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SOUTH DAKOTA
SCHOOL OF MINES
& TECHNOLOGY
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Syllabus, ATM 519 [Fall 2010] Computing Methods in Atmospheric Sciences
Who Where When
Reference Text
Chivers & Sleightholme,
Introduction to Programming with Fortran
Robbins:
UNIX in a Nutshell (I don't recommend the Linux version)
You should view these texts as reference manuals as much as you would
treat them like text books. My approach in this class also presumes that you
have a pressing need to learn Fortran quickly. The bare minimum skill set
needed to get you started will be "fast-tracked". Other skills that are not
frequently used in ad-hoc two-fisted programming will be tabled for later in
the class or set aside completely for you to teach yourself in the future.
Like many modern Fortran books, Introduction to Programming with
Fortran presumes that many readers will have previous experience with
other languages. We will also be treating the text mostly as an as-you-go
reference manual rather than a front-to-back reference text. I will assign
readings before class (typically at the end of the previous lecture) on various
topics, typically by chapter, but these will bounce about the text's natural
order to accommodate skills that I set as priorities. As such, you will
experience a goodly amount of foreshadowing and Fortran-by-Immersion as
you read through the pre-class prep where you will get a taste of things
before we formally introduce them.
Books on Reserve
To be determined
Scope of the Course
Catalog Entry:
(2-1) Prerequisite:
CSC
150 or equivalent.
Introduction to the Linux/UNIX operating system from the user’s
perspective.
Fundamentals of the Fortran 90/95 programming languages.
Introduction to scientific data formats commonly used in the meteorology
community (netCDF,
GRIB,
Climate and Forecast Metadata
Convention).
Additional material may include shell scripts, and visualization of
meteorological data using community based software (IDV,
NCAR Command
Language). This experimental course is a candidate for the ATM
MS
Techniques requirement but has not been formally established as
such.
Overview: Programming,
Data Smithing
and "Code Jockeying" and other aspects of Scientific Computing
are not things you learn in one
semester. It is a skill you accrue,
hone and develop throughout your career.
As such, the goal of this class is not to make you a scientific programmer
overnight or over four months. Rather, our goal is to make you
unafraid of making a working "two-fisted"
programming solution to most geosciences problem and likewise make you
unafraid
to "code dive"ť or otherwise jump into community code (or two-fistedly
programmed
code!) and make the necessary changes for your own agendas.
This class focuses on meteorologically-oriented
programming
using the Fortran family of programming languages. Fortran, while some
consider it to be dated, remains the lingua franca of scientific
computing and number crunching. Unfortunately it unfairly receives
bad
(and often rabidly prejudicial)
PR by people who are not number-crunchers, have never had, used nor
learned
Fortran, stopped looking at Fortran since Fortran 77, or simply have neither
realized nor
appreciated the upgrades in Fortran 90 and Fortran 95, as well as more recent
upgrades of Fortran 2003 (which have not fully yet percolated down to the
user community).
Some of these improvements include access to Object Oriented Programming
that
once again make Fortran very attractive to those working in Finite Element
Modeling. Moreover, many
small and even larger Computer Science programs lack the resources and
enrolments to support Fortran instruction at the introductory level, favoring
the C-family or Java. As meteorologists (and those students working
in
computational fluid dynamics and companion fields who wish to join us),
Fortran
is an important language to have ready to work for you.
In this
course, we wish to
familiarize you with Fortran 90 so as to reduce your learning curve later (or
now if you are working with MM5, WRF or other model code). Some screedy
goodness on the continued relevance and need for Fortran can be found
here.
Additionally, high performance computing is rarely
done in
the Windows with friendly workbenches by most users. It's done
in the
Linux/UNIX-family of OS environments. Therefore, we will be working
exclusively with Linux using the GNU family and Portland Group compilers for
Fortran.
