楼主: vmzy

[项目新闻] United Devices [已结束]

 楼主| 发表于 2006-5-24 23:56:35 | 显示全部楼层
May 24, 2006
New cancer job

I have rolled up the results for the previous cancer job and submitted a new one. As usual, outstanding results will be credited until Monday.




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 楼主| 发表于 2006-5-31 12:49:14 | 显示全部楼层
May 30, 2006
Rosetta Job

The latest Rosetta job completed over the weekend. This caused some members to experience the "cannot connect..." messages. I have reset the job so that outstanding results can still be credited and verified that I could download a workunit. Everyone should be able to connect now.


上周末Rosetta完成了一个任务。这导致一些用户收到“cannot connect...”信息。我已经更新了任务,现在一切应该已经恢复正常了。

[ Last edited by vmzy on 2006-5-31 at 13:39 ]


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 楼主| 发表于 2006-6-2 09:38:00 | 显示全部楼层
Jun 01, 2006
New Cancer Job

I have rolled up the results for the previous Cancer job and submitted a new one. This is normally done on Wednesday, but the Monday holiday put me a bit behind. As usual, results from the previous job will be credited until Monday. If you are using UD Mon, you may wish to dump your cache in order to pick up the new workunits.


[ Last edited by vmzy on 2006-6-2 at 09:43 ]


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 楼主| 发表于 2006-6-6 12:32:20 | 显示全部楼层
Jun 05, 2006 Status

Cancer job - Oxford would like us to finish the current batch of data by the end of June. This means I will have to start submitting multiple jobs and rolling them up a bit sooner than we have been doing. Since these workunits process so quickly even on slow machines, it should not affect anyones ability to return results for credit even if I cut the processing time by a few days. I will make posts as I submit/rollup jobs.

2006 年6月 05 日

癌症任务 -  牛津想要我们在六月底之前完成当前这一批数据。这意谓着,我必须开始一次发放多个任务,而且要加快回收速度。因为这些任务在慢的机器上的处理速度也很快,我想如果我把任务期限减短些,也应该不会影响太多的人。当我发放/回收任务的时候,我会发帖通知大家。

[ Last edited by vmzy on 2006-6-6 at 21:45 ]


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 楼主| 发表于 2006-6-8 11:45:41 | 显示全部楼层
Jun 07, 2006
Cancer Job

I have rolled up the previous cancer job and submitted two more. You will find that these workunits have twice as many Ligands as the previous ones. I verified that I could download one and it appears to be processing fine. Depending on how many results we receive, I may roll these up sooner than next Wednesday.





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 楼主| 发表于 2006-6-13 11:03:42 | 显示全部楼层
Jun 12, 2006
Cancer Job

As I mentioned last week, I am having to accelerate the cancer jobs so that I can have results to Oxford by the end of the month. Today I rolled up the results from the previous two jobs and submitted two more. Results for the previous job will be credited until Wednesday, which should give everyone a chance to return their results.




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 楼主| 发表于 2006-6-20 12:47:51 | 显示全部楼层
Jun 19, 2006
I have rolled up the results from the last two jobs. Note that unlike the other jobs that had 1 or 2 bad WUs, these last jobs had several 40 - 50. This would account for the higher rates of aborts seen in this last batch. I have submitted three more jobs. Results for the previous jobs will be credited until at least Wednesday.



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 楼主| 发表于 2006-6-29 11:28:19 | 显示全部楼层
Jun 28, 2006 status

Here is the (late) update for I apologize for my late post, but there have been some support issues that have consumed much of my time recently.

Cancer job: I will be submitting a new job today that will actually consist of workunits that we have already processed. The reason for this is that I must submit at least something before I do my result rollup or else members will get the "cannot connect..." message. I will then rollup the results of the current cancer jobs. This will be the final results for all data that Oxford has provided for us to crunch. They will analyze it and hopefully will not require a respin.

I will then look at submitting this same cancer data set against the previous protein that was used. It may take a couple of days to get the job correct so please be patient.

