I'm trying to get the output of another process in python3
Here si my code
proc = subprocess.Popen(BIN, stdout=subprocess.PIPE)
try:
outs = proc.communicate(timeout=10)[0]
except subprocess.TimeoutExpired:
proc.kill()
outs = proc.communicate()[0]
The problem is :
BIN is an executable that never finish, so TimeoutExpired is always raised. But I'm unabled to get the output in the except block
Thank's for reading
Related
I'm using papermill in a web app, and running execute_notebook inside of celery tasks. I'm logging the output, and the entire notebook finishes, I get the export I'm waiting for in GCS, and it all seems perfect. but my execute_notebook statement never returns, so my celery task never finishes either.
Here's some pared down code:
def execute_nb(parameters: NotebookParameters, product_type: ProductType, notebook_name: str = None):
try:
nb_path = f"{settings.NOTEBOOK_DIR_PATH}/{product_type}.ipynb"
if notebook_name:
nb_path = f"{settings.NOTEBOOK_DIR_PATH}/{notebook_name}.ipynb"
nb_content = NOTEBOOK_REPO.get_contents(nb_path, ref=settings.NOTEBOOK_REF).decoded_content
except Exception as e:
print(e)
raise NotebookDoesNotExistException(path=nb_path)
# Make sure these local notebook folders exist locally
if not os.path.isdir(settings.NOTEBOOK_DIR_PATH):
os.makedirs(settings.NOTEBOOK_DIR_PATH)
if not os.path.isdir(f"{settings.NOTEBOOK_DIR_PATH}/outputs"):
os.makedirs(f"{settings.NOTEBOOK_DIR_PATH}/outputs")
# Writes the notebook from git to a local file (at the same relative path as git, from main.py)
open(nb_path, "wb").write(nb_content)
parameters_dict = json.loads(parameters)
pm.execute_notebook(
nb_path, f"{settings.NOTEBOOK_DIR_PATH}/outputs/{product_type}_output.ipynb", parameters=parameters_dict, log_output=True
)
print('done!')
return True
It never prints that done statement, so my celery task never finishes. The logs in my container show this:
data-layer-generation-service-worker-1 | [2022-11-16 01:48:43,496: WARNING/ForkPoolWorkerExecuting: 100%|##########| 7/7 [00:39<00:00, 6.36s/cell]
So it's reaching the end. Am I supposed to do something to trigger the end of execute_notebook?
I am using dask to process 10 files which the size of each file is about 142MB. I build a method with delayed tag, following is an example:
#dask.delayed
def process_one_file(input_file_path, save_path):
res = []
for line in open(input_file_path):
res.append(line)
df = pd.DataFrame(line)
df.to_parquet(save_path+os.path.basename(input_file_path))
if __name__ == '__main__':
client = ClusterClient()
input_dir = ""
save_dir = ""
print("start to process")
cvss = [process_one_file(input_dir+filename, save_dir) for filename in os.listdir(input_dir)]
dask.compute(csvs)
However, dask does not always run successfully. After processing all files, the program often hangs.
I used the command line to run the program. The program often huangs after printing start to process. I know the program runs correctly, since I can see all output files after a while.
But the program never stops. If I disabled tls, the program can run successfully.
It was so strange that dask can not stop the program if I enable tls connection. How can I solve it?
I found that if I add to_parquet method, then the program cannot stop, while if I remove the method, it runs successfully.
I have found the problem. I set 10GB for each process. That means I set memory-limit=10GB. I totally set 2 workers and each has 2 processes. Each process has 2 threads.
Thus, each machine will have 4 processes which occupy 40GB. However, my machine only have 32GB. If I lower the memory limit, then the program will run successfully!
Although I am quite familiar with Tcl this is a beginner question. I would like to read and write from a pipe. I would like a solution in pure Tcl and not use a library like Expect. I copied an example from the tcl wiki but could not get it running.
My code is:
cd /tmp
catch {
console show
update
}
proc go {} {
puts "executing go"
set pipe [open "|cat" RDWR]
fconfigure $pipe -buffering line -blocking 0
fileevent $pipe readable [list piperead $pipe]
if {![eof $pipe]} {
puts $pipe "hello cat program!"
flush $pipe
set got [gets $pipe]
puts "result: $got"
}
}
go
The output is executing go\n result:, however I would expect that reading a value from the pipe would return the line that I have sent to the cat program.
What is my error?
--
EDIT:
I followed potrzebie's answer and got a small example working. That's enough to get me going. A quick workaround to test my setup was the following code (not a real solution but a quick fix for the moment).
cd /home/stephan/tmp
catch {
console show
update
}
puts "starting pipe"
set pipe [open "|cat" RDWR]
fconfigure $pipe -buffering line -blocking 0
after 10
puts $pipe "hello cat!"
flush $pipe
set got [gets $pipe]
puts "got from pipe: $got"
Writing to the pipe and flushing won't make the OS multitasking immediately leave your program and switch to the cat program. Try putting after 1000 between the puts and the gets command, and you'll see that you'll probably get the string back. cat has then been given some time slices and has had the chance to read it's input and write it's output.
