diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 000000000..b0ff81123 --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +README.md merge=ours diff --git a/.gitignore b/.gitignore new file mode 100644 index 000000000..496ee2ca6 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +.DS_Store \ No newline at end of file diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 000000000..84186759f --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,125 @@ +# Contributing + +Thank you for taking an interest in contributing to our repository! Please consult the information below (we tried to keep it brief and reasonable) prior to making a pull request. These guidelines help avoid hassle between us (the maintainers) and you (the contributors) that give us a common target to shoot for, and makes what our standards are transparent and obvious. + +If you desire, you may credit yourself as author within any content you contribute. + +### Who can contribute? +Can you read this? Then you! Simply consult the short [style guidelines](#style-guidelines) below to get familiar with our content standards. + +### What should be contributed? +* Tutorials on your software-stack of choice (something you'd give a new member of your team) +* Scripts/notebooks/cheatsheets that automate a convoluted task or explain something succinctly +* Explanations of system aspects of Linux and specific NREL HPC systems (e.g. "What is the `/var` directory for?") +* Anything you think another HPC user might benefit from! + +### How do I contribute? + +If the below instructions are foreign to you, consider giving a reading to the [`git` module](/git/README.md) to "*git*" familiar with git! The git workflow has some colorful jargon but none of the concepts should be new to you if you have used a computer before. If you *haven't* used a computer before, then it might be best to [start somewhere more basic](https://www.pcworld.com/article/2918397/how-to-get-started-with-linux-a-beginners-guide.html). + +1. Fork this repo +2. _(optional)_ To edit locally on your machine, do either of: + * `git clone https://github.com/`\`/HPC` for only the base repo. + * `git clone https://github.com/`\`/HPC.wiki` to clone and edit the [Wiki](https://github.com/NREL/HPC/wiki) if you intend to have highly verbose documetation. + + ***Note that there does not have to be an entry for your content in both repos.** If you only want to construct explanitory documents, they do not need a directory in the base repo. Similarly, example or utility scripts that don't need a lot of explanation don't need an entry in the [Wiki](https://github.com/NREL/HPC/wiki). For more info on the intended purpose of each repo, see the [style guidelines](#style-guidelines) below.* +3. Change something (_after_ consulting the [style guidelines](#style-guidelines)) +4. `git add` the change(s) +5. `git commit` with a useful commit message! +6. `git push` +7. Make a pull-request (shiny green button on your fork of the repo's GitHub webpage.) + +Alternatively, you may send your contributions via e-mail attachment to HPC-Help@nrel.gov with subject of "NREL HPC GitHub Contribution" and the body detailing what changes you made (the more specific the better). + +### Why should I contribute? +Something something good Samaritan, benefit the community, searchable knowledge-base, etc. + +--- + +## Style Guidelines + +>### **TL;DR—this repository should be predominantly composed of scripts/source code/executables or other things that _do_ something on the HPC systems, and the Wiki should predominantly be for explanations about what/how/why.** +>### That said, still getting familiar with the details below will improve the chance your contributions are submitted in a a readily-acceptable format. + +### ***New to Markdown?*** +Appropriately enough, we have a documentation for that! Simply start with the [README in the Markdown module](/markdown/README.md). Not to mention, the raw-contents of any `.md` file can be used as a reference for how to style content a certain way. + +Note that git (the version control protocol) is not equivalent to GitHub (the git repository hosting web service, which implements the git protocol). This is an important distinction to be sure of before proceeding. There are other git-hosting services such as GitLab which function similarly to GitHub, but both use the git protocol. These hosting-services provide different decorative features to make the repositories more visually pleasing/intuitive to interact with. + +One such feature of GitHub's frontend is the "[Wiki](https://github.com/NREL/HPC/wiki)" (found in the tab at the top of the repository webpage). This is essentially its own child git repository that is intended to only hold template documents (like markdown files) and be more sensible to navigate as a web interface than a git repo. To edit the material in the Wiki of this repository, you will need to clone it separately (it's the same URI to clone this repository just with `.wiki` at the end.) + +## Files and directories + +### Naming files +* Files need an appropriate extension so it is obvious what purpose they serve. Compiled binaries shouldn't be pushed here (the most common type of extension-lacking files) so there's no reason a file should be without an extension. + * This includes Markdown files, which should carry a ".md" extension (not .txt or lackthereof). +* No capitals or spaces (with the exception of any `README.md` files serving as landing pages within directories per GitHub markdown rendering). Separate words in the filename with underscores or hyphens—whichever reduces ambiguity the most and is most pleasant for you to type. + * For example, using underscores in a potential filename containing a hyphenated command like `llvm-g++` would make it clear that the command has a hyphen: `how_to_use_llvm-g++.md` vs `how-to-use-llvm-g++.md`. + * Spaces aren't allowed because referencing such files by name from a command-line has extra caveats, and is generally a pain if you aren't prepared. + * If you are fond of word-wise traversal in text-editors you may prefer hyphens to underscores. Whichever is more sensible for your preferences and the content. +* Files should be named in a way that makes clear their content and role in the training scheme, but should not carry metadata. GitHub is a revision control system, so don't use filenames for versioning, ownership, or stamping date/time. +* Everything in this repository is instructional. You do not need to include qualifiers like `tutorial` or `walkthrough` in the name of the module files or directory. + +### Directory structure + +Here is a brief overview of how files and directories should be organized within this repository. Explicitly named files or directories should remain fixed in location and name, and assumed to exist as such by other files: + +```bash +HPC # i.e. the root of this repo +├── assets +│ ... +│ └── <...> # This directory should contain all non-text files used within other markdown files. +├── CONTRIBUTING.md # This is the document you're currently reading. +├── LICENSE.txt +├── README.md # The homepage of the repository. Should contain a link to each module's README. +... +└── <...> # Modules that exist or will exist + ... + ├─ README.md # Any directory should contain a "README.md" to serve as the landing page. + ... + └ ... ─ <...> # Sub-modules that exist or will exist +``` + +* Module directories should go in the root of the repository, both here and the wiki. The `README.md` is responsible for sorting the modules into a reasonably traversable hierarchy, sorted by expected user-competency and expertise with HPC principles or specific components of your module (e.g. expertise in Python). + +* Per tool/software/language tutorials should have a dedicated directory and relevant source code or scripts stored within that, accompanied by a `README.md` that briefly explains how to use the content present there. + +* Long-form, highly verbose documentation should be contained in an identically named directory within the [Wiki](https://github.com/NREL/HPC/wiki) of this repository. If there is content on the wiki, it should be linked there from a module that shares its name. + +Example of a module directory: + * In the repository itself: + ```bash + plexos-quickstart + ├── data + │ └── RTS-GMLC-6.400.xml + ├── env-6.4.2.sh + ├── env-7.3.3.sh + ├── env-7.4.2.sh + ├── README.md # Contains enough instruction to use these scripts. Links to the wiki for extra info. + └── util + └── get_week.py + ``` + * The respective [Wiki](https://github.com/NREL/HPC/wiki) directory featuring verbose explanations: + ```bash + plexos-quickstart + ├── initial-session.md + ├── README.md # The "home page" of the module which introduces, links to, and structures neighboring pages. + ├── run-magma.md + ├── run-plexos.md + └── setup-plexos.md + ``` + +### Markdown content and structure +* The intent of training or tutorial materials is to show someone who does not know how to do what you do how to do it. Err on the side of verbosity. + +* Where you can assume that a user should have worked through training materials conceptually prior to the current ones, cross-reference them (mention and hyperlink). This also applies to information on the HPC website. In general, where you can refer someone to well crafted information online that's more extensive or well constructed than you have time or space to write, do so through a hyperlink. + +* **Images and other reusable non-textual files go in `assets/`** in the root of both the repository and the [Wiki](https://github.com/NREL/HPC/wiki) of this repository, so as to be easily and mutually referred to throughout various pages. The image can then be linked to anywhere with markdown like `![alt text](/assets/name_of_image.png)`, If an image can replace lots of text, by all means include it. However, don't take terminal screenshots when `inline code` or a codeblock will suffice. + +* GitHub doesn't support embedded videos, so if you need that please just insert it as a regular hyperlink (or hyperlinked thumbnail image of the video). + +### General Advice + +* As the content generation process evolves, some contributions will undoubtedly stand out as exemplary. Don't be shy about copying those in style, syntax, etc. + +* Always preview the rendered output. GitHub's specific rendering has unique features and inconsistencies with other platforms. diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 000000000..25e7ebc60 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. http://fsf.org/ + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. Therefore, you have +certain responsibilities if you distribute copies of the software, or if +you modify it: responsibilities to respect the freedom of others. