12/13/2005
What is going on

The old NAS performs a chkdsk every time it boots, during which it finds no errors. This takes 4+ hours to validate the drives and is, how shall we say ... inconvenient.

The Drives check out OK physically, but the RAID does not. When it completes boot, at least one drive is deactivated and the RAID is offline. I must manually activate the Drive, bring the RAID back online and then ... wait ... while it rebuilds the array.

Oh, and guess what. It's a SOFTWARE RAID.

It has come to pass that there is irreparable data corruption in the operating system partition. With power failures and inadequate generators, when the NAS fails, this is bound to happen. With software RAID, this is a tragic thing.

The Current NAS has been offline for some time during this diagnosis and evaluation. I have secured a new NAS that has upgraded spindle speed, a hardware backplane with hardware RAID, and improved network connectivity. It is enroute.

The key here was to replace the device without the need to recode the software. Migrating the data will be dicey as the current NAS is not stable at all  I have unplugged it from the network to prevent y'all from using it and uploading doomed data.

Yes the project is down. No, the project has not ended. It will simply take longer than we had hoped to march forward.

2005年12月13日
发生了什么？

每次老NAS启动时都要执行一次chkdsk，却找不到任何错误。检测驱动器需要4+小时，怎么说呢……很不方便。

驱动器检查结果显示是好的，但RAID却老出错。当它完成启动后，只要有一个驱动器有问题，RAID就会当掉。我必须手工激活驱动器，重开RAID...然后等它重建磁盘列阵。

噢，猜到什么了。对我们用的是软RAID系统。

在操作系统分区出现了不可恢复的数据丢失。当遇到电源故障和发电机功率不足，NAS出错时，这经常发生。就软RAID而言，这简直是一个恶梦。

在当前查错期间NAS已经当掉了一段时间了。我已经找到了新的NAS系统，升级了核心速度，硬件支持硬RAID，加强了网络连接性能。不过它还在运送途中。

当前最重要的是要在不需要重新编译软件的前提下替换设备。就当前的NAS的稳定性而言转移数据是非常危险的，我已经将它和网络断开了，防止用户们使用它或上传要命的数据。

是的，项目现在当了。但，项目不会因此而结束的。不过我们要等很长一段时间才能恢复正常。


P.S.看来D2OL的结果分析服务器要当掉相当长的一段时间。（此间可以下载数据，但无法上传）
    请各位D2OLer慢慢算，等新服务器到了，一次上传它几万个结果，这样才有成就感。反正D2OL的任务没有时间限制，在机子上多存几天不碍事。

12/20/2005
NAS Ship Date
The New NAS has shipped. The Holiday season may affect shipping times but I will begin configuration as soon as it arrives. We may encounter obstacles migrating data and we will tackle them one at a time - my priority is to get a working NAS in place ASAP. Target is to complete this before the end of the year.

2005年12月20日
新NAS今天发货了
新NAS今天发货了。节日也许会影响运输时间，但当它一到达我就将开始配置。我们也许在转移数据时会遇到许多难题，不过我们将尽量一一解决他们 - 我的优先事项是使新的NAS尽快开工。目标是尽量在年底之前完成这项任务。

January 17, 2006
Stats froze - but that is nothing new. When this happens, we restart the process and use the backup, flushing the current queue (and offending task that it was processing). However, we have experienced a serious file error during recovery and are currently analyzing what our options are. This is the first time the Backup has been bad

2006年1月17日
统计挂了 - 这是老问题了。当它发生后，我们重启进程，并使用备份，清空当前的队列(禁用处理任务)。但是，在修复期间，我们遇到了一个严重的文件错误，当前我们正在考虑对策。这是备份第一次出错。

January 17, 2006
Things look poor at the moment - we experienced some disk errors on top of the typical "stats are down" Not sure what to expect as recovery options. :/

Because we are transitioning the development from Sengent to Adam the recovery may take longer than average as it is much more valuable to have Adam work with Sengent on the repair to facilitate knowledge tenasfer. I am coordinating now.

