I was doing some experiments to learn more about Linux process states.
So, there's a directory(named big_dir) with over a billion files in it(the directory has many sub-directories recursively), and then I run tar -cv big_dir | ssh anotherServer "tar -xv -C big_dir" and found out via executing top that, the tar process stays in D status. Meanwhile, the tar command keeps outputting the paths of the files.
I know that, the process was in D status because it was doing disk I/O, but why didn't its status keep switching between D and R? Printing the file names under the directory must have used some CPU computation, isn't it? Otherwise how could the find command know that it should print something?
If I run dd if=/dev/zero of=/dev/null, then the dd process status kept in R status from the top output. But why wasn't it in D status? Wasn't it doing I/O all the time?
/dev/zero and /dev/null are pseudo-devices. So there's no physical device behind them.
If I do
dd if=/dev/zero of=/tmp/zeroes
then top does show me dd in the D status. However it does spend a lot of it's time in R (in CPU time). top will simply sample the process table and consequently you may need to watch it for some time in order to see transient states.
I suspect for your tar example above that the amount of time outputting to stdout is negligible compared to the disk time. Note also that outputting to stdout will also involve the windowing system writing and whilst it's doing that the process will be sleeping. e.g. I'm running yes right now, and the majority of the work is being performed by my X server. The yes process is sleeping for most of the time I'm watching it (via top)
I'm sure your tar process SOMETIMES goes to R, but it's probably for a very short period of time, because it doesn't do that much - particularly since you are sending the data through a network. Unless that's a 10Gb/s network card [and everything else to "anotherServer" is really working at 1GB/s], this will be the slowest part of the chain. ssh itself will take a little bit of overhead as it encrypts the data.
It probably takes tar a few microseconds to ask for some data from the disk, and a few milliseconds for the disk to move its head and read the actual data. So you have about 0.1% of the time in "R", the rest is in "D".
Related
I am planning to write a linux command which is going to process (with a custom logic) a very big file. Once this command is run, it will take hours to finish the task.
What is the best way to give eta output?
What about the idea of writing a 100 byte progress status file? In specific stages I can write bytes to the file. Say at 40% I can write 40 bytes to the file. Once the file size reaches 100 bytes size it means the process is finished. So to monitor the progress we have to check only the size of this file.
Is there any general way of handling such progress information? I don't want to include too much logic in my program for displaying the progress information. I am looking for a simple solution.
Any suggestions?
The normal way would be to set up a signal handler like dd does, and then you send the process a SIGUSR1 or somesuch using the kill command and it catches the signal and outputs a status message. Try
man dd
So, on my iMac, for example, dd uses SIGINFO, so
# Move a whole load of nothing to nowhere in the background
dd if=/dev/zero of=/dev/null &
[1] 11232
# No output, till I want some a few seconds later
kill -SIGINFO 11232
12875835+0 records in
12875834+0 records out
6592427520 bytes transferred in 9.380158 secs (702805581 bytes/sec)
# No more output, till I want some a few more seconds later
kill -SIGINFO 11232
19163866+0 records in
19163865+0 records out
9811898880 bytes transferred in 14.015095 secs (700095068 bytes/sec)
A signal handler is pretty easy to set up, even in a shell script. For example:
#!/bin/bash
trap "echo Progress report..." SIGINT
echo "My process id is $$"
while : ; do
sleep 10 # Do something - admittedly little :-)
done
I'm afraid you can't do this nicely in Linux but if the result of your program can be an output stream like in unzip then you just can use pv - Pipe Viewer command. You can redirect the output into pv input and it will show you the progress.
In Windows you can use Taskbar Extensions API with methods SetProgressState and SetProgressValue.
I have a script that produces a lot of output. The script pauses for a few seconds at point T.
Now I am using the less command to analyze the output of the script.
So I execute ./script | less. I leave it running for sufficient time so that the script would have finished executing.
Now I go through the output of the less command by pressing Pg Down key. Surprisingly while scrolling at the point T of the output I notice the pause of few seconds again.
The script does not expect any input and would have definitely completed by the time I start analyzing the output of less.
Can someone explain how the pause of few seconds is noticable in the output of less when the script would have finished executing?
Your script is communicating with less via a pipe. Pipe is an in-memory stream of bytes that connects two endpoints: your script and the less program, the former writing output to it, the latter reading from it.
As pipes are in-memory, it would be not pleasant if they grew arbitrarily large. So, by default, there's a limit of data that can be inside the pipe (written, but not yet read) at any given moment. By default it's 64k on Linux. If the pipe is full, and your script tries to write to it, the write blocks. So your script isn't actually working, it stopped at some point when doing a write() call.
