RNA World:常见问题解答

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RNA World 的常见问题解答

目录

RNA World的目标是什么?为什么我要参与呢?(In simple words, what are the goals of RNA World and why should I participate?)

RNA World focuses on RNA research and as such it is the first distributed computing project of its kind. If you take a look for what discoveries the recent Nobel Prizes in chemistry and medicine were awarded (telomerase, ribosome: all RNA-based cell machineries; and before that for RNA interference / miRNAs: small RNAs that regulate cell development and are involved in cancer), you will realize that RNA research is a highly important subject. But maybe you have also once taken antibiotics to help your immune system to battle a bacterial infection. Such antibiotics usually bind to the RNA components of bacterial ribosomes and thereby inactivate protein synthesis and consequently growth of these microbes. Other small RNAs in bacteria are required for attaching to and eventually even invading human host cells. And of course, many aspects of fundamental cellular processes where RNAs are involved are of additional interest to researchers, as e.g. the question whether microorganisms such as bacteria might even possess some sort of primitive immune system (CRISPR RNA family). So as you can see, identifying non-protein-coding RNAs in as many organisms as possible establishes a fundamental basis of knowledge for a diverse range of questions and may even promote the development of drugs to combat diseases. For further information, please see the project description.

RNA World是第一个致力于核糖核酸(RNA)研究的分布式计算项目.从基于RNA结构的细胞器如端粒酶,核糖体,再到能够调控细胞周期,应对癌症的小干扰核糖核酸(siRNA),关于RNA的研究一直是近年来诺贝尔奖的热点.我们平时为了抵御细菌感染而吃的抗生素,通常就是结合在细菌的核糖体RNA上,从而干扰细菌的生长,抑制它们的繁殖;而且,细菌也是依靠一些小RNA来依附和感染人体细胞的.正是因为RNA广泛的参与了许多细胞基础代谢过程,它们也吸引了广泛的研究兴趣,例如:是不是细菌也具有(由CRISPR RNA,即含有规律成簇的间隔短回文重复序列的RNA组成的)某种原始免疫系统呢?于是,在多种有机体内发现和鉴别非编码蛋白质的RNA,能够让我们更多地了解生命的基础,并且促进开发新的药物.如想了解更多的知识,请参见"项目描述".

RNA World目前支持哪些项目?(What applications are currently supported by RNA World?)

type
application
purpose
INFERNAL 1.0.2 CMBUILD, CMCALIBRATE, CMSEARCH RNA covariance analysis
RNA协方差统计
InReAlyzer 1.0 Converter to produce high-resolution graphics
from INFERNAL output files (in-house development)
将INFERNAL项目输出的文件转化并制作高分辨能力的图像(内部支持)


目前有哪些任务类型?(What types of work units are available?)

At present we have four types of work units, which are based on (1) CMBUILD, (2) CMCALIBRATE, (3) CMSEARCH and (4) InReAlyzer. CMBUILD work units produce an RNA co-variance model from a text alignment of members of RNAs belonging to the same RNA family. CMCALIBRATE work units calibrate an RNA co-variance model produced by CMBUILD such that it can be used to score the probability that a potential RNA identified as a member of a certain RNA family is indeed a true candiate of that family. CMSEARCH work units use the output of CMBUILD, i.e. a calibrated co-variance model to search for an RNA family in the genome of a specified organism. InReAlyzer work units convert the somewhat cryptic text output of CMSEARCH work units into high-resolution PNG graphics that allow for convenient visual judgement whether or not a given CMSEARCH candidate belongs to the RNA family under investigation.

目前我们有四种任务单元类型,分别基于(1)CMBUILD,(2)CMCALIBRATE,(3)CMSEARCH以及(4)InReAlyzer。 CMBUILD任务单元创建同一系的不同RNA模型。CMCALIBRATE任务单元(用来)校准由CMBUILD生成的RNA模型,以便检测该模型是否可能是该系中潜在的一种RNA。CMSEARCH任务单元利用CMBUILD的输出结果,即一种不同以往的经过校正的模型,来为某一种特殊的组织的基因寻找RNA系。InReAlyzer任务单元将CMBUILD中一些意义深远的任务单元转换成高分辨率的PNG图片,以便方便的进行视觉判断某个给定的 CMSEARCH的候选结构属不属于正在研究的RNA系的一员。

RNA World支持GPU/CUDA/STREAM运算吗?(Does RNA World support GPU/CUDA/STREAM processing?)

At present, RNA World applications do not profit from GPU processing, but we can think of applications that will and if that applies, we will certainly try our best to make clients available that support such performance improvements.

目前,RNA World尚未从GPU运算中受益。不过我们会为参与者考虑。一旦有相关需求,我们一定会尽全力让参与者获得对这类计算性能提升技术的支持。

RNA World有存盘点吗?(Does RNA World support checkpointing?)