Because meteorologically-based programming also
requires
specific constructs not seen in externally-offered programming courses, we
will
introduce you one such construct: the netCDF Application Programming
Interface
(API). This format is use in
observational, archival, and numerical weather prediction applications and is
one of the more widely used “standard data formats” along with WMO
GRIB.
Students will also learn how to develop data
products that
are readily sharable with the larger meteorological community through the
Climate and Forecast (CF) Metadata conventions.
Finally, we shall explore other programming and
computing
skills that are nice to have under your belt, such as how to write a simple
shell script, and work with some viewing/analysis software commonly used in
the
atmospheric sciences community that also follow language-based, not GUI-
based
formats.
Prerequisites and Qualification Standards
This course requires CSC 150 (Computer Science I) or
equivalent
study as a prerequisite. Students are expected to have previous
coursework in
programming (e.g., the C- or BASIC-families) but not the Fortran family.
Students whose programming coursework and work
experience already includes proficiency in Fortran 77/90/95 but are waiting
to learn netCDF and NCL may expect to
be drafted into assisting their peers and in the meanwhile should use this as
an opportunity to practice, perfect and upgrade their skillset. We are
not planning for this course
to replace coursework in the C-family of languages at the undergraduate
level
(CSC 150) since C is frequently used in meteorological code in concert with
Fortran programming elements, especially in areas of Input and Output.
We will presume that you have had some course work in programming
(e.g., C or
C++) but may be somewhat rusty at first due to time and lack of use of those
skills. We, therefore, will have a short period of repressed false
memory
therapy with some re-familiarization drills with you as we spin up to more
aggressive tasks. However, we wish to keep this period as short as
possible. Students will be expected to bring themselves up to speed by
investing significant time out of class to rebuild their computing skills
portfolio.
Current undergraduates wishing to enroll should interview with the
professor-in-charge the semester beforehand. Students with
"As" in CSC 150
will be permitted to enroll. Students with high "B"s (or
would have had
B+'s if the SD University System had a +/- system like Tech had in
the good
old days), will be need a short interview and short evaluation
of programming skills.
This class will be taught completely in the Linux/UNIX environment as
used
within IAS (Fedora and Mandriva).
We
will be working with the GNU Fortran (gfortran) and G95 compilers.
Commercial compilers (Portland Group) may also be used. This class
will
not use MPICH or OpenMPI. Students interested in learning parallel
programming,
as opposed to being an end user of parallel code (e.g., MM5 or WRF), may
wish to also consider
CSC
410/510 (Parallel Computing)
which also includes elements of Fortran.
Students, staff and faculty alike are also Strongly encouraged™ to
attend the Spring Semester offerings of Henry Neeman's Supercomputing in Plain
English. This class is offered every spring through our campus's
Access Grid node.
This course will count as an ATM MS
"Techniques"
course.
Anticipated Travel
I expect to be on Institute Travel on the following dates
13-20 September
04-08 October
25-29 October
You will be given activities to keep you sharp, abused and entertained during
these windows. At least one guest lecture is in the planning.
2010 Course Concepts and Take-home Skills
- Navigating the Linux/Unix Operating System (distributed through
the course)
- UNIX for Dummies 101,201,301,401 & 501 (the basics of
walking and working
around a "shell"ť)
- Typical Linux User Tasks
- Account maintenance
- Environment variables
- Working with a networked system, at work and from
home
- Understanding what is really where
- Archiving
- Efficient and responsible account use for community
systems
- GUI[s]
[K]SUX!:
Weaning you from the Graphical User Interface
- Terminal Linux Usage and the secure shell
- Navigating in a Linux shell
- Editing in "vi" (Linux's no-frills in-terminal
editor)
- GUI-oriented umbrella-drink editors (e.g., gedit, kwrite,
kedit,
nedit)
- Introduction to the basics of Fortran 90/95 and Two Fisted
Programming
- The Obligatory Starters (a.k.a., "The Most Important
Program You Will Ever
Write")
- Compiling Fortran programs with GNU's
gfortran
and/or
pgf90 on a
Linux system
- Sample Activity: "Hello Kitty!
