How can I copy a file in fortran 90 in a portable, cross plaform way ?
Use the SYSTEM with your OS's copy command. Practically all compilers support this feature.
You can read/write the file through a stream in Fortran 2003, but in Fortran 90/95 I think this would work to copy an arbitrary file (extremely inefficient though!!)
OPEN(UNIT=ISRC, FILE='', ACCESS='DIRECT', STATUS='OLD', ACTION='READ', IOSTAT=IERR, RECL=1)
OPEN(UNIT=IDST, FILE='', ACCESS='DIRECT', STATUS='REPLACE', ACTION='WRITE', IOSTATE=IERR, RE)
IREC = 1
DO
READ(UNIT=ISRC, REC=IREC, IOSTAT=IERR) CHAR
IF (IERR.NE.0) EXIT
WRITE(UNIT=IDST, REC=I) CHAR
IREC = IREC + 1
END DO
Of course, if it was a fortran generated file, you could use that information to make it more efficient.
On a personal note: if you need invoke system calls from inside fortran, what are you doing? Isn't it better to use some other language that is better suited for the task?
Yes, Fortran has pathetic I/O and shouldn't be used for this sort of thing if at all possible. What a shame that some of us are forced to do it.
I just read the source file and simultaneously write to the destination, line-by-line. So far this works for me, but is very inefficient.
Dealing with files and portability is annoying with Fortran, and SYSTEM calls are often not very good either. The windows OS doesn't properly follow linux linked files, and Windows/Linux/MacOS have different separaters, I have been caught out with stack limits inherent in the SYSTEM call, and so on.
Good luck !
For Intel Fortran
subroutine copy_file (file_name, file_name_new)
! copies a file file_name to file_name_new
! file_name and file_name_new must include the path information and may include wildcard characters
USE ifport
implicit character*100 (f)
character*1000 fnam
logical*4 logical_result
len1 = len_trim(file_name); len2 = len_trim(file_name_new)
fnam = 'copy/y ' //file_name(1:len1) //' '//file_name_new(1:len2)
l = len_trim(fnam)
logical_result = systemqq(fnam(1:l))
return
end
The previous answer didn't work for me so I wrote the following subroutine
!=============================================================================================================================!
! !
! This subroutine copies file_name to file_name_new writing command to cmd !
! !
!=============================================================================================================================!
subroutine copy_file (file_name, file_name_new)
use ifport
implicit none
!=============================================================================================================================
! D e c l a r a t i o n s
!=============================================================================================================================
character(len=*),intent(IN) :: file_name_new,file_name
!-----------------------------------------------------------------------------------------------------------------------------
logical :: logical_result
!=============================================================================================================================
! S t a t e m e n t s
!=============================================================================================================================
logical_result = systemqq('copy "'//trim(file_name) //'" "'//trim(file_name_new)//'"')
!==============================================================================================================================
end subroutine copy_file
! For Compaq/Intel Visual Fortran
subroutine copy_file(source_,dest_)
use kernel32,only:CopyFile,FALSE
implicit none
integer ret
character*(*), intent(in) :: source_, dest_
ret = CopyFile(trim(source_)//""C, trim(dest_)//""C, FALSE)
end subroutine copy_file
Related
GCC version 4.6
The Problem: To find a way to feed in parameters to the executable, say a.out, from the command line - more specifically feed in an array of double precision numbers.
Attempt: Using the READ(*,*) command, which is older in the standard:
Program test.f -
PROGRAM MAIN
REAL(8) :: A,B
READ(*,*) A,B
PRINT*, A+B, COMMAND_ARGUMENT_COUNT()
END PROGRAM MAIN
The execution -
$ gfortran test.f
$ ./a.out 3.D0 1.D0
This did not work. On a bit of soul-searching, found that
$./a.out
3.d0,1.d0
4.0000000000000000 0
does work, but the second line is an input prompt, and the objective of getting this done in one-line is not achieved. Also the COMMAND_ARGUMENT_COUNT() shows that the numbers fed into the input prompt don't really count as 'command line arguments', unlike PERL.
If you want to get the arguments fed to your program on the command line, use the (since Fortran 2003) standard intrinsic subroutine GET_COMMAND_ARGUMENT. Something like this might work
PROGRAM MAIN
REAL(8) :: A,B
integer :: num_args, ix
character(len=12), dimension(:), allocatable :: args
num_args = command_argument_count()
allocate(args(num_args)) ! I've omitted checking the return status of the allocation
do ix = 1, num_args
call get_command_argument(ix,args(ix))
! now parse the argument as you wish
end do
PRINT*, A+B, COMMAND_ARGUMENT_COUNT()
END PROGRAM MAIN
Note:
The second argument to the subroutine get_command_argument is a character variable which you'll have to parse to turn into a real (or whatever). Note also that I've allowed only 12 characters in each element of the args array, you may want to fiddle around with that.