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must pass on to the recipients the same +freedoms that you received. You must make sure that they, too, receive +or can get the source code. And you must show them these terms so they +know their rights. + + Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License +giving you legal permission to copy, distribute and/or modify it. + + For the developers' and authors' protection, the GPL clearly explains +that there is no warranty for this free software. For both users' and +authors' sake, the GPL requires that modified versions be marked as +changed, so that their problems will not be attributed erroneously to +authors of previous versions. + + Some devices are designed to deny users access to install or run +modified versions of the software inside them, although the manufacturer +can do so. This is fundamentally incompatible with the aim of +protecting users' freedom to change the software. The systematic +pattern of such abuse occurs in the area of products for individuals to +use, which is precisely where it is most unacceptable. Therefore, we +have designed this version of the GPL to prohibit the practice for those +products. If such problems arise substantially in other domains, we +stand ready to extend this provision to those domains in future versions +of the GPL, as needed to protect the freedom of users. + + Finally, every program is threatened constantly by software patents. +States should not allow patents to restrict development and use of +software on general-purpose computers, but in those that do, we wish to +avoid the special danger that patents applied to a free program could +make it effectively proprietary. To prevent this, the GPL assures that +patents cannot be used to render the program non-free. + + The precise terms and conditions for copying, distribution and +modification follow. + + TERMS AND CONDITIONS + + 0. Definitions. + + "This License" refers to version 3 of the GNU General Public License. + + "Copyright" also means copyright-like laws that apply to other kinds of +works, such as semiconductor masks. + + "The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + + To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of an +exact copy. The resulting work is called a "modified version" of the +earlier work or a work "based on" the earlier work. + + A "covered work" means either the unmodified Program or a work based +on the Program. + + To "propagate" a work means to do anything with it that, without +permission, would make you directly or secondarily liable for +infringement under applicable copyright law, except executing it on a +computer or modifying a private copy. Propagation includes copying, +distribution (with or without modification), making available to the +public, and in some countries other activities as well. + + To "convey" a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user through +a computer network, with no transfer of a copy, is not conveying. + + An interactive user interface displays "Appropriate Legal Notices" +to the extent that it includes a convenient and prominently visible +feature that (1) displays an appropriate copyright notice, and (2) +tells the user that there is no warranty for the work (except to the +extent that warranties are provided), that licensees may convey the +work under this License, and how to view a copy of this License. If +the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + + 1. Source Code. + + The "source code" for a work means the preferred form of the work +for making modifications to it. "Object code" means any non-source +form of a work. + + A "Standard Interface" means an interface that either is an official +standard defined by a recognized standards body, or, in the case of +interfaces specified for a particular programming language, one that +is widely used among developers working in that language. + + The "System Libraries" of an executable work include anything, other +than the work as a whole, that (a) is included in the normal form of +packaging a Major Component, but which is not part of that Major +Component, and (b) serves only to enable use of the work with that +Major Component, or to implement a Standard Interface for which an +implementation is available to the public in source code form. A +"Major Component", in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system +(if any) on which the executable work runs, or a compiler used to +produce the work, or an object code interpreter used to run it. + + The "Corresponding Source" for a work in object code form means all +the source code needed to generate, install, and (for an executable +work) run the object code and to modify the work, including scripts to +control those activities. However, it does not include the work's +System Libraries, or general-purpose tools or generally available free +programs which are used unmodified in performing those activities but +which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for +the work, and the source code for shared libraries and dynamically +linked subprograms that the work is specifically designed to require, +such as by intimate data communication or control flow between those +subprograms and other parts of the work. + + The Corresponding Source need not include anything that users +can regenerate automatically from other parts of the Corresponding +Source. + + The Corresponding Source for a work in source code form is that +same work. + + 2. Basic Permissions. + + All rights granted under this License are granted for the term of +copyright on the Program, and are irrevocable provided the stated +conditions are met. This License explicitly affirms your unlimited +permission to run the unmodified Program. The output from running a +covered work is covered by this License only if the output, given its +content, constitutes a covered work. This License acknowledges your +rights of fair use or other equivalent, as provided by copyright law. + + You may make, run and propagate covered works that you do not +convey, without conditions so long as your license otherwise remains +in force. You may convey covered works to others for the sole purpose +of having them make modifications exclusively for you, or provide you +with facilities for running those works, provided that you comply with +the terms of this License in conveying all material for which you do +not control copyright. Those thus making or running the covered works +for you must do so exclusively on your behalf, under your direction +and control, on terms that prohibit them from making any copies of +your copyrighted material outside their relationship with you. + + Conveying under any other circumstances is permitted solely under +the conditions stated below. Sublicensing is not allowed; section 10 +makes it unnecessary. + + 3. Protecting Users' Legal Rights From Anti-Circumvention Law. + + No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + + When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such circumvention +is effected by exercising rights under this License with respect to +the covered work, and you disclaim any intention to limit operation or +modification of the work as a means of enforcing, against the work's +users, your or third parties' legal rights to forbid circumvention of +technological measures. + + 4. Conveying Verbatim Copies. + + You may convey verbatim copies of the Program's source code as you +receive it, in any medium, provided that you conspicuously and +appropriately publish on each copy an appropriate copyright notice; +keep intact all notices stating that this License and any +non-permissive terms added in accord with section 7 apply to the code; +keep intact all notices of the absence of any warranty; and give all +recipients a copy of this License along with the Program. + + You may charge any price or no price for each copy that you convey, +and you may offer support or warranty protection for a fee. + + 5. Conveying Modified Source Versions. + + You may convey a work based on