Stats: The team stats did not update the other day so I had to manually rerun the task yesterday. This would affect the stats task that was supposed to run last night so I am rerunning again currently. Everything should be caught up by tomorrow.

Connectivity: Some members have reported some connectivity problems to the portal - members services, forums, etc. Other members are able to connect with no problem. We have not been able to identify what may be happening here. I have not been able to reproduce this issue and there have been no changes to the UD hardware/network. We are still looking into this and if anyone has any additional info, please let me know.



癌症工作:我今天将会上传一个新的工作,实际上是由我们已经处理过的任务所组成。因为,在我进行结果回收之前,我必需至少要上传一些东西让大家算,否则用户们又将会收到"cannot connect..."的信息。然后我会回收当前的癌症任务的结果。至此,牛津大学提供给我们的所有癌症数据就都处理完了。他们将会分析所有的结果,希望不需要返工。

然后我将会用这些癌症数据针对以前的蛋白质(Phase I)再进行计算。因此请耐心等候,我可能需要花几天时间才能把它们搞定。


连接问题:一些用户已经向grid.org报告 - members services、论坛等出现一些连接问题,其他的用户却能够顺利地连接。我们不能够确定究竟发生了什么事。我不能够再现这个问题,故没有对UD硬件/网络做任何改动。我们仍在调查这个事件,如果有人遇到这种情况,请告诉我。


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 楼主| 发表于 2006-6-30 12:55:58 | 显示全部楼层
Jun 29, 2006
Cancer Job Status

I have rolled up the results from the last batches of data, which completes that batch of data against the current protein. I was also asked by Oxford to run the same data against the previous protein. Until I hear otherwise, that is what we are going to do. Today I submitted a new job that runs the first batch of the latest data against the previous protein we ran against late last year.

This job seems to be taking much longer than the ones we have been running lately. Therefore, I have reduced the ligand count back down to 600. Some members may have received a slow 1200 ligand workunit. If so, please dump that workunit because I have deleted the job and no credit will be given for results.

Finally, it will take a while for one of these workunits to complete. It is possible that there is some sort of problem with these workunits and that they may fail in the final stages of execution. I do not expect this, but I did not get a chance to test this on another system first. If there is some sort of a problem, we will deal with it quickly.

It will be interesting to see if we get any aborts like we did against the previous protein and what that rate is.



这个任务似乎比近来我们一直在算的任务要慢很多。因此,我已经把 ligand 数量减回至 600。一些用户可能已经收到大的 1200 ligand 任务。 如果如此,请删除任务,因为我已经把任务作废了,上传结果无效,没有积分。



[ Last edited by vmzy on 2006-7-19 at 13:33 ]


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 楼主| 发表于 2006-7-4 09:35:59 | 显示全部楼层
Jul 03, 2006 / Cancer Job Status

Cancer Job - Obviously, the WUs are taking too long to process. I tried to upload a new job as soon as possible after rolling up the last batch because many members were talking about leaving. Therefore I did not test how long the new WUs would take, but just that they would indeed process. These long running WUs have caused a harsher response apparently than not having anything to crunch. I guess I can't win either way.  

I have suspended the 600 ligand job so that no more WUs will be sent out. I have uploaded a new job with a total of 100 ligands. I have not tested how long these will now take. If it is still takes too long, we will reduce the number of ligands further. There is no built in timeout in the previous 600 ligand WUs, so if you want to continue crunching on them you can. I will wait a reasonable amount of time before deleting that job so that credit may be given. If you do not want to continue, delete the WU and you will get one of the 100 ligand ones.

Rosetta Job - I think I mentioned this before, but some members have asked me recently. The HPF project that we were working on is apparently done. There are no more new batches of data available to us to work on. I have heard nothing about participating in HPF2 if there is such a thing. The WUs that are currently active have all been previously processed so the work is redundant. I am not going to delete it though until I am sure that there will be no more HPF projects for to work on.


