Conda-Build Documentation Release 3.21.5+15.G174ed200.Dirty
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Hsafew2019 S2b.Pdf
How to work with SSM products From Download to Visualization Apostolos Giannakos Zentralanstalt für Meteorologie und Geodynamik (ZAMG) https://www.zamg.ac.at 1 Topics • Overview • ASCAT SSM NRT Products • ASCAT SSM CDR Products • Read and plot ASCAT SSM NRT Products • Read and plot ASCAT SSM CDR Products • Summary 2 H SAF ASCAT Surface Soil Moisture Products ASCAT SSM Near Real-Time (NRT) products – NRT products for ASCAT on-board Metop-A, Metop-B, Metop-C – Swath orbit geometry – Available 130 minutes after sensing – Various spatial resolutions • 25 km spatial sampling (50 km spatial resolution) • 12.5 km spatial sampling (25-34 km spatial resolution) • 0.5 km spatial sampling (1 km spatial resolution) ASCAT SSM Climate Data Record (CDR) products – ASCAT data merged for all Metop (A, B, C) satellites – Time series format located on an Earth fixed DGG (WARP5 Grid) – 12.5 km spatial sampling (25-34 km spatial resolution) – Re-processed every year (in January) – Extensions computed throughout the year until new release 3 Outlook: Near real-time surface soil moisture products CDOP3 H08 - SSM ASCAT NRT DIS Disaggregated Metop ASCAT NRT SSM at 1 km (pre-operational)* H101 - SSM ASCAT-A NRT O12.5 Metop-A ASCAT NRT SSM orbit 12.5 km sampling (operational) H102 - SSM ASCAT-A NRT O25 Metop-A ASCAT NRT SSM orbit 25 km sampling (operational) H16 - SSM ASCAT-B NT O12.5 Metop-B ASCAT NRT SSM orbit 12.5 km sampling (operational) H103 - SSM ASCAT-B NRT O25 Metop-B ASCAT NRT SSM orbit 25 km sampling (operational) 4 Architecture of ASCAT SSM Data Services -
What If What I Need Is Not in Powerai (Yet)? What You Need to Know to Build from Scratch?
IBM Systems What if what I need is not in PowerAI (yet)? What you need to know to build from scratch? Jean-Armand Broyelle June 2018 IBM Systems – Cognitive Era Things to consider when you have to rebuild a framework © 2017 International Business Machines Corporation 2 IBM Systems – Cognitive Era CUDA Downloads © 2017 International Business Machines Corporation 3 IBM Systems – Cognitive Era CUDA 8 – under Legacy Releases © 2017 International Business Machines Corporation 4 IBM Systems – Cognitive Era CUDA 8 Install Steps © 2017 International Business Machines Corporation 5 IBM Systems – Cognitive Era cuDNN and NVIDIA drivers © 2017 International Business Machines Corporation 6 IBM Systems – Cognitive Era cuDNN v6.0 for CUDA 8.0 © 2017 International Business Machines Corporation 7 IBM Systems – Cognitive Era cuDNN and NVIDIA drivers © 2017 International Business Machines Corporation 8 IBM Systems – Cognitive Era © 2017 International Business Machines Corporation 9 IBM Systems – Cognitive Era © 2017 International Business Machines Corporation 10 IBM Systems – Cognitive Era cuDNN and NVIDIA drivers © 2017 International Business Machines Corporation 11 IBM Systems – Cognitive Era Prepare your environment • When something goes wrong it’s better to Remove local anaconda installation $ cd ~; rm –rf anaconda2 .conda • Reinstall anaconda $ cd /tmp; wget https://repo.anaconda.com/archive/Anaconda2-5.1.0-Linux- ppc64le.sh $ bash /tmp/Anaconda2-5.1.0-Linux-ppc64le.sh • Activate PowerAI $ source /opt/DL/tensorflow/bin/tensorflow-activate • When you -
Python Default File Format for Download Download Files with Progress in Python
python default file format for download Download files with progress in Python. This is a coding tip article. I will show you how to download files with progress in Python. The sauce here is to make use of the wget module. First, install the module into the environment. The wget module is pretty straight-forward, only one function to access, wget.download() . Let say we want to download this file http://download.geonames.org/export/zip/US.zip, the implementation will be following: The output will look like this: As you can see, it prints out the progress bar for us to know the progress of downloading, with current bytes retrieved with