Kill -9!
Kill -9!" "Hello World!"
- Variable Types and Simple Math Operations (including
intrinsic
functions)
- Variable Types, Implicit vs. Explicit Declarations (and
why you should default
to the latter!)
- Simple Arithmetic and Intrinsic Functions
- Sample Activity: Various Conversion Programs (Units,
Physical Properties, Etc)
- Intro to Input and Output and Intro to Arrays
- Console Input
- Formatted Output in Fortran
- Sample Activity: Interactive Conversion Programs
- Program Flow: If/Then/Else Blocks and Loops
- Arrays and how to manage them
- If/Then/Else Conditional Blocks
- Cases
- Do Loops and While Loops
- What will happen to you if we ever catch
you using a GOTO statement
- Other college-educated-stupid things we'd rather
you not do that you could
have gotten
away with in F77 if you knew you could have done it
- Sample Activity: Decisions and Multiple Line
I/O
- Sample Activity: Input a data field, Calculate its
Gradient, Output the Field - i.e., create a geostrophic wind vector set
- Characters and Strings
- Files and File-based I/O
- Reading and Writing to ASCII files
- Column(Fortran)-major vs. row(C)-major Arrays and
I/O
- Introduction to Binary Files and How Fortran binary I/O is
different than C-family
I/O
- Sample Activity: Read and Process ASCII Formatted Meteo
Data
- Functions, Subroutines and Modules
- Partitioning repeated or common tasks into functions
and
subroutines
- Creating a personal toolbox of support code
- Compiling and running a set of source code files using
a
simple Makefile
- Modules
- Sample Activity: Do all of the above in a demonstration
code
exercize
- Scientific Data Formats and Creating Meteorologically-Friendly Files
for
Colleagues and Applications
- Introduction to netCDF (your community's Common
Data
Format)
- The concept of self-describing files
- Dimensions, Variables, Attributes (Global and
Local) and
Data
- Common Data form Language (CDL) -- netCDF for
humans and
professors
- The netCDF Convention
- Dimensions, Attributes, Data and Globals
- The basic netCDF command line utilities:
ncdump and
ncgen
- Sample Activity: Crack a netCDF file into an ASCII
CDL file with ncdump, edit the CDL file, and rebuild the
"corrected" netCDF
file with ncgen.
- The Climate and Forecast (CF) Metadata Standard:
- Storage Conventions (t-z-y-x)
- Standardized Names
- Standardized Units
- Geospatial References and Horizontal/Vertical
Coordinates
- Programming with the netCDF API
- Sample Activity: Read/Edit/Create netCDFs file in
Fortran
- Sample Activity: Create a community-readable netCDF
File in
Fortran
(and why you may never want to use ncgen after this -
but you
will continue to worship ncdump)
- If you can do this. You should be
afraid of
NOTHING.
- WMO Gridded Binary (GRIB)
- The GRIB Product (Versions 1 and Versions 2)
- wgrib and wgrib2
- GRIB around the World! The devil everyone
knows, but
only in their native tounge.
- Sample Activity: Explore and Crack a GRIB file
NCAR Command Language (NCL)
- NCL File Input (GRIB and netCDF)
- Simple Plotting
- Mapping
- Color!
- Analysis
- NCL File Output (netCDF)
The BIG Measurable Goal of this Class : The Project Activity
- Solve a Meteorology Problem as Meteorologists (or
someone taking a class with Meteorologists)
- If you aren't a meteorologist, be your advisor's
abused graduate
student, for CREDIT!
Additional Material Time Permitting
- Simple shell scripts
- Two-fisted Makefiles
- A heads-up on Fortran 2003/2008, Earth System Modeling
Framework
(ESMF) APIs, and GRID Technologies
Grading
Lab Assignments (1/3)
Lab exercises will often be based on recent lectures and building off the
material learned in previous labs and lectures
Quizlets and Drills (1/3)
There will be staggered quizzes proficiency drills every two weeks (one week
topic quiz, one week drill)
Project (1/3)
Students will demonstrate proficiency in programming through a project that
ingests meteorological or climatological data, processes the data, and
outputs
the results in a community-readable NetCDF/CF compatible file.
