I'm running multiple processes in parallel and each of these processes read the same file in parallel. It looks like some of the processes see a corrupted version of the file if I increase the number of processes to > 15 or so. What is the recommended way of handling such a scenario?
More details:
The file being read in parallel is actually a perl script. The multiple jobs are python processes, and each of them launch this perl script independently with different input parameters. When the number of jobs is increased, some of these jobs give errors that the perl script has invalid syntax (which is not true). Hence, I suspect that some of these jobs read in corrupted versions of the perl script.
I'm running all of this on a 32core machine.
If any process is also writing to the file, then you need to enforce some synchronization, for example with a global named mutex.
If there is no asynchronous writing going on, I would not expect to see corruption during the reads. Are you opening the files with "r" access? If you're still encountering troubles, it might be worth experimenting with reducing read buffer size. Or call out to a native win32 API for the file access.
Good luck!
Related
I am running some tests from shell (currently zsh but could be bash as well) concurrently that will output the results by appending to the same file (results.txt).
Each result will be a few lines and some hundred bytes long (not longer than 1000).
I want to be able to read the output of each test in whole in the results file, without any interleaving from any test that might have finished at the same time.
I see a couple of obvious options from a theoretical point of view:
Atomic write(append)
Use a mutex to acquire the results file
The problem is that I have no idea whether how to do any of the 2 in a shell.
More specifically, I don't know if appends are atomic by nature and I don't know how to use a mutex in a shell context.
Any help appreciated.
My process creates a log file and appends a new line at the end of the file by using a, e.g:
fopen("log.txt", "a");
The order of the writes is not critical, but I need to ensure that fopen always succeeds. My question is, can the call above be executed from multiple processes at the same time on Windows, Linux and macOS without any race-condition?
If not, what is the most common and easy way to ensure I can write to the log file? There is file-lokcing, but also a file-lock (aka log.txt.lock) possible. Could anyone share some insights or resources which go more into detail?
If you do not use any synchronization between processes, you'll highly likely have moment when several processes will try to write to the file and the best you can get is mesh of input strings.
In order to synchronize any work in several processes (multiprocessing module). Use Lock. It will prevent several processes to do some work simultaneously.
It will look something like this:
import multiprocessing
# create lock in main process and "send" it to child processes.
lock = multiprocessing.Lock()
# ...
# in child Process
with lock:
do_some_work()
If you need more detailed example, feel free to ask.
Also you can check example in official docs
Im writing a bash script that essentially fires off a python script that takes roughly 10 hours to complete, followed by an R script that checks the outputs of the python script for anything I need to be concerned about. Here is what I have:
ProdRun="python scripts/run_prod.py"
echo "Commencing Production Run"
$ProdRun #Runs python script
wait
DupCompare="R CMD BATCH --no-save ../dupCompareTD.R" #Runs R script
$DupCompare
Now my issues is that often the python script can generate a whole heap of different processes on our linux server depending on its input, with lots of different PIDs AND we have heaps of workers using the same server firing off scripts. As far as I can tell from reading, the 'wait' command must wait for all processes to finish or for a specific PID to finish, but when i cannot tell what or how many PIDs will be assigned/processes run, how exactly do I use it?
EDIT: Thank you to all that helped, here is what caused my dilemma for anyone google searching this. I broke up the ProdRun python script into its individual script that it was itself calling, but still had the issue, I think found that one of these scripts was also calling another smaller script that had a "&" at the end of it that was ignoring any commands to wait on it inside the python script itself. Simply removing this and inserting a line of "os.system()" allowed all the code to run sequentially.
It sounds like you are trying to implement a job scheduler with possibly some complex dependencies between different tasks. I recommend to use a job scheduler instead. It allows you to specify to run those jobs whilst also benefitting from features like monitoring, handling exceptional cases, errors, ...
Examples are: the open source rundeck https://github.com/rundeck/rundeck or the commercial one http://www.bmcsoftware.uk/it-solutions/control-m.html
Make your Python program wait on the children it spawns. That's the proper way to fix this scenario. Then you don't have to wait for Python after it finishes (sic).
(Also, don't put your commands in variables.)
I have close to a million files over which I want to run a shell script and append the result to a single file.
For example suppose I just want to run wc on the files.
So that it runs fast I can parallelize it with xargs. But I do not want the scripts to step over each other when writing the output. It is probably better to write to a few separate files rather than one and then cat them later. But I still want the number of such temporary output files to be significantly smaller than the number of input files. Is there a way to get the kind of locking I want, or is it the case that is always ensured by default?
Is there any utility that will recursively cat two files in parallel?
I can write a script to do that, but have to deal with the temporaries and clean up. So was wondering if there is an utility which does that.
GNU parallel claims that it:
makes sure output from the commands is
the same output as you would get had
you run the commands sequentially
If that's the case, then I presume it should be safe to simple pipe the output to your file and let parallel handle the intermediate data.
Use the -k option to maintain the order of the output.
Update: (non-Perl solution)
Another alternative would be prll, which is implemented with shell functions with some C extensions. It is less feature-rich compared to GNU parallel but should the the job for basic use cases.
The feature listing claims:
Does internal buffering and locking to
prevent mangling/interleaving of
output from separate jobs.
so it should meet your needs as long as order of output is not important
However, note on the following statement on this page:
prll generates a lot of status
information on STDERR which makes it
harder to use the STDERR output of the
job directly as input for another
program.
Disclaimer: I've tried neither of the tools and am merely quoting from their respective docs.
I want to increase the throughput of a script which does net I/O (a scraper). Instead of making it multithreaded in ruby (I use the default 1.9.1 interpreter), I want to launch multiple processes. So, is there a system for doing this to where I can track when one finishes to re-launch it again so that I have X number running at any time. ALso some will run with different command args. I was thinking of writing a bash script but it sounds like a potentially bad idea if there already exists a method for doing something like this on linux.
I would recommend not forking but instead that you use EventMachine (and the excellent em-http-request if you're doing HTTP). Managing multiple processes can be a bit of a handful, even more so than handling multiple threads, but going down the evented path is, in comparison, much simpler. Since you want to do mostly network IO, which consist mostly of waiting, I think that an evented approach would scale as well, or better than forking or threading. And most importantly: it will require much less code, and it will be more readable.
Even if you decide on running separate processes for each task, EventMachine can help you write the code that manages the subprocesses using, for example, EventMachine.popen.
And finally, if you want to do it without EventMachine, read the docs for IO.popen, Open3.popen and Open4.popen. All do more or less the same thing but give you access to the stdin, stdout, stderr (Open3, Open4), and pid (Open4) of the subprocess.
You can try fork http://ruby-doc.org/core/classes/Process.html#M003148
You can get the PID in return and see if this process run again or not.
If you want manage IO concurrency. I suggest you to use EventMachine.
You can either
implement (or find an equivalent gem) a ThreadPool (ProcessPool, in your case), or
prepare an array of all, let's say 1000 tasks to be processed, split it into, say 10 chunks of 100 tasks (10 being the number of parallel processes you want to launch), and launch 10 processes, of which each process right away receives 100 tasks to process. That way you don't need to launch 1000 processes and control that not more than 10 of them work at the same time.