total bytes. The s econd parameter is to set output filename or directory for output file. There is another parameter, bar=callback(current, total, width=80) . This is to define how the progress bar is rendered to output screen. Canonical specification. The canonical version of the wheel format specification is now maintained at https://packaging.python.org/specifications/binary-distribution-format/ . This may contain amendments relative to this PEP. Abstract. This PEP describes a built-package format for Python called "wheel". A wheel is a ZIP-format archive with a specially formatted file name and the .whl extension. It contains a single distribution nearly as it would be installed according to PEP 376 with a particular installation scheme. Although a specialized installer is recommended, a wheel file may be installed by simply unpacking into site-packages with the standard 'unzip' tool while preserving enough information to spread its contents out onto their final paths at any later time. -
Using the GNU Compiler Collection (GCC)
Using the GNU Compiler Collection (GCC) Using the GNU Compiler Collection by Richard M. Stallman and the GCC Developer Community Last updated 23 May 2004 for GCC 3.4.6 For GCC Version 3.4.6 Published by: GNU Press Website: www.gnupress.org a division of the General: [email protected] Free Software Foundation Orders: [email protected] 59 Temple Place Suite 330 Tel 617-542-5942 Boston, MA 02111-1307 USA Fax 617-542-2652 Last printed October 2003 for GCC 3.3.1. Printed copies are available for $45 each. Copyright c 1988, 1989, 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004 Free Software Foundation, Inc. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with the Invariant Sections being \GNU General Public License" and \Funding Free Software", the Front-Cover texts being (a) (see below), and with the Back-Cover Texts being (b) (see below). A copy of the license is included in the section entitled \GNU Free Documentation License". (a) The FSF's Front-Cover Text is: A GNU Manual (b) The FSF's Back-Cover Text is: You have freedom to copy and modify this GNU Manual, like GNU software. Copies published by the Free Software Foundation raise funds for GNU development. i Short Contents Introduction ...................................... 1 1 Programming Languages Supported by GCC ............ 3 2 Language Standards Supported by GCC ............... 5 3 GCC Command Options ......................... -
Bash Shell Scripts
Bash Shell Scripts Writing Bash shell scripts Bash shell scripts are text files Text files most efficiently built with programming editors (emacs or vi) File must be executable and in search path chmod 700 my_script PATH environment variable may not include .! An example shell script: #!/bin/bash #My first script echo "Hello World!" Bash Shell Scripts Writing Bash shell scripts Compile a Verilog file with vlog #!/bin/bash if [ ! d work ] ; then echo work does not exist, making it vlib work fi if [ ! s adder.v ] ; then vlog adder.v fi work directory must exist before compilation Get scripts via wget, eg: wget http://web.engr.oregonstate.edu/~traylor/ece474/script --- Bash Shell Scripts Writing Bash shell scripts File attribute checking #!/bin/bash if [ ! s junk_dir ] ; then mkdir junk_dir fi Spaces around brackets are needed! File attribute checking d exists and is a directory e, a file exists f exists and is a regular file s file exists and is not empty --- Bash Shell Scripts Writing Bash shell scripts Compile Verilog then run a simultion #!/bin/bash if [ ! -d "work" ] ; then vlib work fi if [ -s "adder.v" ] ; then vlog adder.v #runs simulation with a do file and no GUI vsim adder -do do.do quiet c else echo verilog file missing fi --- Bash Shell Scripts Writing Bash shell scripts vsim command and arguments vsim entity_name do dofile.do quiet -c -quiet (do not report loading file messages) -c (console mode, no GUI) -do (run vsim from a TCL do file) +nowarnTFMPC (don’t warn about mismatched ports, scary) +nowarnTSCALE (don’t warn about timing mismatches) Try vsim help for command line arguements --- Bash Shell Scripts Writing Bash Shell Scripts (TCL Script) In another text file, we create a TCL script with commands for the simulator. -
