The following is a data set I am working with:
2 19.000000E-01 4.246377E+24 9000.0 100.0 106.0 1400.0
2.601629E+4 1E+24 2.232456E+2 0.100000E+00
0.000000E+00 0.20000E+00 1.000000E+00 5.169046E+4
0.000000E+00 0.000000E+00 0.000000E+00
I want to read the elements of this text data set from left to right using Gfortran. However, my code is reading it from top to bottom. In addition, it's not reading all of the elements. Is there any way I can make my GFortran code read from left to right and read all of the elements?
Here is my code:
PROGRAM S1
IMPLICIT NONE
REAL :: col1
REAL :: col2, col3
REAL :: col4, col5
REAL :: col6, col7
INTEGER :: IOstatus=0
open (unit = 1, file = "testing.txt", STATUS = "OLD")
readloop: DO
READ (1,*,IOSTAT=IOstatus) col1,col2,col3,col4,col5,col6,col7
IF (IOstatus /=0) EXIT
WRITE (*, *) col1,col2,col3,col4,col5,col6,col7
END DO readloop
END PROGRAM
Thanks. If there's any other information I can give, let me know.
The problem is that Fortran reads records line-by-line (row-by-row). Reading column-by-column is not very simple.
When I run this, this is the output I get:
2.00000000 1.89999998 4.24637708E+24 9000.00000 100.000000 106.000000 1400.00000
26016.2891 1.00000001E+24 223.245605 0.100000001 0.00000000 0.200000003 1.00000000
Since Fortran reads row by row, it will try to read everything in the first row, then the second, and so on. In this case, the first iteration of the loop read seven items from the first row. The second iteration read four items from the second row and then three from the third row. The third iteration attempted to read the rest, but as there were no additional items to read, the READ failed and the loop exited.
To read columns will take some work. The first step is probably to make your column variables arrays. You may have to read records (lines/rows) and parse them yourself, or read items one at a time and manually sort them into columns.
Also, check out this post; it may offer some help: Reading columns from data file in fortran
Related
So I have some code that does essentially this:
REAL, DIMENSION(31) :: month_data
INTEGER :: no_days
no_days = get_no_days()
month_data = [fill array with some values]
WRITE(1000,*) (month_data(d), d=1,no_days)
So I have an array with values for each month, in a loop I fill the array with a certain number of values based on how many days there are in that month, then write out the results into a file.
It took me quite some time to wrap my head around the whole 'write out an array in one go' aspect of WRITE, but this seems to work.
However this way, it writes out the numbers in the array like this (example for January, so 31 values):
0.00000 10.0000 20.0000 30.0000 40.0000 50.0000 60.0000
70.0000 80.0000 90.0000 100.000 110.000 120.000 130.000
140.000 150.000 160.000 170.000 180.000 190.000 200.000
210.000 220.000 230.000 240.000 250.000 260.000 270.000
280.000 290.000 300.000
So it prefixes a lot of spaces (presumably to make columns line up even when there are larger values in the array), and it wraps lines to make it not exceed a certain width (I think 128 chars? not sure).
I don't really mind the extra spaces (although they inflate my file sizes considerably, so it would be nice to fix that too...) but the breaking-up-lines screws up my other tooling. I've tried reading several Fortran manuals, but while some of the mention 'output formatting', I have yet to find one that mentions newlines or columns.
So, how do I control how arrays are written out when using the syntax above in Fortran?
(also, while we're at it, how do I control the nr of decimal digits? I know these are all integer values so I'd like to leave out any decimals all together, but I can't change the data type to INTEGER in my code because of reasons).
You probably want something similar to
WRITE(1000,'(31(F6.0,1X))') (month_data(d), d=1,no_days)
Explanation:
The use of * as the format specification is called list directed I/O: it is easy to code, but you are giving away all control over the format to the processor. In order to control the format you need to provide explicit formatting, via a label to a FORMAT statement or via a character variable.
Use the F edit descriptor for real variables in decimal form. Their syntax is Fw.d, where w is the width of the field and d is the number of decimal places, including the decimal sign. F6.0 therefore means a field of 6 characters of width with no decimal places.