Students from other academic divisions may be given an equivalent project
that
meets their discipline's equivalents and advisor's
expectations.
ADA Statement and Specific Special Needs
"Students with special needs
or requiring special accommodations should contact the instructor, (Bill
Capehart, at 394-1994) and/or the campus ADA coordinator, Jolie
McCoy,
at 394-1924 at the earliest opportunity."
SD School of
Mines Specifically for ATM
519: This course uses skills that require color
recognition, keyboard work and computer vision. Students with vision
problems
(e.g., color blindness) or any other possible impediment should bring these
issues to the professor ASAP so as to assess accommodation. Most
issues ought not prevent participation in the class.
SDSM&T Electronic Devices Policy
"Please turn off your cell phone before class starts. No text messaging
in class. No headphones. If you wish to use a laptop in this class for purposes
of note taking, that's great; however, you will be required to download
DyKnow software and then join
ATM 450 to activate. Any attempt to circumvent the DyKnow monitoring
system will be considered a form of cheating and a breach of academic
integrity. Note that according to
"Policy Governing Academic Integrity" in the SDSM&T
Undergraduate Catalog, the instructor of record for this course has discretion
of how acts of academic dishonesty are penalized, subject to the appeal
process, and that
"Penalties may range from requiring the student to repeat the work in
question to failure in the course" (72-73). No other use of any other
electronic/computer media is allowed during class time."
SD School of Mines
Specifically for ATM 519: As ATM upperclassmen
and
graduate students you are "on duty"
professionals in this course. I will treat you as such. Therefore,
cell phones on vibrate only under
reasonable (e.g., emergency) use. Instant Messaging and other
non-relevant, inappropriate and otherwise non-directed internet usage is
absolutely forbidden. The traditional "Old
School" Honor Code applies to programming assignments,
drills and projects, as well as account access and will be enforced. You
will be given a secure UNIX/LINUX account
for use with the IAS computing network. Observe all proper security
and
acceptable use policies, regarding access, internet use, general use, and disk
discipline. Any "Live OS" CDs issued in the class are for at-
home use
only. The unauthorized use of "Live OS" CDs on the Tech
campus
machines connected to the internet is not endorsed by IAS or ATM, and may
be seen and interpreted as an attempt to circumvent university security
measures. Violation of
University
and IAS acceptable use policies may mean the revoking of computer
privileges.
SD BOR Freedom of Learning Statement
"Students are responsible for learning the content of any course of
study in which they are enrolled. Under Board of Regents and University
policy, student academic performance shall be evaluated solely on an
academic basis and students should be free to take reasoned exception to the
data or views offered in any course of study. Students who believe that an
academic evaluation is unrelated to academic standards but is related instead
to judgment of their personal opinion or conduct should contact the dean of
the college which offers the class to initiate a review of the
evaluation."
SD Board of Regents
Specifically for ATM 519: While the faculty
of
IAS accepts the use of a diverse range of problem solving environments (from
tablet PCs to Linux to Macs, from single systems to clusters to GRIDs), we are
operationally limited to those that we can provide. As such, we
don't care
what OS or Linux distribution you prefer. IAS uses Mandriva on
its fleet machines. We don't care if you prefer Intel or Lahey
compilers. IAS
uses those by GNU and the Portland Group (and due to the latter, can't
afford
much else!). Those wanting to use
those OSs, distros or compilers not supported by IAS are welcome to do so on
their own time and their own systems so long as they produce the same
results.
Unfortunately we will not be able to support them.
Those wanting us to do so are
offered and engraved
invitation
to back up those
recommendations by showering IAS and ATM with very
generous and
welcome
gifts of filthy
lucre through the SDSMT Foundation to support said changes. No,
really! Cut that check and send it
in!
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