swirl_done

AquaFortR_Swirl/First_Lesson/customTests.R

@@ -1,12 +1,9 @@
 # Put custom tests in this file.
-
-      # Uncommenting the following line of code will disable
-      # auto-detection of new variables and thus prevent swirl from
-      # executing every command twice, which can slow things down.
-
-      # AUTO_DETECT_NEWVAR <- FALSE
-
-      # However, this means that you should detect user-created
-      # variables when appropriate. The answer test, creates_new_var()
-      # can be used for for the purpose, but it also re-evaluates the
-      # expression which the user entered, so care must be taken.
+# Uncommenting the following line of code will disable
+# auto-detection of new variables and thus prevent swirl from
+# executing every command twice, which can slow things down.
+# AUTO_DETECT_NEWVAR <- FALSE
+# However, this means that you should detect user-created
+# variables when appropriate. The answer test, creates_new_var()
+# can be used for for the purpose, but it also re-evaluates the
+# expression which the user entered, so care must be taken.

AquaFortR_Swirl/First_Lesson/dependson.txt

@@ -0,0 +1,2 @@
+ggplot2
+microbenchmark

AquaFortR_Swirl/First_Lesson/initLesson.R

@@ -1,13 +1,15 @@
 # Code placed in this file fill be executed every time the
-      # lesson is started. Any variables created here will show up in
-      # the user's working directory and thus be accessible to them
-      # throughout the lesson.
+# lesson is started. Any variables created here will show up in
+# the user's working directory and thus be accessible to them
+# throughout the lesson.
 
-.get_course_path <- function(){
+.get_course_path <- function() {
   tryCatch(swirl:::swirl_courses_dir(),
-           error = function(c) {file.path(find.package("swirl"),"Courses")}
+    error = function(c) {
+      file.path(find.package("swirl"), "Courses")
+    }
   )
 }
 
 
-add_f_txt <- readLines(file.path(.get_course_path(), "AquaFortR_Swirl", "First_Lesson", "add_f.f90"))
+add_f_txt <- readLines(file.path(.get_course_path(), "AquaFortR_Swirl", "First_Lesson", "add_f.f90"))

AquaFortR_Swirl/First_Lesson/lesson.yaml

@@ -12,17 +12,17 @@
   Fortran-accelerated R."'
 
 - Class: text
-  Output: 'In the first leason we will try to write a small Fortran subroutine 
-  and use it in R'
+  Output: 'In our initial lesson, we will endeavour to create a modest Fortran 
+  subroutine and employ it in R'
 
 - Class: cmd_question
-  Output: Define one variable 'a' in R. and it has a value of 7
+  Output: Define one variable 'a' in R, and it has a value of 7
   CorrectAnswer: a <- 7
   AnswerTests: omnitest(correctExpr='a <- 7')
-  Hint: Just type a <- 7.
+  Hint: Type a <- 7.
 
 - Class: cmd_question
-  Output: Define one variable 'b' in R. and it has a value of 15
+  Output: Define one variable 'b' in R, and it has a value of 15
   CorrectAnswer: b <- 15
   AnswerTests: omnitest(correctExpr='b <- 15')
   Hint: Just type b <- 15.
@@ -32,38 +32,127 @@
   CorrectAnswer: c <- a + b
   AnswerTests: omnitest(correctExpr='c <- a + b')
   Hint: Just type c <- a + b
-
 - Class: text
   Output: 'We did simple summation in R, Let us try to do that in Fortran togethor'
 
 - Class: text
-  Output: 'Start by creating a txt file and save it as "add_f.f90"'
+  Output: 'To achieve that, we need to write a Fortran file called "add_f.f90"'
 
+- Class: text
+  Output: 'If you look at the enviroment subwindow, you will find "add_f_txt". 
+   this Fortran subroutine we will use.' 
+
 