How to overcome this? Adjusting defaults is a bad option; what is used instead is allocating a buffer in the reader, so that it reads into the buffer, freeing the pipe and thus letting the writing program work, but shows to you (or handles) only a part of the output. less has such a buffer, and, by default, expands it automatically, However, it doesn't fill it in the background, it only fills it as you read the input.
So what would solve your problem is reading the file until the end (like you would normally press G), and then going back to the beginning (like you would normally press g). The thing is that you may specify these commands via command line like this:
./script | less +Gg
You should note, however, that you will have to wait until the whole script's output loads into memory, so you won't be able to view it at once. less is insufficiently sophisticated for that. But if that's what you really need (browsing the beginning of the output while the ./script is still computing its end), you might want to use a temporary file:
./script >x & less x ; rm x
The pipe is full at the OS level, so script blocks until less consumes some of it.
Flow control. Your script is effectively being paused while less is paging.
If you want to make sure that your command completes before you use less interactively, invoke less as less +G and it will read to the end of the input, you can then return to the start by typing 1G into less.
For some background information there's also a nice article by Alexander Sandler called "How less processes its input"!
http://www.alexonlinux.com/how-less-processes-its-input
Can I externally enforce line buffering on the script?
Is there an off the shelf pseudo tty utility I could use?
You may try to use the script command to turn on line-buffering output mode.
script -q /dev/null ./script | less # FreeBSD, Mac OS X
script -c "./script" /dev/null | less # Linux
For more alternatives in this respect please see: Turn off buffering in pipe.
I have two programs A and B. I can't change the program A - I can only run it with some parameters, but I have written the B myself, and I can modify it the way I like.
Program A runs for a long time (20-40 hours) and during that time it produces output to the file, so that its size increases constantly and can be huge at the end of run (like 100-200 GB). The program B then reads the file and calculates some stuff. The special property of the file is that its content is not correlated: I can divide the file in half and run calculations on each part independently, so that I don't need to store all the data at once: I can calculate on the first part, then throw it away, calculate on the second one, etc.
The problem is that I don't have enough space to store such a big files. I wonder if it is possible to pipe somehow the output of the A to B without storing all the data at once and without making huge files. Is it possible to do something like that?
Thank you in advance, this is crucial for me now, Roman.
If program A supports it, simply pipe.
A | B
Otherwise, use a fifo.
mkfifo /tmp/fifo
ls -la > /tmp/fifo &
cat /tmp/fifo
EDIT: Adjust buffer sizes with ulimit -p and then:
cat /tmp/fifo | B
It is possible to pipeline output of one program into another.
Read here to know the syntax and know-hows of Unix pipelining.
you can use socat which can take stdout and feed it to network and get from network and feed it to stdin
named or unnamed pipe have a problem of small ( 4k ? ) buffer .. that means too many process context switches if you are writing multi gb ...
Or if you are adventurous enough .. you can LD_PRELOAD a so in process A, and trap the open/write calls to do whatever ..
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I typically end up in the following situation: I have, say, a 650 MB MPEG-2 .avi video file from a camera. Then, I use ffmpeg2theora to convert it into Theora .ogv video file, say some 150 MB in size. Finally, I want to upload this .ogv file to an ssh server.
Let's say, the ffmpeg2theora encoding process takes some 15 minutes on my PC. On the other hand, the upload goes on with a speed of about 60 KB/s, which takes some 45 minutes (for the 150MB .ogv). So: if I first encode, and wait for the encoding process to finish - and then upload, it would take approximately
15 min + 45 min = 1 hr
to complete the operation.
So, I thought it would be better if I could somehow start the upload, in parallel with the encoding operation; then, in principle - as the uploading process is slower (in terms of transferred bytes/sec) than the encoding one (in terms of generated bytes/sec) - the uploading process would always "trail behind" the encoding one, and so the whole operation (enc+upl) would complete in just 45 minutes (that is, just the time of the upload process +/- some minutes depending on actual upload speed situation on wire).
My first idea was to pipe the output of ffmpeg2theora to tee (so as to keep a local copy of the .ogv) and then, pipe the output further to ssh - as in:
./ffmpeg2theora-0.27.linux32.bin -v 8 -a 3 -o /dev/stdout MVI.AVI | tee MVI.ogv | ssh user#ssh.server.com "cat > ~/myvids/MVI.ogv"
While this command does, indeed, function - one can easily see in the running log in the terminal from ffmpeg2theora, that in this case, ffmpeg2theora calculates a predicted time of completion to be 1 hour; that is, there seems to be no benefit in terms of smaller completion time for both enc+upl. (While it is possible that this is due to network congestion, and me getting less of a network speed at the time - it seems to me, that ffmpeg2theora has to wait for an acknowledgment for each little chunk of data it sends through the pipe, and that ACK finally has to come from ssh... Otherwise, ffmpeg2theora would not have been able to provide a completion time estimate. Then again, maybe the estimate is wrong, while the operation would indeed complete in 45 mins - dunno, never had patience to wait and time the process; I just get pissed at 1hr as estimate, and hit Ctrl-C ;) ...)