the Program, or the modifications to +produce it from the Program, in the form of source code under the +terms of section 4, provided that you also meet all of these conditions: + + a) The work must carry prominent notices stating that you modified + it, and giving a relevant date. + + b) The work must carry prominent notices stating that it is + released under this License and any conditions added under section + 7. This requirement modifies the requirement in section 4 to + "keep intact all notices". + + c) You must license the entire work, as a whole, under this + License to anyone who comes into possession of a copy. This + License will therefore apply, along with any applicable section 7 + additional terms, to the whole of the work, and all its parts, + regardless of how they are packaged. This License gives no + permission to license the work in any other way, but it does not + invalidate such permission if you have separately received it. + + d) If the work has interactive user interfaces, each must display + Appropriate Legal Notices; however, if the Program has interactive + interfaces that do not display Appropriate Legal Notices, your + work need not make them do so. + + A compilation of a covered work with other separate and independent +works, which are not by their nature extensions of the covered work, +and which are not combined with it such as to form a larger program, +in or on a volume of a storage or distribution medium, is called an +"aggregate" if the compilation and its resulting copyright are not +used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work +in an aggregate does not cause this License to apply to the other +parts of the aggregate. + + 6. Conveying Non-Source Forms. + + You may convey a covered work in object code form under the terms +of sections 4 and 5, provided that you also convey the +machine-readable Corresponding Source under the terms of this License, +in one of these ways: + + a) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by the + Corresponding Source fixed on a durable physical medium + customarily used for software interchange. + + b) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by a + written offer, valid for at least three years and valid for as + long as you offer spare parts or customer support for that product + model, to give anyone who possesses the object code either (1) a + copy of the Corresponding Source for all the software in the + product that is covered by this License, on a durable physical + medium customarily used for software interchange, for a price no + more than your reasonable cost of physically performing this + conveying of source, or (2) access to copy the + Corresponding Source from a network server at no charge. + + c) Convey individual copies of the object code with a copy of the + written offer to provide the Corresponding Source. This + alternative is allowed only occasionally and noncommercially, and + only if you received the object code with such an offer, in accord + with subsection 6b. + + d) Convey the object code by offering access from a designated + place (gratis or for a charge), and offer equivalent access to the + Corresponding Source in the same way through the same place at no + further charge. You need not require recipients to copy the + Corresponding Source along with the object code. If the place to + copy the object code is a network server, the Corresponding Source + may be on a different server (operated by you or a third party) + that supports equivalent copying facilities, provided you maintain + clear directions next to the object code saying where to find the + Corresponding Source. Regardless of what server hosts the + Corresponding Source, you remain obligated to ensure that it is + available for as long as needed to satisfy these requirements. + + e) Convey the object code using peer-to-peer transmission, provided + you inform other peers where the object code and Corresponding + Source of the work are being offered to the general public at no + charge under subsection 6d. + + A separable portion of the object code, whose source code is excluded +from the Corresponding Source as a System Library, need not be +included in conveying the object code work. + + A "User Product" is either (1) a "consumer product", which means any +tangible personal property which is normally used for personal, family, +or household purposes, or (2) anything designed or sold for incorporation +into a dwelling. In determining whether a product is a consumer product, +doubtful cases shall be resolved in favor of coverage. For a particular +product received by a particular user, "normally used" refers to a +typical or common use of that class of product, regardless of the status +of the particular user or of the way in which the particular user +actually uses, or expects or is expected to use, the product. A product +is a consumer product regardless of whether the product has substantial +commercial, industrial or non-consumer uses, unless such uses represent +the only significant mode of use of the product. + + "Installation Information" for a User Product means any methods, +procedures, authorization keys, or other information required to install +and execute modified versions of a covered work in that User Product from +a modified version of its Corresponding Source. The information must +suffice to ensure that the continued functioning of the modified object +code is in no case prevented or interfered with solely because +modification has been made. + + If you convey an object code work under this section in, or with, or +specifically for use in, a User Product, and the conveying occurs as +part of a transaction in which the right of possession and use of the +User Product is transferred to the recipient in perpetuity or for a +fixed term (regardless of how the transaction is characterized), the +Corresponding Source conveyed under this section must be accompanied +by the Installation Information. But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + + The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or updates +for a work that has been modified or installed by the recipient, or for +the User Product in which it has been modified or installed. Access to a +network may be denied when the modification itself materially and +adversely affects the operation of the network or violates the rules and +protocols for communication across the network. + + Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + + 7. Additional Terms. + + "Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + + When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + + Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders of +that material) supplement the terms of this License with terms: + + a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or + + b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or + + c) Prohibiting misrepresentation of the origin of that material, or + requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or + + d) Limiting the use for publicity purposes of names of licensors or + authors of the material; or + + e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or + + f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions of + it) with contractual assumptions of liability to the recipient, for + any liability that these contractual assumptions directly impose on + those licensors and authors. + + All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + + If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + + Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; +the above requirements apply either way. + + 8. Termination. + + You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + + However, if you cease all violation of this License, then your +license from a particular copyright holder is reinstated (a) +provisionally, unless and until the copyright holder explicitly and +finally terminates your license, and (b) permanently, if the copyright +holder fails to notify you of the violation by some reasonable means +prior to 60 days after the cessation. + + Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + + Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + + 9. Acceptance Not Required for Having Copies. + + You are not required to accept this License in order to receive or +run a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + + 10. Automatic Licensing of Downstream Recipients. + + Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + + An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + + You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + + 11. Patents. + + A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + + A contributor's "essential patent claims" are all patent claims +owned or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + + Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + + In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + + If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + + If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + + A patent license is "discriminatory" if it does not include within +the scope of its coverage, prohibits the exercise of, or is +conditioned on the non-exercise of one or more of the rights that are +specifically granted under this License. You may not convey a covered +work if you are a party to an arrangement with a third party that is +in the business of distributing software, under which you make payment +to the third party based on the extent of your activity of conveying +the work, and under which the third party grants, to any of the +parties who would receive the covered work from you, a discriminatory +patent license (a) in connection with copies of the covered work +conveyed by you (or copies made from those copies), or (b) primarily +for and in connection with specific products or compilations that +contain the covered work, unless you entered into that arrangement, +or that patent license was granted, prior to 28 March 2007. + + Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + + 12. No Surrender of Others' Freedom. + + If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you may +not convey it at all. For example, if you agree to terms that obligate you +to collect a royalty for further conveying from those to whom you convey +the Program, the only way you could satisfy both those terms and this +License would be to refrain entirely from conveying the Program. + + 13. Use with the GNU Affero General Public License. