SOLVED see Edit 2
Hello,
I've been writing a Perl program to handle automatic upgrading of local (proprietary) programs (for the company I work for).
Basically, it runs via cron, and unfortunately has a memory leak (or something similar). The problem is that the leak only happens when I'm not looking (aka when run via cron, not via command line).
My code does not contain any circular (or other) references, so the commonly cited tools will not help me (Devel::Cycle, Devel::Peek).
How would I go about figuring out what is using so much memory that the kernel kills it?
Basically, the code SFTPs into a server (using ```sftp...`` `), calls OpenSSL to verify the file, and then SFTPs more if more files are needed, and installs them (untars them).
I have seen delays (~15 sec) before the first SFTP session, but it has never used so much memory as to be killed (in my presence).
If I can't sort this out, I'll need to re-write in a different language, and that will take precious time.
Edit: The following message is printed out by the kernel which led me to believe it was a memory leak:
[100023.123] Out of memory: kill process 9568 (update.pl) score 325406 or a child
[100023.123] Killed Process 9568 (update.pl)
I don't believe it is an issue with cron because of the stalling (for ~15 sec, sometimes) when running it via the command-line. Also, there are no environmental variables used (at least by what I've written, maybe underlying things do?)
Edit 2: I found the issue myself, with help from the below comment by mobrule (in response to this question). It turns out that the script was called from a crontab of a user (non-root) just once a day and that (non-root privs) caused a special infinite loop situation.
Sorry guys, I feel kinda stupid for not finding this before, but thanks.
mobrule, if you submit your comment as an answer, I will accept it as it lead to me finding the problem.
End Edits
Thanks,
Brian
P.S. I may be able to post small snippets of code, but not the whole thing due to company policy.
You could try using Devel::Size to profile some of your objects. e.g. in the main:: scope (the .pl file itself), do something like this:
use Devel::Size qw(total_size);
foreach my $varname (qw(varname1 varname2 ))
{
print "size used for variable $varname: " . total_size($$varname) . "\n";
}
Compare the actual size used to what you think is a reasonable value for each object. Something suspicious might pop out immediately (e.g. a cache that is massively bloated beyond anything that sounds reasonable).
Other things to try:
Eliminate bits of functionality one at a time to see if suddenly things get a lot better; I'd start with the use of any external libraries
Is the bad behaviour localized to just one particular machine, or one particular operating system? Move the program to other systems to see how its behaviour changes.
(In a separate installation) try upgrading to the latest Perl (5.10.1), and also upgrade all your CPAN modules
How do you know that it's a memory leak? I can think of many other reasons why the OS would kill a program.
The first question I would ask is "Does this program always work correctly from the command line?". If the answer is "No" then I'd fix these issues first.
On the other hand if the answer is "Yes", I would investigate all the differences between having the program executed under cron and from the command line to find out why it is misbehaving.
If it is run by cron, that shouldn't it die after iteration? If that is the case, hard for me to see how a memory leak would be a big deal...
Are you sure it is the script itself, and not the child processes that are using the memory? Perhaps it ends up creating a real lot of ssh sessions , instead of doing a bunch of stuff in one session?
Related
I'm using a a few system() commands in my perl script that is running on Linux.
The commands I run with the system() function output their data to a log which I then parse to decide what to do next.
I noticed that sometimes it looks like the code that parses the log file (which comes after the system() function) doesn't use the final log.
For example, I search for a "test pass" phrase in the log file - and the script doesn't find it even though when I open the log it is there.
Another example - I try to delete the folder where the log was placed but it doesn't let me because it's "Not empty". When I try to delete it manually it is deleted with errors.
(These examples happen every now and then, but most of the time they don't)
It looks like some kind of "timing" problem to me. How can I solve it?
If you want to be safe and are on Linux, call system sync; after every command that writes to the disk before reading from the disk. That will force the OS to write everything still buffered to the filesystem and only return afterwards. Thus you can be sure that when it is finished, everything you wrote to files now actually has arrived there.
But be aware, that may be overkill in many situations. There are reasons for those buffers and manually calling sync constantly is most likely not the fastest way of achieving things. See also http://linux.die.net/man/8/sync
If, for example, you have something else that you could do between the writing and the reading, like some calculations or whatever, that would likely be enough and you would not waste time by telling the OS that you know better how and when it has to do it's jobs. ^^
But if perfect efficiency is not your main concern (and you should not be using Perl if it was), system sync; after everything that modifies files and before accessing those files is probably okay and safe.
Got stuck with one problem in our live server.
Have script (perl) which runs almost 15 to 18 hrs a day. it creates 100+ sub process every day . One place it has command (product command which we run in command line solaris box) which is being triggerred with back ticks inside perl code.