As you've already figured out read isn't used for reading command line arguments in Fortran programs.
Since you want to read an array of real numbers, you might be better off using the approach you've already figured out, that is reading them from the terminal after the program has started, it's up to you.
The easiest way is to use a library. There is FLAP or f90getopt available. Both are open source and licensed under free licenses.
The latter is written by Mark Gates and me, just one module and can be learned in minutes but contains all what is needed to parse GNU- and POSIX-like command-line options. The first is more sophisticated and can be used even in closed-source projects. Check them out.
Furthermore libraries at https://fortranwiki.org/fortran/show/Command-line+arguments
What READ (*,*) does is that it reads from the standard input. For example, the characters entered using the keyboard.
As the question shows COMMAND_ARGUMENT_COUNT() can be used to get the number of the command line arguments.
The accepted answer by High Performance Mark show how to retrieve the individual command line arguments separated by blanks as individual character strings using GET_COMMAND_ARGUMENT(). One can also get the whole command line using GET_COMMAND(). One then has to somehow parse that character-based information into the data in your program.
I very simple cases you just need the program requires, for example, two numbers, so you read one number from arg 1 and another form arg 2. That is simple. Or you can read a triplet of numbers from a single argument if they are comma-separated like 1,2,3 using a simple read(arg,*) nums(1:3).
For general complicated command line parsing one uses libraries such as those mentioned in the answer by Hani. You have set them up so that the library knows the expected syntax of the command line arguments and the data it should fill with the values.
There is a middle ground, that is still relatively simple, but one already have multiple arguments, that correspond to Fortran variables in the program, that may or may not be present. In that case one can use the namelist for the syntax and for the parsing.
Here is an example, the man point is the namelist /cmd/ name, point, flag:
implicit none
real :: point(3)
logical :: flag
character(256) :: name
character(1024) :: command_line
call read_command_line
call parse_command_line
print *, point
print *, "'",trim(name),"'"
print *, flag
contains
subroutine read_command_line
integer :: exenamelength
integer :: io, io2
command_line = ""
call get_command(command = command_line,status = io)
if (io==0) then
call get_command_argument(0,length = exenamelength,status = io2)
if (io2==0) then
command_line = "&cmd "//adjustl(trim(command_line(exenamelength+1:)))//" /"
else
command_line = "&cmd "//adjustl(trim(command_line))//" /"
end if
else
write(*,*) io,"Error getting command line."
end if
end subroutine
subroutine parse_command_line
character(256) :: msg
namelist /cmd/ name, point, flag
integer :: io
if (len_trim(command_line)>0) then
msg = ''
read(command_line,nml = cmd,iostat = io,iomsg = msg)
if (io/=0) then
error stop "Error parsing the command line or cmd.conf " // msg
end if
end if
end subroutine
end
Usage in bash:
> ./command flag=T name=\"data.txt\" point=1.0,2.0,3.0
1.00000000 2.00000000 3.00000000
'data.txt'
T
or
> ./command flag=T name='"data.txt"' point=1.0,2.0,3.0
1.00000000 2.00000000 3.00000000
'data.txt'
T
Escaping the quotes for the string is unfortunately necessary, because bash eats the first quotes.
GCC version 4.6
The Problem: To find a way to feed in parameters to the executable, say a.out, from the command line - more specifically feed in an array of double precision numbers.
Attempt: Using the READ(*,*) command, which is older in the standard:
Program test.f -
PROGRAM MAIN
REAL(8) :: A,B
READ(*,*) A,B
PRINT*, A+B, COMMAND_ARGUMENT_COUNT()
END PROGRAM MAIN
The execution -
$ gfortran test.f
$ ./a.out 3.D0 1.D0
This did not work. On a bit of soul-searching, found that
$./a.out
3.d0,1.d0
4.0000000000000000 0
does work, but the second line is an input prompt, and the objective of getting this done in one-line is not achieved. Also the COMMAND_ARGUMENT_COUNT() shows that the numbers fed into the input prompt don't really count as 'command line arguments', unlike PERL.
If you want to get the arguments fed to your program on the command line, use the (since Fortran 2003) standard intrinsic subroutine GET_COMMAND_ARGUMENT. Something like this might work
PROGRAM MAIN
REAL(8) :: A,B
integer :: num_args, ix
character(len=12), dimension(:), allocatable :: args
num_args = command_argument_count()
allocate(args(num_args)) ! I've omitted checking the return status of the allocation
do ix = 1, num_args
call get_command_argument(ix,args(ix))
! now parse the argument as you wish
end do
PRINT*, A+B, COMMAND_ARGUMENT_COUNT()
END PROGRAM MAIN
Note:
The second argument to the subroutine get_command_argument is a character variable which you'll have to parse to turn into a real (or whatever). Note also that I've allowed only 12 characters in each element of the args array, you may want to fiddle around with that.