癌症任务 - 很显然,任务的计算量太大了。因为许多用户正在考虑离开项目,所以我试着在上一批任务回收之后尽快地上传了一个新的任务。因此我还来不及测试新的任务需要多久,但是他们肯定要全算完。这些计算时间过长的任务所引起的反响显然比没有任务算还要糟糕。我只能在这里受夹板气。

我已经中止 600 ligand 任务的发放,以免扩大负面影响。我已经上传了一组新的总数为 100 ligands的任务。我还没有测试这些任务要算多久。如果它仍然很难算,我们将会更进一步减少 ligands 的数量。先前的600 ligand任务并没有设定时间限制,因此,如果你愿意的话也可以继续慢慢算他们。我正在等大家反馈时间计算时间,以决定是否删除该任务,所以不一定会给予积分。如果你不想继续算,就删掉它吧,而且你将会立即收到新的 100 ligand 的任务。

Rosetta任务 - 我想我以前说过了,但是一些用户最近老问我。HPF项目已经结束了。我们没有计算数据。据我所知目前 没有参与 HPF2 的打算。现在发放的任务全部是先前计算过的,因此任务是无意义的。在我没有确定 将会停止HPF之前,不会删除它们。

[ Last edited by vmzy on 2006-7-19 at 15:51 ]


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 楼主| 发表于 2006-7-11 13:01:35 | 显示全部楼层
Jul 10, 2006 Status

Cancer - After a few false starts, I think we have a good Ligand number at 100. These take much longer than the previous ones, but it seems that even a slow machine should be able to crunch a single WU in one week. Unless I hear otherwise, we will stick with 100 ligand WUs.

It also appears that the aborts have gone away. Since nothing has changed other than the protein we are working on (as was the case when they started happening), I think this proves that there was something in the last protein that the Ligandfit application had an occassional problem with and not an issue with UD hardware. Since Oxford delivered the protein, they would have to be the ones to figure out what is different in the two proteins.

Regarding the 600 ligand job, I will let that one spin for another week or two to give everyone a chance to return their results. Otherwise, we will go back to the one week cycle we were on previously with the 100 ligand WUs.

Rosetta - This project is apparently complete. Since I do not know if we will be doing any other Rosetta projects, I am going to leave this running until I hear something official. This means currently any Rosetta work is for points only. The actual work will be ignored. If I turn the job off, I am sure that many machines will get the flashing explanation point and cause an uproar. Active members who read the boards can make a decision whether they want to set their profile to the cancer job only or not. Maybe some members think the Rosetta screensaver is cool.  

Connection issues - We have had random connection issues recently. Restarting the load balancer last week appeared to have fixed the issue, but I noticed a few complaints today. I do not know if this is the same issue or something different. There is a request into IT to check the load balancer again to see if it has some sort of chronic problem. In the meantime, I can only suggest to retry until you get the page you want. There is a 50/50 chance you will get directed correctly if the load balancer is acting up. Luckily these are not agent connection issue, but limited to the member web pages.


癌症 - 在经过一些尝试之后,我认为 Ligand 数量定在 100比较合适。这些任务比较早先的要难算些,但是似乎绝大部分的机器都能够在一个星期内算完。如果没有异议,我们将会把任务定位 100 ligand。

异常退出现象好像也没有了。因为除了蛋白质之外什么都没有改变,我想这证明早些的蛋白质与 Ligandfit 程序有些许兼容性问题,UD 硬件没有问题。因为是牛津大学给的蛋白质,所以只有他们才知道两种蛋白质间有什么不同。

关于 600 ligand 任务,我将会在1~2星期后回收他们的结果。另外,我们将会和以前一样把 100 ligand 任务期限设为1周。

Rosetta - 这个项目已经中止了。因为我不知道我们是否会有任何其他的 Rosetta 项目,所以在我收到官方的通知前,我不会关掉它。这意谓现在的 Rosetta 任务只有赚积分而已,没有任何现实意义。真实的任务总数不会增加。如果我把任务关掉,我确定许多机器将会,而且可能会引发抗议。读到这个帖子的用户,可以自己决定是否将他们的喜好设定为只算癌症任务。也许一些用户认为 Rosetta 屏保程序比较好看。