Spaces can be added with the X control edit descriptor.
Repetitions of edit descriptors can be indicated with the number of repetitions before a symbol.
Groups can be created with (...), and they can be repeated if preceded by a number of repetitions.
No more items are printed beyond the last provided variable, even if the format specifies how to print more items than the ones actually provided - so you can ask for 31 repetitions even if for some months you will only print data for 30 or 28 days.
Besides,
New lines could be added with the / control edit descriptor; e.g., if you wanted to print the data with 10 values per row, you could do
WRITE(1000,'(4(10(F6.0,:,1X),/))') (month_data(d), d=1,no_days)
Note the : control edit descriptor in this second example: it indicates that, if there are no more items to print, nothing else should be printed - not even spaces corresponding to control edit descriptors such as X or /. While it could have been used in the previous example, it is more relevant here, in order to ensure that, if no_days is a multiple of 10, there isn't an empty line after the 3 rows of data.
If you want to completely remove the decimal symbol, you would need to rather print the nearest integers using the nint intrinsic and the Iw (integer) descriptor:
WRITE(1000,'(31(I6,1X))') (nint(month_data(d)), d=1,no_days)
I have often observed that unformatted file writing (as shown below) is way faster than formatted file writing (also as shown below) in Fortran 90.
Unformatted file writing
OPEN ( Unit=86, File='out.dat', Form='unformatted', Action='Write')
WRITE (86) A, B, C
CLOSE (86)
Formatted file writing
OPEN ( Unit=86, File='out.dat', Form='formatted', Action='Write')
DO ii = 1,N
DO jj = 1,N
WRITE (*,86) A(ii,jj), B(ii,jj), C(ii,jj)
END DO
END DO
CLOSE (86)
Where A,B,C are two-dimensional arrays of size(N,N). I found that in this case the difference in CPU_Time was around 12s.
Why is there a huge difference? Is it just the time taken by looping in formatted procedure?
Notice that in one case you write the whole A first, then whole B then whole C. In the second you are writing A11, B11, C11, A21, B21, C21, ... That is a difference, but the impact will be small.
It takes a lot of CPU time to convert the numbers from the binary memory representation to human readable numbers. That is mostly what makes it slower in formatted case. Also the file is larger so writing it takes more time.
I have a formatted data file which is typically billions of lines long, with several lines of headers of variable length. The data file takes the form:
# header 1
# header 2
# headers are of variable length.
# data begins from next line.
1.23 4.56 7.89 0.12
2.34 5.67 8.90 1.23
:
:
# billions of lines of data, each row the same length, same format.
-- end of file --
I would like to extract a portion of data from this file, and my current code looks like:
<pre>
do j=1,jmax !Suppose I want to extract jmax lines of data from the file.
[algorithm to determine number of lines to skip, "N(j)"]
!This determines the number of lines to skip from the previous file
!position, when the data was read on j-1th iteration.
!Skip N-1 lines to go to the next data line to read off:
do i=1,N-1
read(unit=unit,fmt='(A)')
end do
!Now read off the line of data I want:
read(unit=unit,fmt='(data_format)'),data1,data2,etc.
!Data is stored in some arrays.
end do
</pre>
The problem is, N(j) can be anywhere between 1 and several billion, so it takes some time to run the code.
My question is, is there a more efficient way of skipping millions of lines of data? The only way I can think of, while sticking to Fortran, is to open the file with direct access and jump to the desired line upon opening the file.
As you suggest, direct access seems like the best option. But that requires the records to all have the same length, which your headers violate. Also, why used formatted output? With a file of this length, its hard to imagine a person reading the file. If you use unformatted IO, the file will be both smaller and IO will be faster. Perhaps create two files, one with the headers (metadata) in human reader form, and the other with the data in native form. Native / binary representation means a loss of portability, which is something to consider if you want to move the files to different computer architectures or have them be useable for decades. Otherwise it's probably worth the convenience. Other options would be to use a more sophisticated file format that combines metadata and data, such as HDF5 or FITS, but for communication between two programs of one person, that's probably excessive.