As you've already figured out read isn't used for reading command line arguments in Fortran programs.
Since you want to read an array of real numbers, you might be better off using the approach you've already figured out, that is reading them from the terminal after the program has started, it's up to you.
The easiest way is to use a library. There is FLAP or f90getopt available. Both are open source and licensed under free licenses.
The latter is written by Mark Gates and me, just one module and can be learned in minutes but contains all what is needed to parse GNU- and POSIX-like command-line options. The first is more sophisticated and can be used even in closed-source projects. Check them out.
Furthermore libraries at https://fortranwiki.org/fortran/show/Command-line+arguments
What READ (*,*) does is that it reads from the standard input. For example, the characters entered using the keyboard.
As the question shows COMMAND_ARGUMENT_COUNT() can be used to get the number of the command line arguments.
The accepted answer by High Performance Mark show how to retrieve the individual command line arguments separated by blanks as individual character strings using GET_COMMAND_ARGUMENT(). One can also get the whole command line using GET_COMMAND(). One then has to somehow parse that character-based information into the data in your program.
I very simple cases you just need the program requires, for example, two numbers, so you read one number from arg 1 and another form arg 2. That is simple. Or you can read a triplet of numbers from a single argument if they are comma-separated like 1,2,3 using a simple read(arg,*) nums(1:3).
For general complicated command line parsing one uses libraries such as those mentioned in the answer by Hani. You have set them up so that the library knows the expected syntax of the command line arguments and the data it should fill with the values.
There is a middle ground, that is still relatively simple, but one already have multiple arguments, that correspond to Fortran variables in the program, that may or may not be present. In that case one can use the namelist for the syntax and for the parsing.
Here is an example, the man point is the namelist /cmd/ name, point, flag:
implicit none
real :: point(3)
logical :: flag
character(256) :: name
character(1024) :: command_line
call read_command_line
call parse_command_line
print *, point
print *, "'",trim(name),"'"
print *, flag
contains
subroutine read_command_line
integer :: exenamelength
integer :: io, io2
command_line = ""
call get_command(command = command_line,status = io)
if (io==0) then
call get_command_argument(0,length = exenamelength,status = io2)
if (io2==0) then
command_line = "&cmd "//adjustl(trim(command_line(exenamelength+1:)))//" /"
else
command_line = "&cmd "//adjustl(trim(command_line))//" /"
end if
else
write(*,*) io,"Error getting command line."
end if
end subroutine
subroutine parse_command_line
character(256) :: msg
namelist /cmd/ name, point, flag
integer :: io
if (len_trim(command_line)>0) then
msg = ''
read(command_line,nml = cmd,iostat = io,iomsg = msg)
if (io/=0) then
error stop "Error parsing the command line or cmd.conf " // msg
end if
end if
end subroutine
end
Usage in bash:
> ./command flag=T name=\"data.txt\" point=1.0,2.0,3.0
1.00000000 2.00000000 3.00000000
'data.txt'
T
or
> ./command flag=T name='"data.txt"' point=1.0,2.0,3.0
1.00000000 2.00000000 3.00000000
'data.txt'
T
Escaping the quotes for the string is unfortunately necessary, because bash eats the first quotes.
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.
I'm trying to verify that a directory exists using Fortan90. On various sites I found:
logical :: dir_e
inquire(file='./docs/.', exist=dir_e)
if ( dir_e ) then
write(*,*) "dir exists!"
else
! workaround: it calls an extern program...
call system('mkdir docs')
end if
However, inquire returns False whether or not the directory exists and if I execute this code twice, I get an error message
cannot make dir, file already exists
If I use:
inquire(file='./docs/test', exist=dir_e)
with an existing file test, inquire returns true.
How can I check for the existence of a directory? I am using ubuntu 11.04 and the ifort compiler.
The Fortran standard 95, 2003 and 2008 do not specify, how inquire should treat directories. From my experience under Linux, gfortran treats them as files, ifort does not. The directory statement is a proprietary feature of ifort and should therefore be avoided.
The safest would be to test for a file in the said directory.
The following should work:
INQUIRE (DIRECTORY=dir, EXIST=ex [, DIRSPEC=dirspec] [, ERR=label] [, IOSTAT=i-var] )
I don't have ifort on this machine so I can't test it.
Addendum: The code posted originally works with gfortran. The DIRECTORY statement works with ifort but not with gfortran.