2006年1月17日
现在情况不容乐观 - 在"统计挂掉"的情况下，我们遇到了一些磁盘错误，不清楚下一步该怎么做。:/

由于我们的开发团队正处于由Sengent向Adam的转型期中，所以也许要多花些时间才能恢复，只有Adam和Sengent鼎立合作才能尽快恢复。我现在在协调完成它。

February 02, 2006
Task Outage
I have new hardware for the Structures NAS and it has been exceedingly difficult to migrate data while y'all are crushing it. It will be offline temporarily while I try and get the brand spanking new hardware up to speed.

2006年2月2日
断粮通知
我已经为NAS结构安装了新硬件，如果在大家计算的时候进行数据转移将非常困难。所以我们将暂时关闭项目，以便让新硬件能全力以赴工作。

February 08, 2006
Tasks ... what's going on?
The new hardware for the Task Assignment is just dandy, but getting the data moved from the old hardware to the new has turned into a nightmare.
Copying the data has repeatedly failed. A new file replication tool has produced the first successful result so far, but the hardware decay on the old NAS is such that the speed is severely limited. We are copying over 100 million files and 102 gigs of data at approximately .5 - 1 gig an hour. 200 hours of downtime is NOT what we signed up for, but we are more than half way there.

2006年2月8日
任务...咋了？
新硬件很爽，但移动数据成了我们的恶梦。
数据拷贝总是失败。我们使用新的复制工作，已经成功拷贝了，但老NAS的硬件很慢，所以速度受到一定的限制。我们正在以大约0.5～1GB/小时的速度拷贝超过1亿个文件，102GB数据。我们大约要拷贝200个小时，现在已经拷贝了一半多的数据。

[ Last edited by vmzy on 2006-2-11 at 17:18 ]

February 10, 2006
2006 Project Goals
My first visit to TRI (February 3 – 6) is now in the books, and I wanted to take a few minutes here to update the community on the activities from this weekend. We were able to accomplish a great deal of knowledge transfer from Charles and Wolfgang to myself, which will be very important as we move forward. Of more immediate concern to the science and community of the project, we established a strong set of goals for the coming year that will help to revitalize the project and give us a firm foundation for future improvements.

First and foremost, this project is about finding drugs that can help fight diseases. You all have done a lot of work over the last few years in crunching the candidates and targets that we have given you, and your efforts have whittled the field down to several top conformers. While we need to keep working on the current libraries and targets in order to find all of the promising conformers that we can, we realize that a large percentage of the solution space has already been visited. It is for this reason that our top priority for this quarter is the release of a new target and new candidate libraries. To that end, we have identified a promising Avian Flu target and two large libraries of commercially-available drug candidates. I am currently working on formatting the associated files for use with our software.

While the science of drug discovery is the central focus of the project, contributor statistics provide tangible, up-to-date metrics for users to gauge their activity and the contributions they have made to the search for drug treatments. To make tracking our progress a better, more meaningful experience for you (and us!), we are planning to update the statistics processing code to improve both accuracy and currency. I am working with Sengent to make sure we have access to a stable, up-to-date code base before I begin my development work.

Finally, this transition period in the project’s life cycle provides a good opportunity to step back and look at where we’ve been and where we would like to go in the future. Fairly soon, I will be releasing Vision and Values statements for the project, which will help guide our actions moving forward. These will be living documents, and I encourage you to participate in shaping the project by giving me your thoughts on these topics. Then, later in the year, we plan to publish a review article detailing D2OL’s accomplishments and our place in the historical and current Distributed Computing landscape for computational chemistry. This will serve as the perfect celebratory capstone on the first phase of the project as we turn the page and move forward.

As you can see, we had a busy weekend, and there is a lot of work to do in the coming year. I’m confident, though, that we’ll be able to make important improvements to the project and continue to do good science, and I look forward to working with the talented people at TRI and all of you in our dedicated user communities. Please don’t hesitate to contact me with any questions or concerns.