Introduction to Linux by Lars Eklund Based on Work by Marcus Lundberg
Introduction to Linux By Lars Eklund Based on work by Marcus Lundberg ● What is Linux ● Logging in to UPPMAX ● Navigate the file system ● “Basic toolkit” What is Linux ● The Linux Operating system is a UNIX like UNIX compatible Operating system. ● Linux is a Kernel on which many different programs can run. The shell(bash, sh, ksh, csh, tcsh and many more) is one such program ● Linux has a multiuser platform at its base which means permissions and security comes easy. Many Flavours Connect to UPPMAX ● (Download XQuartz or other X11 server for Mac OS ) ● Linux and MacOS: – start Terminal – $ ssh -X [email protected] Connect to UPPMAX for windows users ● Download a X-server such as GWSL or X-ming or VcXsrv or an other of your choosing ● Install WSL and a Distribution such as ubuntu or a ssh program such as MobaXTerm ● Connect to $ ssh -X [email protected] Windows links ● https://sourceforge.net/projects/vcxsrv/ ● https://mobaxterm.mobatek.net/ ● https://opticos.github.io/gwsl/ ● https://sourceforge.net/projects/xming/ ● https://docs.microsoft.com/en-us/windows/wsl/install-wi n10 ● Don’t forget to update to wsl2 X11-forwarding graphics from the command line ● Graphics can be sent through the SSH connection you’re using to connect - Use ssh -Y or ssh -X ● MacOS users will need to install XQuartz. ● When starting a graphical program, a new window will open, but your terminal will be “locked”. - Run using & at the end to run it as a background proccess e.g. “gedit &” - Alternatively, use ctrl-z to put gedit to sleep and -
Conda Build Meta.Yaml
Porting legacy software packages to the Conda Package Manager Joe Asercion, Fermi Science Support Center, NASA/GSFC Previous Process FSSC Previous Process FSSC Release Tag Previous Process FSSC Release Tag Code Ingestion Previous Process FSSC Release Tag Code Ingestion Builds on supported systems Previous Process FSSC Release Tag Code Ingestion Push back Builds on changes supported systems Testing Previous Process FSSC Release Tag Code Ingestion Push back Builds on changes supported systems Testing Packaging Previous Process FSSC Release Release Tag Code Ingestion All binaries and Push back Builds on source made changes supported systems available on the FSSC’s website Testing Packaging Previous Process Issues • Very long development cycle • Difficult dependency • Many bottlenecks management • Increase in build instability • Frequent library collision errors with user machines • Duplication of effort • Large number of individual • Large download size binaries to support Goals of Process Overhaul • Continuous Integration/Release Model • Faster report/patch release cycle • Increased stability in the long term • Increased Automation • Increase process efficiency • Increased Process Transparency • Improved user experience • Better dependency management Conda Package Manager • Languages: Python, Ruby, R, C/C++, Lua, Scala, Java, JavaScript • Combinable with industry standard CI systems • Developed and maintained by Anaconda (a.k.a. Continuum Analytics) • Variety of channels hosting downloadable packages Packaging with Conda Conda Build Meta.yaml Build.sh/bld.bat • Contains metadata of the package to • Executed during the build stage be build • Written like standard build script • Contains metadata needed for build • Dependencies, system requirements, etc • Ideally minimalist • Allows for staged environment • Any customization not handled by specificity meta.yaml can be implemented here. -
Application of Bagit-Serialized Research Object Bundles for Packaging and Re-Execution of Computational Analyses
