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.
Related
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.
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.
I am using Fortran to make a subroutine to use in a CFD shallow water software.
I have written this code to read and use the values stored.
PROGRAM hieto
! Calcula la precipitacion efectiva en funcion del tiempo
!IMPLICIT NONE
real::a
!Abrir CSV
!OPEN(UNIT=10,FILE="datos.txt",FORM="formatted",STATUS="replace",ACTION="readwrite",ACCESS='sequential')
open(unit=10, file='datos.txt')
!Leer el archivo
read(10, *, iostat=ios)a
print*,ios
print*, a
close (UNIT=10)
END PROGRAM hieto
My text file datos, looks like this
1
2
3
When I run the code as is, I get the following output
-1
0.0000000000
Process return 0 (0x0) execution time: 0.002 s
the first number in the row one is one not zero, so I don't know why this happens.
And if I remove the iostat=ios from the read statement, I get the following error:
At ine 13 (the line od the read stament) of file /home/Dropbox/scripts_tesis/fortran/hieto_telemac.f90 (unit=10, file=datos.txt')
Fortran runtime error: end of file.
Proceess returned 2 (0x2)
I have read some answers here so I tried adding end=3 in the read statement, and also to end my text file with a blank line at the end.
The end=3 gives an error saying 3 is not a defined label and putting a blank row in the text file does nothing.
I am using ubuntu 16.04 LTS and Gfortran compiler.
What happens is that your file is empty.
Make sure that there is indeed a file called datos.txt in that directory. Pay attention to the exact name. datos.txt and just datos is not the same thing.
If you tried to open it before with the commented command that includes STATUS="replace" your old file would have been replaced.
And because the file is empty, you didn't real anything useful. If iostat is non-zero, and your is -1, then the value of the variable being read is undefined. So your a is undefined. Again, because your file is empty.
Additionally, you cannot just blindly put end=3 in your code because you saw it somewhere on Stack Overflow. You must first understand what it is supposed to do. There is no reason to combine iostat= and end=. The iostat is perfectly sufficient.
I am using a Fortran 90 program that writes a file. The first line of this file is supposed to indicate the number of lines in the remaining file. The file is written by the program when a certain criterion is met and that can't be determined beforehand. Basically, I will know the total number of lines only after the run is over.
I want to do it in the following manner:
1) open the file and write the first line with some text say, "Hello"
2) Write rows in the file as desired and keep a counter for number of rows.
3) Once the run is over and just before closing the file, replace the first line string ("Hello") with the counter.
The problem is in step 3. I don't know how to replace the first line.
Another option that I can think of is to write to 2 files. First, write a file as above without the counter. Once the run is over, close the file and write another file and this time, I know the value of the counter.
I believe there is a way to proceed with the first approach. Can someone please help me with this?
Fortran supports three forms of file access - DIRECT, STREAM (F2003+) and SEQUENTIAL. Both DIRECT and STREAM access support being able to rewrite earlier parts of a file, SEQUENTIAL access does not (a rewrite to an earlier record truncates the file at the rewritten record).
With direct access, all the records in the file are the same length. An arbitrary record can be [must be] accessed by any input/output statement by simply specifying the relevant record number in the statement. Note though, that the typical disk format of a direct access file may not match your idea of a file with "lines".
With formatted stream access, the current position in the file can be captured using an INQUIRE statement, and then a later input/output statement can begin data transfer at that position by using a POS specifier. The typical disk format of a formatted stream access file usually matches with what people expect of a text file with lines.
Stream access is likely what you want. Examples for both approaches are shown below.
Direct access:
PROGRAM direct
IMPLICIT NONE
INTEGER :: unit
REAL :: r
INTEGER :: line
OPEN( NEWUNIT=unit, &
FILE='direct.txt', &
STATUS='REPLACE', &
ACCESS='DIRECT', &
RECL=15, & ! The fixed record length.
FORM='FORMATTED' )
CALL RANDOM_SEED()
! No need to write records in order - we just leave off
! writing the first record until the end.
line = 0
DO
CALL RANDOM_NUMBER(r)
IF (r < 0.05) EXIT
line = line + 1
PRINT "('Writing line ',I0)", line
! All the "data" records are offset by one, to allow the
! first record to record the line count.
WRITE (unit, "('line ',I10)", REC=line+1) line
END DO
! Now update the first record with the number of following "lines".
WRITE (unit, "(I10)", REC=1) line
CLOSE(unit)
END PROGRAM direct
Stream access:
PROGRAM stream
IMPLICIT NONE
INTEGER :: unit
REAL :: r
INTEGER :: line
INTEGER :: pos
OPEN( NEWUNIT=unit, &
FILE='stream.txt', &
STATUS='REPLACE', &
ACCESS='STREAM', &
POSITION='REWIND', &
FORM='FORMATTED' )
CALL RANDOM_SEED()
! Remember where we are. In this case, the position
! is the first file storage unit in the file, but
! it doesn't have to be.
INQUIRE(unit, POS=pos)
! Leave some space in the file for later overwriting
! with the number of lines. We'll stick the number
! zero in there for now.
WRITE (unit, "(I10)") 0
! Write out the varying number of lines.
line = 0
DO
CALL RANDOM_NUMBER(r)
IF (r < 0.05) EXIT
line = line + 1
PRINT "('Writing line ',I0)", line
WRITE (unit, "('line ',I10)") line
END DO
! Now update the space at the start with the number of following "lines".
