Good morning. This is our annual Bloomberg Library Grand Rounds. We do this, we try to do this every year to get you up to speed with what's going on in the library and today we're really excited because we've got, there are three of us that are speaking. First will be Christy Jarvis and I'm going to introduce her. Brian Jones from the research side and then I'm going to give you an update about what's new in our library and a little bit about novel. But Christy Jarvis is a wonderful resource. You have to get to know her. She did her undergraduate work at the State University of New York in Buffalo and got her library of science master's degree at San Jose State and she is the information specialist library for Eccles Health Sciences Library. And there is one or two things she's going to tell us today that could change your career or at least make it a lot easier to keep writing papers. So Christy. Thank you. I am fairly new here at the University. I've only been here about eight months, so I haven't had a chance to meet a lot of you yet. But I'm looking forward to working with you in the future. Again, my name is Christy Jarvis. I've been asked to kind of talk a little bit about the resources that are available at the University and most importantly how you access those resources because if we have them available and you can't get to them, it doesn't do anyone any good. This is an overview of some of the things I'm going to talk about today. I'm going to talk about how you access things remotely, the databases that are available, e-books that are available, e-journals that are available and most importantly how you get to those e-journals. I'll talk quickly about interlibrary loan and document delivery and then ways that the library can help you. So the first thing I want to talk about is remote access because even though I'm sure that everyone here is very dedicated to their job and their patience and their research, at some point I hope you go home. Or you go on vacation or you're at a conference and you're not here at the University and most of the library's resources are subscription based meaning you cannot use them unless the resource provider knows that you are a member of the University of Utah. When you're here on campus that's easily accomplished because everything happens through IP ranges but when you're not here you have to tell the resource that you want to use that you belong to the University. The easiest way to do that is to use something called the easy proxy. Many of you here probably have never heard of the easy proxy. It's relatively new. It doesn't completely replace VPN but it works the same way but much, much better so I'm going to walk you through how that works. From the library's home page which you might want to bookmark because that's the easiest way to get to the library's resources. The URL is library.med.utah.edu. This is what the page looks like. There are two places on the home page where you can access in remotely.  When you click on this off campus access button you are going to be prompted to log into the proxy server. Looks like this. That should look familiar to most people. You've seen these login screens before. You're going to enter your unit and your password. Click log in. It's going to log you into the proxy server and then take you right back to where you were which was the library home page. What's different is that now the library home page URL has that easy proxy business up there in the URL. That lets you know you are connected to the easy proxy. From now on any library resource that you use from here will let you in because you've accessed the easy proxy and from the easy proxy you're going to access all the resources. All the library resources know. Any person who comes from this easy proxy server is affiliated with the University of Utah and will let you in. Using these easy proxy off campus login icons is far and away the easiest way to access subscription based resources. Yes it does. If you're a long standing VPN user and you love it and you have no problems with it by all means keep using it. I can tell you that in five to six years. Well vendors are being less cooperative about making their resources available by VPN and we get the university have very little control over access by the VPN. The easy proxy is actually something that is here controlled by the University of Utah and we configure it with every resource that we subscribe to. So we have a lot of control over it over time. I think the VPN is going to be less effective. You're welcome to use it for now if it's still working but I say try the easy proxy. I'm pretty sure you'll become a convert once you've logged into this easy proxy you're able to go to any of the e-journals databases resources etc.  I suggest going to this alphabetical list you can just pick the letter corresponds to the name of the database you want click on it and go right in. If you don't know what database you want you want to see what's available there is this databases a to z list that's in the quick links box on the main library homepage. A couple of the databases that I want to just by no means comprehensive just a couple of databases that I want to point out to make sure everyone is aware of one of them is the Cochran library. How many of you are familiar with the Cochran library use it the Cochran library is a collection of databases of systematic reviews and meta analysis where they collect and interpret the results of controlled trials and studies. They're very probably as unbiased and objective as things can be in the industry and they're really good for evidence based medicine approaches. So the Cochran library you can sign up to receive alerts of new systematic reviews by a particular discipline so that's a great way to stay on top of things. Faculty of a thousand is a post publication peer review process I guess it's a database where thousands of researchers and they say faculty of one thousand there's actually about five thousand people involved in this process right now where subject experts will go through and identify journal articles that are of high relevance that are game changing that are new information they read the journal they or they read the article they give it a ranking. And they justify why the results of this article are important and are things that people should be aware of. So faculty of one thousand is great for journal clubs it's great for helping you keep on top of what's new in an area that may not be your primary area of research or focus but you know want to know what's going on in a particular area. It's kind of like having someone else sort through the avalanche of articles on a particular subject and identify the three the five the ten that are important that you should know about. So that's faculty of one thousand lexicon is great for pharmacology information diagnostic tests lab tests that kind of thing. Dynamed and up to date I think most of the clinicians here know about it's a point of care tool. I'll answer the question that I'm sure some of you are asking which is can we access up to date remotely sadly the answer is still no. However that is very likely to change this coming fall. So stay tuned for that. And also Scopus would be our citation journal abstract database. So those are just some of the ones that I wanted to want to point out. E books the library has a rapidly expanding collection of electronic books. And there's two different ways really to get at those books. The first one is to browse an entire ebook collection and I'm going to show you some of those. The other is to search the library catalog for the name of a particular book to see if it's available and an electronic format. So ebook collections can be accessed again. This is the library home page this quick link box here over on the left is where you get