2006年2月10日
2006计划目标
我的对TRI的第一次访问已经提上日程(2月3-6日)，我想在论坛这里花几分钟说一下下星期的活动安排。我们能够完成从Charles、Wolfgang到我的交接，这对以后的发展很重要。对科学和论坛比较关心的几个方面，我们确立了一套今年的工作目标，这将会帮助为项目恢复生气，并给我们今年的发展奠定一个坚实的基础。

首先，这是一个寻找能帮助对抗疾病的药物的项目。在过去的几年中大家已经计算了很多我们给你的目标和候选药物，而且你们的努力已经成功筛选出了一些最好的分子。然而我们现在仍然需要在现有的数据库和目标上继续努力，以找到所有可能的最佳药物分子，我们已经完成了大部分的计算任务。因此，这个季度我们的首要任务是发布新的目标和新的候选药物库。到目前为止，我们已经确认了一个禽流感目标和二个大的商业药物数据库-可用的候选药物。我现在正在将它们格式化为我们的软件能用的文件。

药物寻找科学是项目关注的焦点，贡献者的统计资料为贡献者们搜寻治疗药物的过程，提供翔实的、最新的统计数据。为了更好的记录我们的过程，对你们(和我们!)都有好处，我们正在计划更新处理程序，改善准确性和统计速度。我正在与Sengent合作确保，在我开始我的开发工作之前，我们有一个稳定、且最新的数据库。

最后, 项目的这次转变给我们提供一个很好的回首过去、展望未来的机会。很快，我将会发布项目的目标和功能说明，这将会我们未来的行动指明方向。它们将会以在线文档的形式发布，而且我鼓励你参我们的项目计划，积极发表您的看法。然后，在年末，我们计划出版一篇回顾文章，详细描述D2OL的成就，和在计算化学领域所作的贡献。这将会为项目的第一阶段画上一个圆满的句号。

如您所见，我们周末很忙，而且今年还有许多工作要做。我有信心，我们的项目将会有重大进步，而且继续做好科学研究，我盼望与我们论坛的热衷参与者，及TRI的天才同事们合作。如果有任何的疑问，不要犹豫，请立即联系我。

[ Last edited by vmzy on 2006-4-17 at 14:34 ]

February 10, 2006
tasks
I have implemented the new tasks with all the structures that DID migrate. We're taking a change here wrt: what will the assignment engine do when it can't find the pdbq file  I was starving y'all and as Adam is working on how to load new libraries, it seemed foolish to sweat the old library so much. Everyone needs WORK!

2006年2月10日
任务
我已经实现了所有新任务的数据转换。我们这里正在变更策略:当任务发放引擎找不到pdbq文件时，该怎么办。我知道大家都等着开工，Adam正在处理该如何装载新的候选数据库。太迁就旧数据库的策略，似乎很蠢。每个人都需要新任务!

[ Last edited by vmzy on 2006-4-17 at 14:12 ]

February 19, 2006
Vision and Values
Vision Statement

D2OL will be a premier distributed-computing platform for conducting drug-discovery research, enabling participants to make meaningful contributions in the fight against human diseases. The combination of the latest, most promising computational technologies and scientific knowledge will form the backbone of a community in which participant ownership and engagement are of paramount importance.


Values and Objectives

Value : The D2OL project is dedicated to fighting human diseases through
the use of the latest drug-discovery knowledge and computer simulation
technologies.
Objectives:
• Actively search for new and promising target proteins.
• Maintain fresh candidate libraries.
• Evaluate novel simulation techniques, and implement them in project software where appropriate.


Value : The D2OL project recognizes the importance of high-quality software
and hardware systems in the modern drug-discovery landscape.
Objectives:
• Perform routine maintenance and updating of software to ensure its viability and compatibility with industry standards.
• Regularly enhance the software to improve its function and the user experience.
• Continue to monitor the hardware systems to provide a stable computing environment.
• Evaluate other software and hardware options where appropriate.


Value: The D2OL project values the vital contributions of a vibrant, engaged
user community.
Objectives:
• Provide robust day-to-day software and hardware support to the user community.
• Facilitate community involvement and ownership through frequent, honest communication of project goals and status.
• Aggressively seek means of expanding the user base.


Value: The D2OL project is committed to advancing the science of
computer-aided drug discovery.
Objectives:
• Establish and nurture relationships with drug-discovery researchers in academia and other research venues.
• Share ideas and results through journal articles, presentations, and private communications.

