I'm running a test, and found that the file doesn't actually get written until I control-C to abort the program. Can anyone explain why that would happen?
I expected it to write at the same time, so I could read the file in the middle of the process.
import os
from time import sleep
f = open("log.txt", "a+")
i = 0
while True:
f.write(str(i))
f.write("\n")
i += 1
sleep(0.1)
Writing to disk is slow, so many programs store up writes into large chunks which they write all-at-once. This is called buffering, and Python does it automatically when you open a file.
When you write to the file, you're actually writing to a "buffer" in memory. When it fills up, Python will automatically write it to disk. You can tell it "write everything in the buffer to disk now" with
f.flush()
This isn't quite the whole story, because the operating system will probably buffer writes as well. You can tell it to write the buffer of the file with
os.fsync(f.fileno())
Finally, you can tell Python not to buffer a particular file with open(f, "w", 0) or only to keep a 1-line buffer with open(f,"w", 1). Naturally, this will slow down all operations on that file, because writes are slow.
You need to f.close() to flush the file write buffer out to the file. Or in your case you might just want to do a f.flush(); os.fsync(); so you can keep looping with the opened file handle.
Don't forget to import os.
You have to force the write, so I i use the following lines to make sure a file is written:
# Two commands together force the OS to store the file buffer to disc
f.flush()
os.fsync(f.fileno())
You will want to check out file.flush() - although take note that this might not write the data to disk, to quote:
Note:
flush() does not necessarily write the file’s data to disk. Use flush() followed by os.fsync() to ensure this behavior.
Closing the file (file.close()) will also ensure that the data is written - using with will do this implicitly, and is generally a better choice for more readability and clarity - not to mention solving other potential problems.
This is a windows-ism. If you add an explicit .close() when you're done with file, it'll appear in explorer at that time. Even just flushing it might be enough (I don't have a windows box handy to test). But basically f.write does not actually write, it just appends to the write buffer - until the buffer gets flushed you won't see it.
On unix the files will typically show up as a 0-byte file in this situation.
File Handler to be flushed.
f.flush()
The file does not get written, as the output buffer is not getting flushed until the garbage collection takes effect, and flushes the I/O buffer (more than likely by calling f.close()).
Alternately, in your loop, you can call f.flush() followed by os.fsync(), as documented here.
f.flush()
os.fsync()
All that being said, if you ever plan on sharing the data in that file with other portions of your code, I would highly recommend using a StringIO object.
Related
We have a project where multiple nodes writes a data to a file in sequence and the file resides on NFS.
We were using synchronous NFS before so the flush to file streams just worked fine. Now we have asynchronous NFS and its not working. Not working in a sense obviously the caching comes into picture and other nodes doesnt see the changes made by a particular node.
I wanted to know if there is a way to forcefully flush the data from the cache to disk. I know this is not efficient but it will get things working until we get the real solution in place.
I've had a similar problem using NFS with VxWorks. After some experimentation I've found a way to surely flush data to the device:
int fd;
fd = open("/ata0a/test.dat", O_RDWR | O_CREATE);
write(fd, "Hallo", 5);
/* data is having a great time in some buffers... */
ioctl(fd, FIOSYNC, 0); // <-- may last quite a while...
/* data is flushed to file */
I've never worked with ofstreams neither do I know if your OS provides something similar to the code shown above...
But one thing to try is to simply close the file. This will cause all buffers to be flushed. But be aware that there may be some time between closing the file and all data being flushed which your application does not see since the "close" call may return before the data is written. Additionally this creates a lot of overhead since you have to re-open the file afterwards.
If this is no option you can also write as much "dummy-data" after your data to cause the buffers to fill up. This will also result in the data being written to the file. But this may waste a lot of disk space depending on the size of your data.
I have a fortran code which needs to read a series of ascii data files (which all together are about 25 Gb). Basically the code opens a given ascii file, reads the information and use it to do some operations, and then close it. Then opens another file, reads the information, do some operations, and close it again. And so on with the rest of ascii files.
Overall each complete run takes about 10h. I usually need to run several independent calculations with different parameters, and the way I do is to run each independent calculation sequentially, so that at the end if I have 10 independent calculations, the total CPU time is 100h.
