Fortran I/O, first read is EOF? - fortran

I'm trying to use some old FORTRAN code with some new Java code which works in Windows(as an exe) but not in OS X. I try to build it in eclipse and I get
make: *** [all] Segmentation fault: 11
so I go to terminal and do it that way, even different compilers but still the same result:
Running OS X 10.7.5 and gfortran-4.2 made
with standard -c and -o commands
Program foo
open(unit = 1, file = 'variables.txt',IOSTAT= iost)
write(*,*)iost
read(1,*) P
write(*,*)P
...
end program foo
the program builds manually but the output is:
0
At line 13 of file Cubic42.f
Fortran runtime error: End of file
I have also seen this error:
list in: end of file
apparent state: unit 88 named variables
last format: list io
lately reading sequential formatted external IO
Abort
It shows that IOSTAT returns 0, which means the file is good?
But it will not read the file, even if I change the unit# to say, 88.. and even if I change the CR to mac, windows, or unix.
It seems to be only a problem with the input/output, if i hardcode variables, for example, the program works.
Any ideas on how to fix this?
Thanks in advance.
Edit1
Here is the variables.txt file
-9999
15.6
500
150.9
48.98
0.000
there is a carriage return at the end, and it doesn't matter if i change the -9999 to positive
Edit2
I deleted the text file from the directory and remade the .f to look like this:
program foo
implicit none
real a, b, c, d
open(unit = 1, file = 'variables.2txt', action='write')
write(1, *) -6666
write(1, *) 6.15
write(1, *) -321
write(1, *) 5.16
close(1)
open(unit = 2, file = 'variables.2txt', action='read',form='FORMATTED')
read(2, *) a
write(*,*) a
read(2, *) b
write(*,*) b
read(2, *) c
write(*,*) c
read(2, *) d
write(*,*) d
close(2)
end program foo
Then I compiled it.
Output is:
-6666.000
6.150000
-321.0000
5.160000
as expected, but variables.2txt is nowhere to be found! I'm very confused, please help.
Edit3
I have found the phantom file. It is located at /users/me/phantom.txt
So the question is, how do I make the file save in the same directory as the executable?

I get a very similar error message to yours
0
At line 4 of file proba.f (unit = 1, file = 'variables.txt')
when running your code on Linux with a file variables.txt where I explicitly set the end of line characters according to the old MAC convention to ^M (instead of Unix's ^J). So, I guess, it is an EOL-convention problem. You could eventually try to write two lines to a file and investigate that file in order to decide which EOL-convention gfortran expects on your system:
program foo
implicit none
open(unit = 1, file = 'variables.txt', action='write')
write(1, *) -9999
write(1, *) 15.6
close(1)
end program foo
Also, I'd definitely go for a more recent gfortran compiler (current stable is version 4.7.2).

Related

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.

Fortran inquire return internal file

I have a situation unexpected with my fortran program.
I want to drop some data in a text file. For some reasons, I created a type to deal with this file.
Therefore, I open a file with the commands (where f is my file type object):
open(newunit = f%unit, &
file = trim(adjustl(f%name)), &
form = 'FORMATTED', &
access = 'STREAM', &
action = 'WRITE', &
status = 'REPLACE', &
iostat = ios)
if(ios /= 0) print '("Problem creating file")', trim(f%name)
Then I write stuff like this:
write(unit=f%unit,fmt='(100A)') "#Header"
And when it is done, I want to close the file. To do this, I call the subroutine:
subroutine close_file_ascii(f)
implicit none
class(my_file_type) intent(in) :: f
logical :: file_opened, file_exist
integer :: ios
inquire(unit=f%unit, exist=file_exist, opened=file_opened) !, iostat=ios)
print *,'file_exist:', file_exist, 'file_opened:', file_opened, 'ios:', ios
if ((file_opened) .and. (file_exist)) then
close(unit=f%unit)
else
print *,"[WARNING]"
end if
end subroutine close_file_ascii
My problem is in this last subroutine. When I run the program on windows, I get the following error:
Fortran runtime error: Inquire statement identifies an internal file
Error termination. Backtrace
Therefore, I tried to create MWE to understand the problem, but all of them where working well. So couldn't really isolate the problem. Also a strange thing is that when I compile and execute with gfortran on my linux there is no problem, but when I do so on my windows I get the previous error. ( I compile on windows with gfortran version 7.3.0 x86_64-posix-sjlj-rev0, Built by MinGW-W64 )
I already work-around this problem by uncommenting the end of inquire line in the close subroutine, and everything seems to work fine. And I get the following print:
file_exist: T file_opened: T ios: 5018
But I would to understand what is going on. So what could create such internal file error (while the file should not be internal but external)? Is my workaround could be harmful ? Is it a bug ? Is there a better way to close safely an opened file? Any ideas to isolate the problem ?
EDIT
From roygvib's comment, the following test seems to replicate the problem:
program bug
implicit none
integer :: i
character(len=1) :: s
write (s,'(i1)') 0
open(newUnit=i,file='bug.txt',status='unknown')
inquire(unit=i)
end program bug
The update to gfortran 8.1 solved the problem.