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + {one line to give the program's name and a brief idea of what it does.} + Copyright (C) {year} {name of author} + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see http://www.gnu.org/licenses/. + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + {project} Copyright (C) {year} {fullname} + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +http://www.gnu.org/licenses/. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +http://www.gnu.org/philosophy/why-not-lgpl.html. diff --git a/README.md b/README.md new file mode 100644 index 000000000..a43ace1bb --- /dev/null +++ b/README.md @@ -0,0 +1,36 @@ +

+

+ + + + +

+ +This repository serves as a collection of walkthroughs, utilities, and other resources to improve the NREL HPC user's quality of life, both novice and veteran. + +### How to Use This Repository + +1. [Login to an NREL HPC system](https://www.nrel.gov/hpc/system-access.html) +2. From your login shell, run `git clone https://github.com/NREL/HPC` +3. View the `README.md` within any directories that interest you, or see the [table of contents](#table-of-contents) below. + +### Contributing +Please see our [contribution guidelines](CONTRIBUTING.md) for a rundown on how we'd like the contents of this repository to be formatted. + +## Table of Contents + +### 🔧 Utilities and Tools +* [Sample Slurm Batch Scripts](/slurm/README.md) +* [Workshops and Presentations Hosted by NREL HPC Operations Team](/workshops/README.md) + +### 🎓 Tutorials +> #### Beginner +> * [Markdown](/markdown/README.md) +> * [Bash](/bash/README.md) +> * [Git](/git/README.md) + +> #### Intermediate +> * [HPC Benchmarking: STREAM](/stream_benchmark/StreamTutorial.ipynb) + +> #### Advanced +> * [\](/markdown/README.md) diff --git a/assets/circ.jpg b/assets/circ.jpg new file mode 100644 index 000000000..9af98b368 Binary files /dev/null and b/assets/circ.jpg differ diff --git a/assets/hpc-style.png b/assets/hpc-style.png new file mode 100644 index 000000000..8ed3b77dc Binary files /dev/null and b/assets/hpc-style.png differ diff --git a/assets/hpc.png b/assets/hpc.png new file mode 100644 index 000000000..dcdbbd2b7 Binary files /dev/null and b/assets/hpc.png differ diff --git a/assets/paraview.png b/assets/paraview.png new file mode 100755 index 000000000..01ee56909 Binary files /dev/null and b/assets/paraview.png differ diff --git a/bash/README.md b/bash/README.md new file mode 100644 index 000000000..53a69b050 --- /dev/null +++ b/bash/README.md @@ -0,0 +1,7 @@ +# Bash (***B***ourne ***A***gain ***Sh***ell) + +`bash` is the default shell application on NREL HPC systems and the terminal environment on many operating systems. + +Bash has a lot of quirks; even for the experienced Bash wizard, there are a lot of caveats and odd syntax details to remember. We recommend all users take a look at our [writeup on bash](https://nrel.github.io/HPC/bash) for some explanation of some of Bash's idiosyncrasies and to get justification for why some of the notation is the way it is. + +Afterwards, please see this very thorough and concise [cheatsheet that documents most of Bash's features](./cheatsheet.sh). \ No newline at end of file diff --git a/bash/cheatsheet.sh b/bash/cheatsheet.sh new file mode 100644 index 000000000..7d5aa7092 --- /dev/null +++ b/bash/cheatsheet.sh @@ -0,0 +1,433 @@ +#!/bin/bash + +# Copied from https://raw.githubusercontent.com/LeCoupa/awesome-cheatsheets/master/languages/bash.sh + +############################################################################## +# SHORTCUTS +############################################################################## + +: ' # Begin multi-line comment + +CTRL+A # move to beginning of line +CTRL+B # moves backward one character +CTRL+C # halts the current command +CTRL+D # deletes one character backward or logs out of current session, similar to exit +CTRL+E # moves to end of line +CTRL+F # moves forward one character +CTRL+G # aborts the current editing command and ring the terminal bell +CTRL+J # same as RETURN +CTRL+K # deletes (kill) forward to end of line +CTRL+L # clears screen and redisplay the line +CTRL+M # same as RETURN +CTRL+N # next line in command history +CTRL+O # same as RETURN, then displays next line in history file +CTRL+P # previous line in command history +CTRL+R # searches backward +CTRL+S # searches forward +CTRL+T # transposes two characters +CTRL+U # kills backward from point to the beginning of line +CTRL+V # makes the next character typed verbatim +CTRL+W # kills the word behind the cursor +CTRL+X # lists the possible filename completions of the current word +CTRL+Y # retrieves (yank) last item killed +CTRL+Z # stops the current command, resume with fg in the foreground or bg in the background + +ALT+B # moves backward one word +ALT+D # deletes next word +ALT+F # moves forward one word + +DELETE # deletes one character backward +!! # repeats the last command +exit # logs out of current session + +' # End multi-line comment + +############################################################################## +# BASH BASICS +############################################################################## + +env # displays all environment variables + +echo $SHELL # displays the shell you're using +echo $BASH_VERSION # displays bash version + +bash # if you want to use bash (type exit to go back to your previously opened shell) +whereis bash # finds out where bash is on your system +which bash # finds out which program is executed as 'bash' (default: /bin/bash, can change across environments) + +clear # clears content on window (hide displayed lines) + + +############################################################################## +# FILE COMMANDS +############################################################################## + + +ls # lists your files in current directory, ls to print files in a specific directory +ls -l # lists your files in 'long format', which contains the exact size of the file, who owns the file and who has the right to look at it, and when it was last modified +ls -a # lists all files, including hidden files (name beginning with '.') +ln -s # creates symbolic link to file +touch # creates or updates (edit) your file +cat # prints file raw content (will not be interpreted) +any_command > # '>' is used to perform redirections, it will set any_command's stdout to file instead of "real stdout" (generally /dev/stdout) +more # shows the first part of a file (move with space and type q to quit) +head # outputs the first lines of file (default: 10 lines) +tail # outputs the last lines of file (useful with -f option) (default: 10 lines) +vim # opens a file in VIM (VI iMproved) text editor, will create it if it doesn't exist +mv # moves a file to destination, behavior will change based on 'dest' type (dir: file is placed into dir; file: file will replace dest (tip: useful for renaming)) +cp # copies a file +rm # removes a file +diff # compares files, and shows where they differ +wc # tells you how many lines, words and characters there are in a file. Use -lwc (lines, word, character) to ouput only 1 of those informations +chmod -options # lets you change the read, write, and execute permissions on your files (more infos: SUID, GUID) +gzip # compresses files using gzip algorithm +gunzip # uncompresses files compressed by gzip +gzcat # lets you look at gzipped file without actually having to gunzip it +lpr # prints the file +lpq # checks out the printer queue +lprm # removes something from the printer queue +genscript # converts plain text files into postscript for printing and gives you some options for formatting +dvips # prints .dvi files (i.e. files produced by LaTeX) +grep # looks for the string in the files +grep -r # search recursively for pattern in directory + + +############################################################################## +# DIRECTORY COMMANDS +############################################################################## + + +mkdir # makes a new directory +cd # changes to home +cd # changes directory +pwd # tells you where you currently are + + +############################################################################## +# SSH, SYSTEM INFO & NETWORK COMMANDS +############################################################################## + + +ssh user@host # connects to host as user +ssh -p user@host # connects to host on specified port as user +ssh-copy-id user@host # adds your ssh key to host for user to enable a keyed or passwordless login + +whoami # returns your username +passwd # lets you change your password +quota -v # shows what your disk quota is +date # shows the current date and time +cal # shows the month's calendar +uptime # shows current uptime +w # displays whois online +finger # displays information about user +uname -a # shows kernel information +man # shows the manual for specified command +df # shows disk usage +du # shows the disk usage of the files and directories in filename (du -s give only a total) +last # lists your last logins +ps -u yourusername # lists your processes +kill # kills the processes with the ID you gave +killall # kill all processes with the name +top # displays your currently active processes +bg # lists stopped or background jobs ; resume a stopped job in the background +fg # brings the most recent job in the foreground +fg # brings job to the foreground + +ping # pings host and outputs results +whois # gets whois information for domain +dig # gets DNS information for domain +dig -x # reverses lookup host +wget # downloads file + + +############################################################################## +# VARIABLES +############################################################################## + + +varname=value # defines a variable +varname=value command # defines a variable to be in the environment of a particular subprocess +echo $varname # checks a variable's value +echo $$ # prints process ID of the current shell +echo $! # prints process ID of the most recently invoked background job +echo $? # displays the exit status of the last command +export VARNAME=value # defines an environment variable (will be available in subprocesses) + +array[0]=valA # how to define an array +array[1]=valB +array[2]=valC +array=([2]=valC [0]=valA [1]=valB) # another way +array=(valA valB valC) # and another + +${array[i]} # displays array's value for this index. If no index is supplied, array element 0 is assumed +${#array[i]} # to find out the length of any element in the array +${#array[@]} # to find out how many values there are in the array + +declare -a # the variables are treaded as arrays +declare -f # uses function names only +declare -F # displays function names without definitions +declare -i # the variables are treaded as integers +declare -r # makes the variables read-only +declare -x # marks the variables for export via the environment + +${varname:-word} # if varname exists and isn't null, return its value; otherwise return word +${varname:=word} # if varname exists and isn't null, return its value; otherwise set it word and then return its value +${varname:?message} # if varname exists and isn't null, return its value; otherwise print varname, followed by message and abort the current command or script +${varname:+word} # if varname exists and isn't null, return word; otherwise return null +${varname:offset:length} # performs substring expansion. It returns the substring of $varname starting at offset and up to length characters + +${variable#pattern} # if the pattern matches the beginning of the variable's value, delete the shortest part that matches and return the rest +${variable##pattern} # if the pattern matches the beginning of the variable's value, delete the longest part that matches and return the rest +${variable%pattern} # if the pattern matches the end of the variable's value, delete the shortest part that matches and return the rest +${variable%%pattern} # if the pattern matches the end of the variable's value, delete the longest part that matches and return the rest +${variable/pattern/string} # the longest match to pattern in variable is replaced by string. Only the first match is replaced +${variable//pattern/string} # the longest match to pattern in variable is replaced by string. All matches are replaced + +${#varname} # returns the length of the value of the variable as a character string + +*(patternlist) # matches zero or more occurrences of the given patterns ++(patternlist) # matches one or more occurrences of the given patterns +?(patternlist) # matches zero or one occurrence of the given patterns +@(patternlist) # matches exactly one of the given patterns +!(patternlist) # matches anything except one of the given patterns + +$(UNIX command) # command substitution: runs the command and returns standard output + + +############################################################################## +# FUNCTIONS +############################################################################## + + +# The function refers to passed arguments by position (as if they were positional parameters), that is, $1, $2, and so forth. +# $@ is equal to "$1" "$2"... "$N", where N is the number of positional parameters. $# holds the number of positional parameters. + + +function functname() { + shell commands +} + +unset -f functname # deletes a function definition +declare -f # displays all defined functions in your login session + + +############################################################################## +# FLOW CONTROLS +############################################################################## + + +statement1 && statement2 # and operator +statement1 || statement2 # or operator + +-a # and operator inside a test conditional expression +-o # or operator inside a test conditional expression + +# STRINGS + +str1 = str2 # str1 matches str2 +str1 != str2 # str1 does not match str2 +str1 < str2 # str1 is less than str2 (alphabetically) +str1 > str2 # str1 is greater than str2 (alphabetically) +-n str1 # str1 is not null (has length greater than 0) +-z str1 # str1 is null (has length 0) + +# FILES + +-a file # file exists +-d file # file exists and is a directory +-e file # file exists; same -a +-f file # file exists and is a regular file (i.e., not a directory or other special type of file) +-r file # you have read permission +-s file # file exists and is not empty +-w file # your have write permission +-x file # you have execute permission on file, or directory search permission if it is a directory +-N file # file was modified since it was last read +-O file # you own file +-G file # file's group ID matches yours (or one of yours, if you are in multiple groups) +file1 -nt file2 # file1 is newer than file2 +file1 -ot file2 # file1 is older than file2 + +# NUMBERS + +-lt # less than +-le # less than or equal +-eq # equal +-ge # greater than or equal +-gt # greater than +-ne # not equal + +if condition +then + statements +[elif condition + then statements...] +[else + statements] +fi + +for x in {1..10} +do + statements +done + +for name [in list] +do + statements that can use $name +done + +for (( initialisation ; ending condition ; update )) +do + statements... +done + +case expression in + pattern1 ) + statements ;; + pattern2 ) + statements ;; +esac + +select name [in list] +do + statements that can use $name +done + +while condition; do + statements +done + +until condition; do + statements +done + +############################################################################## +# COMMAND-LINE PROCESSING CYCLE +############################################################################## + + +# The default order for command lookup is functions, followed by built-ins, with scripts and executables last. +# There are three built-ins that you can use to override this order: `command`, `builtin` and `enable`. + +command # removes alias and function lookup. Only built-ins and commands found in the search path are executed +builtin # looks up only built-in commands, ignoring functions and commands found in PATH +enable # enables and disables shell built-ins + +eval # takes arguments and run them through the command-line processing steps all over again + + +############################################################################## +# INPUT/OUTPUT REDIRECTORS +############################################################################## + + +cmd1|cmd2 # pipe; takes standard output of cmd1 as standard input to cmd2 +< file # takes standard input from file +> file # directs standard output to file +>> file # directs standard output to file; append to file if it already exists +>|file # forces standard output to file even if noclobber is set +n>|file # forces output to file from file descriptor n even if noclobber is set +<> file # uses file as both standard input and standard output +n<>file # uses file as both input and output for file descriptor n +n>file # directs file descriptor n to file +n>file # directs file description n to file; append to file if it already exists +n>& # duplicates standard output to file descriptor n +n<& # duplicates standard input from file descriptor n +n>&m # file descriptor n is made to be a copy of the output file descriptor +n<&m # file descriptor n is made to be a copy of the input file descriptor +&>file # directs standard output and standard error to file +<&- # closes the standard input +>&- # closes the standard output +n>&- # closes the ouput from file descriptor n +n<&- # closes the input from file descripor n + + +############################################################################## +# PROCESS HANDLING +############################################################################## + + +# To suspend a job, type CTRL+Z while it is running. You can also suspend a job