WRITE (unit, "(I10)", POS=pos) line
CLOSE(unit)
END PROGRAM stream
Going back on a sequential access file is tricky, because lines can vary in length. And if you change the length of one line, you'd have to move all the stuff behind.
What I recommend is to write your output to a scratch file while counting the number of lines. Then, once you're finished, rewind the scratch file, write the number of lines to your output file, and copy the contents of the scratch file to that output file.
Here's what I did:
program var_file
implicit none
character(len=*), parameter :: filename = 'delme.dat'
integer :: n, io_stat
character(len=300) :: line
open(unit=200, status='SCRATCH', action="READWRITE")
n = 0
do
read(*, '(A)') line
if (len_trim(line) == 0) exit ! Empty line -> finished
n = n + 1
write(200, '(A)') trim(line)
end do
rewind(200)
open(unit=100, file=filename, status="unknown", action="write")
write(100, '(I0)') n
do
read(200, '(A)', iostat=io_stat) line
if (io_stat /= 0) exit
write(100, '(A)') trim(line)
end do
close(200)
close(100)
end program var_file
I have a shell script from which I pass a binary file to a fortran program such that
Mth=$1
loop=1
it=1
while test $it -le 12
do
Mth=`expr $Mth + $loop`
file="DataFile"$Mth".bin"
./fort_exe ${Yr} ${nt} ${it}
# Increment loop
it=`expr $it + 1`
done
This script is used to pass 12 files within a do loop to the fortran program. In the fortran program, I read the binary file passed from the shell script and I am trying to write a 2nd file which would compile in a single file all the data that was read from the consecutive files e.g.
!Open binary file passed from shell script
open(1,file='Datafile'//TRIM{Mth)//.bin',action='read',form='unformatted',access='direct', &
recl=4*x*y, status='old')
! Open write file for t 1. The status is different in t 1 and t > 1 so I open it twice: I guess there is a more elegant way to do this...
open(2,file='Newfile.bin',action='write',form='unformatted', &
access='stream', position='append', status='replace')
irec = 0
do t = 1, nt
! Read input file
irec = irec + 1
read(1,rec=irec) val(:,:)
! write output file
irecW= irec + (imonth-1)*nt
if ( t .eq. 1) write(2,pos=irecW) val(:,:)
! Close file after t = 1, update the status to old and reopen.
if ( t .eq. 2) then
close (2)
open(2,file='Newfile.bin',action='write',form='unformatted', &
access='stream', position='append',status='old')
endif
if ( t .ge. 2) write(2,pos=irecW) val(:,:)
enddo
I can read the binary data from the first file no problem but when I try and read from another program the binary data from the file that I wrote in the first program such that
open(1,file='Newfile.bin',action='read',form='unformatted', &
access='stream', status='old')
irec=0
do t = 1, nt
! Read input file
irec = irec + 1
read(1,pos=irec) val(:,:)
write(*,*) val(:,:)
enddo
val(:,:) is nothing but a list of zeros. This is the first time I use access=stream which I believe is the only way I can use position='append'. I have tried compiling with gfortran and ifort but I do not get any error messages.
Does anyone have any idea why this is happening?
Firstly, I do not think you need to close and reopen your output file as you are doing. The status specifier is only relevant to the open statement in which it appears: replace will delete Newfile.bin if it exists at that time, before opening a new file with the same name. The status is implicitly changed to old, but this does not affect any operations done to the file.
However, since your Fortran code does not know you run it 12 times, you should have a way of making sure the file is only replaced the first time and opened as old afterwards; otherwise, Newfile.bin will only contain the information from the last file processed.
As for reading in the wrong values, this most likely occurs because of the difference between direct access (where you can choose a record length) and stream access (where you cannot). With stream access, data is stored as a sequence of "file storage units". Their size is in general compiler-dependent, but is available through the module iso_fortran_env as file_storage_size; it is usually 8 bits. This means that each entry will usually occupy multiple storage units, so you have to take care that a read or write with the pos = specifier does not access the wrong storage units.
Edit:
Some example code writing and reading with stream access:
program stream
use, intrinsic :: iso_fortran_env
implicit none
integer :: i, offset
real(real32), dimension(4,6) :: val, nval
open(unit=2, file='Newfile.bin', action='readwrite', form='unformatted', &
access='stream', status='replace')
do i = 1,2
call random_number(val)
write(2) val
enddo
! The file now contains two sequences of 24 reals, each element of which
! occupies the following number of storage units:
offset = storage_size(val) / file_storage_size
! Retrieve the second sequence and compare:
read(2, pos = 1 + offset*size(val)) nval
print*, all(nval == val)
close(2)
end program
The value true should be printed to the screen.
Note also that it's not strictly necessary to specify a pos while writing your data to the file, because the file will automatically be positioned beyond the last record read or written.
That said, direct or stream access is most beneficial if you need to access the data in a non-sequential manner. If you only need to combine input files into one, it could be easier to write the output file with sequential access, for which you can also specify recl and position = 'append'.
You can check for the existence of a file in standard Fortran, by using the inquire statement:
logical :: exist
inquire(file="test.dat", exist=exist)
if (exist) then
print *, "File test.dat exists"
else
print *, "File test.dat does not exist"
end if
Alternatively you can have a look at the modFileSys library which provides libc like file manipulation routines.
As for appending and streams: Appending files is also possible when you use "classical" record based fortran files, you do not have to use streams for that.