to most things. And there's an ebooks link that takes you to an alphabetical list of all of the ebook collections that we have. And I wanted to highlight just a few of them here access medicine the NCB NCB eyes bookshelf and then MD console. All of these ebook collections in this list have multiple titles that the publishers have assembled into a. Subject collection if you will. So access medicine if you were to click on that takes you into this main screen where you can browse all of the clinical textbooks that are available on access medicine. You can browse them by subject area you can drill down to the exact title that you want for example access medicine has general ophthalmology. You can go right into a particular chapter in this case I went into chapter 10 for the retina. You can read this chapter or read this whole book online if you want. I will say that if you are interested in reading online be aware that most of our ebooks have a limited number of seats associated with them. So there's a limited number of people who can be in the book at the same time. So if you do decide to read the book online when you're done reading please log out so that you don't block someone else from having a seat. And also if you try and go into a book and you get a message that says something like current user limit exceeded or no seats available that just means that however many seats we have are currently being used. Just check back in a few minutes and see if a spot has opened up. I will say that if you forget to log yourself out of a book when you're done. Most books will kick you out within about 10 minutes of you not doing anything. So you're not taking up a seat permanently. But also be aware that if you're reading online and then you run off to go to the bathroom and drive some coffee and run into a colleague in the hall. And by the time you come back half an hour has passed you've probably been locked logged out of the book and you'll have to go back in. So that's if you're going to read it online. Almost every ebook that the library subscribes to has this download for handheld option which is great because you can click that link and just put the content of the whole book the whole chapter onto either your laptop or your handheld device. Put it on your iPad so you can read it on the plane and you're reading it offline so you're not using one of the available seats. Here's another one of the ebook collections that I want to point out because it's free. It's put out by PubMed there. I think it's their archive department has been working with publishers to have the publishers turn over the content of these ebooks and then the National Library of Medicine hosts them on this bookshelf format. You can browse all the titles or you can do what I've done here in this example which is search for a topic and just search across all available ebooks. And it will show you where that concept is in. So for example I searched for glaucoma and there's 134 books on the PubMed bookshelf that have chapters or sections that deal with that topic. The cool thing about bookshelf is that it's expanding pretty rapidly. You can actually sign up for an RSS feed to get notification of when new books and new editions are added to the bookshelf. Most but not all of the books that are on bookshelf are exempt from copyright so you can use images from them, chapters, whole sections. So about a year ago I would have said bookshelf wasn't that great of a resource because they didn't have that many titles but it's growing in leaps and bounds. And then the third ebook collection I want to point out is MD Consult. MD Consult has clinical texts, educational things, e-journals, patient handouts. But the people who use MD Consult for the most part are unaware that it has a large ebook collection. You can search the ebook titles by a particular discipline. Down here I showed ophthalmology or again you can search for a concept. So I searched for diabetic retinopathy across all of the ebooks that are part of MD Consult. And you get a list of all the books that that concept is in. One of the nice things about MD Consult is that after you search within books if you want you can expand your search to everything on MD Consult and get additional information about diabetic retinopathy. You can get patient hand out information, images. Both Access Medicine, the first ebook collection I showed you and MD Consult have thousands of images available as well that you can download and insert into presentations and that kind of thing. So those are ebook collections that the library has. If you're looking for a particular book and you want to know if we have it as an ebook. The best thing to do is to go to the library catalog and put in, I should not have picked something that's generic but I just put in ophthalmology. But you could put in actually the title of a book. When you search the catalog using that kind of information you're going to get a result list of something like 42 billion because our library catalog is enormous. So when you search for the title that you want and you get this massive result list. The thing that you want to do is to use these limiters, these search refining options over here on the left hand side. So search for your book and then use these restrictors over here on the side to say I only want to see books. And on top of that I only want to see books that have full text online. That's how you get to ebooks that are in our collection. So in this example I searched for ophthalmology and then said show me only books. Only books that have full text online and then I get this long list of books that are all ebooks. For each record that's an ebook, clicking on this view resource link right here opens up the book. This book now can be browsed chapter by chapter online. Or again if you don't want to sit at your computer and read the book use this download link and you can download it onto your iPad, your BlackBerry, your laptop, whatever and read it offline. Okay e-journals, that's the big one. There are thousands of journal titles that the university subscribes to and I actually this morning just to satisfy my own curiosity I wanted to find out how many journals do we subscribe to anyway. And you may or may not be surprised to know that the university has access to in the neighborhood of about 88,000 journals. So you're asking yourself, why can't I find the one I need in 88,000? We do subscribe to a lot. There's no way that we can subscribe to everything. So the first thing I want to talk about is how do you find access to the things that we do subscribe to. And there are three different ways to go about trying to access electronic journals. The first one I'm going to talk about because it's the one that I think most of you are familiar with is using the link out icons in PubMed. So before I show you what that looks like I want to make two points about PubMed. The first is that those link out icons only appear if you are using the library specific URL for PubMed. And I'll show you what that looks like in a minute. And the second thing that's important to note is that these little icons that you see in PubMed are actually browser cookies. So if your browser is not set to accept cookies you won't see these icons. Just two things to keep in mind. So if you go to the library homepage again and you use this quick links box and click on PubMed. That's taken you into PubMed and it's small so I don't know how well you can see it. But the URL for PubMed includes this Utah library holdings bit which means now that all of the holdings that the University of Utah has will appear to you using these link out icons assuming that your browser accepts cookies. So I've done an example here going into PubMed and searching for a journal. You would never really search this way I just put in the ID number of the