You can't control when cat reads your input and writes it back, so you'll have to either use fileevent and enter the event loop to wait (or periodically call update), or periodically try reading from the stream. Or you can keep it in blocking mode, in which case gets will do the waiting for you. It will block until there's a line to read, but meanwhile no other events will be responded to. A GUI for example, will stop responding.
The example seem to be for Tk and meant to be run by wish, which enters the event loop automatically at the end of the script. Add the piperead procedure and either run the script with wish or add a vwait command to the end of the script and run it with tclsh.
PS: For line-buffered I/O to work for a pipe, both programs involved have to use it (or no buffering). Many programs (grep, sed, etc) use full buffering when they're not connected to a terminal. One way to prevent them to, is with the unbuffer program, which is part of Expect (you don't have to write an Expect script, it's a stand-alone program that just happens to be included with the Expect package).
set pipe [open "|[list unbuffer grep .]" {RDWR}]
I guess you're executing the code from http://wiki.tcl.tk/3846, the page entitled "Pipe vs Expect". You seem to have omitted the definition of the piperead proc, indeed, when I copy-and-pasted the code from your question, I got an error invalid command name "piperead". If you copy-and-paste the definition from the wiki, you should find that the code works. It certainly did for me.
I need to use Lua to run a binary program that may write something in its stdout and also returns a status code (also known as "exit status").
I searched the web and couldn't find something that does what I need. However I found out that in Lua:
os.execute() returns the status code
io.popen() returns a file handler that can be used to read process output
However I need both. Writing a wrapper function that runs both functions behind the scene is not an option because of process overhead and possibly changes in result on consecutive runs. I need to write a function like this:
function run(binpath)
...
return output,exitcode
end
Does anyone has an idea how this problem can be solved?
PS. the target system rung Linux.
With Lua 5.2 I can do the following and it works
-- This will open the file
local file = io.popen('dmesg')
-- This will read all of the output, as always
local output = file:read('*all')
-- This will get a table with some return stuff
-- rc[1] will be true, false or nil
-- rc[3] will be the signal
local rc = {file:close()}
I hope this helps!
I can't use Lua 5.2, I use this helper function.
function execute_command(command)
local tmpfile = '/tmp/lua_execute_tmp_file'
local exit = os.execute(command .. ' > ' .. tmpfile .. ' 2> ' .. tmpfile .. '.err')
local stdout_file = io.open(tmpfile)
local stdout = stdout_file:read("*all")
local stderr_file = io.open(tmpfile .. '.err')
local stderr = stderr_file:read("*all")
stdout_file:close()
stderr_file:close()
return exit, stdout, stderr
end
This is how I do it.
local process = io.popen('command; echo $?') -- echo return code of last run command
local lastline
for line in process:lines() do
lastline = line
end
print(lastline) -- the return code is the last line of output
If the last line has fixed length you can read it directly using file:seek("end", -offset), offset should be the length of the last line in bytes.
This functionality is provided in C by pclose.
Upon successful return, pclose() shall return the termination status
of the command language interpreter.
The interpreter returns the termination status of its child.
But Lua doesn't do this right (io.close always returns true). I haven't dug into these threads but some people are complaining about this brain damage.
http://lua-users.org/lists/lua-l/2004-05/msg00005.html
http://lua-users.org/lists/lua-l/2011-02/msg00387.html
If you're running this code on Win32 or in a POSIX environment, you could try this Lua extension: http://code.google.com/p/lua-ex-api/
Alternatively, you could write a small shell script (assuming bash or similar is available) that:
executes the correct executable, capturing the exit code into a shell variable,
prints a newline and terminal character/string onto standard out
prints the shell variables value (the exit code) onto standard out
Then, capture all the output of io.popen and parse backward.
Full disclosure: I'm not a Lua developer.
yes , your are right that os.execute() has returns and it's very simple if you understand how to run your command with and with out lua
you also may want to know how many variables it returns , and it might take a while , but i think you can try
local a, b, c, d, e=os.execute(-what ever your command is-)
for my example a is an first returned argument , b is the second returned argument , and etc.. i think i answered your question right, based off of what you are asking.
I wrote the following two functions, and call the second ("callAndWait") from JavaScript running inside Windows Script Host. My overall intent is to call one command line program from another. That is, I'm running the initial scripting using cscript, and then trying to run something else (Ant) from that script.
function readAllFromAny(oExec)
{
if (!oExec.StdOut.AtEndOfStream)
return oExec.StdOut.ReadLine();
if (!oExec.StdErr.AtEndOfStream)
return "STDERR: " + oExec.StdErr.ReadLine();
return -1;
}
// Execute a command line function....
function callAndWait(execStr) {
var oExec = WshShell.Exec(execStr);
while (oExec.Status == 0)
{
WScript.Sleep(100);
var output;
while ( (output = readAllFromAny(oExec)) != -1) {
WScript.StdOut.WriteLine(output);
}
}
}
Unfortunately, when I run my program, I don't get immediate feedback about what the called program is doing. Instead, the output seems to come in fits and starts, sometimes waiting until the original program has finished, and sometimes it appears to have deadlocked. What I really want to do is have the spawned process actually share the same StdOut as the calling process, but I don't see a way to do that. Just setting oExec.StdOut = WScript.StdOut doesn't work.
