAM running a 6 X 146 GB RAID-5 from a LSI MegaRAID controller, providing redundancy.

太平洋时间今天下午三点的例行维护中我们将备份数据库并优化数据表。我们还将替换一个更健壮的数据文件服务器。我们原来的文件服务器使用的是由5个146G的Ultra3 SCSI硬盘组成的一个逻辑卷。其中一个硬盘的问题导致整个逻辑卷不再安全。新文件服务器的配置是双2.8G至强和2G内存以及由6个146G硬盘组成的RAID5以提供冗余。

January 12, 2006
We stated below that we will grant credit to users who have run and aborted bad work units that were initially released on December 20th. This has finally been done for aborted and failed results from work units in batch 205 and work units that were issued bad random number seeds. The claimed_credit from these results was added to the total_credit in the user, host, and team database tables. A total of 274609.56 credits were granted. A tab delimited list of userid, hostid, teamid, and granted credit is available online (4.2M) for anyone curious.

我们之前已声明将授予那些运行并中止了12月20日分发的错误任务的用户相应积分。最后,所有被中止或出错的批号205的任务以及那些错误的随机数种子相关的任务的结果都被授予了积分。来自这些结果的“声请积分”都被增加到了数据库中相应用户、主机、团队的总积分上。总共有274609.56的积分被授予。如何你想了解详细的情况(具体的用户、主机、团队及授予的积分),请看如下列表(大小为4.2兆):http://boinc.bakerlab.org/rosett ... edit_2006-01-12.txt

January 13, 2006
The University of Washington experienced a campus wide network slowdown today related to the Windows WMF vulnerability. See more here


January 17, 2006
The project will be down for maintenance starting today at 3pm PST. Today's down time is expected to be a bit longer than usual because, in addition to backing up our database and optimizing tables, we are also going to move our project files over to the file server.


February 14, 2006
We've modified the webserver to address the problems connecting to the server. This should improve matters for all.


February 17, 2006
Today we backed up our database and upgraded our production database server which now uses mysql-max and has a SCSI controller serving a RAID10 of 14 drives.


February 22, 2006
Starting at around 8:20 (PST) this morning the University of Washington network began to experience widespread connectivity problems. They are working on it.


[ Last edited by Youth on 2006-2-26 at 10:11 ]


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发表于 2006-2-19 15:38:13 | 显示全部楼层

February 18, 2006

Rosetta application update! Graphics are now available for Mac OSX platforms.


// 机器里最新的一个任务包已经是用4.82在计算了,屏保里面多了个model数的显示。


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发表于 2006-3-4 11:41:38 | 显示全部楼层

March 2, 2006

The default cpu run time is now set at 2 hours instead of 8. This change will effect new work units only.


// 好像只是为了减少出错的几率,如果大家算着没问题的话,建议将任务时间设置成8-10小时,这样对网络对服务器的压力都会小很多。

[ Last edited by Youth on 2006-3-4 at 11:42 ]


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发表于 2006-3-4 13:46:16 | 显示全部楼层


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发表于 2006-3-4 14:02:16 | 显示全部楼层
嗯,不用的。  // 我一般一台机器就算一个项目,所以设得比较大一些:)

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发表于 2006-3-14 12:38:51 | 显示全部楼层

March 13, 2006

We will now be posting top predictions each day!

以后我们将会每天对“最佳预测”进行更新!  // 看来官方终于是把这个做成自动的了:)

Today's protein: 1tif


Lowest Energy Structure predicted by: BurnHard (Team Dutch Power Cows)
Lowest RMSD Structure predicted by: Al83

For details and pictures of the predicted structures, see the top predictions page
Congratulations to today's winners!



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发表于 2006-3-14 12:48:00 | 显示全部楼层


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