journal. But it takes you to the article abstract. It's only on the article abstract view that you will see these icons here on the right. I don't know how well you can see this. There are three icons. The first one says Elsevier full text something. That is a publisher link. If you click on that link it will take you to the publisher's website where you will be invited to spend the $86 required to purchase the article. You don't want to click on the publisher link. The other two links means that the Eccles library has access to this journal. The first one that says Eccles catalog means that we have it in print. Eccles library online means that we have online access to this journal article. Most of the time I'm going to say maybe 85% of the time these link out icons work correctly and when you click on them it will take you directly into the full text of the article. The way that link out icon works is behind the icon there is information that we have given to PubMed saying this journal for this range and this issue is available to us here. So take them over here. What happens is sometimes publishers change that information and it takes us a while to be made aware of that so we can make changes in PubMed. So sometimes that lovely link that says that you should get it from the library doesn't work. So here's an example of it working lovely right took me right to the article. Here's another article update on treatments for diabetic macular edema and it's from current opinion and ophthalmology. According to PubMed Eccles library online has this journal article. Sadly when I click on it I get this message that says the following article requires subscription by now and that tends to lead to some frustration and despair and why didn't it work. So when that happens don't despair. You can either contact a librarian for assistance or you can try using one of the other options for accessing journals. So option two is to leave PubMed and to come back to the library homepage and use this e-journal list. Again this quick links box on the homepage has this e-journal option. When you click on that it opens up a search window. Find e-journal and I'm putting in the title of that journal that I was unable to get in PubMed. So current opinion and ophthalmology. Click go. I get a list of journal articles sorry of journal titles. Down here on the bottom the first one says current opinion and ophthalmology. This little tiny eye icon that's over here on the right. If you click on that little box pops up and it tells you exactly what range of years we have coverage for that title. Pretty useful to know. And if you just click on the actual link for the journal title itself it opens up a screen where you can see the various places you can go to find this journal. Now this bottom one says that we have this journal in this Lippincott legacy archive but it's only from 1990 to 1999. The article we want is from 2008 so that's not going to work. This top one though journals at Ovid says we have this journal from 1997 on. So I'm going to click on that go into journals at Ovid to see I'm now in current opinion and ophthalmology and I'm going to search for the journal title. If I remembered the citation information I could have searched for it that way. You can also just use the menu over here. I could have drilled down to the correct the correct year but I just searched by title and there we are. Ovid found the title that I want and look it says it has PDF full text so I click on that and there is my journal. So there's the article that PubMed said we didn't have and we had to pay for and blah blah blah. PubMed was wrong. So going through the option two for accessing journals which is to look up the journal title I was able to navigate to where we have the full text. Option three for accessing journal articles is to use the citation linker tool which is on the library homepage. You could get to it in a way very similar to we just had in the last example you go to this quick links box on the homepage of the library click on e-journals. But this time instead of searching by title I'm going to search on citation linker and enter as much citation information as I have for a particular journal article. When I click on go the citation linker tool goes out and it looks at every single database that's available here at the University of Utah to identify every place that that citation is likely to be available in full text. So when I put in the citation information and click on go the citation linker tool is now telling me this thing that you asked for this American Journal of Ophthalmology. This issue this volume issue in page number is available in full text in both of these places. So option one you're in PubMed you click on the link you get the article works well then you don't have to worry but that doesn't always work. Option two go back to the library homepage use the e-journal link type in the title of the journal. And then go into that whole journal record and either navigate to the article you want or type in the article title. Option three is to come back to the library homepage and use the citation linker tool. Enter the citation information of the journal and then the tool will go and find every single place that it says we have access to that journal article. And actually I should say option four is you can call the reference desk and ask a librarian that's option four for accessing journal titles. So let's say you've done all of that and you've actually verified there's no access to this journal article that I want. Can't get it electronically what am I going to do. You can use interlibrary loan and document delivery which are kind of interchangeable terms. If you are in PubMed you can use Lonesome Dock. If you're not in PubMed you can use Iliad. For both of those services I should say that the turnaround time we say 24 to 48 hours I rarely see an article request that takes less than. Well I would say I rarely see a request that takes more than 24 hours they're usually pretty pretty quick. There is a fee for requesting articles through ILL it's either $5 or $11. $5 is if the article is able to be filled by another institution in our state $5. If it has to go to an institution outside of our state it's $11. So it's kind of stinky because when you place the article request you're not sure whether it's going to cost you $5 or $11. But I guess you should go in with the assumption that this could cost up to $11. But having said that if you remember back with our slide of PubMed where we had the icons for ways you could get articles that else have your link. If you had used that link to get the article it would have cost you $86 so $11 is still a much better deal. So document delivery if you are in PubMed and you have signed up for a Lonesome Dock account registering for Lonesome Dock is free.  