Is there an alternate way to spawn processes that will share the StdOut & StdErr of the launching process? I tried using "WshShell.Run(), but that gives me a "permission denied" error. That's problematic, because I don't want to have to tell my clients to change how their Windows environment is configured just to run my program.
What can I do?
You cannot read from StdErr and StdOut in the script engine in this way, as there is no non-blocking IO as Code Master Bob says. If the called process fills up the buffer (about 4KB) on StdErr while you are attempting to read from StdOut, or vice-versa, then you will deadlock/hang. You will starve while waiting for StdOut and it will block waiting for you to read from StdErr.
The practical solution is to redirect StdErr to StdOut like this:
sCommandLine = """c:\Path\To\prog.exe"" Argument1 argument2"
Dim oExec
Set oExec = WshShell.Exec("CMD /S /C "" " & sCommandLine & " 2>&1 """)
In other words, what gets passed to CreateProcess is this:
CMD /S /C " "c:\Path\To\prog.exe" Argument1 argument2 2>&1 "
This invokes CMD.EXE, which interprets the command line. /S /C invokes a special parsing rule so that the first and last quote are stripped off, and the remainder used as-is and executed by CMD.EXE. So CMD.EXE executes this:
"c:\Path\To\prog.exe" Argument1 argument2 2>&1
The incantation 2>&1 redirects prog.exe's StdErr to StdOut. CMD.EXE will propagate the exit code.
You can now succeed by reading from StdOut and ignoring StdErr.
The downside is that the StdErr and StdOut output get mixed together. As long as they are recognisable you can probably work with this.
Another technique which might help in this situation is to redirect the standard error stream of the command to accompany the standard output.
Do this by adding "%comspec% /c" to the front and "2>&1" to the end of the execStr string.
That is, change the command you run from:
zzz
to:
%comspec% /c zzz 2>&1
The "2>&1" is a redirect instruction which causes the StdErr output (file descriptor 2) to be written to the StdOut stream (file descriptor 1).
You need to include the "%comspec% /c" part because it is the command interpreter which understands about the command line redirect. See http://technet.microsoft.com/en-us/library/ee156605.aspx
Using "%comspec%" instead of "cmd" gives portability to a wider range of Windows versions.
If your command contains quoted string arguments, it may be tricky to get them right:
the specification for how cmd handles quotes after "/c" seems to be incomplete.
With this, your script needs only to read the StdOut stream, and will receive both standard output and standard error.
I used this with "net stop wuauserv", which writes to StdOut on success (if the service is running)
and StdErr on failure (if the service is already stopped).
First, your loop is broken in that it always tries to read from oExec.StdOut first. If there is no actual output then it will hang until there is. You wont see any StdErr output until StdOut.atEndOfStream becomes true (probably when the child terminates). Unfortunately, there is no concept of non-blocking I/O in the script engine. That means calling read and having it return immediately if there is no data in the buffer. Thus there is probably no way to get this loop to work as you want. Second, WShell.Run does not provide any properties or methods to access the standard I/O of the child process. It creates the child in a separate window, totally isolated from the parent except for the return code. However, if all you want is to be able to SEE the output from the child then this might be acceptable. You will also be able to interact with the child (input) but only through the new window (see SendKeys).
As for using ReadAll(), this would be even worse since it collects all the input from the stream before returning so you wouldn't see anything at all until the stream was closed. I have no idea why the example places the ReadAll in a loop which builds a string, a single if (!WScript.StdIn.AtEndOfStream) should be sufficient to avoid exceptions.
Another alternative might be to use the process creation methods in WMI. How standard I/O is handled is not clear and there doesn't appear to be any way to allocate specific streams as StdIn/Out/Err. The only hope would be that the child would inherit these from the parent but that's what you want, isn't it? (This comment based upon an idea and a little bit of research but no actual testing.)
Basically, the scripting system is not designed for complicated interprocess communication/synchronisation.
Note: Tests confirming the above were performed on Windows XP Sp2 using Script version 5.6. Reference to current (5.8) manuals suggests no change.
Yes, the Exec function seems to be broken when it comes to terminal output.
I have been using a similar function function ConsumeStd(e) {WScript.StdOut.Write(e.StdOut.ReadAll());WScript.StdErr.Write(e.StdErr.ReadAll());} that I call in a loop similar to yours. Not sure if checking for EOF and reading line by line is better or worse.
You might have hit the deadlock issue described on this Microsoft Support site.
One suggestion is to always read both from stdout and stderr.
You could change readAllFromAny to:
function readAllFromAny(oExec)
{
var output = "";
if (!oExec.StdOut.AtEndOfStream)
output = output + oExec.StdOut.ReadLine();
if (!oExec.StdErr.AtEndOfStream)
output = output + "STDERR: " + oExec.StdErr.ReadLine();
return output ? output : -1;
}