How do we read a specific file line by line while skipping some columns in it?
For example, I have a text file which has data, sorted out in 5 columns, but I need to read only two columns out of it, they can be first two or any other random combination (I mean, need a solution which would work with any combination of columns like first and third only).
Code something like this
open(1, file=data_file)
read (1,*) ! to skip first line, with metadata
lmax = 0
do while (.true.)
! read column 1 and 3 here, either write
! that to an array or just loop through each row
end do
99 continue
close (1)
Any explanation or example would help a lot.
High Performance Mark's answer gives the essentials of simple selective column reading: one still reads the column but transfers it to a then-ignored variable.
To extend that answer, then, consider that we want to read the second and fourth columns of a five-column line:
read(*,*) junk, x, junk, y
The first value is transferred into junk, then the second into x, then the third (replacing the one just acquired a moment ago) into junk and finally the fourth into y. The fifth is ignored because we've run out of input items and the transfer statement terminates (and the next read in a loop will go to the next record).
Of course, this is fine when we know it's those columns we want. Let's generalize to when we don't know in advance:
integer col1, col2 ! The columns we require, defined somehow (assume col1<col2)
<type>, dimension(nrows) :: x, y, junk(3) ! For the number of rows
integer i
do i=1,nrows
read(*,*) junk(:col1-1), x(i), junk(:col2-col1-1), y(i)
end do
Here, we transfer a number of values (which may be zero) up to just before the first column of interest, then the value of interest. After that, more to-be-ignored values (possibly zero), then the final value of interest. The rest of the row is skipped.
This is still very basic and avoids many potential complications in requirements. To some extent, it's such a basic approach one may as well just consider:
do i=1,nrows
read(*,*) allofthem(:5)
x(i) = allofthem(col1)
y(i) = allofthem(col2)
end do
(where that variable is a row-by-row temporary) but variety and options are good.
This is very easy. You simply read 5 variables from each line and ignore the ones you have no further use for. Something like
do i = 1, 100
read(*,*) a(i), b, c(i), d, e
end do
This will overwrite the values in b, d, and e at every iteration.
Incidentally, your line
99 continue
is redundant; it's not used as the closing line for the do loop and you're not branching to it from anywhere else. If you are branching to it from unseen code you could just attach the label 99 to the next line and delete the continue statement. Generally, continue is redundant in modern Fortran; specifically it seems redundant in your code.
this is my first time trying to program in Fortran. I'm trying to write a program that prints the first 1476 terms of the Fibonacci sequence, then examines the first digit of each term and stores the number of 1s, 2s, 3s, ..., 9s that occur in an array.
The problem that I can't seem to figure out is how to read the first digit of each term. I've tried several things but am having difficulty with my limited knowledge of Fortran techniques. I write the terms to a text file and the idea is to read the first digit of each line and accumulate the respective number in the array. Does anyone have any suggestions of how to do this?
Here is my code so far:
(edit: I included the code I have for reading the file. Right now it just prints out 3.60772951994415996E-313,
which seems like an address of some sort, because it's not one of the Fibonacci numbers. Also, it is the only thing printed, I expected that it would print out every line of the file...)
(edit edit: After considering this, perhaps there's a way to format the writing to the text file to just the first digit. Is there a way to set the number of significant digits of a real number to one? :P)
subroutine writeFib(n)
integer :: i
real*8 :: prev, current, newFib
prev = 0
current = 1
do i = 1, n
newFib = prev + current
prev = current
current = newFib
write(7,*) newFib
end do
return
end subroutine
subroutine recordFirstDigits(a)
integer :: openStat, inputStat
real*8 :: fibNum
open(7, file = "fort.7", iostat = openStat)
if (openStat > 0) stop "*** Cannot open the file ***"
do
read(7, *, iostat = inputStat) fibNum
print *,fibNum
if (inputStat > 0) stop "*** input error ***"
if (inputStat < 0) exit ! end of file
end do
close(7)
end subroutine
program test
integer :: k, a(9)
k = 1476
call writeFib(k)
call recordFirstDigits(a)
end program
Although the suggestions were in place, there were also several things that were forgotten. Range of the REAL kind, and some formatting problems.
