Less talking, more doing: Crowd-sourcing the integration of Galaxy with a high-performance computing cluster
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On March 5th, 2014 a team of system administrators and bioinformaticians conducted a hack-a-thon to integrate Galaxy on top of the high-performance computing cluster at Michigan State University complete with single-sign-on and the ability to run jobs as the submitting user. They elicited and received strong community support during the hack-a-thon and engaged Galaxy developers and users through IRC and Twitter. In eight hours this hack-a-thon was able to quickly navigate the various integration hurdles via real time assistance from the Galaxy community. The entire deployment was done as openly as possible with coordination of the various efforts via a separate public chat channel. While there were a couple person-days of prep and follow up, the scheduling of a single day to do the bulk of the installation proved to be critical in getting the job done and was far more effective than the many hours talking about the idea of deploying Galaxy prior. The format allowed for rapid progress as communication time was reduced and developers could modify or add components, receive prompt feedback and continue to build on the growing infrastructure. We advocate a similar recipe of using virtual machines, the Puppet configuration management system, and agile development enabled by the built-in implementations of various components of Galaxy to enable forward progress.
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Reusable infrastructure (systems created by one or more people and intended to be used by other people) has become essential for many types of research over the last century, from microscopes to telescopes, and from sequencers to colliders. Over the past few decades, much research infrastructure has become digital, and many new digital systems have been developed. Here we discuss e-Research infrastructure (also called cyberinfrastructure), which has been defined by Craig Stewart as consisting of “... computing systems, data storage systems, advanced instruments and data repositories, visualization environments, and people, all linked together by software and high performance networks to improve research productivity and enable breakthroughs not otherwise possible.” While the research infrastructure as a whole is important, it is useful to consider infrastructure elements as well, as they comprise the overall infrastructure. Each element has a technical context (which allows one to ask questions about its architecture, such as: How does it fit into the overall infrastructure? How does it interact with other infrastructure elements?), a social context (which allows one to ask questions about its developers, such as: Who has developed the element?, and it users, such as: Who uses the element?, and its purpose, such as: What is the intended use of the element?), and a political context (which allows one to ask questions about its funders, such as: Who funds the development and maintenance?, and about its political scope, such as: Is the element national? International?). Understanding how a particular infrastructure element can be created and sustained requires answering two pairs of questions: What resources are needed to create it, and how can those resources be assembled and applied? What resources are needed to sustain it, and how can those resources be assembled and applied? In this paper, we focus on the second half of the two questions, since the amount and type of needed resources vary with the specific element being discussed. We believe elements of e-Research infrastructure can be placed in a three-dimensional space, consisting of temporal duration, spatial extent, and purpose. Note that the number of users of a given element should be larger the farther the element is from the origin in any direction, as should the cost. These two elements (number of users and cost) can be generically called ‘scale’ in this context. Alternatively, we can attempt to map impact, rather than usage, as an element of scale. In either case, scale is thus a metric of the space, though it is not orthogonal to any of the three axes. This talk with discuss how placing potential elements in this space allows decisions to be made on which elements should be pursued.
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"The mission of the US Department of Energy (DOE) Exascale Computing Project (ECP) was initiated in 2016 as a formal DOE project and extends through 2022. The ECP is designing the software infrastructure to enable the next generation of supercomputers—systems capable of more than 1018 operations per second—to effectively and efficiently run applications that address currently intractable problems of strategic importance. The ECP is creating and deploying an expanded and vertically integrated software stack on US Department of Energy (DOE) HPC exascale and pre-exascale systems, thereby defining the enduring US exascale ecosystem."
Watch the video: https://wp.me/p3RLHQ-kep
Learn more: https://www.exascaleproject.org/
Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter
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Talk given at the 2018 Association of Biomolecular Resource Facilities Mid-Atlantic Directors and Staff of Scientific Cores meeting
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Chemical Databases and Open Chemistry on the Desktop
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本公司拥有海外各大学样板无数，能完美还原海外各大学 Bachelor Diploma degree, Master Degree Diploma
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原版定制美国纽约州立大学奥尔巴尼分校毕业证学位证书原版一模一样
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此贴长年有效【贴心专线/微-信: 95270640】敬请保留此联系方式以备用！如有不在线请给我们留言！我们将在第一时间给您回复!上散发着一抹抹的光晕而这每处自然形成的细节融合在一起浑然天成的美实在令人心生愉悦小道的周边无秩序的生长着几株艳丽的野花红的粉的紫的虽混乱无章却给这幅美景更增添一份性感夹杂着一份纯洁的妖娆毫无违和感实在给人带来一份悠然幸福的心情如果说现在的审美已经断然拒绝了无声的话那么在树林间飞掠而过的小鸟叽叽咋咋的叫声是否就是这最后的点睛之笔悠然走在林间的小路上宁静与清香一丝丝的盛夏气息吸入身体昔日生活里的繁忙多
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About the event
14th Edition of International conference on computer vision
Computer conferences organized by ScienceFather group. ScienceFather takes the privilege to invite speakers participants students delegates and exhibitors from across the globe to its International Conference on computer conferences to be held in the Various Beautiful cites of the world. computer conferences are a discussion of common Inventions-related issues and additionally trade information share proof thoughts and insight into advanced developments in the science inventions service system. New technology may create many materials and devices with a vast range of applications such as in Science medicine electronics biomaterials energy production and consumer products.