with CTRL+Y. +# This is slightly different from CTRL+Z in that the process is only stopped when it attempts to read input from terminal. +# Of course, to interrupt a job, type CTRL+C. + +myCommand & # runs job in the background and prompts back the shell + +jobs # lists all jobs (use with -l to see associated PID) + +fg # brings a background job into the foreground +fg %+ # brings most recently invoked background job +fg %- # brings second most recently invoked background job +fg %N # brings job number N +fg %string # brings job whose command begins with string +fg %?string # brings job whose command contains string + +kill -l # returns a list of all signals on the system, by name and number +kill PID # terminates process with specified PID + +ps # prints a line of information about the current running login shell and any processes running under it +ps -a # selects all processes with a tty except session leaders + +trap cmd sig1 sig2 # executes a command when a signal is received by the script +trap "" sig1 sig2 # ignores that signals +trap - sig1 sig2 # resets the action taken when the signal is received to the default + +disown # removes the process from the list of jobs + +wait # waits until all background jobs have finished + + +############################################################################## +# TIPS & TRICKS +############################################################################## + + +# set an alias +cd; nano .bash_profile +> alias gentlenode='ssh admin@gentlenode.com -p 3404' # add your alias in .bash_profile + +# to quickly go to a specific directory +cd; nano .bashrc +> shopt -s cdable_vars +> export websites="/Users/mac/Documents/websites" + +source .bashrc +cd $websites + + +############################################################################## +# DEBUGGING SHELL PROGRAMS +############################################################################## + + +bash -n scriptname # don't run commands; check for syntax errors only +set -o noexec # alternative (set option in script) + +bash -v scriptname # echo commands before running them +set -o verbose # alternative (set option in script) + +bash -x scriptname # echo commands after command-line processing +set -o xtrace # alternative (set option in script) + +trap 'echo $varname' EXIT # useful when you want to print out the values of variables at the point that your script exits + +function errtrap { + es=$? + echo "ERROR line $1: Command exited with status $es." +} + +trap 'errtrap $LINENO' ERR # is run whenever a command in the surrounding script or function exits with non-zero status + +function dbgtrap { + echo "badvar is $badvar" +} + +trap dbgtrap DEBUG # causes the trap code to be executed before every statement in a function or script +# ...section of code in which the problem occurs... +trap - DEBUG # turn off the DEBUG trap + +function returntrap { + echo "A return occurred" +} + +trap returntrap RETURN # is executed each time a shell function or a script executed with the . or source commands finishes executing \ No newline at end of file diff --git a/c/c.md b/c/c.md new file mode 100644 index 000000000..2622856b6 --- /dev/null +++ b/c/c.md @@ -0,0 +1,164 @@ +1. [HPC User Wiki](index.html) +2. [NREL HPC User Community + Wiki](NREL-HPC-User-Community-Wiki_15171667.html) +3. [Tips and Tricks](Tips-and-Tricks_18593769.html) + + HPC User Wiki : C Programs +=========================== + +Created by Southerland, Jennifer on 2018-01-23 + +Compiling and Running C Programs on the Peregrine System +======================================================== + +### Simple "Hello, world" Program + +Follow these instructions to compile and run your first programs written +in C on Peregrine. + +Copy this text to a file named hello\_world.c with your favorite text +editor (nano, vi, emacs, etc.). + + /* C Example */ + #include + + int main (argc, argv) +    int argc; +    char *argv[]; + { +    printf( "Hello, world \n" ); +    return 0; + } + +Compile this program using the Intel C compiler, icc: + + $ icc -o hello_world hello_world.c + +The compiler will create a Linux executable file called hello\_world. + +To run this program, use your editor to create a job script containing +the following text: + + #!/bin/bash -l + #PBS -j oe + #PBS -N job_hello_world + #PBS -l walltime=01:00:00 + #PBS -l nodes=1 + + # this ensures your job runs from the directory from which you run the qsub command + cd $PBS_O_WORKDIR + + ./hello_world + +Give the file a name like hello\_world.sh. + +Submit the script using the qsub command and a valid project handle. +Because this is a very quick job, let's submit it to the "short" queue. + + $ qsub -q short -A CSC000 hello_world.sh + +The output from this job is in a file with the name +job\_hello\_world.o<JID> where JID is the job id. You can see the +contents of that file using the "cat" command: + + [icarpent@login4 ~]$ cat job_hello_world.o1112070 + Warning: no access to tty (Bad file descriptor). + Thus no job control in this shell. + Hello, world + +### Parallel "Hello, world" Program + +For this example, we'll use MPI to write a parallel Hello World program +written in C. The Message Passing Interface (MPI)( is one way to create +programs that run on more than one processor. + +Copy this text to a file named hello\_world.c with your favorite text +editor (vi, emacs, etc.)  If you are not familiar with text editors, try +"nano hello\_world.c" + + /* C Example */ + #include + #include   + + + int main (argc, argv) +    int argc; +    char *argv[]; + { +    int rank, size; +    MPI_Init (&argc, &argv); /* starts MPI */ +    MPI_Comm_rank (MPI_COMM_WORLD, &rank);     /* get current process id */ +    MPI_Comm_size (MPI_COMM_WORLD, &size);     /* get number of processes */ + +    printf( "Hello, world from process %d of %d\n", rank, size ); + +    MPI_Finalize(); +    return 0; + } + +Compile this program using mpicc, which is a C compiler that knows about +MPI. + + mpicc hello_world.c -o hello_world + +The compiler will create a linux executable file called hello\_world. + +### Running your Parallel “Hello, world” program + +Peregrine is a cluster: a collection of computers connected together +with a special network (InfiniBand in this case) and software (Torque) +that allows a single program to run across multiple physical computers. +Create a submit script which contains options for torque, including the +number of nodes you want your parallel program to run on and +instructions for how to start the parallel program. For example, create +a file named **hello.qsub** with the contents below. + + #!/bin/bash -l + #PBS -j oe + #PBS -N job_hello_world + #PBS -l walltime=01:00:00 + #PBS -l nodes=2                 # this asks for 2 nodes  + + # this ensures your job runs from the directory from which you run the qsub command + cd $PBS_O_WORKDIR + set -x + + mpirun -np 32 ./hello_world >& my_results.out + +Because this is an MPI program, we execute it using the mpirun command +and we tell it how many processors to run it on with the -np option. In +this case we have told the system to run the hello\_world program on 32 +processors.  The nodes assigned to your job will have either 16 or 24 +processors so to use 32 we have asked for 2 nodes. The system will use +some processors on the first node and some on the second node. Each +processor will run the program and print a line of output. + +Once you've saved this file, next create your run directory in /scratch +using the mkdir command and copy your program and job script to it. + + $ mkdir /scratch/$USER/hello + $ cp hello_world /scratch/$USER/hello + $ cp hello.qsub /scratch/$USER/hello + +Go to this directory using the cd command: + + $ cd /scratch/$USER/hello + +Now, submit your job script using the qsub command with a valid project +handle: + + $ qsub hello.qsub -A project-handle + +The job will run, then you should see an output file named +"my\_results.out" with one line of output from each MPI process. + + [kregimba@login1 hello]$ cat my_results.out + Hello world from process 14 of 32 + Hello world from process 30 of 32 + ... + Hello world from process 26 of 32 + [kregimba@login1 hello]$ + +Document generated by Confluence on 2019-04-03 10:15 + +[Atlassian](http://www.atlassian.com/) diff --git a/fortran/fortran.md b/fortran/fortran.md new file mode 100644 index 000000000..5859d7795 --- /dev/null +++ b/fortran/fortran.md @@ -0,0 +1,68 @@ +1. [HPC User Wiki](index.html) +2. [NREL HPC User Community + Wiki](NREL-HPC-User-Community-Wiki_15171667.html) +3. [Tips and Tricks](Tips-and-Tricks_18593769.html) + + HPC User Wiki : Fortran Programs +================================= + +Created by Southerland, Jennifer, last modified on 2018-01-23 + +Compiling and Running Fortran Programs on the Peregrine System +============================================================== + +Follow these instructions to compile and run your Fortran program on +Peregrine. + +Create Program +-------------- + +Using a text editor such as nano, vi or emacs, create a file called +hello.F90. + +If you don't already know how to use a text editor, we suggest you learn +to use nano. To create the file named hello.F90, enter the following +command on the login node on Peregrine: + + $ nano hello.F90 + +This will start the nano program, which will allow you to type text into +the file. Commands to tell nano what to do are located at the bottom of +your screen. The ^ symbol