If you have an account set up you're in PubMed and you come across an article and you realize that the only option here is to buy it from the publisher, library doesn't have it, you've checked. The only way you can get it is through ILL. If you have a Lonesome Dock account just while you're in PubMed you can click on this send to link and that opens a drop down box. You can say that you want to order the article, you click on order, you say order the article, takes you to your Lonesome Dock sign in page, you put in your username and password, you've ordered the article. Easy enough. If you're not in PubMed and you just have a journal citation that you scribbled down on the back of a napkin while you were talking to a colleague rather than going into PubMed to find it you can go directly to the library home page. Under services and technology you can scroll down to where it says interlibrary loan. That opens up a new window that just explains what interlibrary loan is and you just click on this request items via ILLIED. ILLIED also you have to register for an account the first time but once you have an account you just put in your username and your password, you log into ILLIED. In this case we're going to click on request an article and then you fill in the article request with however much of the citation information you have and then you click go and you submit that request to interlibrary loan. I don't know whether now is the correct time for me to have it Elaine talk about this that when you set up your account in ILLIED, when you register for ILLIED, there is a spot where you can put down either a chart field that you want to charge these article fees to or you can put down the name of a contact person. Okay so Elaine says put her down she'll pay your article fees. Yeah a lot of programs will have the residents just put a responsible party in their department who will receive the invoices for articles that are delivered through interlibrary loan. That way you don't have to worry about pulling out a credit card or knowing a chart field you just put in Elaine's name and she'll take care of that. So that's access to databases and e-books and e-journals and if you can't get the e-journal how do you get it through ILL. There are other things that the library can help you with that I want to make sure that you're aware of. This is just a slide showing you actually how to contact us. If it's during pretty much regular operating hours 7 in the morning till about 7 o'clock at night at the library the fastest way to get help is to use the IM. There's pretty much always someone on IM and they'll respond immediately or phone. If you send an email your response time is going to be probably an hour or two because there's not someone constantly monitoring that inbox. But the IM chat and the phone you'll get quick response. Some things that the reference staff at EQUALS can help you with. They can help you select the right databases to find published literature. They can help you develop effective search strategies. A big one is they can help you set up saved searches and alerts so that you're not constantly have to go out and look for information that you can have things set up that information is just pushed to you which is very useful. They can assist with bibliographic management tools. So if you've ever found yourself in the middle of the night saying bad words at your end note account talk to the library. We have several people on staff who are end note geniuses. We actually offer end note training and they can assist you along the way using those kind of tools. They can also do orientation or point of need instruction on any of the resources that are available. I didn't realize that a lot of people at the university did not know that you could order a literature search from the library. It is a customized professional literature database searching by reference staff. The library does charge mediated search fees but not to the University of Utah students faculty and staff. So for you ordering a comprehensive literature search is free. They're very good at it. They do it all the time and it's a service that I was amazed to find that a lot of people aren't even aware of. So that's just something to keep in mind. The library offers a lot of workshops and trainings. I mentioned end note. There's going to be a further training next Wednesday for those of you who have been introduced to further. I wanted to point out some of the resources that are available for researchers. The library actually has a research librarian on staff, Abby, who does a lot of one-on-one consulting training on how to use biomedical databases. Does extensive literature searches, can help with compliance support, scholarly publishing, navigating. She's a dedicated person to help support researchers in the health sciences. Some other resources that are specific to researchers are MIRA, which is my research assistant. It is a program that is just getting off the ground that is designed to, right now, it functions by funneling researchers in the direction of where they can find answers to questions at various stages in the research cycle. Eventually this whole MIRA website will be interactive where that research cycle, by clicking anywhere in that cycle, it will pull information that's necessary to you at that point in the cycle. Further, which is the Federated Utah Research and Translational Health eRepository, is not that this is specific to researchers, I think, but it has a lot of value for researchers. This is a new informatics database that's just gotten off the ground. Joyce Mitchell was the driver behind it. I don't know whether your department has had further training. I know some of the departments have had whole department trainings, but if yours hasn't, the library offers further training on an ongoing basis. I think the next class is next Wednesday, and that's something you might want to look into. Some other help for researchers that's coming soon. The first is the university is going to be acquiring SyVal experts in SyVal funding, which if you don't know much about, pretty slick. SyVal experts is kind of a database of researcher expertise and projects and funding and a way to network with other people, not only here at the university, but across the country. And then the SyVal funding piece links project interests with available funding sources throughout the country. So those are coming. They were actually expected to roll out at the very end of 2011, and they're spending a little bit more time beefing up the content. So I think it's slated for later, late spring, early summer, but I think those are going to be a great help for researchers. And then the last thing I want to mention that's coming soon is that the university has just funded a new position in the School of Medicine for someone who's very official job title will be Research Concierge, who is going to be responsible to be the human linking element between what various labs on campus are doing. So it will be his or her job to know what projects various researchers are working on. And when a researcher contacts him or her, he can say, well, you know what, you're actually looking for this. And so and so over here has just submitted a grant for this, and I think you too should talk. So it's actually meant to, we'll have Syval experts, we'll have Syval funding, and then the Concierge piece is the human brain who will make a lot of the connections. I actually personally think of him as being the person that has like the old school operator, you know, that plugs, you know, I'd like to talk to person number 42. He's going to try and make those connections between researchers on campus. So that was a very quick run through of things that the library has available and things that we can do for you. I would say the takeaway message is number one, use the easy proxy when you're not on campus. It will save you a lot of heartache and a lot of frustration. And number two, if you can't find the full text of the journal article you need by using the icons in PubMed link out, don't despair, most of the time we actually do have it. If that icon ever showed up there, it means that we have it. It's probably just means that the link has died. So try using one of the other options to get to the journal article that you need or contact a librarian. So anyone have any questions, any comments? I'm happy to feel if you have complaints, issues, things that aren't working, no questions?