RNA World is a universal framework comprising a diverse set of RNA-relevant bioinformatic tools. Originally, these tools were not designed for incorporation in a distributed computing environment although most of these require significant compute ressources. Traditional checkpointing, however, must be supported by the scientific application. Consequently, checkpointing is not available, but: The RNA World development team is seeking ways to establish novel, universal checkpointing procedures. These novel methods rely on either creating "suspend RAM to disk" images at the system level or the establishment of RNA World as a system that generally runs in a virtual machine (VM). For the former we have a functional 32-bit Linux workaround that, however, requires that memory randomization is deactivated in the Linux kernel. For the latter we have a promising cooperation with CERN.

RNA World是一个通用的框架,包括一系列有关的的生物信息工具。一开始,这些工具并没有设计在分布式计算环境内,尽管它们需要大量(显著)的计算资源。传统的存盘点必须要被科学任务所支持。因此,存盘点并未被RNA World所支持。不过RNA World的技术小组正在试图建立新颖的、通用的存盘过程。这些新颖的方法包括在系统水平上创建将内存(数据)存入硬盘(的功能)或者将RNA World建成系统以便在虚拟机上运行。对于前者,我们可以在一台32-bit的Linux工作环境中实现,不过(事先)要将随机内存功能从Linux内核中移除。对于后者,我们与CERN有着密切的合作且前景良好。

RNA Word 的内存需求如何?(What is the RAM requirement of RNA World?)

type
application
RAM requirements
INFERNAL 1.0.2 CMCALIBRATE up to 2.5 GB of RAM,
usually below 600 MB of RAM
最多需要2.5GB,通常小于600MB
CMSEARCH up to 1 GB of RAM,
usually below 100 MB of RAM
最多需要1GB,通常小于100MB
InReAlyzer 1.0 below 50 MB of RAM
小于50MB

Please note one important thing: If you are using a multi-core machine, RNA World might engage on all of your cores simultaneously. As long as we do not use the OpenMPI-based multi-threaded application mode, this means that the RAM required to successfully complete all of the work units is additive.

请注意一个重要的事实:如果你使用的是多核处理器,RNA World可能会同时使用所有的核心,前提是我们不使用基于OpenMPI的多线程任务模式。这就意味着未来完成任务内存需求会增加。

运行在Ubuntu Linux X64上的英特尔Core2Due 2.4GHz的计算机通常运行RNA World需要多长时间? (What are the typical running times of RNA World work units using an Intel P8600 Core2Duo 2,4 GHz machine with Ubuntu Linux x64?)

type
application
runtime
INFERNAL 1.0.2 CMCALIBRATE 20 minutes to 10 days,
typically a day
20分钟-10天
通常1天
CMSEARCH a few minutes to 100 hours,
typically a few hours
几分钟-100小时
通常几小时
InReAlyzer 1.0 a few seconds to 5 hrs,
typically a few minutes
几秒-5小时
通常几分钟



RNA World支持多线程任务吗?(Does RNA World support multithreaded (MT) applications?)

RNA World supports whatever its scientific applications support. In case of INFERNAL, multithreaded applications are nicely supported on the basis of OpenMPI. While MT applications run well in a local computing environment under Linux, validation of results generated in a distributed computing environment that employ MT applications for unknown reasons fails in a subset of cases, although technically MT applications work excellent. We have not yet identified the cause of this inconsistent behavior, but INFERNAL makes use of random number generation that is tied to the processor core time at which individual threads are started. On a multicore system, an MT application therefore is initiated at slightly different times on each of the cores involved. Consequently, on a different (distributed) system, the random numbers differ and so do the results - although differences are only minor. If the random number generator is supplied with a fixed value, issues are largely solved but, strangely, not entirely and that is a problem for BOINC-based WU validation. The RNA World team is currently corresponding with the INFERNAL developers to solve this issue to fully enable distributed MT applications as soon as possible.

只要是它的科学任务所支持的,RNA World都支持。以INFERNAL为例。基于OpenMPI,多线程任务可以被很好的支持。多线程任务可以在Linux下的传统计算平台下良好运行,但事实结果证实了在分布式计算平台下多线程任务无故的在一些任务的子集中遭遇失败,尽管技术上认为多线程任务工作正常。我们还没有探明这些矛盾的行为的原因,不过INFERNAL使用率随机数生成技术。该技术与独立线程的初始点:核心时钟联系紧密。因此在多核系统中,多线程任务受每个核心的影响在不同的时间被创建(尽管时间差很小)。因此,在不同的系统下(分布式运算),随机数不相同,结果也是如此(尽管差距很小)。如果随机数生成器支持混合数值,问题将在很大程度(奇怪的是,并不是全部)得到解决。而这就是基于BOINC的WU的难题。RNA World小组现在正在于INFERNAL小组进行合作来解决这个问题,以期多线程任务可以尽早展开。

什么是多线程任务?(What is a multithreaded (MT) application?)

