Fortran is reading beyond endfile record - fortran

I'm trying to read some data from a file, and the endfile record detection is important to stop reading. However, depending of the array dimensions of the array used to read data, I cannot detect properly the endfile record and my Fortran program stops.
The program is below:
!integer, dimension(3) :: x ! line 1.1
!integer, dimension(3,10) :: x ! line 1.2
integer, dimension(10,3) :: ! line 1.3
integer :: status,i=1
character(len=100) :: error
open( 30, file='data.dat', status='old' )
do
print *,i
!read( 30, *, iostat=status, iomsg=error ) x ! line 2.1
!read( 30, *, iostat=status, iomsg=error ) x(:,i) ! line 2.2
read( 30, *, iostat=status, iomsg=error ) x(i,:) ! line 2.3
if ( status < 0 ) then print *,'EOF'
print *,'total of ',i-1,' lines read.'
exit
else if ( status > 0 ) then
print *,'error cod: ',status
print *,'error message: ', error
stop
else if ( status == 0 ) then
print *,'reading ok.'
i = i + 1
end if
end do
With 'data.dat' file been:
10 20 30
30 40 50
When lines 1.3 and 2.3 are uncommented the mentioned error appears:
error cod: 5008
error message: Read past ENDFILE record
However, using lines 1.1 and 2.1, or 1.2 and 2.2, the program works, detecting endfile record.
So, I would like some help on understanding why I cannot use lines 1.3 and 2.3 to read properly this file, since I'm giving the correct number of array elements for read command.
I'm using gfortran compiler, version 6.3.0.
EDIT: simpler example
the following produces a 5008 "Read past ENDFILE record" error:
implicit none
integer x(2,2),s
open(20,file='noexist')
read(20,*,iostat=s)x
write(*,*)s
end
if we make x a scalar or a one-d array ( any size ) we get the expected -1 EOF flag. It doesn't matter if the file actually doesn't exist or is empty. If the file contains some, but not enough, data its hard to make sense of which return value you might get.

I am not sure if I am expressing myself correctly but it has to do with the way fortran is reading and storing 2d-arrays. When you are using this notation: x(:,i), the column i is virtually expanded in-line and the items are read using this one line of code. In the other case where x(i,:) is used, the row i is read as if you called read multiple times.
You may use implied loops if you want to stick with a specific shape and size. For example you could use something like that:read( 30, *, iostat=status, iomsg=error ) (x(i,j), j=1,3)
In any case you should check that your data are stored properly (as expected at least) in variable x.

Please note this is only a guess. Remember that Fortran stores arrays in column major order. When gfortran compiles read() x(:,i), the 3 memory locations are next to each other so in the executable, it produces a single call to the operating system to read in 3 values from the file.
Now when read() x(i,:) is compiled, the three data elements x(i,1), x(i,2) and x(i,3) are not in contiguous memory. So I am guessing the executable actually has 3 read calls to the operating system. The first one would trap the EOF but the 2nd one gives you the read past end of file error.
UPDATE: I have confirmed that this does not occur with Intel's ifort. gfortran seems to have had a similar problem before: Bad IOSTAT values when readings NAMELISTs past EOF. Whether this is a bug or not is debatable. The code certainly looks like it should trap an EOF.

Related

moving the file position back by one single character to over-write it, in fortran [duplicate]