Application of BagIt-Serialized Research Object Bundles for Packaging and Re-execution of Computational Analyses Kyle Chard Bertram Ludascher¨ Thomas Thelen Computation Institute School of Information Sciences NCEAS University of Chicago University of Illinois at Urbana-Champaign University of California at Santa Barbara Chicago, IL Champaign, IL Santa Barbara, CA [email protected] [email protected] [email protected] Niall Gaffney Jarek Nabrzyski Matthew J. Turk Texas Advanced Computing Center Center for Research Computing School of Information Sciences University of Texas at Austin University of Notre Dame University of Illinois at Urbana-Champaign Austin, TX South Bend, IN Champaign, IL [email protected] [email protected] [email protected] Matthew B. Jones Victoria Stodden Craig Willisy NCEAS School of Information Sciences NCSA University of California at Santa Barbara University of Illinois at Urbana-Champaign University of Illinois at Urbana-Champaign Santa Barbara, CA Champaign, IL Champaign, IL [email protected] [email protected] [email protected] Kacper Kowalik Ian Taylor yCorresponding author NCSA Center for Research Computing University of Illinois at Urbana-Champaign University of Notre Dame Champaign, IL South Bend, IN [email protected] [email protected] Abstract—In this paper we describe our experience adopting and can be used for verification of computational reproducibil- the Research Object Bundle (RO-Bundle) format with BagIt ity, for example as part of the peer-review process. serialization (BagIt-RO) for the design and implementation of Since its inception, the Whole Tale platform has been “tales” in the Whole Tale platform. A tale is an executable research object intended for the dissemination of computational designed to bring together existing open science infrastructure. -
Luarocks Fostering an Ecosystem of Lua Modules
LuaRocks fostering an ecosystem of Lua modules Hisham Muhammad [email protected] @hisham_hm FOSDEM !"# $russels% $elgium &hat is LuaRocks 'ackage manager... like d(kg (a(t*get+% RPM% etc. like Ruby-ems, Python eggs, npm% C'/0% etc. ...for Lua e1tension modules written in Lua (.lua files) or ,inary modules (.so4.dll files) Fostering an ecosystem of Lua modules Some uni5ue challenges ...related to Lua as a language ...related to Lua as a community Lessons learned ...on building an ecosystem / one*slide introduction to Lua function process(filename, fn, ...) local f = io.open(filename) local rets = {} for line in f:lines() do rets[#rets+1] = { fn(line, ...) } end f:close() return rets end matches = process("file.txt", string.find, "foo") for i, match in ipairs(matches) do print(i, table.concat(match, ", ")) end / one*slide introduction to Lua function process(filename, fn, ...) local f = io.open(filename) local rets = {} o,6ects for line in f:lines() do rets[#rets+1] = { fn(line, ...) } end f:close() return rets end matches = process("file.txt", string.find, "foo") for i, match in ipairs(matches) do print(i, table.concat(match, ", ")) end / one*slide introduction to Lua function process(filename, fn, ...) local f = io.open(filename) local rets = {} for line in f:lines() do rets[#rets+1] = { fn(line, ...) } end f:close() return rets 3rst*class functions end matches = process("file.txt", string.find, "foo") for i, match in ipairs(matches) do print(i, table.concat(match, ", ")) end / one*slide introduction to Lua function process(filename, fn, ...) -
Real Time Operating Systems Rootfs Creation: Summing Up
Real Time Operating Systems RootFS Creation: Summing Up Luca Abeni Real Time Operating Systems – p. System Boot System boot → the CPU starts executing from a well-known address ROM address: BIOS → read the first sector on the boot device, and executes it Bootloader (GRUB, LILO, U-Boot, . .) In general, load a kernel and an “intial ram disk” The initial fs image isn’t always needed (example: netboot) Kernel: from arm-test-*.tar.gz Initial filesystem? Loaded in RAM without the kernel help Generally contains the boot scripts and binaries Real Time Operating Systems – p. Initial Filesystem Old (2.4) kernels: Init Ram Disk (initrd); New (2.6) kernels: Init Ram Filesystem (initramfs) Generally used for modularized disk and FS drivers Example: if IDE drivers and Ext2 FS are modules (not inside the kernel), how