Second area was solid, but just a real gutsy effort. And I don't mean I say gutsy effort because it was after that first inning and kind of getting out of it a little bit unscathed after the two-run homer. To be able to give us six innings tonight after that first inning is pretty impressive. But I think it was part because I thought he's throwing the ball really well too. Lindsey. Karen, in your discussions about the called strikes on Judge and others, have you gotten any sense of if there's any other factors here aside from just sheer size? No. There have been any. Is there any sort of? I don't know what to tell you guys on this, OK?  I answer this question every so often. I don't know what to tell you. To the right. Karen, the boos and the frustration, I think, keep building for Gallo. Are you seeing any signs that he can snap out of this? Yeah, I mean, I've seen it over the last 10 days. Couple really good at bats last night where he worked walks in a tight game. Nobody ever mentioned those, so he's grinding. It's a challenge. It's been a struggle without question. He has had some good at bats along the way here. I feel like over the last week or 10 days hasn't got a lot of traction with hits. But he's just got to keep fighting. Keep passing in front. I apologize that this was asked already. But during your ejection, it looked like you were saying, it's not too late. It's not too late. Did Rayburn tell you that it's too late in the game to be arguing? No, he didn't say anything. I was just saying it's not too late to change. And then during Chapman's outing, you had a map Lakewood for a mount visit mid at bat, which is kind of unusual. Did you guys see something there? Or just you wanted to talk to him about it? Yeah, we just wanted to make sure he was doing something. We wanted to make sure he was doing. Brian, to the left. Aaron, I know you were out of the game by that point, but the decision to pinch at Donaldson instead of Gonzalez, what was the call there? Yeah, Josh Donaldson, I agree with the call with them going there in that spot. Yeah. Eric, Judge and Stanton have never been ejected in their careers. They very rarely say anything to umpires. As a player, guys have different philosophies on that. What was your view? Can that impact, when you say something to an umpire, when you got thrown out as a player, can that, does that have any impact on balls and strikes? No, these guys are pros, you know, umpires are pros, you know, they obviously, so I would like to think in the vast majority of cases, you know, things happen and we all move on from it and with the players as well. I certainly don't want them or any of my players whenever possible to not, you know, get ejected out of a game, you know, especially position player front nowadays where you play with shorter benches and stuff. So, you know, I prefer that they leave it to me. You can say things, you know, in a professional way, which they do and, you know, but I don't think guys, you know, umpires are holding grudge of their pros, you know, and I have a lot of respect for what they do and who they are, um, and I think, no, I don't think things have big carry over effectual. Dan.  Oh, yeah, yeah, just running for him. And Castro, any update on him? I gotta get, I gotta get with them. I think it's gonna be an IL situation, so I don't have the diagnosis and timeframe yet though.


Cuing systems, we're going to start general and go back on specifics for what BayoCAD actually does here. A queuing system, just like a queue in a theme park or whatever, is jobs are submitted and then processed according to the scheduler. So you take your place in line, essentially. It's more like a mainframe, the old batch computing systems of the 60s and 70s than it is like a desktop or single server. You can't preempt what other people are already doing. Yes. Is that a question? You use those? Me too. I'm old. We do have preemptive scheduling, so we have some nodes that are actually owned by particular groups. So that that means that they have priority access on that machine and if your job happens running on their machine then they kick you off because they bought it. So that's the way life works. But in the meantime, you get to use it for free in the mean and so you're not really at anything. So the utilizing resources is a gameless BayoCAD. The biggest users we have of BayoCAD are people who have set up their own clusters and have realized within a couple of years that the really expensive part about setting up a cluster is not the hardware that's in it. There's a lot of hardware there, but that's not the expensive part. This expensive part is keeping it going and good system administration, keeping up on the latest security patches, all that kind of stuff. That's the hard part of a system and security and all that kind of stuff.  So we started this on a budget of zero using used equipment and a few grants, that kind of thing. It's how it all got started. It's built up from there. We also have researchers that are buying their own resources on others. Some in this room that are in that group just from the names I saw that were registered for the class that they bought some of those particular machines with their money and so now they have priority access either to general to the whole machine or to their particular nodes. Not saying that there's no disadvantage. The disadvantage is that you don't always have immediate access to everything. You do have to take your place in line. This is kind of a schematic of Baocat and it's kind of hard to see here. What we've got here is we've got the campus network. We have our Nichols Hall router comes into our firewall and our firewall actually has four networks sitting off of it. Actually, we just added a fifth. So we have our management network, which is how we nobody else has access to that except for actually Adam and I. That's how we turn machines off and on and do our monitoring that kind of thing. OpenStack, which is kind of shaky right now. The future plan is for OpenStack to be a place where you can spin up your own VM kind of like your own Amazon cloud sort of service. We're not we're not ready to go real live with that yet, but we're getting there. We have a production network, which is our main what we consider Baocat and then we have a hosted virtual hosted network, which where we we have a few researchers that have a particular Windows machine or some licensed software.  So we set them up on a virtual machine so they can run that kind of in their own space. We have several different types of connectivity here. OpenStack, try to think. The orange is our fiber channel. That's very fast disk access. That's what that orange is. Infiniband. Normally orange is fiber channel. Yeah, this is our Infiniband. Infiniband is a very, very fast network mesh capability. It talks at 40 gigabits per second, which is quite a bit faster. Most of our other machines are down getting up to 10 gigabits per second, which is pretty fast, but it's also very low latency. So if you're talking MPI stuff, MPI stuff runs very well over Infiniband. We have our regular network, which is in the blue. We have some other strange things going throughout, like Hadoop, and we have a Ceph network for our OpenStack. But it's not just like you'd see in a lab, something like this, where you got to switch and you got a bunch of machines out there. It's a little more complicated than that. I wasn't able to get more recent numbers, or at least not in the short time frame that I had to update these slides. But I think we have somewhere near 600 people on Beocat now. So you can see that it's gone up through and we're over 2,500 cores now. I probably should have been able to get those numbers, but like I said, I just I grabbed the slides from our last class and it was a couple years old and I forgot to update them before now. So getting new numbers is fast, but so we're still growing. We're always growing. We usually buy more resources at least twice a year, sometimes three times to add into Beocat. There are times we take the oldest stuff when we kick it out and we give it to other parts on campus. We have, in our main network, we have several different classes