2006年2月19日
目标和功能
目标说明

D2OL将会成为寻找药物研究分布式平台的先锋，能让参加者在抗击人类疾病方面作出贡献。最新的计算技术和科学知识的组合，将会促进一个主要依靠参加者的贡献的社区的形成。


功能和目的
功能:D2OL项目利用最新的药物寻找和计算机模拟技术来抗击人类疾病。
目的:
* 积极地寻找新的、可能的蛋白质目标。
* 维持更新的候选药物库。
* 测试新的模拟技术，而且在项目软件中尽量使用他们。

功能:D2OL项目认识到在现代的药物搜寻领域中高质量软件的重要性。
目的:
* 按照工业标准进行例行维护和软件的更新，已确保它的可用性和兼容性。
* 经常地改进软件的功能和易用性。
* 继续监测硬件系统，提供稳定的计算机环境。
* 采用一切好的软件和硬件。


价值:D2OL项目意识到活泼团结的用户论坛的重要性。
目的:
* 提供对用户论坛日常软件和硬件支持。
* 通过经常和用户真诚的交流项目目标和状态，促进论坛团结。
* 努力寻求招揽更多用户方法。

价值: D2OL项目改进计算机-援助药物搜寻科学。
目的:
* 与学术界和其他的研究机构的药物-搜寻研究员建立和发展关系。
* 通过杂志文章，书籍和私下通讯共享主意和结果。

[ Last edited by vmzy on 2006-4-27 at 15:08 ]

February 23, 2006
An Update on Tasks
As you may have noticed, there have been some problems in loading tasks over the last couple of weeks since the new NAS was installed. These problems are due to the fact that many of the files on the old NAS were not able to be copied to the new NAS. Because you all have done such a great job and found so many promising conformers, we feel that we can spend the enormous time and effort involved in a complete replication of the data on the old NAS in more worthwhile pursuits, like the deployment of new libraries. However, we’re still a month or so away from that point, and we DO want to continue to find any good remaining conformers from the present setup in the meantime. With that in mind, here is our plan for going forward.

Charles has switched out the new NAS and re-installed the old NAS. This change should eliminate the warnings you are seeing, such as “loaded 9 of 0 tasks”, etc. It will also allow your computations to continue to span the entire existing problem space, and not just a small segment of it. I am working on formatting new libraries (and a new target) for use with this project, and I expect to have that work done sometime around the end of March. At that point, the new tasks will have been loaded on the new NAS, and we will remove the old NAS and re-install the new NAS. The old tasks will be purged from the database, and you can start crunching on completely fresh material. Note that while the old TASKS will be gone, THE OLD RESULTS WILL BE SAVED, so that they’re available for future laboratory tests.

What all this means to you is that you can continue to do valuable work by loading existing tasks and helping us to fill any holes that we still have in our solution space. It also means that you should be thinking about uploading any cached results within the next month or so. We want to make sure that ALL of your results are counted and saved, and the best way to do this is for you to upload before the new NAS comes on line permanently.

Thanks for your time and efforts, and please let me know if you have any concerns or questions.

just my two cents ... I finally received a new KVM over IP that I needed to install for the 24 servers in the rack and since I had to require the whole dang thing anyway, I just gave some power and network to the old NAS and crossed my fingers. No matter how fragile the disks are, they do have data on them. We will all realize improved use of the client if they bloody well have some work to do  

Further, this will also provide a quiet and stable NAS onto which Adam can load the new Library - with no one hitting it, it will be less painfull (I assure you, it is never painless). When that is complete, I move a plug and life goes on with new tasks.

When we release the new library, we will no longer be handing out tasks from the OLD library - we will be closing that chapter if you will as have to do it SOME time and call it a complete dataset for analysis. Please don't hoard results - results that come in after we take the old library down will NOT be useful from the perspective of stats or the SCIENCE!