can the kernel load them from disk? Solution: boot drivers can be on initrd / initramfs The bootloader loads it from disk with the kernel The kernel creates a “fake” fs based on it Modules are loaded from it Embedded systems can use initial FS for all the binaries Qemu does not need a bootloader to load kernel and initial FS (-kernel and -initrd) Real Time Operating Systems – p. Init Ram Filesystem Used in 2.6 kernels It is only a RAM FS: no real filesystem metadata on a storage medium All the files that must populate the FS are stored in a cpio package (similar to tar or zip file) The bootloader loads the cpio file in ram At boot time, the kernel “uncompresses” it, creating the RAM FS, and populating it with the files contained in the archive The cpio archive can be created by using the cpio -o -H newc command (see man cpio) Full command line: find . -
R Markdown Cheat Sheet I
1. Workflow R Markdown is a format for writing reproducible, dynamic reports with R. Use it to embed R code and results into slideshows, pdfs, html documents, Word files and more. To make a report: R Markdown Cheat Sheet i. Open - Open a file that ii. Write - Write content with the iii. Embed - Embed R code that iv. Render - Replace R code with its output and transform learn more at rmarkdown.rstudio.com uses the .Rmd extension. easy to use R Markdown syntax creates output to include in the report the report into a slideshow, pdf, html or ms Word file. rmarkdown 0.2.50 Updated: 8/14 A report. A report. A report. A report. A plot: A plot: A plot: A plot: Microsoft .Rmd Word ```{r} ```{r} ```{r} = = hist(co2) hist(co2) hist(co2) ``` ``` Reveal.js ``` ioslides, Beamer 2. Open File Start by saving a text file with the extension .Rmd, or open 3. Markdown Next, write your report in plain text. Use markdown syntax to an RStudio Rmd template describe how to format text in the final report. syntax becomes • In the menu bar, click Plain text File ▶ New File ▶ R Markdown… End a line with two spaces to start a new paragraph. *italics* and _italics_ • A window will open. Select the class of output **bold** and __bold__ you would like to make with your .Rmd file superscript^2^ ~~strikethrough~~ • Select the specific type of output to make [link](www.rstudio.com) with the radio buttons (you can change this later) # Header 1 • Click OK ## Header 2 ### Header 3 #### Header 4 ##### Header 5 ###### Header 6 4. -
Installation Instructions
Installation instructions The following instructions should be quite detailed and easy to follow. If you nevertheless encounter a problem which you cannot solve for yourself, please write an email to Thomas Foesel. Note: the monospaced text in this section are commands which have to be executed in a terminal. • for Linux/Mac: The terminal is simply the system shell. The "#" at the start of the line indicates that root privileges are required (so log in as root via su, or use sudo if this is configured suitably), whereas the commands starting with "$" can be executed as a normal user. • for Windows: Type the commands into the Conda terminal which is part of the Miniconda installation (see below). Installing Python, Theano, Keras, Matplotlib and Jupyter In the following, we show how to install these packages on the three common operating systems. There might be alternative ways to do so; if you prefer another one that works for you, this is also fine, of course. • Linux ◦ Debian/Mint/Ubuntu/... 1. # apt-get install python3 python3-dev python3- matplotlib python3-nose python3-numpy python3-pip 2. # pip3 install jupyter keras Theano ◦ openSUSE 1. # zypper in python3 python3-devel python3- jupyter_notebook python3-matplotlib python3-nose python3-numpy-devel 2. # pip3 install Theano keras • Mac 2. Download the installation script for the Miniconda collection (make sure to select Python 3.x, the upper row). In the terminal, go into the directory of this file ($ cd ...) and run # bash Miniconda3-latest-MacOSX-x86_64.sh. 3. Because there are more recent Conda versions than on the website, update it via conda update conda.