A more rapid way would be to run the 10 independent calculations at the same time using different processors on a cluster machine, but the problem is that if a given calculation needs to open and read data from a given ascii file which has been already opened and it's being used by another calculation, then the code gives obviously an error.
I wonder whether there is a way to verify if a given ascii file is already being used by another calculation, and if so to ask the code to wait until the ascii file is finally closed.
Any help would be of great help.
Many thanks in advance.
Obamakoak.
Two processes should be able to read the same file. Perhaps action="read" on the open statement might help. Must the files be human readable? The I/O would very likely be much faster with unformatted (sometimes call binary) files.
P.S. If your OS doesn't support multiple-read access, you might have to create your own lock system. Create a master file that a process opens to check which files are in use or not, and to update said list. Immediately closing after a check or update. To handle collisions on this read/write file, use iostat on the open statement and retry after a delay if there is an error.
I know this is an old thread but I've been struggling with the same issue for my own code.
My first attempt was creating a variable on a certain process (e.g. the master) and accessing this variable exclusively using one-sided passive MPI. This is fancy and works well, but only with newer versions of MPI.
Also, my code seemed happy to open (with READWRITE status) files that were also open in other processes.
Therefore, the easiest workaround, if your program has file access, is to make use of an external lock file, as described here. In your case, the code might look something like this:
A process checks whether the lock file exists using the NEW statement, which fails if a file already exists. It will look something like:
file_exists = .true.
do while (file_exists)
open(STATUS='NEW',unit=11,file=lock_file_name,iostat=open_stat)
if (open_stat.eq.0) then
file_exists = .false.
open(STATUS='OLD',ACTION=READWRITE',unit=12,file=data_file_name,iostat=ierr)
if (ierr.ne.0) stop
else
call sleep(1)
end if
end do
The file is now opened exclusively by the current process. Do the operations you need to do, such as reading, writing.
When you are done, close the data file and finally the lock file
close(12,iostat=ierr)
if (ierr.ne.0) stop
close(11,status='DELETE',iostat=ierr)
if (ierr.ne.0) stop
The data file is now again unlocked for the other processes.
I hope this may be useful for other people who have the same problem.
I am going to read a file in C++. The reading itself is happening in a while-loop, and is reading from one file.
When the function reads information from the file, it is going to push this information up some place in the system. The problem is that this file may change while the loop is ongoing.
How may I catch that new information in the file? I tried out std::ifstream reading and changing my file manually on my computer as the endless-loop (with a sleep(2) between each loop) was ongoing, but as expected -- nothing happend.
EDIT: the file will overwrite itself at each new entry of data to the file.
Help?
Running on virtual box Ubuntu Linux 12.04, if that may be useful info. And this is not homework.
The usual solution is something along the lines of what MichaelH
proposes: the writing process opens the file in append mode, and
always writes to the end. The reading process does what
MichaelH suggests.
This works fine for small amounts of data in each run. If the
processes are supposed to run a long time, and generate a lot of
data, the file will eventually become too big, since it will
contain all of the processed data as well. In this case, the
solution is to use a directory, generating numbered files in it,
one file per data record. The writing process will write each
data set to a new file (incrementing the number), and the
reading process will try to open the new file, and delete it
when it has finished. This is considerably more complex than
the first suggestion, but will work even for processes
generating large amounts of data per second and running for
years.
EDIT:
Later comments by the OP say that the device is actually a FIFO.
In that case:
you can't seek, so MichaelH's suggestion can't be used
literally, but
you don't need to seek, since data is automatically removed
from the FIFO whenever it has been read, and
depending on the size of the data, and how it is written, the
writes may be atomic, so you don't have to worry about partial
records, even if you happen to read exactly in the middle of
a write.
With regards to the latter: make sure that both the read and
write buffers are large enough to contain a complete record, and
that the writer flushes after each record. And make sure that
the records are smaller than the size needed to guarantee
atomicity. (Historically, on the early Unix I know, this was
4096, but I would be surprised if it hasn't increased since
then. Although... Under Posix, this is defined by PIPE_BUF,
which is only guaranteed to be at least 512, and is only 4096
under modern Linux.)