It looks like the back ticks command gets skipped or failed randomly.
for eg. if i need to run for 50 customers 2 or 3 gets failed randomly.
I do not see the evidence that the command has been triggerred in anywhere.
since its live server we can't even try making much in code change until we are sure about the problem.
here is the code..
my $comm = "inventory -noX customer1"; #sample command i have given here
my $newLogFile = "To capture command output here we have path whre the file gets created");
my $piddy = `$comm 2>&1 > $newLogFile`;
Is it because of the back ticks it happens I am really not sure :(.
Also tried various analysis like memory/CPU/diskspace/Adding librtld_db.so in LD_LIBRARY_PATH etc....but no luck...Also the perl is in 64 bit ...what else Can i? :(
I suspect you are not checking for errors (and perl doesn't make that easy to do correctly for backticks).
Consider using IPC::System::Simple's capture in place of your backticks/qx.
As its doc says, "If there's an error, it will die with a detailed description of what went wrong."
It shouldn't fail just because of backticks, however because it is spawning a new process, that process may be periodically subject to failure due to system conditions (eg. sysLoad). Backticks are really a "fire and forget" method and should never be used for anything critical in a production environment. As previously suggested, there are far more detailed ways to manage spawning external processes.
If the command's output is being lost due to buffering, you might try turning off buffering, but keep an eye on it for performance degradation (it's usually not significant).
Buffering can be turned off for an entire script by adding this near the top:
$|=1;
When calling external commands, I'm using system of IPC::System::Simple or open3 of IPC::Open3.
We have a pretty big perl codebase.
Some processes that run for multiple hours (ETL jobs) suddenly started consuming a lot more RAM than usual. Analysis of the changes in the relevant release is a slow and frustrating process. I am hoping to identify the culprit using more automated analysis.
Our live environment is perl 5.14 on Debian squeeze.
I have access to lots of OS X 10.5 machines, though. Dtrace and perl seem to play together nicely on this platform. Seems that using dtrace on linux requires a boot more work. I am hoping that memory allocation patterns will be similar between our live system and a dev OS X system - or at least similar enough to help me find the origin of this new memory use.
This slide deck:
https://dgl.cx/2011/01/dtrace-and-perl
shows how to use dtrace do show number of calls to malloc by perl sub. I am interested in tracking the total amount of memory that perl allocates while executing each sub over the lifetime of a process.
Any ideas on how this can be done?
There's no single way to do this, and doing it on a sub-by-sub basis isn't always the best way to examine memory usage. I'm going to recommend a set of tools that you can use, some work on the program as a whole, others allow you to examine a single section of your code or a single variable.
You might want to consider using Valgrind. There's even a Perl module called Test::Valgrind that will help set up a suppression file for your Perl build, and then check for memory leaks or errors in your script.
There's also Devel::Size which does exactly what you asked for, but on a variable-by-variable basis rather than a sub-by-sub basis.
You can use Devel::Cycle to search for inadvertent circular memory references in complex data structures. While a circular reference doesn't mean that you're wasting memory as you use the object, circular references prevent anything in the chain from being freed until the cycle is broken.
Devel::Leak is a little bit more arcane than the rest, but it basically will allow you to get full information on any SVs that are created and not destroyed between two points in your program's execution. If you check this across a sub call, you'll know any new memory that that subroutine allocated.
You may also want to read the perldebguts section of the Perl manual.
I can't really help more because every codebase is going to wind up being different. Test::Valgrind will work great for some codebases and terribly on others. If you are going to try it, I recommend you use the latest version of Valgrind available and Perl >= 5.10, as Perl 5.8 and Valgrind historically didn't get along too well.
You might want to look at Memory::Usage and Devel::Size
To check the whole process or sub:
use Memory::Usage;
my $mu = Memory::Usage->new();
# Record amount of memory used by current process
$mu->record('starting work');
# Do the thing you want to measure
$object->something_memory_intensive();
# Record amount in use afterwards
$mu->record('after something_memory_intensive()');
# Spit out a report
$mu->dump();
Or to check specific variables:
use Devel::Size qw(size total_size);
my $size = size("A string");
my #foo = (1, 2, 3, 4, 5);
my $other_size = size(\#foo);
my $foo = {
a => [1, 2, 3],
b => {a => [1, 3, 4]}
};
my $total_size = total_size($foo);
The answer to the question is 'yes'. Dtrace can be used to analyze memory usage in a perl process.
This snippet of code:
https://github.com/astletron/perl-dtrace-malloc/blob/master/perl-malloc-total-bytes-by-sub.d
tracks how memory use increases between the call and return of every sub in a program. As an added bonus, dtrace seems to sort the output for you (at least on OS X). Cool.