+- Class: cmd_question
+  Output: Look at the content of add_f_txt in the console by typing the variable name
+  CorrectAnswer: add_f_txt
+  AnswerTests: omnitest(correctExpr='add_f_txt')
+  Hint: add_f_txt
+
+
+- Class: cmd_question
+  Output: 'Now, we can use the writeLines function to write the add_f_txt variable to
+  the "add_f.f90" file.'
+  CorrectAnswer: writeLines(add_f_txt, "add_f.f90")
+  AnswerTests: omnitest(correctExpr='writeLines(add_f_txt, "add_f.f90")')
+  Hint: writeLines(add_f_txt, "add_f.f90")
+
+- Class: text
+  Output: 'Take some time to look at the add_f.f90 to understand its basic structure.'
+
+- Class: text
+  Output: 'Great! Now, we need to complie the Fortran subroutine in order to use it.
+  In most mashines, you can simply run "R CMD SHLIB add_f.f90" allowing R to help
+  with compilation. Otherwise, you can use "gfortran -shared -o add_f.so add_f.o". Hint:
+  it should be done in the terminal, not the console.'
+
 - Class: text_question
-  Output: Have you created the "add_f.f90" file?
-  CorrectAnswer: Yes
-  AnswerTests: omnitest(correctVal='Yes')
-  Hint: In RStudio, you can go to File then New File and then choose Text File
-
-- Class : text
-  Output: |-
-    Now we write the Fortran subroutine in the 'add_f.f90'. The subroutine content is
-    
-     subroutine add_f(x, y, answer)
-     
-      ! add 2 numbers
-      
-      implicit none
-      
-      double precision :: x, y, answer
-      
-      answer = x + y
-      
-    end
-    
-- Class: text 
-  Output: Copy the subroutine from the last message starting from "subroutine" to "end".
-      And place the subroutine in the add_f.90 file. Please, omit the pipe sign | from the text.
+  Output: After compilation, do you see the add_f.so file in your working directory? 
+  CorrectAnswer: 'yes'
+  AnswerTests: omnitest(correctVal = 'yes')
+  Hint: yes or no 
+
+- Class: text
+  Output: 'The compiled library file contains the subroutine that we will use in 
+  summation. In order to use the add_f.so file we need to load it in R using dyn.load("add_f.so")' 
+
+- Class: cmd_question
+  Output: Please load the compiled library file.
+  CorrectAnswer: dyn.load("add_f.so")
+  AnswerTests: omnitest(correctExpr='dyn.load("add_f.so")')
+  Hint: dyn.load("add_f.so")
+
+- Class: text
+  Output: 'You cans also explore is.loaded function. It is helpful to check if the 
+  subroutine is actually loaded.'
+
+- Class: text
+  Output: 'Moving further, we need to use add_f subroutine now in R. We will use
+  .Fortran function as follows: .Fortran("add_f", a, b, c_f = 0). Since it is a subroutine,
+  we need to provide input and output variables. c_f is the output variable.'
+
+- Class: cmd_question
+  Output: Now, we can test the .Fortran code above. 
+  CorrectAnswer: .Fortran("add_f", a, b, c_f = 0)
+  AnswerTests: omnitest(correctExpr='.Fortran("add_f", a, b, c_f = 0)')
+  Hint: .Fortran("add_f", a, b, c_f = 0)
+
+- Class: text
+  Output: 'You notice that the output in the console is different from just running a + b. 
+  It is a list and this is because .Fortran retuens all input and ouput variables. We can get
+  c_f variable only by using .Fortran("add_f", a, b, c_f = 0)$c_f'
+
+- Class: text
+  Output: Now, we can write a small function to do that. Also, to have a nicer code!
+   add_f<-function(a,b){dyn.load("add_f.so");.Fortran("add_f", a, b, c_f = 0)$c_f}
+
+- Class: mult_question
+  Output: What did we do in the add_f function?
+  AnswerChoices: Loaded the .so file only;Loaded the .so file & extracted output variable from .Fortran; Used .Fortran function only
+  CorrectAnswer: Loaded the .so file & extracted output variable from .Fortran
+  AnswerTests: omnitest(correctVal= 'Loaded the .so file & extracted output variable from .Fortran')
+  Hint: Be aware of the ; sign. 
+
+- Class: text
+  Output: "We can compare the perfomance of addition in R vs Fortran."
+
+- Class: text
+  Output: 'Now, we compare the two functions using a microbenchmark() function. 
+  Please have a look at the documentation of this function.'
+
+- Class: cmd_question
+  Output: 'Using the microbenchmark() is easy! We provide expressions that we want to compare.
+  It could be something such: mbm <- microbenchmark(R = a + b, F = add_f(a,b))'
+  CorrectAnswer:  mbm <- microbenchmark(R = a + b, F = add_f(a , b))
+  AnswerTests: omnitest(correctExpr=' mbm <- microbenchmark(R = a + b, F = add_f(a,b))')
+  Hint:  mbm <- microbenchmark(R = a + b, F = add_f(a + b))
+
+- Class: cmd_question
+  Output: We can explore the mbm variables in the console. 
+  CorrectAnswer: mbm
+  AnswerTests: omnitest(correctExpr='mbm')
+  Hint: type mbm in console 
+
+- Class: cmd_question
+  Output: "We can also use autoplot() to show the results graphically."
+  CorrectAnswer: autoplot(mbm)
+  AnswerTests: omnitest(correctExpr='autoplot(mbm)')
+  Hint: autoplot(mbm)
+
+- Class: text
+  Output: 'From the mbm values and plot, Fortran was not faster than R. 
+  Nevertheless, it is a very simple process, and probably most computation 
+  time is due to copying the variables to Fortran.'
+
+- Class: text
+  Output: 'We reached the end of the 1st lesson. In the next lesson, we will check
+  more computationally complicated example to see the benefits of integrating Fortran in R.' 
+
+
+#- Class: cmd_question
+  #Output: "Do not forget to load the two packages after installation."
+  #CorrectAnswer: library(microbenchmark); library(ggplot2)
+  #AnswerTests: omnitest(correctExpr='library(microbenchmark); library(ggplot2)')
+  #Hint: library(microbenchmark); library(ggplot2)
 