of machines that serve different purposes. Our scouts are the oldest ones that we have. We bought 76 of them. I was guessing we have about 50 of them in operation now. There's eight cores, two 4-core optorons, grabbed this off the website. Eight gigs of RAM. There's some of those. We stole eight gigs out of some of them. We kicked out and put them in another one. So yeah, we should have some with 16. Kind of a strange lot there. There are the paladins. The paladins have 24 cores, two 6-core, 12 cores, sorry, 12 cores, 24 gigs of RAM. They're the ones that are GPUs on them. If you wouldn't do any CUDA type programming with the high-end GPUs, that's what we have out there. Please do if you have anything that could take advantage of it. They sit mostly not doing anything most of the time. So if you can take advantage of those GPUs, please have at it. We have the mages. We have six of those. These are our big monsters. They've got 80 cores, eight 10-core CPUs in it, and a terabyte of RAM. I tell this to other play other schools and they all start drooling because very few places have machines with that much RAM in them. They've got InfiniBand and 15 gig yet. Yes, they have 10 gig up to those. I don't think I'm going to worry. The old ones, I think we have 80 and 79 or 80. Something like that. 80's squeeze has got the new ones. Yeah. So they are from 16 to 20 cores. These are the fastest ones we have available. Most time we can have people specify something that went around the elves because they run really fast on there. We have at least 64 gigs of RAM on the 16 core machines. On the 24 core machines, we have 96. Sometimes we even have 384. InfiniBand, Andor, 10 gig Ethernet on them.  Sorry. Baocat itself. How to get an account. Baocat is available to any researcher in the state of Kansas or collaborating with a researcher in the state of Kansas. Well over 90 percent, probably 95 percent or more of our users are on the K-State University campus. We do have some from other universities. We have a couple from Washburn, Pittsburgh State. I think we even have one from Benedictine, if I remember right, and people that collaborate with them. So we have some people from Michigan, for instance, that are dealing with some researchers on campus. All you have to do is get an EID and then fill out the account request page. And if you hold it out correctly and you get approved, which is pretty much a given if you're a researcher, then you're getting an account. Logging in. Everybody here is probably a user already. User name, we use EID credentials. So we do have a couple times a year, somebody say, hey, I forgot my Baocat password. I said, I don't know what it is either. You have to go talk to the EID people. And usually we get a cheapest response like, oh, yeah, I forgot that. I just changed my EID password and didn't work. Um, creating programs. We talked a lot about the programming, that type of thing. Running your own toolkits. I'm not going to go into that in any great detail. But we do have all the development resources out there. So you can do your own programming. If you want to, you can download your own toolkits. We've gone over how to install things in your home directory, that type of thing. We do have, whenever you log in, you'll either see Athena or Minerva on the command line. That's the machine you're logged in to. Those are our two head nodes. There's maybe a few of you that get a Pade. If you're in one particular working group they bought in a head node because they're doing some special things on there. I'm not thinking if this group was on there or not. You'd probably nodding at me now if you were because you do that on purpose. But running jobs on the head nodes. We try to limit to one hour CPU time. We don't enforce that. Um, right? Rules change all the time. So these are meant for like light prep work. A lot of your pipelining stuff that you use in genomics where it submits the jobs for you. That serial part until you go serial and parallel, serial and parallel, serial. A lot of times that serial part is not real heavy duty workload stuff. So we'll run those on the head nodes and let it submit the jobs. That's fine. And used mostly for testing. I mean if you've got a program that's going to run for 30 seconds and even using the entire thing, we're not really going to care if it's taking 30 seconds. The idea of it is just used for testing. Get it tested out there. Make sure it's working right. On our system before you submit a job. Hey, Catur. Hey, we already did that. Okay. Submitting a job. Yes it is. Dang it. I'll get that corrected before I put these out there too. We'll go out into the... There is a page here called SGE Basics that talks about how to do all this stuff that we're talking about. This is what I was talking about. I try to lead you through step by step on this because I know that when I first got started personally I had lots of Linux experience and that part wasn't the assembling block for me. But when I first came here I'd never used a queuing system or anything like that. So this was kind of the hurdle for me. So I just kind of wrote up some documentation on how to make this happen. We use the queue sub-command to submit to our schedule. Our schedule is called grid engine. Sometimes they call SGE for sun grid engine, which is where it came from. Although technically we got the fork of it, which is now sun of grid engine. So we call it SGE or grid engine. That's our queuing system. There are several different queuing systems out there that all do essentially the same thing. If you come from other universities you might have seen Torque and Maui or PBS, Slurm. Yeah, there's several of them out there. They all essentially operate in the same way. They're ways of scheduling resources mapping that onto the system. Basically if you can think of having a giant spreadsheet of all your resources out here along the top and all the people who want resources out here along the side and trying to map those up. That's what it does. It tries to say US for eight quarters and 16 gigs of RAM. I can fit that in over here. That's what it does. Or it might say I can get you in anywhere for a while, but I'll be able to in... We're here and so kind of reserve your spot there. That's what the idea behind a scheduler is. So I'm not going to read to you. I try to do that very limitedly. I doubt I did a little bit there, but here's a Q sub command that might, for an example here, I created one called myhost by SH which just echoes the host name. Q sub it with a time limit of 60 seconds because I know this isn't going to run very long. I use the move amount of memory possible, one processor, and I ran it. All that does is it submits it to the Q and that goes and brings the host name back out. Your output, whereas your... Yes, between a Q and... Which Q you submit to. You can. However, if you give it the correct resources, it will do a better job scheduling it for you than you probably can yourself because it's going to try to optimize that for wherever it'll fit. So if you tell it what resources you need, you tell it how much RAM you need, you tell it how many cores you need, how long you need it for, it will schedule that for you. That is its job, is a schedule it for you. We have people that try to use the... As a matter of fact, we had somebody just today try to use a specific host. Well, that host was busy, so the job is going to sit there forever and it could have already been finished somewhere else. So that's the reason why you tell it what resources you need as opposed to which machines that you want, by and large. We do that part automatically. So here's what I did. I created the file, I submitted my job and it popped back up because it can schedule that just about anywhere. When I did that, this is what I started off to begin with. I started off with