My second attempt was to run the encoding process in one terminal window, i.e.:
./ffmpeg2theora-0.27.linux32.bin -v 8 -a 3 MVI.AVI # MVI.ogv is auto name for output
..., and the uploading process, using scp, in another terminal window (thereby 'forcing' 'parallelization'):
scp MVI.ogv user#ssh.server.com:~/myvids/
The problem here is: let's say, at the time when scp starts, ffmpeg2theora has already encoded 5 MB of the output .ogv file. At this time, scp sees this 5 MB as the entire file size, and starts uploading - and it exits when it encounters the 5 MB mark; while in the meantime, ffmpeg2theora may have produced additional 15 MB, making the .ogv file 20 MB in total size at the time scp has exited (finishing the transfer of the first 5 MB).
Then I learned (joen.dk ยป Tip: scp Resume) that rsync supports 'resume' of partially completed uploads, as in:
rsync --partial --progress myFile remoteMachine:dirToPutIn/
..., so I tried using rsync instead of scp - but it seems to behave exactly the same as scp in terms of file size, that is: it will only transfer up to the file size read at the beginning of the process, and then it will exit.
So, my question to the community is: Is there a way to parallelize the encoding and uploading process, so as to gain the decrease in total processing time?
I'm guessing there could be several ways, as in:
A command line option (that I haven't seen) that forces scp/rsync to continuously check the file size - if the file is open for writing by another process (then I could simply run the upload in another terminal window)
A bash script; say running rsync --partial in a while loop, that runs as long as the .ogv file is open for writing by another process (I don't actually like this solution, since I can hear the harddisk scanning for the resume point, every time I run rsync --partial - which, I guess, cannot be good; if I know that the same file is being written to at the same time)
A different tool (other than scp/rsync) that does support upload of a "currently generated"/"unfinished" file (the assumption being it can handle only growing files; it would exit if it encounters that the local file is suddenly less in size than the bytes already transferred)
... but it could also be, that I'm overlooking something - and 1hr is as good as it gets (in other words, it is maybe logically impossible to achieve 45 min total time - even if trying to parallelize) :)
Well, I look forward to comments that would, hopefully, clarify this for me ;)
Thanks in advance,
Cheers!
May be you can try sshfs (http://fuse.sourceforge.net/sshfs.html).This being a file system should have some optimization though I am not very sure.
I have an application (video stream capture) which constantly writes its data to a single file. Application typically runs for several hours, creating ~1 gigabyte file. Soon (in a matter of several seconds) after it quits, I'd like to have 2 copies of file it was writing - let's say, one in /mnt/disk1, another in /mnt/disk2 (the latter is an USB flash drive with FAT32 filesystem).
I don't really like an idea of modifying the application to write 2 copies simulatenously, so I though of:
Application starts and begins to write the file (let's call it /mnt/disk1/file.mkv)
Some utility starts, copies what's already there in /mnt/disk1/file.mkv to /mnt/disk2/file.mkv
After getting initial sync state, it continues to follow a written file in a manner like tail -f does, copying everything it gets from /mnt/disk1/file.mkv to /mnt/disk2/file.mkv
Several hours pass
Application quits, we stop our syncing utility
Afterwards, we run a quick rsync /mnt/disk1/file.mkv /mnt/disk2/file.mkv just to make sure they're the same. In case if they're the same, it should just run a quick check and quit fairly soon.
What is the best approach for syncing 2 files, preferably using simple Linux shell-available utilities? May be I could use some clever trick with FUSE / md device / tee / tail -f?
Solution
The best possible solution for my case seems to be
mencoder ... -o >(
tee /mnt/disk1/file.mkv |
tee /mnt/disk2/file.mkv |
mplayer -
)
This one uses bash/zsh-specific magic named "process substitution" thus eliminating the need to make named pipes manually using mkfifo, and displays what's being encoded, as a bonus :)
Hmmm... the file is not usable while it's being written, so why don't you "trick" your program into writing through a pipe/fifo and use a 2nd, very simple program, to create 2 copies?
This way, you have your two copies as soon as the original process ends.
Read the manual page on tee(1).