Nomination are Open!! Don't Miss it
Visit: computer.scifat.com
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Could you use a simple piece of Scala validation code (granted, a very simplistic one too!) that you can rewrite, now and again, to refresh your basic understanding of Applicative operators <*>, <*, *>?
The goal is not to write perfect code showcasing validation, but rather, to provide a small, rough-and ready exercise to reinforce your muscle-memory.
Despite its grandiose-sounding title, this deck consists of just three slides showing the Scala 3 code to be rewritten whenever the details of the operators begin to fade away.
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一比一原版(USF毕业证)旧金山大学毕业证如何办理
USF硕士毕业证成绩单【微信95270640】一比一伪造旧金山大学文凭@假冒USF毕业证成绩单+Q微信95270640办理USF学位证书@仿造USF毕业文凭证书@购买旧金山大学毕业证成绩单USF真实使馆认证/真实留信认证回国人员证明
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国外毕业证学位证成绩单办理方法：
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2开始安排制作毕业证成绩单电子图；
3毕业证成绩单电子版做好以后发送给您确认；
4毕业证成绩单电子版您确认信息无误之后安排制作成品；
5成品做好拍照或者视频给您确认；
6快递给客户（国内顺丰国外DHLUPS等快读邮寄）。
教育部文凭学历认证认证的用途：
如果您计划在国内发展那么办理国内教育部认证是必不可少的。事业性用人单位如银行国企公务员在您应聘时都会需要您提供这个认证。其他私营 #外企企业无需提供！办理教育部认证所需资料众多且烦琐所有材料您都必须提供原件我们凭借丰富的经验帮您快速整合材料让您少走弯路。
实体公司专业为您服务如有需要请联系我: 微信95270640奈一次次令他失望山娃今年岁上五年级识得很多字从走出小屋开始山娃就知道父亲的家和工地共有一个很动听的名字——天河工地的底层空空荡荡很宽阔很凉爽在地上铺上报纸和水泥袋父亲和工人们中午全睡在地上地面坑坑洼洼山娃曾多次绊倒过也曾有长铁钉穿透凉鞋刺在脚板上但山娃不怕工地上也常有五六个从乡下来的小学生他们的父母亲也是高楼上的建筑工人小伙伴来自不同省份都操着带有浓重口音的普通话可不知为啥山娃不仅很快与他们熟识了
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Preparing Non - Technical Founders for Engaging a Tech Agency
Preparing non-technical founders before engaging a tech agency is crucial for the success of their projects. It starts with clearly defining their vision and goals, conducting thorough market research, and gaining a basic understanding of relevant technologies. Setting realistic expectations and preparing a detailed project brief are essential steps. Founders should select a tech agency with a proven track record and establish clear communication channels. Additionally, addressing legal and contractual considerations and planning for post-launch support are vital to ensure a smooth and successful collaboration. This preparation empowers non-technical founders to effectively communicate their needs and work seamlessly with their chosen tech agency.Visit our site to get more details about this. Contact us today www.ishtechnologies.com.au
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Less talking, more doing: Crowd-sourcing the integration of Galaxy with a high-performance computing cluster
- 1. Less talking, more doing Crowd-sourcing the integration of Galaxy with a high-performance computing cluster
- 2. The Goal Enable users of the Michigan State University Genomics Core to perform their own analysis using their High Performance Computing Cluster infrastructure Via: 1. Integrated institutional login 2. Import/export data from/to cluster storage while respecting permissions 3. Utilize existing node allocations and quotas; jobs must run as a HPCC user not a generic Galaxy user 4. Use the existing installed bioinformatics tools (no installs from the tool- shed)
- 3. The Resources Institute for Cyber-Enabled Research • $10 million for developing collaborative, interdisciplinary computational projects through a faculty scholars program and post-doctoral fellowships • Home of Michigan State University’s HPCC High Performance Computing Center • 8, 16, 32, or 64 cores • 8GiB - 2TiB of memory/node • Advanced GPU and Intel PHI capabilities also available • > 7000 cores in main cluster incl 800 core HTCondor system • 339 TB scratch storage, 192TB user storage
- 4. The Plan Do It Ourselves: open agile deployment All stakeholders set aside a single work day to get as much done as possible Community support solicited via galaxy-dev@ and Twitter Public chat room to document our work
- 6. Community Assistance 6 people joined our chat room to provide encouragement and very useful advice Thanks to Marten Martenson, Alper Kucukural, Dannon Baker, Lauren M and Nate Coraor!
- 7. Zero to Success in 8 Hours • No code changes needed • Only minimal prep beforehand • Login using existing Shibboleth infrastructure (no new accounts or passwords) • Jobs running as the user’s account with quota control on the existing compute cluster • Frontend + database running on a VMware ESXi 5.1 virtual machine (4 cores, shared, NetApp NFS backed) • Deployed using Puppet • Will be migrating to the community’s Puppet configuration
- 9. The Future • Filesystem permissions automation (each homedir is own filesystem & needs the SHARENFS property managed) • Galaxy upgrade procedure & testing • More user outreach courtesy @nodoubleg
- 10. Credits Dirk Colbry1, Michael R. Crusoe2, Andy Keen1, Greg Mason1, Jason Muffett1, Matthew Scholz1, Tracy K. Teal21 Michigan State University, Institute for Cyber-Enabled Research 2 Michigan State University, Department of Microbiology and Molecular Genetics Nicholas Beckloff, Genomics Core Director