And in case for more information check: http://software.intel.com/sites/products/documentation/hpc/compilerpro/en-us/fortran/win/compiler_f/lref_for/source_files/rfinquir.htm#rfinquir
Most of the time, one checks if the directory exists so to write something in it. What I do is just create the directory. If it already exists there is no problem.
CALL system("mkdir video")
CALL chdir("video")
CALL getcwd(path)
You could use C routines to test the files :
C side (OK with ifort and gfortran on Win32 and Linux 32/64)
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <errno.h>
#include <sys/stat.h>
#if defined(_WIN32) && defined(__INTEL_COMPILER)
# include "dirent_windows.h"
#else
# include <dirent.h>
#endif
void file_info(const char*filename,int*mode,int*exist,int*time){
int k;
struct stat buf;
k=stat(filename,&buf);
if(k != 0) {
*mode=0;
*exist=0;
*time=0;
}else{
*mode=buf.st_mode;
if(*mode == 0) *exist=0; else *exist=1;
*time=buf.st_mtime;
}
}
Fortran side :
MODULE file
USE iso_c_binding
INTERFACE
SUBROUTINE file_info(filename,mode,exist,time) BIND(C,name="file_info")
USE iso_c_binding
CHARACTER(kind=C_CHAR),INTENT(in) :: filename(*)
INTEGER(C_INT),INTENT(out) :: mode,exist,time
END SUBROUTINE
END INTERFACE
END MODULE
How to use in a Fortran routine :
..
use file
use iso_c_binding
...
integer(c_int) :: mode,exist,time
...
call file_info("./docs"//char(0),mode,exist,time)
Advantage : it works for any kind of file and provides additional pieces of information like the mode (read/write/execute permission) and the creation time.
Here's a subroutine I use often -- it uses the conditional you asked about:
subroutine create_directory( newDirPath )
! Author: Jess Vriesema
! Date: Spring 2011
! Purpose: Creates a directory at ./newDirPath
implicit none
character(len=*), intent(in) :: newDirPath
character(len=256) :: mkdirCmd
logical :: dirExists
! Check if the directory exists first
! inquire( file=trim(newDirPath)//'/.', exist=dirExists ) ! Works with gfortran, but not ifort
inquire( directory=newDirPath, exist=dirExists ) ! Works with ifort, but not gfortran
if (dirExists) then
! write (*,*) "Directory already exists: '"//trim(newDirPath)//"'"
else
mkdirCmd = 'mkdir -p '//trim(newDirPath)
write(*,'(a)') "Creating new directory: '"//trim(mkdirCmd)//"'"
call system( mkdirCmd )
endif
end subroutine create_directory
Depending on which compiler you use, you'll have to decide which of those conditionals is right for you.
Unfortunately, I do not have access to nagfor and don't know how it treats directories.
Another non-portable solution is to let the shell (Bash, in this case) do the work:
call system('[[ ! -e docs ]] && mkdir docs')
I had the same problem. If you want a compiler independent way of doing this, you can try to open a small file within the directory. The open statement allows for the code to jump to a particular line (specified by err=) if the open statement fails:
! Tests whether the directory exists
subroutine checkdir(dir)
implicit none
character(len=*), intent(in) :: dir
integer :: unitno
! Test whether the directory exists
open(newunit=unitno,file=trim(dir)//'deleteme.txt',status='replace',err=1234)
close (unitno)
return
! If doesn't exist, end gracefully
1234 write(*,*) 'Data directory, '//trim(dir)//' does not exist or could not write there!'
STOP
end subroutine
Note that this is not foolproof, as it is assumed "dir" has the trailing "/" or "\" depending on the OS being used.
I need to develop a library that opens a file and parses the stuff.
The unit number, due to fortran IO style, must be decided by me, but I can't know what other units are open in the client code. Is there a standard function like give_me_any_unit_number_that_is_free() ?
In fortran 2008, there's a newunit clause to open that you can use
integer :: myunit
..
open(newunit=myunit,file='file.dat')
...
close(myunit)
but that's new enough that not all compilers support it yet. If yours doesn't yet, you can mock one up yourself; there's a good example on the fortran wiki.
You can use INQUIRE to find a unit number that is not in use:
integer*4 function get_file_unit (lu_max)
!
! get_file_unit returns a unit number that is not in use
integer*4 lu_max, lu, m, iostat
logical opened
!
m = lu_max ; if (m < 1) m = 97
do lu = m,1,-1
inquire (unit=lu, opened=opened, iostat=iostat)
if (iostat.ne.0) cycle
if (.not.opened) exit
end do
!
get_file_unit = lu
return
end function get_file_unit