Anyways, here's one patched up solution, compiled and working, so try to see if this will work for you. I've took the liberty of choosing my own method for fibonacci numbers calculation.
program SO1658805
implicit none
integer, parameter :: iwp = selected_real_kind(15,310)
real(iwp) :: fi, fib
integer :: i
character(60) :: line
character(1) :: digit
integer :: n0=0, n1=0, n2=0, n3=0, n4=0, n5=0, n6=0, n7=0, n8=0, n9=0
open(unit=1, file='temp.txt', status='replace')
rewind(1)
!-------- calculating fibonacci numbers -------
fi = (1+5**0.5)/2.
do i=0,1477
fib = (fi**i - (1-fi)**i)/5**0.5
write(1,*)fib,i
end do
!----------------------------------------------
rewind(1)
do i=0,1477
read(1,'(a)')line
line = adjustl(line)
write(*,'(a)')line
read(line,'(a1)')digit
if(digit.eq.' ') n0=n0+1
if(digit.eq.'1') n1=n1+1
if(digit.eq.'2') n2=n2+1
if(digit.eq.'3') n3=n3+1
if(digit.eq.'4') n4=n4+1
if(digit.eq.'5') n5=n5+1
if(digit.eq.'6') n6=n6+1
if(digit.eq.'7') n7=n7+1
if(digit.eq.'8') n8=n8+1
if(digit.eq.'9') n9=n9+1
end do
close(1)
write(*,'("Total number of different digits")')
write(*,'("Number of digits 0: ",i5)')n0
write(*,'("Number of digits 1: ",i5)')n1
write(*,'("Number of digits 2: ",i5)')n2
write(*,'("Number of digits 3: ",i5)')n3
write(*,'("Number of digits 4: ",i5)')n4
write(*,'("Number of digits 5: ",i5)')n5
write(*,'("Number of digits 6: ",i5)')n6
write(*,'("Number of digits 7: ",i5)')n7
write(*,'("Number of digits 8: ",i5)')n8
write(*,'("Number of digits 9: ",i5)')n9
read(*,*)
end program SO1658805
Aw, ... I just read you need the number of digits stored in to an array. While I just counted them.
Oh well, ... "left as an exercise for the reader ..." :-)
Can you read with a FORMAT(A1)? It's been 20 years so I don't remember the exact syntax.
I wonder why the open statement succeeds when file 7 hasn't been closed. I think you need an endfile statement and/or a rewind statement in between writing and reading.
Paul Tomblin posted what you have to do after you solve your problem in getting reads to work in the first place.
I am getting an 'end of line' runtime error
You don't show the ! code to read here... which makes it kind of difficult to guess what you are doing wrong :-)
Perhaps you need a loop to read each line and then jump out of the loop to a continue statement when there are no more lines.
Something like this:
do
read(7,*,end=10) fibNumber
end do
10 continue
Better still - look at the more modern style used in this revcomp program.
here are some hints:
You don't need to use characters,
much less file i/o for this problem
(unless you forgot to state that a
file must be created).
Therefore, use math to find your statistics. There are lots of resources on Fibonacci numbers that might provide a simplifying insight or at least a way to independently spot check your answers.
Here is a complicated hint in non-Fortran lingo:
floor(10^(frac(log_10(7214989861293412))))
(Put this in Wolfram Alpha to see what it does.)
A simpler hint (for a different approach) is that you can do very
well in Fortran with simple
arithmetic inside of looping
constructs--at least for a first pass at the solution.
Accumulate your statistics as you
go. This advice would even apply to your character-driven approach. (This problem is ideally suited
for coming up with a cute indexing
scheme for your statistics, but some
people hate cute schemes in
programming. If you don't fear
cuteness ... then you can have associative
arrays in Fortran as long as your
keys are integers ;-)
The most important aspect of this
problem is the data type you will
use to calculate your answers. For
example, here's the last number you
will have to print.
Cheers, --Jared