means to hold the Control key while you type +the letter, so ^o (pronounced "control-o") is entered by holding the +control key and the o key at the same time. + +Enter the following text, being careful to include the spaces and +symbols as shown: + + program hello + write(6,*)'hello, world' + stop + end program hello + +Save this file by entering ^o. Exit nano by entering ^x. + +Compile Program +--------------- + +To convert your program from a human-readable language like Fortran +(which is used in the example above) to the language used inside the +computer, a program called a "compiler" is used. Peregrine has several +different compilers for each commonly used language. For this example, +we will use the compilers that are developed by Intel. The command used +to run the Intel Fortran compiler is "ifort". To run it on the file you +just created, type + + $ ifort -o hello hello.F90 + +The -o hello part of the command tells the compiler to store its output +in a file called hello. This file contains the program that will execute +on the computer. + +Execute this program with the following command: + + $ ./hello + +Document generated by Confluence on 2019-04-03 10:15 + +[Atlassian](http://www.atlassian.com/) diff --git a/git/README.md b/git/README.md new file mode 100644 index 000000000..4b7a58150 --- /dev/null +++ b/git/README.md @@ -0,0 +1,17 @@ +# Git + +To begin, let's start by clearing up some common misconceptions about git. You probably have heard of git through the popular git-repository hosting web-service [GitHub](https://github.com). GitHub (the the hosting service) is to git (the open-source version control software) what the internet is to computers—git is used locally to track incremental development and modifications to a collection of files, and GitHub gets those changes to serve as a synchronized, common access point. GitHub also has social aspects, like tracking who changed what and why. There are other git hosting services like [GitLab](https://gitlab.com) which are similar to GitHub but offer slightly different features. + +The git workflow has some pretty colorful vocabulary, so let's define some of the terms to avoid confusion going forward: +* **Repository/repo**: A git repository is an independent grouping of files to be tracked. A git repo has a "root" which is the directory that it sits in, and tracks further directory nesting from that. A single repo is often thought of as a complete project or application, though it's not uncommon to nest modules of an application as child repositories to isolate the development history of those submodules. + +* **Commit**: A commit, or "revision", is an individual change to a file (or set of files). It's like when you save a file, except with Git, every time you save it creates a unique ID (a.k.a. the "SHA" or "hash") that allows you to keep record of what changes were made when and by who. Commits usually contain a commit message which is a brief description of what changes were made. + +* **Fork**: A fork is a personal copy of another user's repository that lives on your account. Forks allow you to freely make changes to a project without affecting the original. Forks remain attached to the original, allowing you to submit a pull request to the original's author to update with your changes. You can also keep your fork up to date by pulling in updates from the original. + +* **Pull**: Pull refers to when you are fetching in changes and merging them. For instance, if someone has edited the remote file you're both working on, you'll want to pull in those changes to your local copy so that it's up to date. + +* **Pull request:** Pull requests are proposed changes to a repository submitted by a user and accepted or rejected by a repository's collaborators. Like issues, pull requests each have their own discussion forum. For more information, see "About pull requests." + +* **Push**: Pushing refers to sending your committed changes to a remote repository, such as a repository hosted on GitHub. For instance, if you change something locally, you'd want to then push those changes so that others may access them. + diff --git a/markdown/README.md b/markdown/README.md new file mode 100644 index 000000000..16c15b19e --- /dev/null +++ b/markdown/README.md @@ -0,0 +1,5 @@ +# Markdown + +These documents are quite literally self-explanitory. You can compare the raw contents of `.md` files here to how they appear when rendered to see what the relatively minimal set of markdown syntax results in when converted to mark*up*. + +Simply follow along with the [template file](template.md) which will showcase most common Markdown features and link to the other markdown files in this directory at relevant points to demonstrate the linking feature. That's honestly all you need to get up and running with Markdown, it's designed to be simple to learn and use! diff --git a/markdown/RenameStep1.md b/markdown/RenameStep1.md new file mode 100644 index 000000000..4afa9a9fb --- /dev/null +++ b/markdown/RenameStep1.md @@ -0,0 +1,7 @@ +## Consider using heading levels to signify a breadcrumb trail of topics. + +This content is more to summarize formatting considerations, and possibly a general organization for how content might be laid out. +Naturally, this will need to be adapted to the training or tutorial at hand. + +A reasonable high-level layout is to use the top-level README.md as a master navigation, with a list of sequential steps to be followed that are linked to their respective detailed documents. + diff --git a/markdown/RenameStep2.md b/markdown/RenameStep2.md new file mode 100644 index 000000000..bd413260c --- /dev/null +++ b/markdown/RenameStep2.md @@ -0,0 +1,18 @@ +## Consider using heading levels to signify a breadcrumb trail of topics. + +* Each top-level step should be relatively self-contained, and ideally persistent. So, install/setup/build/etc. are good, since one can leave off after one step, and pick right up at the next one. +* If possible, transient results like login/get-a-compute-node/etc. would be grouped under a larger topic to signify that one will have to start over again if all list items at that nested level aren't completed as a unit. + +### Example + +1. Obtain an account on NREL HPC +2. Install X and Y locally. +3. Prepare the Z environment on Peregrine + a. Login to Peregrine + b. View software and get access to a compute node + c. First-time setup for Z on Peregrine +4. Run example 1. +5. Run example 2. +6. Visualize examples 1 and 2. + + diff --git a/markdown/template.md b/markdown/template.md new file mode 100644 index 000000000..c673eeda9 --- /dev/null +++ b/markdown/template.md @@ -0,0 +1,55 @@ +# Level 1 heading for the top-level page on the topic. +A one-sentence summary of paragraph text, summarizing the purpose of the training or tutorial. + +1. [Summary of step #1](RenameStep1.md) + +2. [Summary of step #2](RenameStep2.md) + +## Sometimes you might need a level-2 heading! If not, delete this. +### Sometimes you might need a level-3 heading! If not, delete this. +#### And so forth. + +*Italic* text is considered emphasis, and uses _single_ asterisks or underscores. +**Bold** text is considered strong emphasis, and uses __double__ asterisks or underscores. +Emphases _can be **combined**_. +~~Strikethrough~~ text can be used inline if needed. + +* Unordered +- lists + * are + - easy +* to make, if you take note of nested bullet alignment with the previous line in the plaintext file (in, e.g., vi). +- (As you can see, the characters you use as bullets are irrelevant to the renderer on Github.) + +1. Ordered +2. lists + a. number + b. themselves (sometimes you'll need to add extra spaces after list items, otherwise + c. separate items may render as concatenated). +3. when rendered, independent of what you type in raw text. + +If you've got a lot of natural language to quote, +> sometimes a block quote +> is best, terminated with a blank line. +> As with lists, add 2 spaces at the end of a line to force a line break. + +That is different from computer code, like +``` +git status # To find added or changed files. +git add +... +git commit -m 'Use comments to identify changes' +git push +``` + +On the other hand, `` can be useful as well. + +If for some reason a list of tasks is useful, +- [x] Make an unordered list with leading square brackets. +- [ ] Put a space in between the brackets for unfinished tasks. +- [x] Put an "x" in between the brackets for finished tasks. +- [ ] \(Escape leading parentheses with a backslash) + +:angry: Don't :collision: overdue :see_no_evil: it :trollface: with :clap: [emoji codes](https://www.webpagefx.com/tools/emoji-cheat-sheet/). + + diff --git a/paraview/rendering.md b/paraview/rendering.md new file mode 100644 index 000000000..76edc113d --- /dev/null +++ b/paraview/rendering.md @@ -0,0 +1,133 @@ +# High-quality rendering on peregrine with ParaView + +How to use batch ParaView with OSPRay to generate single frames and +animations on peregrine + +![](/assets/paraview.png) + +Step-by-step guide +------------------ + + + +1. Log on to a peregrine login node: + + ssh peregrine + +   + +2. Start an interactive session: + + qsub -A YOURALLOC -I + +   + +3. Once the session starts, load the appropriate modules: + + module purge + module load gcc/6.2.0 openmpi-gcc/2.0.1-6.2.0 python/2.7.6 paraview/5.4.1-compute + +   + +4. And start your render job: + + pvbatch --use-offscreen-rendering pvrender.py + +  + +Once you feel that your script is automated enough, start submitting +batch jobs. + +1. Prepare your script for `qsub`. A short job might look like this: + + #!