A multithreaded application makes use of multiple CPU cores on modern machines to compute a single RNA World work unit. Our measurements for CMCALIBRATE running in a Linux environment showed that a quadcore crunches one work unit in even slightly less (!) than a fourth of the computation time that was required for singlethreaded computation of the same work unit. This shows that CMCALIRATE scales excellent in MT mode.

多线程任务可以让现代计算机上多个CPU核心只运行单一RNA World任务。对在Linux环境下CMCALIBRATE运行情况的测量显示一个4核处理器处理一个任务所需的计算时间甚至少于同一个任务使用单线程所需时间的四分之一。这表明CMCAIBRATE可以在多线程模式下完美的运行。

RNA World的研究最终是否会促进医药的发展?(Will RNA World research ultimately lead to the development of medications?)

Although nobody can forsee this for sure, it seems highly likely that the results generated by RNA World will contribute to the development of medications (see application section of this F.A.Q.).

尽管没有人预见并确信这一点,不过看上去RNA World有很高的可能性可以为医药的发展做出贡献。(参见本FAQ中的任务(介绍)部分)

RNA World项目有什么潜在的应用呢?(What are potential applications of the RNA World project?)

RNAs like proteins are macromolecules of defined structure that serve vital cellular tasks. Consequently, structural knowledge of RNAs is of similar importance for drug design as is the case for proteins. What you know as antibiotics are actually small molecule drugs that mainly target RNA components of bacterial ribosomes. This illustrates nicely how important RNAs are and what huge potential they represent in the context of drug design. However, before we can take on RNA structures to design drugs, we first need to identify which RNAs are present and where exactly they are located in the genome of any given organism. This we presently try to accomplish in a global manner using the RNA World supercomputer.

核糖核酸(RNA)如蛋白质一样,是拥有精妙结构的大分子,在细胞内起着必不可少的作用.因此,了解RNA的结构就如同了解蛋白质的结构一样,对于药物设计有着重要的作用.也许你已经了解到,抗生素分子通常就是攻击细菌核糖体RNA,因此了解RNA的结构就可以帮助我们设计抗生素.但是,在我们利用RNA 结构设计药物之前,我们首先需要了解在目标微生物中有哪些RNA,且都在哪里.这就是我们的目标,是我们需要大规模计算能力的原因.

RNA World项目的结果会被公开吗?是的话,在什么样的许可下?(Will the RNA World project results be published and if so under what license?)

All RNA World results will be published in high-quality peer-reviewed science journals, preferrably in those offering an open access policy for the general public.

RNA World的所有成果将会发表在高品质,优秀的科学期刊上,尤其是那些为普通公众开放的期刊。

任务单元是自动还是手动生成的?(Are work units generated automatically or manually?)

BOINC-based work units are always generated in a fully automated manner from operator-supplied input files. RNA World currently relies on operator-curated input archives that will be automatically processed by the RNA World server to yield several thousands of work units per archive. Archives can be placed in a on-hold queue such that once the server is running low on work units, it can process new ones from this supply.

基于BOINC的任务单元一直完全由运行支持出入文件自动生成。RNA World目前依赖于运作辅助输出档案,它可以自动被RNA World服务器所运行以在每个档案中生成数千个任务单元。档案可以被安置在一个冻结队列中这样一旦服务器任务不足时可以从这里生成新的任务。

We are currently working on implementing user job submission interfaces such that, under strict security guidelines, researches can use the RNA World distributed supercomputer to process their own project files. Here, we do not plan to allow batch job processing for security reasons and the users will have to register and use a digital certificate for clear identification.

目前我们正在完善用户任务提交界面,因此在严格的安全保证下,研究人员可以利用RNA World分布式计算运行它们自己的项目文件。现在,出于安全原因我们不打算引入分批任务,用户也需要注册并使用数字证书进行验证。

It is also planned to derive work units fully automated by regularly scanning RNA-relevant databases for novel sequences that could be analyzed.

我们还计划通过常规扫描RNA相关数据库,将任务单元完全自动导出以便寻找可以被分析的新奇的序列。

持续性的任务供应有保证吗?(Is a continuous work supply guaranteed?)

Our objective is to continuously recruit more and more RNA-relevant bioinformatic tools to RNA World. Moreover, the data sources containing RNA-relevant information that require analysis by RNA World are growing daily. To cope with these two facts, we expect that RNA World will require increasing compute capacities and consequently should be expected not to run out of work, soon. However, we are computing on an individual project basis plus we try to build up databases containing pre-computed results e.g. for listing potential RNA candidate genes in any given organism. Once our objectives are reached, we will naturally stop sending out work units until we have new projects in store. This will be announced in time on the RNA World website to avoid machines to run idle.

我们的目标是不断地在RNA World中引入越来越多的RNA World相关的生物结构的工具。而且,需要由RNA World进行分析的包含有RNA相关信息的资源与日俱增。为了应对这两个事实,我们预期RNA World将需要更强的计算能力并最终能够稳定运行。但是,我们正在一个个体项目基端上运行外加我们准备建立包含有运算前结果的数据库,即列举任意给定组织的潜在RNA候选基因。一旦我们的目标完成,很自然,我们将停止发送任务单元,除非我们又有了新的项目。这将被及时的在RNA World网站上宣布以防(用户)机器白白的运行。

不同的操作系统下任务单元有所区别吗?(Are the work units identical for different operating systems?)