网络连接问题 - 最近我们遇到了几次网络连接问题。上星期我通过重启网络负载平衡路由解决了这个问题,但是我今天注意到又一些人诉苦无法访问UD了。我不知道这是相同的问题,还是新的问题。我已经请求IT部门的人来检查一下负载平衡路由是否有毛病。在此,我只能建议你多刷新几次页面试试。即使负载平衡路由有毛病,你也有 50%的机会打开页面。幸好,这些不是客户端的连接问题,仅仅是用户网页而已。

[ Last edited by vmzy on 2006-7-19 at 16:28 ]


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 楼主| 发表于 2006-7-18 12:43:35 | 显示全部楼层
Jul 17, 2006 Job Status

Cancer Job - I received several PMs asking to extend the result credit time on the previous jobs since they were taking so long. Even the 100 Ligand WUs were taking a while for some members. I have submitted a new 50 Ligand WU job to try to get the processing time down. We will see how this works out.

We want all members to be able to participate regardless of the power of their machines. I will leave the current jobs active for at least another week to give time for results to come in. Note that the jobs must be set inactive as always while I roll up the results. Hopefully you will not have the bad luck of trying to return one of these large WU results while the job is inactive.

Please post in a couple days to let me know how the 50 Ligand WUs are working out.


癌症任务 - 我收到一些论坛消息要求延长先前的任务的期限,因为他们太难算了。甚至这种 100 Ligand的任务也不好算。我已经上传了一个新的 50 Ligand 任务,试着把计算时间降下来。我们将会看看这样是否可行。


请在接下来的几天里,发帖让我知道这种 50 Ligand的任务的工作情况。

[ Last edited by vmzy on 2006-7-19 at 16:52 ]


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 楼主| 发表于 2006-8-1 12:33:01 | 显示全部楼层
Jul 31, 2006 status

I am planning on rolling up the results from the previous Cancer jobs and submitting a new one tomorrow. Everyone should be done with the larger Ligand WUs - 600, 300, and 100. I will leave the 50 Ligand WU job active for a week to allow results to be returned. If there is some reason you think this should not happen, please let me know today.


我想大多数600, 300和100 Ligand 的大包都应该算完了。我打算明天回收以前的任务,并上传一个新的。50 Ligand 的任务在一星期后再回收。如果你对此有什么意见,请今天尽早告诉我。

[ Last edited by vmzy on 2006-8-1 at 21:47 ]


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 楼主| 发表于 2006-8-22 13:11:07 | 显示全部楼层
Aug 21, 2006 status

Rosetta (HPF) - The Rosetta job has been turned off. I wanted to leave this up to the individual members as to whether they still wished to run Rosetta (some like the screensaver), but some members were very vocal about having it turned off so that is what we did.

Cancer - As I mentioned before and someone confirmed with Inibox, we are rerunning the previous protein against the newest database from Oxford. This is not respinning old data for the sake of running something on I have deleted all of the previous jobs (1200, 600, 100 ligands) since they should have been processed by now. The newer 50 ligand WUs seem to be working for all. Some members have complained that they are processing too fast, but since we do not want to exclude members with slower machines, 50 ligands is what we are sticking with.

Rosetta (HPF) - Rosetta项目已经正式结束。我本不想这样做,有些人仍然想要运行 Rosetta(一些人喜欢它的荧屏保护程序),但是多数用户强烈要求关掉它,所以我们就只好把它关了。

癌症 - 以前我说过,但现在仍有人在问,我们在用以前的蛋白质针对牛津的最新的分子数据库进行计算。这并不是重复计算。我把以前所有的任务都取消了(1200、600、100 ligands),因为他们现在应该已经算完了。新的50 ligand任务似乎一切正常。一些用户抱怨,他们算得太快,但是因为我们不想排斥机器慢的用户,所以我们坚持以后就使用50 ligands任务了。


[ Last edited by vmzy on 2006-8-22 at 17:20 ]


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 楼主| 发表于 2006-8-29 12:39:08 | 显示全部楼层
Aug 28, 2006 Status

There is not much to report on this week. We continue to process cancer data and I think this is working for everyone.




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