I want to display the progress of a calculation done with a DO-loop, on the console screen. I can print out the progress variable to the terminal like this:
PROGRAM TextOverWrite_WithLoop
IMPLICIT NONE
INTEGER :: Number, Maximum = 10
DO Number = 1, MAXIMUM
WRITE(*, 100, ADVANCE='NO') REAL(Number)/REAL(Maximum)*100
100 FORMAT(TL10, F10.2)
! Calcultations on Number
END DO
END PROGRAM TextOverWrite_WithLoop
The output of the above code on the console screen is:
10.00 20.00 30.00 40.00 50.00 60.00 70.00 80.00
90.00 100.00
All on the same line, wrapped only by the console window.
The ADVANCE='No' argument and the TL10 (tab left so many spaces) edit descriptor works well to overwrite text on the same line, e.g. the output of the following code:
WRITE(*, 100, ADVANCE='NO') 100, 500
100 FORMAT(I3, 1X, TL4, I3)
Is:
500
Instead of:
100 500
Because of the TL4 edit descriptor.
From these two instances one can conclude that the WRITE statement cannot overwrite what has been written by another WRITE statement or by a previous execution of the same WRITE satement (as in a DO-loop).
Can this be overcome somehow?
I am using the FTN95 compiler on Windows 7 RC1. (The setup program of the G95 compiler bluescreens Windows 7 RC1, even thought it works fine on Vista.)
I know about the question Supressing line breaks in Fortran 95 write statements, but it does not work for me, because the answer to that question means new ouput is added to the previous output on the same line; instead of new output overwriting the previous output.
Thanks in advance.
The following should be portable across systems by use of ACHAR(13) to encode the carriage return.
character*1 creturn
! CODE::
creturn = achar(13) ! generate carriage return
! other code ...
WRITE( * , 101 , ADVANCE='NO' ) creturn , i , npoint
101 FORMAT( a , 'Point number : ',i7,' out of a total of ',i7)
There is no solution to this question within the scope of the Fortran standards. However, if your compiler understand backslash in Fortran strings (GNU Fortran does if you use the option -fbackslash), you can write
write (*,"(A)",advance="no") "foo"
call sleep(1)
write (*,"(A)",advance="no") "\b\b\bbar"
call sleep(1)
write (*,"(A)",advance="no") "\b\b\bgee"
call sleep(1)
write (*,*)
end
This uses the backslash character (\b) to erase previously written characters on that line.
NB: if your compiler does not understand advance="no", you can use related non-standard tricks, such as using the $ specifier in the format string.
The following worked perfectly using g95 fortran:
NF = NF + 1
IF(MOD(NF,5).EQ.0) WRITE(6,42,ADVANCE='NO') NF, ' PDFs'//CHAR(13)
42 FORMAT(I6,A)
gave:
5 PDFs
leaving the cursor at the #1 position on the same line. On the next update,
the 5 turned into a 10. ASCII 13 (decimal) is a carriage return.
OPEN(6,CARRIAGECONTROL ='FORTRAN')
DO I=1,5
WRITE(6,'(1H+" ",I)') I
ENDDO

How do I skip lines when some conditions are met with Fortran? [duplicate]

It is my understanding that Fortran, when reading data from file, will skip lines starting with and asterisk (*) assuming that they are a comment. Well, I seem to be having a problem with achieving this behavior with a very simple program I created. This is my simple Fortran program:
1 program test
2
3 integer dat1
4
5 open(unit=1,file="file.inp")
6
7 read(1,*) dat1
8
9
10 end program test
This is "file.inp":
1 *Hello
2 1
I built my simple program with
gfortran -g -o test test.f90
When I run, I get the error:
At line 7 of file test.f90 (unit = 1, file = 'file.inp')
Fortran runtime error: Bad integer for item 1 in list input
When I run the input file with the comment line deleted, i.e.:
1 1
The code runs fine. So it seems to be a problem with Fortran correctly interpreting that comment line. It must be something exceedingly simple I'm missing here, but I can't turn up anything on google.
Fortran doesn't automatically skip comments lines in input files. You can do this easily enough by first reading the line into a string, checking the first character for your comment symbol or search the string for that symbol, then if the line is not a comment, doing an "internal read" of the string to obtain the numeric value.
Something like:
use, intrinsic :: iso_fortran_env
character (len=200) :: line
integer :: dat1, RetCode
read_loop: do
read (1, '(A)', isostat=RetCode) line
if ( RetCode == iostat_end) exit ReadLoop
if ( RetCode /= 0 ) then
... read error
exit read_loop
end if
if ( index (line, "*") /= 0 ) cycle read_loop
read (line, *) dat1
end do read_loop
Fortran does not ignore anything by default, unless you are using namelists and in that case comments start with an exclamation mark.
I found the use of the backspace statement to be a lot more intuitive than the proposed solutions. The following subroutine skips the line when a comment character, "#" is encountered at the beginning of the line.
subroutine skip_comments(fileUnit)
integer, intent(in) :: fileUnit
character(len=1) :: firstChar
firstChar = '#'
do while (firstChar .eq. '#')
read(fileUnit, '(A)') firstChar
enddo
backspace(fileUnit)
end subroutine skip_comments
This subroutine may be used in programs before the read statement like so:
open(unit=10, file=filename)
call skip_comments(10)
read(10, *) a, b, c
call skip_comments(10)
read(10, *) d, e
close(10)
Limitations for the above implementation:
It will not work if the comment is placed between the values of a variable spanning multiple lines, say an array.
It is very inefficient for large input files since the entire file is re-read from the beginning till the previous character when the backspace statement is encountered.
Can only be used for sequential access files, i.e. typical ASCII text files. Files opened with the direct or append access types will not work.
However, I find it a perfect fit for short files used for providing user-parameters.