RNA World delivers work units based on available applications. If an RNA World application is available for more than one operating system then the work units assigned are usually identical. This, however, does certainly not mean that identical work units will be computed similarly fast on systems that have identical hardware but different operating systems. The reason for this, among others, is e.g. differences in compiler performance.

如果一个任务可以在多个系统上运行,那么任务单元往往会被特定化分配。不过这并不意味着特定的任务单元可以在特定的硬件上运行的更快,在其他的系统下却表现的不同。这样的原因是因为不同的编译程序的表现不同,而不是其他的原因。

RNA World有项目表现证书吗?(Does RNA World award project performance certificates?)

Yes.

有的。

RNA World项目无存盘点,当我要关机时将如何保存我的任务?(How can I save my work for non-checkpointed RNA World sub-applications when I need to turn my machine off?)

If you run RNA World on a laptop or if you have multiple operating systems installed, from time to time it will be required to turn your machine off. The current RNA World sub-applications INFERNAL and InReAlyzer dot not support checkpointing, so your work would be lost if you shut down your machine the standard way. To avoid loss of your work, set the machine to enter sleep mode. Under these conditions the entire RAM will be saved to hard disk and upon system reboot your work will be reloaded into memory such that even RNA World can continue to calculate where it left off.

当您在笔记本电脑上或者在多系统计算机上运行RNA World,关机将是必须的。目前,RNA World的主项目INFERNAL和InReAlyzer均不支持存盘点,所以关机意味着任务的丢失。避免任务丢失的方法是使计算机进入休眠模式。在休眠模式下整个内存的数据将会被保存在硬盘中,当系统重新加载时数据也将一同重新加载,这样RNA World能够继续运行。

RNA World支持哪些操作系统?(What operating systems (32/64-bit) are supported by RNA World?)

Since RNA World is a framework consisting of many different bioinformatic applications, support of operating systems will always depend on the individual application. If its source code is available, the RNA World development team will do its best to make it available for as many operating systems as possible, i.e. Linux, Windows and OSX at the minimum. In addition, care will be taken to support 32-bit as well as 64-bit versions and special assembly codes (SSE, SSE2, etc.) wherever possible and useful.

由于RNA World只是一个框架,它包括众多不同的生物信息任务,因此它所支持的操作系统将取决于个人。如果它的资源代码可以获得,RNA World技术小组将尽全力支持尽可能多的操作系统平台。至少包括Linux、Windows和OSX。另外,32bit和64bit系统一样会的得到支持,特殊指令集(SSE,SSE2等)也将被支持,因为它们十分有用。

加入RNA World需要哪些花费?(What are the costs of participating in RNA World?)

None, except for your private electricty, network and hardware maintenance costs.

无,只有电费网费以及硬件的维修保养费用。

Rechenkraft.net 的团队成员是否有什么特权?(Are there privileges that apply only to Rechenkraft.net team members?)

As fairness dictates: No.

为了公平起见:答案是否定的。

RNA World网站支持哪些语言?(What are the plans concerning language support on the RNA World website?)

Just take a look here: http://www.rnaworld.de/rnaworld/language_select.php

只需点击即可获知:http://www.rnaworld.de/rnaworld/language_select.php。

有没有针对CPU特性进行优化的计算程序?(Will there be CPU-optimized applications?)

These are already implemented, i.e. the initially downloaded package contains a program that checks which type of application is optimal for your machine (x86/x64, diverse SSE versions).

这些已经被实施了,初始下载包中包含有一个检测计算机最适合运算项目的程序。(包括X86/X64,各种指令集)

参与者有没有可能(选择)免于计算某个子项目?(Is it possible to exclude participation in certain sub-applications?)

Yes. In your RNA World project settings you can decide on your own which RNA World sub-applications to support and which not. In fact, if you have an older machine it might be recommended, e.g. to exclude CMCALIBRATE as work units for this program demand huge amounts of RAM and often take a long time to complete.

是的,在你的RNA World项目参数中你可以自己决定参与哪些子项目而又不参加哪些。如果你的机器相对较旧,推荐不参与CMCALIBRATE。该项目的任务单元需要大量的内存并需要很长时间才可完成。

在RNA World中用户能否使用一个简单的设置来决定是否参加alpha/beta 测试?(Is it possible to enable/disable participation in alpha/beta tests using a simple switch in the RNA World user profile?)

Yes.

可以。

我是一名科技工作者,我可以在RNA World上面提交我自己的任务么?(Can I as a scientist submit tasks to RNA World?)

Hopefully soon. We are working on implementing user job submission interfaces for each of the various RNA World applications. However, you will have to register and receive a digital certificate such that jobs submitted to our system are clearly correlated to an individual known to us.