ABAQUS fortran subroutine write command doesn't write anything

I need to save an Abaqus simulation output to an external file. To do this I tried to use a subroutines but I saw it doesn't print anything. I did some test using this code:
SUBROUTINE UMAT(STRESS,STATEV,DDSDDE,SSE,SPD,SCD,
1 RPL,DDSDDT,DRPLDE,DRPLDT,
2 STRAN,DSTRAN,TIME,DTIME,TEMP,DTEMP,PREDEF,DPRED,CMNAME,
3 NDI,NSHR,NTENS,NSTATV,PROPS,NPROPS,COORDS,DROT,PNEWDT,
4 CELENT,DFGRD0,DFGRD1,NOEL,NPT,LAYER,KSPT,JSTEP,KINC)
C
INCLUDE 'ABA_PARAM.INC'
C
CHARACTER*80 CMNAME
DIMENSION STRESS(NTENS),STATEV(NSTATV),
1 DDSDDE(NTENS,NTENS),DDSDDT(NTENS),DRPLDE(NTENS),
2 STRAN(NTENS),DSTRAN(NTENS),TIME(2),PREDEF(1),DPRED(1),
3 PROPS(NPROPS),COORDS(3),DROT(3,3),DFGRD0(3,3),DFGRD1(3,3),
4 JSTEP(4)
C user coding to define DDSDDE, STRESS, STATEV, SSE, SPD, SCD
C and, if necessary, RPL, DDSDDT, DRPLDE, DRPLDT, PNEWDT
C
OPEN (UNIT=1, FILE='D:\Temp\workspace\fortan\data_fortran.dat',
1 STATUS='UNKNOWN', ACCESS='DIRECT',FORM='FORMATTED')
WRITE (1,*) 'WRITE TEST'
CLOSE (1)
RETURN
END
-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-°-
SUBROUTINE UGENS(DDNDDE,FORCE,STATEV,SSE,SPD,PNEWDT,STRAN,
1 DSTRAN,TSS,TIME,DTIME,TEMP,DTEMP,PREDEF,DPRED,CENAME,NDI,
2 NSHR,NSECV,NSTATV,PROPS,JPROPS,NPROPS,NJPROP,COORDS,CELENT,
3 THICK,DFGRD,CURV,BASIS,NOEL,NPT,KSTEP,KINC,NIT,LINPER)
C
INCLUDE 'ABA_PARAM.INC'
C
CHARACTER*80 CENAME
DIMENSION DDNDDE(NSECV,NSECV),FORCE(NSECV),STATEV(NSTATV),
1 STRAN(NSECV),DSTRAN(NSECV),TSS(2),TIME(2),PREDEF(*),
2 DPRED(*),PROPS(*),JPROPS(*),COORDS(3),DFGRD(3,3),
3 CURV(2,2),BASIS(3,3)
C
logical, save :: isFileOpen = .FALSE.
C
CALL GETVRM('TEMP',ARRAY,JARRAY,FLGRAY,JRCD,JMAC,JMATYP,MATLAYO,
1LACCFLA)
C IS THE FILE OPEN?
if (.not. isFileOpen) then
OPEN (UNIT=1, FILE='D:\Temp\workspace\fortan\data.txt',
1 STATUS='NEW')
C CHANGE FILE FLAG
isFileOpen = .TRUE.
end if
write (1,*) 'WRITE TRY'
RETURN
END
The simulation runs without any error but it doesn't write the file, regardless the results (it doesn't print a text).
I thought it could be a link error but everything seems to be ok:
I am using:
Abaqus 6.14
Parallel Studio XE 2013
Intel Composer XE 2013
and all
abaqus verify -user_std
abaqus info=system
abaqus verify -all
gave me PASS.
I don't really know where could be the error. Does anyone have any idea?
I would try to write to an already available channel. For instance in UMAT, Write(6,) prints the Gauss Point info to the .dat file while write(7,) prints to the .msg file. Such procedure may seem a good approach while debugging . When you want info only at the end of each converged increment you may want to pass info to the uexternal routine by common blocks and loop over GP in that routine.
An even better approach is to create SDVs and check them at the odb via UI. In that case you need to declare in the input file how many sdvs you want to pass to the the odb.

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.

Write and read access=stream files in fortran

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.