[BOINC] [生命科学类] Rosetta@home

Youth

Outage Notice: The project will be down for general maintenance starting today at 3pm PST for 1-2 hours.

停机通告：太平洋时间今天下午三点开始进行例行的停机维护，大约持续1到2个小时。

Youth

Work is flowing again. We optimized database tables and backed up the database.

已经恢复正常。我们优化了数据库表并对数据库进行了备份。

Youth

Today's protein: 1di2
Lowest RMSD Structure predicted by: UW-Madison CAE

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

公布1di2蛋白质的最佳预测得主。

Grё@thΙll

现在rosetta的页面不能访问～wu能正常下载～

2006-3-22 20:42:13||Attempting to communicate with [boinc.bakerlab.org] timed out
2006-3-22 20:42:13|rosetta@home|Temporarily failed download of hom017_aa1rnbA09_05.200_v1_3.gz: timeout
2006-3-22 20:42:13|rosetta@home|Backing off 1 minutes and 0 seconds on download of file hom017_aa1rnbA09_05.200_v1_3.gz

[ Last edited by Grё@thΙll on 2006-3-22 at 20:54 ]

Youth

Host Merging has been disabled for the time being... See Technical News for more details.

计算机合并的功能已经被禁用了。详细请看技术新闻贴。

Youth

Recently our database server has been crushed repeatedly resulting in webserver slowdowns. Tracking all of this down has been a real challenge. This AM it was noticed that during every slowdown someone was trying to 'merge' two client hosts. After eliminating everything else as a possibility we were left to wonder if this merging of hosts could really be a problem. After disasterously wasteful searching of many unrelated issues, it was discovered that SETI@home had this very problem last month [see the entry for February 1, 2006 on the SETI@home Technical News Page]. We have disabled host merges until we can upgrade the database software.

最近我们的数据库服务器多次死机，导致网站变慢。问题很难解决。今天上午我们注意到每次变慢的时候都有人正在进行合并计算的操作。在排除了其它所有可能性之后，我们怀疑是不是合并计算机的操作有问题。在多次无用的搜寻之后，我们发现SETI@home项目上个月也碰到了这个问题（详情请看SETI@home项目2月1日的技术新闻）。因此我们已经禁用了合并计算机的功能，直到我们对数据库软件进行升级。

Youth

Today's protein: 1aiu, thioredoxin from humans

Lowest Energy Structure predicted by: Freaknoid
Lowest RMSD Structure predicted by: C5Vette
For details and pictures of the predicted structures, see the top predictions page
Congratulations to today's winners!

公布蛋白质1aiu的最佳预测得主。

[ Last edited by Youth on 2006-3-29 at 09:13 ]

Youth

The rosetta application was updated this morning. The new version includes a fix that Rom Walton (from the BOINC development team) added to the BOINC API for the "leave in memory" bug. See Technical News for more details.

Rosetta的计算程序今天上午进行了升级。新版本引入了Rom Walton对“被抢占时移出内存”臭虫的修正。详细请看技术新闻。

Youth

With Rom Walton's help, we've made good progress debugging rosetta. For starters, Rom has fixed the annoying "leave in memory" bug by updating the BOINC API to use TerminateProcess instead of exit to shut down the application. TerminateProcess halts any executing threads and then cleans up after the application instead of relying on the application to clean up after itself. Additional information for debugging has also been added to help track down remaining bugs like the "1% bug." For example, there are now fractional percent complete values (.01,.02, etc.) that will help us determine where jobs are getting stuck. Windows users can also help us track down bugs further by downloading the program database file (http://boinc.bakerlab.org/rosetta/download/rosetta_X.XX_windows_intelx86.pdb where X.XX is the latest version number) and placing it in the "BOINC/projects/boinc.bakerlab.org_rosetta" directory (the same directory where the rosetta executable resides). Currently, this file is not automatically packaged with the executable to reduce bandwidth usage. The program database file provides additional debug information that gets written to stderr. We are optimistic that with Rom's help and feedback from participants, we will soon be able to track down and fix the remaining issues with rosetta and continue to reduce the error rate for the project.

Rom Walton通过升级BOINC接口修复了“被抢占时移出内存”臭虫，方法是在关闭计算程序时由exit改用TerminateProcess，这样就是由BOINC在计算进程退出后进行清理工作，而不是计算程序自己来进行清理。针对其它如“计算程序僵在1%进度”臭虫，我们增加了新的调试信息。Windows用户可能通过下载计算程序的数据库文件来帮助我们搜寻这些臭虫。数据库文件的下载网址是：http://boinc.bakerlab.org/rosetta/download/rosetta_X.XX_windows_intelx86.pdb，其中X.XX是最新的版本号。下载后请放置在BOINC/projects/boinc.bakerlab.org_rosetta文件夹。目前出于网络带宽的限制，我们并没有将这个数据库文件打包在计算程序中。该数据库文件提供了附加的调试信息。我们相信有了Rom的帮助和用户们的反馈，我们很快就能找到并修正rosetta中残留的问题并进一步减少项目的错误率。

Youth

March 29, 2006

Today's protein: 1a19, ribonuclease inhibitor, homolog from Bacillus licheniformis

Lowest Energy Structure predicted by: dad
Lowest RMSD Structure predicted by: jswitz
For details and pictures of the predicted structures, see the top predictions page
Congratulations to today's winners!

公布蛋白质1a19的最佳预测得主！

March 31, 2006

Short Outage all the routers on the UW campus are being upgraded sometime between 0530PST and 0600PST. There will be a 5 minute outage sometime during that half hour while our router reboots.

因为学校里所有的路由器都将在太平洋时间5:30到6:00间进行升级。轮到我们的路由器重启时，5分钟内项目将不可访问。

Youth

Over 100,000 hosts have joined our project since June 2005. Thank you all for your participation! We are still actively seeking new members to help reach our target of 150 teraflops, so please spread the word out.

从2005年6月开始，已经有超过10万台计算机参加了我们的项目！感谢所有的参与者！我们仍在积极地寻求更多的新成员以达到150Teraflops的计算能力！

Youth

Dramatic increase in success rate: A fix for the "leave in memory bug" in the BOINC API has reduced failure rate from 9.1% to 4.2% for Windows work units with the newest Rosetta@home release.

任务包的成功率有了明显的提高：通过对BOINC API的修正，“被抢占时移出内存”臭虫的修正已经将使用新Rosetta计算程序的Windows任务包的错误率从9.1%降低到了4.2%。

Youth

最近David Baker似乎比较忙，一直没有更新这个页面，倒是下面这个帖子更新很频繁，推荐有兴趣的看看，对了解项目的进展很有帮助。

David Baker's Rosetta@home journal

Grё@thΙll

Youth大哥辛苦咯～
可喜的进步啊～^_^

Grё@thΙll

4.83的确比4.81改进了许多～除了可视化界面的稍微改进之外～现在暂停的出错也大大减少了～^_^