即将推出.我们正在添加用户作业提交界面,让您能够使用RNA World的各种功能.您需要注册并使用收到的数字证书,来确保我们知道每一个任务的来源.

哪些系统将在未来得到支持?(What systems are going to be supported in the future?)

At present we support Linux, Windows and Mac wherever possible. PS3 most likely will not be supported due to its small RAM capacity although it might be possible to use it for other applications in the future which, at present, we have not implemented yet. If we manage to establish a virtual machine approach, however, it might be possible to even support a number of additional systems.

目前无论怎样我们支持Linux,Windows以及Mac。PS3由于其较小的内存而没有得到我们支持,尽管在未来可能有其他的子项目供其运算。如果我们成功的建立一些虚拟机,那样的话甚至可能会支持一些额外的系统。

BOINC以及RNA World任务安全吗?没有病毒以及其他的恶意软件?(Are BOINC and the RNA World applications safe, i.e. free from viruses and other malware?)

Yes. BOINC as well as all RNA World applications are open source, i.e. can be inspected by anyone who is interested. The RNA World applications are compiled in-house using compiler tools that are widely applied public domain tools which e.g. are used to produce the code of the majority of todays webservers. Consequently, if these were malicious, we would already face a much bigger problem.

是的,BOINC以及RNA World任务属于开放资源。即可以被任何对其感兴趣的人检测。RNA World的任务是使用广泛应用于公共领域的家庭用编译工具编译的。它们被用来编写出了当今的主流网络应用(服务)。因此,如果它们使恶意的,我们应该早就面对比目前更加严重的问题了。

运行RNA World需要多大的硬盘空间?(How much hard disk space is required to run RNA World?)

The required disk space varies depending on the types of work units you are being assigned to. At present, RNA World core files require around 25 MB of hard disk space. CMBUILD and CMCALIBRATE work units should not require more than approximately 10 MB while CMSEARCH work units may use up 300 MB at maximum, typically between 2-20 MB. InReAlyzer hard disk space requirements cannot be predicted reliably because the number of images generated depends on the CMSEARCH output file size. However, we do not expect InReAlyzer to require much more than 1-100 MB. Remember that the sum of required hard disk space calculates from the sum of work units that have been downloaded plus the RNA World core files. Currently, a maximum of 10 work units can be downloaded per CPU core. Note that you can specify the maximum hard disk space that RNA World is allowed to occupy manually from either within you local BOINC manager or on the RNA World website.

硬盘空间取决于你所申请的任务种类。目前,RNA World核心文件大约需要25M的硬盘空间。CMBUILD和CMCALIBRATE任务单元一般不超过大约10M的空间,CMSEARCH任务单元可能最多使用300M空间(不过)通常在2-20M之间。InReAlyzer任务所需的硬盘空间大小无法被可靠的预测,因为生成的图片数量取决于 CMSEARCH输出文件的尺寸。不过我们不期望InReAlyzer的硬盘需求超过1-100M。需要记住的是,硬盘空间需求总大小是由下载任务单元以及RNA World核心文件累加而得出的。目前,一个CPU核心最大可下载10个任务单元。注意这一点的话,你便可以通过本地BOINC客户端或RNA World的网站明确硬盘最大允许占用值了。

项目导致的网络流量大约多少?(What Internet traffic can be expected?)

All files are transferred in compressed format and most files contain simple ASCII data such that compression rate is around 30%, i.e. original file sizes will be reduced to 30% of their original size. In general, CMBUILD and CMCALIBRATE work units are the smallest and should require less than 1 MB (usually even less than 100 kB) of data traffic. CMSEARCH work units cause somewhat higher download traffic depending on the size of the genome that is going to be analyzed: Current upper limit: With a maximum of 512 MB for one of the chromosomes of an opossum (uncompressed file size), 150 MB would have to be transferred (compressed file size) for a CMSEARCH work unit plus a few kB for additional control files. Of course, the upload traffic only contains the result file and not the genome that was searched for RNA presence and consequently will be much, much smaller. Normal traffic: A typical bacterial genome such as that of e.g. E. coli is about 4.6 MB (uncompressed) in size. Hence, 1.3 MB (compressed) of data plus the control files (just a few kB) will be transferred. Lower limit: Many viral genomes as well as plasmid sequences contain less than 10 kB of data in uncompressed format. However, note that small CMSEARCH work units are expected to complete quickly such that your machine may request new data over and over again depending on your systems performance.