/bin/bash + #PBS -A YOURALLOC + #PBS -l nodes=1:ppn=1 + #PBS -l walltime=0:01:00 + #PBS -q short + module purge + module load gcc/6.2.0 openmpi-gcc/2.0.1-6.2.0 python/2.7.6 paraview/5.4.1-compute + pvbatch --use-offscreen-rendering pvrender.py + +   + +2. Submit the job and wait: + + qsub batchrender.sh + +   + +Creating the ParaView python script +----------------------------------- + +Your ParaView python script can be made in a number of ways. The easiest +is to run a fresh session of ParaView (use version 5.x on your local +machine) and select "Tools→Start Trace," then "OK". Perform all the +actions you need to set your scene and save a screenshot. Then select +"Tools → Stop Trace" and save the resulting python script (we will use +`pvrender.py` in these examples). + +  + +Here are some useful components to add to your ParaView Python script. + +- Read the first command-line argument and use it to select a data + file to operate on. + + import sys + doframe = 0 + if len(sys.argv) > 1: +   doframe = int(sys.argv[1]) + infile = "output%05d.dat" % doframe + + Note that `pvbatch` will pass any arguments after the script name to + the script itself. So you can do the following to render frame 45: + + pvbatch --use-offscreen-rendering pvrender.py 45 + + But were you to use this in a `qsub` script, your script would need + to have the line + + pvbatch --use-offscreen-rendering pvrender.py $1 + + And you would need to submit the script as such: + + qsub -F "45" batchrender.sh + +   + +- Set the output image size to match FHD or UHD standards: + + renderView1.ViewSize = [3840, 2160] + renderView1.ViewSize = [1920, 1080] + +   + +- Enable OSPRay rendering and set parameters for high-quality output: + + renderView1.LightScale = 1.5 + renderView1.AmbientSamples = 4 + renderView1.SamplesPerPixel = 9 + renderView1.Shadows = 1 + renderView1.EnableOSPRay = 1 + +   + +- Don't forget to actually render the image! + + pngname = "image%05d.png" % doframe + SaveScreenshot(pngname, renderView1) + +  + +  + +Attachments: +------------ + +![](images/icons/bullet_blue.gif) +[frame0100\_img3sm.png](attachments/18594270/28148762.png) (image/png) + +Document generated by Confluence on 2019-04-03 10:15 + +[Atlassian](http://www.atlassian.com/) diff --git a/slurm/README.md b/slurm/README.md new file mode 100644 index 000000000..02cf1f507 --- /dev/null +++ b/slurm/README.md @@ -0,0 +1,5 @@ +# Sample Slurm Batch Scripts + +A showcase various programflow techniques by leveraging bash and slurm features. + +* [`multinode-task-per-core.sh`](./multinode-task-per-core.sh) - Example of mapping process execution to each core on an arbitrary amount of nodes. \ No newline at end of file diff --git a/slurm/multinode-task-per-core.sh b/slurm/multinode-task-per-core.sh new file mode 100644 index 000000000..3ac93d2dd --- /dev/null +++ b/slurm/multinode-task-per-core.sh @@ -0,0 +1,49 @@ +#!/usr/bin/env bash + +: 'By Michael Bartlett + +Example of mapping an echo command to each core on an arbitrary amount +of nodes using slurm. Each node on Eagle has 36 cores, so there should +be an entry for 36 * N CPU ranks in the job output. + +USAGE: sbatch –A -N multinode-task-per-core.sh +' + +#SBATCH --nodes=2 # Change this number to get different outputs +#SBATCH -t 1 +#SBATCH --job-name=node_rollcall +#SBATCH -o node_rollcall.%j # output to node_rollcall. + +PROCS=$(($SLURM_NNODES * $SLURM_CPUS_ON_NODE)) # Number of CPUs * number of nodes + +# Master node in jobs with N > 1 runs these +echo "I am node $SLURMD_NODENAME and I am the master node of this job with ID $SLURM_NODEID" +echo "There are $SLURM_NNODES nodes in this job, and each has $SLURM_CPUS_ON_NODE cores, for a total of $PROCS cores." +printf "Let's get each node in the job to introduce itself:\n\n" + +# Send an in-line bash script to each node to run. The single quotes prevent $var evaluation. +# `srun` uses all resources by default +srun bash <<< 'printf "\tI am $SLURMD_NODENAME, my ID for this job is $SLURM_NODEID\n"' & +wait + +# Do the same, but get each node to get each core to print its "rank" (unique index) +printf "\nLet's get each node to print the ranks of all their cores (concurrently!):\n\n" +srun --ntasks=$PROCS \ + bash <<< 'printf "n${SLURM_NODEID}:c"; awk "{print \$39}" /proc/self/stat' | tr '\n' ' ' +echo + + +################################################################### +: "Example Output + +I am node r5i0n13 and I am the master node of this job with ID 0 +There are 2 nodes in this job, and each has 36 cores, for a total of 72 cores. +Let's get each node in the job to introduce itself: + + I am r5i0n14, my ID for this job is 1 + I am r5i0n13, my ID for this job is 0 + +Let's get each node to print the ranks of all their cores (concurrently!): + +n1:c32 n0:c19 n0:c22 n1:c0 n0:c23 n1:c3 n0:c6 n1:c24 n0:c24 n1:c27 n0:c25 n1:c26 n0:c26 n1:c4 n0:c2 n1:c8 n0:c8 n1:c9 n0:c0 n1:c2 n0:c4 n1:c5 n0:c21 n1:c19 n0:c20 n1:c23 n0:c18 n1:c6 n0:c10 n1:c7 n0:c29 n0:c28 n0:c14 n0:c13 n0:c30 n0:c27 n1:c21 n0:c12 n1:c28 n0:c7 n0:c1 n0:c5 n0:c31 n1:c11 n1:c13 n1:c33 n1:c1 n1:c25 n0:c3 n1:c30 n1:c31 n1:c14 n1:c20 n1:c29 n1:c12 n1:c18 n1:c22 n1:c10 n1:c15 n0:c9 n0:c32 n0:c11 n0:c17 n0:c16 n0:c15 n1:c17 n0:c34 n1:c35 n1:c34 n1:c16 n0:c33 n0:c35 +" \ No newline at end of file diff --git a/stream_benchmark/README.md b/stream_benchmark/README.md new file mode 100644 index 000000000..19d02ddb8 --- /dev/null +++ b/stream_benchmark/README.md @@ -0,0 +1,3 @@ +# STREAM Benchmark + +This module will guide you through the process of running the STREAM benchmark on Eagle. Start by opening the [StreamTutorial](StreamTutorial.ipynb) notebook for a step-by-step walkthrough of the source code, compilation process, and results discussion. \ No newline at end of file diff --git a/stream_benchmark/StreamTutorial.ipynb b/stream_benchmark/StreamTutorial.ipynb new file mode 100644 index 000000000..302259fc4 --- /dev/null +++ b/stream_benchmark/StreamTutorial.ipynb @@ -0,0 +1,351 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# HPC Benchmarking\n", + "\n", + "A common way to characterize the performance of a high-performance computer (HPC) is to run computational benchmarks. These standardized tests are typically designed to stress and measure the performance of different features of the HPC hardware. Generally, there are three different areas that can be tested independently:\n", + "\n", + "1. CPU\n", + "2. **Memory**\n", + "3. Network\n", + "\n", + "In this tutorial, we'll focus on performing and interpreting a memory-intensive test using the STREAM benchmark. We'll also attempt to characterize what happens to the performance as we utilize different configurations of the available HPC hardware.\n", + "\n", + "## The STREAM Benchmark\n", + "\n", + "The STREAM benchmark is a straightforward algorithm that tests the speed at which simple operations can be carried out on a very memory-intensive vector. The four vector operations being iterated are (1) copying, (2) scaling, (3) addition, and (4) a combination of all three, the \"triad\".\n", + "\n", + "| Operation | Sample | Flops |\n", + "|-----------|-----------------------------|--------|\n", + "| Copying | `c[j] = a[j]` | 0 |\n", + "| Scaling | `b[j] = scalar*c[j]` | 1 |\n", + "| Addition | `c[j] = a[j] + b[j]` | 1 |\n", + "| Triad | `a[j] = b[j] + scalar*c[j]` | 2 |\n", + "\n", + "As you can see in the table above, the computational complexity of these operations is quite low. It's important to reiterate that the STREAM benchmark is primarily focused on testing the effects of a memory-intensive operation, *not* a CPU-intensive calculation. The end results of the STREAM benchmark aren't actually the four vectors being computed above; instead, the results are the time it takes to execute these simple operations. The key components of the algorithm and timing steps are printed below.\n", + "\n", + "```C\n", + "for (k=0; k\n", + "\n", + "
\n", + "What about multi-core? For simplicity, the OpenMP commands that parallelize the for loops have been omitted from the example code shown above. The actual source code in stream.c includes all directives for compiling a parallel version of the STREAM benchmark, and can be run on different configurations of cores as shown in the following examples.\n", + "
\n", + "\n", + "## Compiling STREAM\n", + "\n", + "To begin, copy the entire `stream_benchmark` directory to your HPC account (Don't have an account? __[Get one here.](https://www.nrel.gov/hpc/user-accounts.html)__). Once the copying step is finished, navigate to the `stream_benchmark` folder and execute the following compilation commands\n", + "\n", + "`module purge`\n", + "\n", + "`module load intel-mpi`\n", + "\n", + "`icc -o stream_omp -qopenmp stream.c`\n", + "\n", + "In the first line, we purge any previously-loaded modules to ensure this test starts with a blank slate. In the second line, we load the Intel compiler we'll be using to create the stream executable. In the third line, we compile the code using the Intel compiler (icc) which creates an executable, `stream_omp`, from the code contained in `stream.c` to run in parallel using OpenMP.\n", + "\n", + "## Running the benchmark\n", + "\n", + "To run the example, first obtain an interactive debugging node on Eagle (`srun -A -t