just... When I listed, I could see my host.sh. Now when I do the listing, afterwards, I see all these other files that it creates. It creates O files, E files, PE files, and PO files. Those are for output, error, parallel error, parallel output. And if you look at them, usually, when you run something on the command line, it'll just send text back to you. Well, these are happening on the machine, so that's not going to work out so well. That sends it to these files when you queue sub. And if you take a look at them, and I didn't show it on here, yeah, we kind of go with that. I said, cat, this file name. I did it in the order I wanted to on purpose. And it shows nothing. So that file was empty. That file empty. That file was empty. But now, when I did the last one, my output file, you'll see that it has, that's the output that would have come on the screen if I was running it interactively. When you put it in batch mode, your errors are going to go into one file, your output's going to go in the other. Sometimes we'll have people come in and they'll say, I don't have any output. Well, did you check your error file? It'll tell you when the error file or something went wrong. So that's where you really need to look for these. You also have some ways of monitoring jobs. The status command will tell you that things are running and what's waiting. I actually created jobs in particular so that one would be running and one would not be running so that I could make this example up. But the status command will tell you what's running and what's not what's waiting and how and when it was submitted, when it was running up here and status dash r will give you a relative time. So it's saying it started 27 seconds ago in this case. The question people want to know is when my job is going to start, which I think is really a silly question to ask because the real question you want to know is when will my job end? You don't care when it starts, you want to know how soon is my job going to run, but they are related so I can understand that. So I just took a, we have a command out there called QStat and QStat will tell you just about everything you want to know about what's going on. So I took at this point in time before I was writing this article and I just ran a QStat command and I edited stuff out. I can put some things in here, kind of some boring parts just so we can kind of see some things that were running at the time. So anything with the lowercase r in this column, in the state column means it's running. The capital r over here means it was resubmitted. Right, I said they're rerunning, yeah. So something went wrong with it the first time and automatically restarted the job. So the capital r means it was resubmitted. So something went wrong and it's doing it again. The lowercase r means it's actually running. So it's running basically for the second time is what it's telling you here. It's what? Still running, yes. We get down here to the QW. This is where your job will be when they're waiting. That means it's queued and waiting. The Q and W means queued and waiting. Down here you'll see another strange one. HRQ, that means it's queued. It's been resubmitted and it's on hold. I don't know if they did something themselves or if we did something for that person right at that point. Yeah, there are times we'll put jobs on hold. We'll suspend jobs saying, hey you can't do that. We just kind of keep an eye on things and make sure that you're asking for roughly what you are. We don't have any, there are queuing systems out there as a matter of fact we can enforce this on ours that you can say, I want eight gigs of RAM.  You ask for more than what you want to do. We don't do that here. We kind of go on the honor system of you said this is not what you're going to use. We're going to trust that you're using about that.  And another one, this one is also put on hold for some reason or other. But most everything you see is going to be either QW or R. That's queuing and waiting or running. Yes, you have to make good estimates. I didn't have, we could. I don't have that on my thing but we ask us here, we can go through it. Yeah. I've been working to ask for way too much memory. Give another question? More or less. Yeah. Why in large that's the order they're going to be in. So the closer you are to the top of the QW the closer you are to getting your job done. Get the job ID what? Get the command line. When you submit your job it'll tell you the job ID. You can get it from here. This is, that's what this column is with the job ID. If you want to see what jobs are, what jobs of yours are submitted, so what you're saying. Yes, if you do the QStat command, again using GRIP, which is just saying just show me the output. Let's look at the current queue right now. Okay, I'm just looking here. Jeff Cumber has a bunch of stuff here. So we're going to look at just his job, right? Let's say QStat when you use the pipe then take the output of QStat and run it through the next program. Just GRIP, that'll show me just his jobs. Does that make sense? Are you Sophie? I guess from the accent. I knew that Sophie was in the class. Do you have any jobs in the queue right now? You can grab it from here. See what I did out here? So I just used QStat and then I grabbed your username. And those are your two jobs. There'll be one line is 185.11.80. There's a little 185.12.21. You can use Auk or some other command line utility to say grab that as of right now. Monitor node. Here's something nice too. But it won't let me do it even though I'm admin. We'll see if it works or not. Nope, I don't have any jobs running. This is a nice thing. This will let you log into a machine that you already have a job running on. So let me just second here. I think I still have that in my... I'm basically making a job here that's just going to sit there and do nothing for an hour. Should start running pretty quick, I would think. Oh, I see what you're saying. Make it as wide as I can. If the small's it'll let me go. Oh, come on. You should be running by now. I'm not using much memory. The three things you're going to need to know when you submit a job are how many cores you need. It defaults to one. How much time you need. It defaults to one hour. And how much RAM you need, which it defaults to one gig per core. The biggest thing we get is people who don't... who submit jobs with how much RAM they need total. Is it how much they need per core on multi-core jobs? So let's say I need 16 cores and 80 gigs of RAM. That's five gigs per core. So when you do your QSub, you're going to tell it you need five gigs per core. Because if I tell it 16 cores and 80 gigs per core, that's going to be more than we have available. So that's the biggest trick is, especially for big jobs, is you have to specify the amount of RAM per core. Thank you. The limit for what? The RAM and any core? Well, there's not a limit per core. You could ask, if you wanted to mage older yourself, you could have more than a terabyte of RAM. It would do that. So, but I'm saying, when you specify what your memory requirements are within QSub, you're telling it how much RAM per core. So you take your total RAM divided by the number of cores that you're using. Must be busy. Well, I'm waiting for this. I'm going to show you. We showed you how to do a QSub on the command line from this page here. But the better way of doing that is create actually submit script. And I have an example. That's true. But I don't now. That works too. There we are. It's already running. It's running in L51. Okay. This is your question now. How to get on there? Now that I have a job running on L51, it's capital M for monitor node. L51 should come on. Come on. It's waiting for my job to get past the sleep command before it lets me in. I said it was going to be answered your question. Apparently your answer takes a while. I don't think so. I'm proud to put that in there. Somebody could add that to the wiki. Just saying. It is a wiki.  