所有被传输的文件均为压缩格式,大多数包括基本的ASCII数据并且压缩率大约30%,即文件大小将为原始文件的30%。通常,CMBUILD和 CMCALIBRATE的任务单元是最小的,应该不超过1MB(一般小于100KB)的流量。CMSEARCH任务单元会有一些更大流量的下载,取决于它将要分析的基因的尺寸:目前的上限是:一个负鼠染色组的大小不会超过512MB(原始数据),150MB的CMSEARCH任务单元将和一些不到1MB的额外的控制文件一同被传送。当然,上传文件只包括结果而不包括所要寻找的RNA基因组,因此最终(大小)将会非常小。普通流量:一个典型的细菌(比如 coli)基因组大约为4.6MB(未压缩)。因此,1.3MB(压缩后)的数据外加控制文件(仅仅不到1MB)将被传送。更低的限制:很多病毒感染基因组以及质粒顺序在未压缩模式下只有不到10KB的数据。但是,注意到较小的CMSEARCH任务单元可以预见将被更快的完成,因此取决于电脑性能,你的机器可能会不断地申请任务。

RNA World能否在离线模式下运行?(Can RNA World be operated in offline mode?)

Currently not, because we do not allow for caching of large sets of work unit packages because we require a high turn-around time. In case of CMCALIBRATE work units this is quite easy to understand, since the results of these are the basis for all subsequent CMSEARCH work units. Generally, CMBUILD results are the basis for CMCALIBRATE calculations and CMCALIBRATE results are required as input data for CMSEARCH. The output of CMSEARCH in turn then serves as input for InReAlyzer. However, since we are planning to add a set of additional applications in the future which lack these strict interdependencies, it is very likely that certain types of future work units will allow for offline computation.

目前暂不可以,因为我们不允许囤积大量的任务单元包。我们需要一个长期的转变时间。以CMCALIBRATE任务单元为例很容易让人理解,因为它们的结果是所有CMSEARCH任务单元的基础。一般而言,CMBUILD的结果是CMCALIBRATE计算的基础而CMCALIBRATE的结果又是 CMSEARCH的输入数据。CMSEARCH的输出结果反过来作为InReAlyzer的输入。不过,我们正在考虑添加一系列额外的任务。这些任务不需要这些苛刻的相互关联。在未来有很高的可能性特定的任务可以离线计算。

参加RNA World对CPU的最低要求是什么?(What are the minimal CPU requirements for participation in RNA World?)

Concerning the CPU, even processors lacking SSE such as Intel Pentium II (or older) could in principle participate since we have the appropriate applications ready for delivery. However, you should consider the average run times, deadlines and RAM requirements for certain types of work units as detailed elsewhere in this F.A.Q.

考虑到CPU的话,哪怕缺少SSE的英特尔奔腾2(或更早的产品)都可以参与。因为我们准备好了合适的任务,只待发送。不过你得考虑某个类型任务的平均运算时间,截止日期以及内存的占用。这些细节你可以在本文的其他问题下找到。

加入RNA World对网络有什么要求?(What are the network requirements for participation in RNA World?)

Currently we recommend RNA World participation only for machines that are connected to the Internet on a 24/7 basis, i.e. all around the clock.

目前我们推荐那些24*7即始终联网的机器参与RNA World项目。

RNA World 提供屏保功能吗?(Does RNA World offer a screensaver function?)

Yes.

是的。

根据(项目)服务状态页面,任务单元应该是可获得的,但为什么我无法获得任何任务?(According to the server status page, work units should be available, so why don't I get any?)

Assuming you have activated the type of work units announced to be available for processing in your RNA World project profile, the reason is RNA World's homogenous redundancy policy: a work unit delivered to a Linux x64 machine of a certain CPU type for example will only be sent to another Linux x64 machine for validation which has the same CPU type installed. If your system does not get any work units anymore then the remaining work indicated on the server status page can only be delivered to machines that provide an operating system and/or CPU different from yours.

假设你已经激活了在页面中显示可获得的任务的种类,并(申请)在你的RNA World项目文件中运行,那原因就是RNA World的同类冗余政策:例如传送给一台某型号CPU的Linux 64位机器的任务只会传送给另外一台完全相同的Linux 64位机器用以验证有效性。如果服务状态页面上显示有任务但你不能获得的话,那么剩余的任务将只能被传送给与你的系统或CPU型号不同的机器。

我回到家后发现我的机器无法响应而RNA World屏保处于运行状态。这是怎么回事?(I came home and my machine was basically unresponsive with multiple RNA World screensaver windows open - what is going on here?)

This (rarely occuring) strange behaviour is not yet completely understood. For simplicity, our current screensaver makes use of Adobe FlashPlayer. Consequently, the problem you describe can occur only on machines where FlashPlayer is installed (on others, the screensaver function will not work). To resolve the issue, it seems you need to either upgrade to the latest FlashPlayer version or uninstall it completely from your machine (of course, uninstalling is not really a good suggestion as many websites make use of Flash).

这种奇怪的表现目前(我们)尚不能完全理解。(该现象很罕见)简单地说,我们的屏保使用Adobe FlashPlayer软件。因此,你描述的问题只会出现在安装了FlashPlayer的电脑上(在其他电脑上,屏保将不会运行)。解决问题的方法是升级最新的FlashPlayer版本或者从电脑中完全移除它。(显然,移除并不是一个好的建议,因为大量的网站使用Flash)

是不是整个RNA World网站内容只支持德语?(It seems that the entire RNA World website is available only in German?)