Thanks to all that chimed in. I answered this one myself as the question is really specific to dtrace/perl.
You could write a simple debug module based on Devel::CallTrace that prints the sub entered as well as the current memory size of the current process. (Using /proc or whatever.)
I'm about to rewrite a large portion of a project that I have developed over the last 10years while learning perl. There is alot of optimisation that can be gained.
A key part of the code is a large if/elsif block that require xxx.cgi files depending on a POST value. Eg:
if($FORM{'action'} eq "1"){require "1.cgi";}
elsif($FORM{'action'} eq "2"){require "2.cgi";}
elsif($FORM{'action'} eq "3"){require "3.cgi";}
elsif($FORM{'action'} eq "4"){require "4.cgi";}
It has many more irritations but just how expensive is using "require" in perl?
require itself has a relatively low cost in any case and, if you require the same file more than once within a single run of your program, it will detect that the file has already been loaded and not attempt to load it a second time. However, if you have a long and highly-populated search path (#INC) and you require (or use) a lot of files, it's possible that all of the directory searches could add up; this isn't common (and doesn't sound likely in your case), but it can be improved by reorganizing your module directories so that the things you're loading show up earlier in #INC.
The potentially-major performance hit referred to by earlier answers is the cost of compiling the code in the files you require. Getting rid of the require by moving the code into your main program will not help with this, as the code will still need to be compiled. In your case, it would probably make things worse, as it would cause the code for all options to be compiled on every one rather than only compiling the code used by the one action selected by the user.
As has been said, it really depends on the actual code in those files. Your best bet would be to do tests using Devel::NYTProf and/or Benchmark to see where the most time is being spent in your code if you are unhappy with its performance.
You can also read Profiling Perl on perl.com, but it is a bit outdated as it uses Devel::DProf.
Not answer to your primary question, but still a good idea for code refactor i read recently in Ovid blog.
The first time, possibly expensive; Perl has to search a path to find the file and load it up. Subsequent times, it's cheap -- a table is consulted and the file isn't actually loaded a second time. If this is in a CGI that is run once per request and then exited, then this is not too good.
It's really going to depend on the size of the files you're calling to. If you have massive CGI files, then it might detriment the performance of your software. If we're talking 6 or 7 lines of code each, then no issue. Try benchmarking your program's performance with and without, and make your own judgement.
Hi I am using a perl script written by another person who is no longer in the company.
If I run the script as a stand alone, then the output are as expected. But when I call the script from another code repeatedly, the output is wrong except for the first time.
I suspect some variables are not initialised properly. When it is called standalone, each time it exits and all the variable values are initialised to defaults. But when called from another perl script, the modules and the variable values are probably carried over to the next call of the script.
Is there any way to flush out the called script from memory before I call it next time?
I tried enabling warning and it was throwing up 1000s of lines of warning...!
EDIT: How I am calling the other script:
The code looks like this:
do "processing.pl";
...
...
...
process(params); #A function in processing.pl
...
...
...
If you want to force the module to be reloaded, delete its entry from %INC and then reload it.
For example:
sub reload_module {
delete $INC{'Your/Silly/Module.pm'};
require Your::Silly::Module;
Your::Silly::Module->import;
}
Note that if this module relies on globals in other modules being set, those may need to be reloaded as well. There's no easy way to know without taking a peak at the code.
Hi I am using a perl script written by another person who is no longer in the company.
I tried enabling warning and it was throwing up 1000s of lines of warning...!
There's your problem right there. The script was not written properly, and should be rewritten.
Ask yourself this question: if it has 1000s of warnings when you enable strict checking, how can you be sure that it is doing the right thing? How can you be sure that it is not clobbering files, trashing data sets, making a mess of your filesystem? Chances are it is doing all of these things, either deliberately or accidentally.
I wouldn't trust running an error-filled script written by someone no longer with the company. I'd rewrite it and be sure that it was doing what I needed it to do.
Unloading a module is a more difficult task than simply removing the %INC entry of the module. Take a look at Class::Unload from CPAN.
If you don't want to rewrite/fix the script, I suggest calling the script via exec() or one of its varieties. While it is not very elegant to do, it will definitely fix your problem.
Are you sure that you need to reload the module? By using do, you are reading the source every time and executing it. What happens if you change that to require, which will only read and evaluate the source once?
Another possibility (just thinking aloud here) could be to do with the local directory? Are they running from the same place. Probably wouldn't work the first time though.
Another option is to use system ('doprocessing.pl');. Lazily, we do this with a few scripts to force re-initialisation of a number of classes/variables etc. And to force the log files to rotate properly.
edit: I have just re-read your question, and it would appear that you are not calling it like this.