2006年2月23日
任务消息更新
你可能已经注意到，自从安装了新的NAS以来，前两个星期任务载入方面已经出了一些问题。这些问题的起因是由于“旧NAS上的许多文件无法复制到新的NAS上”。因为大家完成了这么多的任务，而且发现了这么多有效的分子构型，我们感觉我们在复制旧 NAS 上的数据花费了太多的时间，应该关注一下更有意义的事情，比如说配置新分子库。然而，我们等一个月左右才能开始做这件事，并且我们确实想继续在现有数据里寻找任何好的构型。综上所述，这是我们未来的计划。

Charles已经关掉了新的 NAS，而且在重装旧的 NAS。这样应该可以消除形如“loaded 9 of 0 tasks”的警告，等等。它也将会让你继续算现有的所有数据，而不只是一小部分。我正在格式化项目将使用新的分子库(和一个新目标)，我希望能在三月底左右完工。届时，新的任务将会放在新的 NAS 上，而且我们将会关掉旧的 NAS，并重装新的 NAS。旧的任务将会从数据库中清除，你就能开始算全新的数据了。注意，当旧的任务不见了的时候，旧的结果将会被保存，所以将来他们可用来进行实验室测试。

总之，通过计算现有任务，帮助我们解决问题，你能继续做有意义的工作。它也意味着，你应该在下个月底左右上传所有的结果。我们想要确保你的全部结果被计算、保存，最好的方法是，等到新的 NAS启用前再上传。

感谢你的时间和努力，如果你有任何疑问请告诉我。

发发牢骚…我终于收到了新 KVM，我需要把它装入架子中的24台刀片伺候器。但这是我份内的事，我刚刚把旧的 NAS，上电和联网，期盼一切顺利。不论磁盘上有多少碎片，但上面确实有数据。我们都意识到，如果有可能一定要改良客户端。

此外，这样也会提供一个纯净和稳定NAS ，好让Adam把新分子库装进去 - 还没有人算过，它将会比较少出问题(我向你保证，它不会出错)。当一切结束的时候，我开放新的任务。

当我们发布新的分子库的时候，我们将会不再发放旧的分子库的任务 - 我们会完全禁用旧分子库，只会拿他们来做分析用。请不要囤积任务 - 在我们把旧的分子库禁用后，那些结果，没有任何科学价值!

[ Last edited by vmzy on 2006-4-28 at 10:53 ]

March 02, 2006
Project Status Reports
Each month, I will provide a very brief project status report in this space so you might get a better idea of what has been going on and what is planned. Only major points will be addressed, and only the "headlines" will be given. More in-depth discussions can happen elsewhere.

D2OL Status – March 2, 2006

This status report provides a brief synopsis of major project activities over the last month and major plans for the next month.


February’s Activities
• Adam visited TRI for project “kick-off” session.
• Avian Flu target protein (H5N1) located and prepped for docking simulations.
• New drug candidate libraries located and file prep started.
• New NAS installed and then backed out when incomplete replication of the existing tasks caused download problems.


Plans for March
• Finish new drug candidate library preparation.
• Load new NAS with new target and libraries; prepare the system for the NAS switchover on April 3.
• Begin source code modifications to enhance the statistics server.
• USERS: Upload all cached results by the end of March.

2006年3月2日
项目状态报告
每个月，我将会在此发表一篇项目状态的简报，这样你就可以更好的了解项目的进展和计划。只会提出要点和“大标题”。可以在论坛其它地方进行比较深入的讨论。

D2OL状态 -2006年3月2日

这一项目状态报告提供上个月的主要项目活动的简述和下个月的主要计划。

二月的活动
• Adam因为项目“开工”拜访了TRI。
• 准备好禽流感目标蛋白质 (H5N1),随时可以开始模拟。
• 新的候选药物库就位，随时可以开始。
• 新的 NAS 安装完毕，当完成复制现有任务后当机了，引起了下载问题。


三月计划
• 完成新的候选药物库的准备工作。
• 把新的目标和分子库装入新的 NAS；准备在4月3日为 NAS 替换系统。
• 开始原代码修正，以提高统计服务器性能。
• 用户：在3月底前上传全部贮存的结果。

[ Last edited by vmzy on 2006-4-28 at 11:09 ]