But this is supposed to be the fast part. The maximum CPUs. If you have a well-written MPI job that will do it, the whole thing is about 2,500. I guess we do have a limit of about 500? 500, of course. Yes. We have MPI spread available. So I've done some work with it on the pelleters. And the infinite air on the pelleters is much more stable. We still have to fix a few issues with the pinnacle. It should take a couple weeks. If you had it fresh on you, we had issues with the few logic and pinnacle on somebody else's node. But again, for me, there are people with MPI code, both in college and online. So I would, if you're doing MPI code, I would try to come in college and do that work. But again, it's not going to work very well for some of you. It's only giving us about one or two to give you this for a second for one, but two, seven. Yeah. And if you do MPI within a node, that will work fine. It's just between nodes. Which is the MPI spread, which is what she was asking was between them. Single connection, please. We'll send out another video. So are you working with the Rue or the Crystal? Do you have one? Okay. So I'm working with them to get it optimized. And so as soon as we get the MPI stuff worked out, then I'll do more testing. Okay. Now the monitor node is actually working. I eventually got me logged in to L51. So now I can use htop and see how things are going, or top, or PS, or that kind of thing. That's the purpose of the monitor node command is to get you into a node that you're currently running on to see how it's doing. Running, John. So here I am. I have my job. And I'm done with it. Make sure I got my numbers right so I don't kill somebody else's job. There. I just deleted my job with QDale. You can also use the QUltra command to change your, if you, before your job starts, if you said, oh shoot, I submitted that with six hours and I really needed 60, I did that wrong. You can go in and change that from before it starts. The very good reason why we don't let you do that after it starts, that's because it's really easy to game the system. If we let you say, oh, I need an hour. Oh, sure, we can schedule it anywhere. No, I was just kidding. I need 400 hours. No, we don't let you do that. So that's why we let you do that before the job starts is the QUltra command. Anything, oh, QSub directives. I have in my BioCAD intro and you'll have this on the slides that I'm going to send to you. Everything I have in here is in this BioCAD intro directly on my folder, which is publicly accessible. Anybody can get to it. But I have some QSub scripts. By putting things in a QSub script, as opposed to typing out the QSub command every time, that keeps you from having to A, remembering all the parameters that you used, and B, it's a whole lot easier to go back and change things if you need to change anything. So here I have it. It's a simple QSub script, blah, blah, blah. Because the directives that QSub sees start with dollar sign or hashtag dollar sign, then I use the double line here. So all these are comments that start with double hashtag. And so if I wanted to change this, all I have to do is delete one of those and then it starts with hashtag dollar sign. And that's what anything that starts with that is a directive toward QSub. So this is how I tell it. I tell it I want how much memory. This is all well documented. Feel free to copy this over to your own home directory and edit it, use it however you want. That's the whole reason why I wrote it is so we wouldn't have to reinvent the wheel. Runtime, this is hours, minutes, seconds. Or you can put the whole thing in seconds if you want. Most people don't want to have mess with thinking about how many seconds is in 300 hours or something. Infiniband, I did put a note in there that if you don't know if you need it, you don't need it most likely. We had a lot of people for a while, so we're looking at our examples and saying, Infiniband, that sounds fast. And they were asking for Infiniband and that was actually keeping their jobs from running on somewhere the way it would run just fine. Same thing with CUDA. CUDA is the GPU processing stuff. So if you don't need it, don't ask for it. Parallel environment.  Single one is the default. It means you're using one core. A single, you're using 12 cores on the same machine. MPI, there's several different MPI options.  MPI spread means to spread it out over as many machines as you can. MPI fill means I'm trying to put it on as few machines as I can. And MPI, we have one, two, four, eight, 80, 16, something like that. We have several of these documented. But that means you're going to allocate this many at a time. So if I had MPI four, 16, that means I'm going to try to run... It's going to allocate four at a time. So four on this machine, four on this machine, four on this machine, and maybe four back on the first machine again. That's going to allocate them in groups of four. Checkpointing, I'm going to skip because we're probably not going to do much of that. Some handy things to put in here. Again, you can put these all in the Q sub command line, but if you're doing a lot of these, put in a sub-script. It's a whole lot easier. CW means change current working directory. By default, all your output files and everything it looks for is going to be looking in your... Is right in your home directory, where you are in your first log in. Most times, if you've been using BioCat for a while, you're going to have your projects in different directories, that type of thing.  At the time you submit it, that's a handy option to have. So all your output files and everywhere it looks for data files are the same. Merge output and error text streams into a single stream. Sometimes you have programs that are expecting, for some strange reason, they try to put their output on error lines. That kind of merges those together. Sometimes it's handy, sometimes it's not, but so that is an option. Name your job. That's a really handy thing to have, especially if you're running lots of different jobs. I know some people submit several different jobs and they'll be N47A2, N47A3, N47A4, you know, on so on and so forth. By doing this, you don't just see, run my job being executable. So that way you can see when you do a QStat, you can see what the job title is. It'll also change the name of your output files, so that it'll be easier to read and easier to tell what's what. And then finally, when you run the program that we're meant to do, especially if you're running executable, so submit script is really a good way of going about things about running your programs. It's almost, is it required? Probably. For R, for Perl, for any scripting language, Python, that kind of thing, you just about have to put it into a scripting, into a submit script, and then you submit this. So here's my sample that I have here, and then if I was wanting to submit that, I'd just say qsub sample.qsub. If you look at our advanced SGE page, it details all this too. So this is all documented. That was what I had for SGE. Again, if you go to our web pages, you can find a lot more complex examples, array jobs, things like that. I think you're going to talk about that in the next... Okay, that type of thing. Some strange things, variable number of quarters. You can do all sorts of strange things. Most everything is documented on our Wiki under the advanced page. I tried to make the beginning page to be really as simple as possible, just trying to get your feet wet and figure out how this thing works with the advanced page being now that you've figured out how it works, here's how to get the most out of it. Questions, comments, or snide your marks? None of the latter even. Okay.