Just read the file, rename the file, open the renamed file. do the processing of data to your system, and at the end of the loop close the file. After a sleep, re-open the file at the top of the white loop, rename it and repeat.
That's the simplest way to approach the problem and saves having to write code to process dynamic changes to the file during the processing stage.
To be absolutely sure you don't get any corruption it's best to rename the file. This guarantees that any changes from another process do not affect the processing. It may not be necessary to do this - it depends on the processing and how the file is updated. But it's a safer approach. A move or rename operation is guaranteed to be atomic - so there should be no concurreny issues if using this approach.
You can use inotify to watch file changes.
If you need simpler solution - read file attributes ( with stat(), and check last_write_time of a file ).
However you still may miss some file modification, while you'll be opening and rereading file. So if you have control over the application which writes to a file, i'd recommend you using something else to communicate between these processes, pipes for example.
To be more explicit, if you want tail-like behavior you'll want to:
Open the file, read in the data. Save the length. Close the file.
Wait for a bit.
Open the file again, attempt to seek to the last read position, read the remaining data, close.
rinse and repeat
Blockquote
how does O.S know that writer is still writing. ?... What is workflow of EOF for file(closing file handle like ^D or ^z) ?
what happens if EOF is never written ?
what happens if readers reading rate is faster than writer's writing speed ? Can a rate mismatch result in deadlock ?
what can be other unwanted scenarios ?
How does O.S calculate EOF while reading file ?
-Nikhil
P.S: Current Operating system is windows but I don't mind learning interesting feature for the same on unix too.
Blockquote
More Edits and More info on the Question
Now that I know EOF is no character,So it cannot be written on the data of file. IF O.S. determines the EOF using File_size like what even #saurabh pointed.
(->) EOF while Reading ( Would probably be determined from file size which would stored in drive table of appropriate File system) )
So does process keeps polling File table for file size to determine EOF as there could be cases of not-fixed files size.
To my little knowledge, EOF is encountered when you read beyond the EOF(in our case file-size). Assume a situation where writer is writing intermittently and reader is reading blocks. SO if reader tries to read more than the available chunk would EOF be thrown ? But Writer has not signalled EOF yet ?
Untill the program dont close the file. OS assumes that the file can be read/written or both (depends on the mode of opening the file).
EOF is nothing, but OS knows it from the size of file. Lets say, your file is of size 100 bytes, and you asks to read from byte 99 and asks for 6 more bytes, then OS knows that file is till only 100th bytes, so it will return EOF.
If you are writing to a file from one process and reading from it from another, you may want to look into using pipes instead. Those are special files designed exactly for your purpose: you can only write at one end, read at the other end and the reader blocks or is notified if there isn't any data to read...
And yes, there is no special EOF marker. If using normal files and you don't like headaches much, just don't mess with them simultaneously from multiple processes.
I have a program that creates pipes between two processes. One process constantly monitors the output of the other and when specific output is encountered it gives input through the other pipe with the write() function. The problem I am having, though is that the contents of the pipe don't go through to the other process's stdin stream until I close() the pipe. I want this program to infinitely loop and react every time it encounters the output it is looking for. Is there any way to send the input to the other process without closing the pipe?
I have searched a bit and found that named pipes can be reopened after closing them, but I wanted to find out if there was another option since I have already written the code to use unnamed pipes and I haven't yet learned to use named pipes.
Take a look at using fflush.
How are you reading the other end? Are you expecting complete strings? You aren't sending terminating NULs in the snippet you posted. Perhaps sending strlen(string)+1 bytes will fix it. Without seeing the code it's hard to tell.
Use fsync. http://pubs.opengroup.org/onlinepubs/007908799/xsh/fsync.html
From http://www.delorie.com/gnu/docs/glibc/libc_239.html:
Once write returns, the data is enqueued to be written and can be read back right away, but it is not necessarily written out to permanent storage immediately. You can use fsync when you need to be sure your data has been permanently stored before continuing. (It is more efficient for the system to batch up consecutive writes and do them all at once when convenient. Normally they will always be written to disk within a minute or less.) Modern systems provide another function fdatasync which guarantees integrity only for the file data and is therefore faster. You can use the O_FSYNC open mode to make write always store the data to disk before returning.