Reading variable length data in FORTRAN

I have an input file that I cannot alter the format. One of the lines in particular can contain either 6 or 7 reals and I don't have any way of knowing ahead of time.
After some reading, my understanding of the list-formatted read statement is that if I attempt to read 7 reals on a line containing 6, it will attempt to read from the next line. The author of the code says that when it was written, it would read the 6 reals and then default the 7th to 0. I am assuming he relied on some compiler specific behavior, because I cannot find a mention of this behavior anywhere.
I am using gfortran as my compiler, is there a way to specify this behavior? Or is there a good way to count a number of inputs on a line and rewind to then chose to read the correct number?
here is a little trick to accomplish that
character*100 line
real array(7)
read(unit,'(a)')line !read whole line as string'
line=trim(line)//' 0' !add a zero to the string
read(line,*)array !list read
If the input line only had 6 values, the zero is now the seventh.
If there were seven to begin with it will do nothing.
I try to avoid using format specifiers on input as much as possible.
Maybe you should use the IOSTAT statement for detecting the wrong format when you attempt to read 7 values when there are only 6. And you should use the ADVANCE statement to be able to retry to read the same line.
READ(LU,'7(F10.3)', IOSTAT=iError, ADVANCE='NO') MyArray(1:7)
IF(iError > 0) THEN
! Error when trying to read 7 values => try to read 6 !
READ(LU, '6(F10.3)') MyArray(1:6)
ELSEIF(iError == 0) THEN
READ(LU, *) ! For skipping the line read with success with 7 values
ENDIF
IOSTAT takes a negative value for example when you reach the end of the file, positive for problem of reading (typically formatting error) and 0 when the read succeed. See this link for a complete definition of gfortran error code: http://www.hep.manchester.ac.uk/u/samt/misc/gfortran_errors.html
Another way to do it could be to read the line as a string and manipulating the string in order to get the vector values :
CHARACTER(LEN=1000) :: sLine
...
READ(LU, '(A)') sLine
READ(sLine,'7(F10.3)', IOSTAT=iError) MyArray(1:7)
IF(iError > 0) THEN
! Error when trying to read 7 values => try to read 6 !
READ(sLine, '6(F10.3)') MyArray(1:6)
ENDIF
If the values are written in fixed format, you can determine the lenght of the vector by testing the lenght of the line:
CHARACTER(LEN=1000) :: sLine
INTEGER :: nbValues
CHARACTER(LEN=2) :: sNbValues
...
READ(LU, '(A)') sLine
nbValues = LEN_TRIM(sLine) / 10 ! If format is like '(F10.x)'
WRITE(sNbValues, '(I2)') nbValues
READ(sLine, '('//TRIM(sNbValues)//'(F10.3))') MyArray(1:nbValues)

Unexpected end of file with the read command

I'm trying to read data from a mesh file in Fortran 2003, but I'm getting an unexpected end of file runtime error. Some lines in the file seem to be skipped by the read command. For example, with this sample.txt file :
1 2 2 0 1 1132 1131 1165
2 2 2 0 2 1099 1061 1060
I want to read the first integer from each line, so my program is :
program read_file
implicit none
integer :: ierr, i, j
open(unit=10,file='sample.txt',status='old',action='read',iostat=ierr)
read(10,*) i
read(10,*) j
write(*,*) i, j
end program read_file
And at runtime, I'm getting
Fortran runtime error: End of file
What is odd is that if I force a carriage return at the end of the file, the program will read the two integers just fine.
If you really need to fix this on the read side (ie. properly terminating the last line of the file is not practical for some reason ) you might try reading each line into a string, then internal reading from the string:
character*80 line
integer i
do ..
read(unit,'(a)')line
read(line,*)i
enddo
Of course this may or may not work depending on the compiler as well..
Obviously fixing the file is the best option ( Whatever program is creating this file should be fixed )
Every record in a sequential file must be properly terminated. The records in text files are the lines. They must be properly terminated. In some editors that means you must add an empty line to the end. Every line containing data must be terminated.
Some compilers are less sensitive to this issue than others and will terminate the last record for you.

mpi rank not valid in do loop

Im updating a program in fortran to run with MPI and have run into an issue with the rank not showing up properly. In the beginning of this subroutine I call MPI_COMM_RANK(MPI_COMM_WORLD,rank,ierr) and it returns the proper rank until this point:
DO IY=2,NY+1
DO IX=2,NX+1
D(IX,IY)=(h_roms(IX,IY)+zeta(IX,IY))*maskr(IX,IY)
call mpi_barrier(mpi_comm_world,ierr)
write(out,12) rank,ix,iy
12 format('disappearing?',i3,'ix:',i3,'iy',i3)
ENDDO
ENDDO
NY and NX are 124,84 respectively and the rank prints properly until iy becomes 125, and ix is 3. after that it only prints out as *** . IT still prints out everything twice (running on 2 processors) but the rank isn't valid, or giving any errors. Ive tried calling MPI_COMM_RANK after the do loop and still nothing. Any ideas would be much appreciated.
Fortran generally prints a sequence of asterisks, your ***, if a numeric output field is too small to contain the number you are trying to write into it. Try changing some of the i3s in the format statement to i6 or even i0; this last form tells the compiler to print an integer in a field wide enough for all its digits but no wider.