 

AquaFortR_Swirl/MANIFEST

@@ -1 +1,2 @@
 First_Lesson
+Second_Lesson

AquaFortR_Swirl/Second_Lesson/customTests.R

@@ -0,0 +1,9 @@
+# Put custom tests in this file.
+# Uncommenting the following line of code will disable
+# auto-detection of new variables and thus prevent swirl from
+# executing every command twice, which can slow things down.
+# AUTO_DETECT_NEWVAR <- FALSE
+# However, this means that you should detect user-created
+# variables when appropriate. The answer test, creates_new_var()
+# can be used for for the purpose, but it also re-evaluates the
+# expression which the user entered, so care must be taken.

AquaFortR_Swirl/Second_Lesson/dependson.txt

@@ -0,0 +1,3 @@
+ggplot2
+microbenchmark
+dotCall64

AquaFortR_Swirl/Second_Lesson/initLesson.R

@@ -0,0 +1,34 @@
+# Code placed in this file fill be executed every time the
+# lesson is started. Any variables created here will show up in
+# the user's working directory and thus be accessible to them
+# throughout the lesson.
+
+.get_course_path <- function() {
+  tryCatch(swirl:::swirl_courses_dir(),
+    error = function(c) {
+      file.path(find.package("swirl"), "Courses")
+    }
+  )
+}
+
+xcorr2D_f_txt <- readLines(file.path(.get_course_path(), "AquaFortR_Swirl", "Second_Lesson", "xcorr2D.f90"))
+
+source(file.path(.get_course_path(), "AquaFortR_Swirl", "Second_Lesson", "xcorr2D_r.R"))
+
+xcorr2D_f0<- function(a, b){
+  m <- nrow(a)
+  n <- ncol(a)
+  p <- nrow(b)
+  q <- ncol(b)
+
+  k <- m + p - 1
+  l <- n + q - 1
+
+  string_vector<-c(rep("integer", 6), rep("double" , 3))
+
+  cc_F <- cc_F<-matrix(0, k,l)
+  result <- .C64("xcorr2d_f", 
+                 SIGNATURE = string_vector,
+                 m, n, p, q, k, l, a, b,
+                 cc_F)$cc_F
+  return(result)}