No, you can individually customize your display language. Forum settings for example are found here. Setting BOINC pages to English (only necessary if it doesn't work properly with the browser's ACCEPT setting) can be done here. Since 18th of January 2010 we have also incorporated the Boinc translation system (BTS).

不,你可以定制显示语言。例如论坛设定在这里。在这里设置BOINC页面(语言)为英语(仅当无法正常工作在浏览器设定下时)。另外,在2010年1月18号之后我们使用BOINC 官方的翻译系统

我得到了“冗余结果”的信息,这是什么意思?(I got the message "redundant result", what exactly does that mean?)

First, a few remarks on the terms used in BOINC. A work unit is defined as a computational job which we would like participants to complete. A result, by contrast, is a collective term for the files which the server generates and sends to the participants. If enough results (quorum) are successful (this includes the data transfer to the participant, computation of the job, return of the result files to the server, etc.) and got validated (i.e. is identical to at least one other result successfully returned to the server), then a work unit is complete.

首先,BOINC中很少有关于术语的意见。任务单元被定义成我们想要参与并完成的计算性的任务。结果,相比而言,对文件是一种收集性的终端,它们由服务器生成并发送至参与者。如果足够的结果(“指定结果”)是成功(这包括传送数据给参与者,计算任务,返回结果给服务器等等)且经验证有效的(即至少与另外一个返回结果进行了验证)这样一个任务就算是完成了。

For example, in RNA World, for each CMSEARCH-based work unit three results are being generated and sent to three different machines. If two of these (quorum) are successful and get validated, the work unit is completed. As a consequence, the third result is no longer required, i.e. it is redundant (redundant result). This third result then (1) will not be sent out again (if it has not yet been sent out), (2) will be aborted on the client machine if it has been sent out but computation has not yet commenced or (3) will be completed on receive credits if its computation has already started.

例如,在RNA World中,每一个基于CMSEARCH的任务单元会被生成并传给三台不同的机器。如果其中两台(“指定机器”)计算成功并验证有效,该任务即为完成。因此,第三个结果就不再需要了,即冗余结果。这第三个结果将(1)不再被发送(如果尚未发送的话),(2)在用户端被删除,但仅当被发送却没有被计算的情况下,或(3)如果已经被计算的话讲正常提供积分。

We generate more results (three) per work unit than required for the quorum (two), to collect results more quickly. If we would not do it this way, we would always have to wait for the deadline to complete until the server detects that the clients do not send anything else in. Only then the server would generate an additional result and send that on out again and again wait for incoming data.

我们每个任务生成比判定有效任务数更多的结果,以便更快的收集结果。如果我们不这么做的话,我们将只能在截止日到来时才由服务器检测到用户没有发送任何数据并完成该任务。只有在这样的情况下,服务器将会生成额外的结果并一次又一次的发送并等待输入的数据。

进度条在100%上停了很长时间,出了什么问题?(The progress bar is at 100% and seems to sit there for hours - what is happening here?)

This is common behavior in BOINC projects, especially if you have just switched from another project to RNA World or if the work units of a given BOINC project are very heterogenous compared to each other. RNA World work units are de facto extremely heterogenous in their system requirements. For each computation, a series of small mini simulations is run on the server to estimate the time required for completion on the server. Since your machine differs from our server hardware, information based on the benchmarks performed from time to time on your machine are used to scale the duration determined for that work unit on the server to your machine. This scaling process is good but not perfectly accurate. So, the first work units often differ detectably in completion time from what the progress bar indicates. But, with more and more work units of that type pouring in on your system, a BOINC-integrated calculation mechanism corrects for that deviation in a progressive manner. So, with time, this "sitting at 100%" should become more and more rare. However, if the incoming work units are extremely different from each other in type (as is often the case for RNA World work units even if based on the same application), this adjustment might again turn out inaccurate for these new work units and an automatic re-adjustment will take place. In the worst case scenario, this might lead to the perception of an apparently constant unreliablity of the progress bar indicator. The bottom line is that you should just expect a work unit to take longer than indicated and not conclude there is something wrong with the work unit or your hardware.

这在BOINC平台是一个很常见的状态,尤其是你刚刚从另外一个项目转换到RNA World或者BOINC项目的任务单元之间非常不同。RNA World任务单元在系统需求方面事实上是极端相异的。每一个计算,在服务器上运行的一系列微型的模拟完整了计算时间需求。因为你的机器和我们的服务器硬件不同,由基准程序实时运行的信息将会被服务器用来度量任务持续时间。这种度量很有好处但并不是完全准确。所以,第一个任务单元的完成时间经常与任务进度条所显示的不符。不过,由于越来越多的该类型任务单元涌入你的系统内,一个BOINC整合计算方法将会以一种渐进的方法修正这种偏差。但是,如果输入任务单元类型之间迥然相异(尽管基于一个子项目,这在RNA World中会有这种情况),这种调整队新任务可能会再次显得不准确,而在调整将会进行(进一步修正)。在最坏的情况下,这可能会导致一种对于进度条的不信任。至少,你应该知道该任务将比所显示的数值消耗更多的时间而不是任务单元本身有误或硬件出了问题。

为什么RNA World不使用标准的BOINC论坛?(Why is RNA World not using the standard BOINC forum?)

