1. FORTRAN Short Course Week 4 Kate Thayer-Calder March 10, 2009

2. Topics for this week Searching in Unix Grep, Regular Expressions Multi-Dimensional Arrays User Defined Datatypes Missing data Reading and writing scientific data

3. Unix Wildcards * - matches all files with none or more of the pattern ls *a returns all files ending in ‘a’ ls a* returns all files starting with ‘a’ ? - matches exactly one character ?ouse would return house and mouse, but not grouse.

4. grep Searches through a file looking for a specific string or pattern, returns the lines where the string occurs grep -i ‘alien’ ufo.txt (case insensitive) grep -w ‘abduct’ ufo.txt (whole word only) grep -riw ‘saucer’ * (recursively thru subdirectories) or lines where it does not occur: grep -v ‘censor’ ufo.txt Can grep multiple files, just add them to the list on the line: grep -i ‘parameterization’ *.txt Unix lexicon: “Can’t grep dead trees.”

5. Regular Expressions aka RegEx, is a special string for describing a pattern of text RegExs can be used with grep or other unix commands and programs for sifting through text They can get really huge, confusing, and powerful, we’ll just look at a few simple options. For more: http://www.regular-expressions.info or just man regexhttp://www.regular-expressions.info

6. Grep and Regex grep foo filessearch files for lines with “foo” grep ‘^foo’ files“foo” at the start of a line grep ‘foo$’ files“foo” at the end of a line grep ‘^foo$’ fileslines containing only the word “foo” grep ‘\^foo’ fileslines containing “^foo” (esc char) grep ‘[fF][oO]o’ filessearch for foo, Foo, fOo, or FOo grep ‘^$’ filessearch for blank lines grep ‘[0-9][0-9]’ filessearch for a pair of numeric digits

7. grep combinations Just some ideas for using grep with other Unix commands: ls -al | grep ‘Jan’ ps -ef | grep ‘501’ man ftp | grep -i ‘directory’ head -30 ‘mydata.txt’ | grep ‘temperature’

8. But... Searching has become much easier than it once was, usually your desktop search engine will filter through files looking for your keywords So, let’s talk about more Fortan!

9. Multi Dimensional Arrays type, dimension(dim1,dim2,...) :: name REAL, dimension(lon,lat,height,time) :: temp Higher dimensional arrays are usually stored contiguously in memory or binary files, in COLUMN MAJOR order See example Multiarrays.f90

10. Column Major Fortran fills up each dimension in order So for i,j,k array, i fills first, then j, then k But do loops work inside out Write out k first, then j, then i To fix this, write your do-loops from the last index in to the first. Do time=1,days Do lon=1,360 Do lat=1,180 Read (10,fmt) Data(lat,lon,time) enddo

11. Array Transformation Reshape function is pretty cool Matrix = RESHAPE( Source, Shape ) A = RESHAPE( B, (/3,2/) ) Another way to index your array elements uses ‘mod’ and integer division lat = array(MOD(i,num_lats)+1) lon = array(i/num_lats + 1) 14 25 36 lons lats

12. Allocatable Arrays Sometimes, you don’t know how large you want your array to be until runtime. Fortran 90 has “allocatable arrays” that can be declared without fixed dimensions, and filled in when the program is running. These can be filled from stdin, or a variable in a file, or a calculation based on previous work, or any other run-time value. See example Multiarrays2.f90

13. WHERE statements An easy way to initialize or set sections of arrays WHERE (array expression) array assignment block ELSEWHERE array assignment block 2 END WHERE This is called “masking”

14. FORALL Construct This statement indicates to the compiler that the operations can be performed in parallel (no operations depend on the value of the operation on other elements in the array) FORALL (triplet) variable = expression

15. Atmospheric Data You’ll see data stored in arrays in many ways: MyData(pressure, temp, mixingratio, height) MyPressure(height), MyTemp(height), MyMixingRatio(height) Pressure(lat,lon,height,time), Temperature(lat,lon,height,time)

16. The Perils of Parallel Arrays It is common in our science to see people using multiple arrays of data that are all the same shape but for different variables (Temperature, Pressure, u wind, v wind,...) This is considered bad form in computer science, it would be better to have one array with multiple values possible at each point. Why? This gets confusing if you implement a 5-D array, however.

17. User Defined Data Types Fortran gives us a nice way to describe more complex data structures by creating new data types. Instead of 4 arrays with different variables in each, we can have one array with four values at each point. TYPE name DataType :: Component_name.... END TYPE name We can create variables with this type or arrays of variables of this type TYPE (name) :: VariableName TYPE (name), Dimension(d1,d2,d3,d4) :: ArrayName Example: StdAtmos.f90

18. IEEE (Eye-Triple-Eee) Institute of Electrical and Electronics Engineers Most members of any technical professional organization in the world. IEEE produces standards for almost everything computer related, and keeps them updated. Today, most IEEE standards have generally been adopted. IEEE 754 is the most widely-used standard for floating- point computation, and is followed by many hardware (CPU and FPU) and software implementations

19. INF and NaN INF is defined as the value given to any Real that is outside the limits of the type. Fortran has +INF and -INF NaN (Not a Number) is produced as the result of an improper floating point calculation. NaN is not equal to either INF. In fact, in the IEEE standard, NaN is not even equal to itself. INF or NaN are occasionally used as placeholders for missing data. See Example: WriteExample2.f90

20. Missing Data Any observational dataset is going to have holes. If missing data is not given as an “outside the bounds” value (-9999 or 9999.0) it is often replaced with INF or NaN. Most Fortran implementations will read INF or NaN in as a Real value (it is a real Real), we need to check for it before doing calculations, or we’ll get a runtime error. See Example: ReadBadData.f90

21. NetCDF Data NetCDF is an I/O library that is widely used in the earth sciences. Once the files are installed, you can use their procedures to open and access the files Each files is “self-describing,” all of the data is annotated (dimension, units, range of values, missing data values, etc...) Examples: read_netCDF.f90 with data from NCEP (NCEP.Precip.0100-1204.nc)

22. Zonal Average Example Modelers and Dynamicists like to look at the atmosphere in latitudinal bands. Don’t have to worry about missing data here... Loading in precip data is pretty simple if you know the parameters. When you do a zonal average, first average in time at each point and then average across all longitudes. Could come up with a less memory intensive way to get the same result... Example: PlayWithPrecip.f90

23. What did we talk about? Searching in Unix Grep, Regular Expressions Multi-Dimensional Arrays User Defined Datatypes Missing data Reading and writing scientific data