The RNA World forums are multilingual which means there is more than just one forum and these are indeed located on a server different from the BOINC servers and from the RNA World server. The reason is that we need to make sure that forum communication remains intact even if the BOINC and the RNA World project severs are non-functional. It is actually surprising that several other DC projects do not do it the same way as we do. A single drawback is that you have to register on our forum server to make use of it but we feel that given the advantages, this drawback is bearable.

RNA World论坛是多语种的,这意味着将会有不止一个论坛并且论坛将置于一个不同于BOINC服务器以及RNA World服务器的(独立)服务器上。这么做的原因是我们要确保论坛交流在BOINC与RNA World项目服务器无法正常工作的情况下仍然完好。其他的几个分布式项目不像我们一样设置着实让我们惊奇。一个不利因素是你得在我们的论坛上注册才能使用。但是我们感觉考虑到它所带来的好处,这个不利因素是可以忍受的。

看上去有一个名字很长的RNA World任务单元堵塞了我的整个BOINC系统。(It seems a long-named RNA World work unit is blocking my entire BOINC system)

This is a known issue which it is occurring only very rarely and relates to a yet unresolved bug in the BOINC manager. It is also exclusively happening on Windows-based machines. The source of the error is the fact that Windows allows only 256 characters at maximum that can be used for the sum of path name plus file name length. RNA World uses explicit file names, i.e. from the long file names the user can easily derive what is being computed on his or her machine. We would like to keep it like that to allow third-party developers to conveniently construct RNA World monitoring programs. The point is that if such a long-named work unit is being sent to your Windows machine, it will get stuck in the downloading process because it can't be written productively to your hard drive. As a baffling consequence, your BOINC manager will stop downloading work units for any DC project it is hooked up to. To resolve the issue you just have to delete that WU from within the BOINC manager. We hope that the BOINC developers will fix this issue, soon.

这是一个由于BOINC管理器bug引发的已知的很少发生的问题。同时这也是一个仅在windows平台下出现的问题。错误的原因是windows中路径名称与文件名总长最大仅仅支持256个字母。RNA World使用详细的名称,即从长长的文件名中用户就可以轻易的知晓他(她)们的电脑在计算什么。我们保留这点是为了给第三方优化RNA World监视程序提供方便。问题在于如果一个名称如此长的任务单元被发送到你的windows电脑中,它将因为无法被写入硬盘中而被困在下载环节。令人困惑的结果是你的BOINC管理器将不会下载任何其他的分布式任务。解决的方法就是把该任务从BOINC管理器中删除。我们希望BOINC的维护者可以在不久的将来解决这个问题。

服务状态页面能否更频繁的更新?(Can't you refresh the server status page more frequently?)

We could, but we will not do that because we need to give priority to server performance. Updating the status page more frequently would cause a considerable increase in database queries which in turn cause additional server load. That power we prefer to dedicate to more important tasks as e.g. WU processing and serving. Anyway, the status page is refreshed every 10 minutes and if you browser shows something different, then you have a caching issue.

我们能做到,但选择不做。因为我们把提升服务体验放在优先位置上。更频繁的更新状态界面将导致基于数据的询问显著增加。这些将导致额外的服务负荷。这些能源我们更愿意贡献给重要的任务,比如WU单元以及服务。不论怎样,状态页面每10分钟更新一次。如果你的浏览器显示了一些不同的内容,那么你有隐藏的问题

我在Debian Etch计算机上运行RNA World,出现了很多的“computer error”信息。但是同样的机器安装RedHat系统运算却根本没有错误。是不是我遇到了一个系统种类的支持问题?(I started RNA World on my Debian Etch machine and got a lot of 'compute error' messages whereas running it on the same machine using RedHat gives no errors at all - is it possible that I experience an OS-dependent problem here?)

Yes. If you have an older glibc version, please check your Linux distibution for an upgrade that employs glibc version 2.4. This will resolve the problem.

是的,如果你有一个较旧的glibc版本,请将你的Linux分布式(指一个系统程序)升级到2.4版本。这样问题将得到解决。

我如何监控单个RNA World任务单元的内存(RAM)使用情况?(How can I monitor the RAM usage of individual RNA World WUs?)

The most simple way to do this under Windows is to use the task manager (TM). But you need to tweak its settings a bit: start the TM -> choose the tab for 'processes' -> go to the TM menu and click 'view' -> 'select columns' and now check the checkbox of 'Peak Memory Usage'.

在windows系统下,最简单的方法是使用任务管理器(TM)但是你需要调整设置:打开TM->选择processes选项->进入TM目录并点击view->选择select columns并且点击Peak Memory Usage。