I am still new to Perl. Since BEGIN blocks are run during compilation can't a virus spread or data loss occur from simply compiling? Does Perl do anything to stop it? If so does it mean the code in BEGIN blocks may act differently outside of it?
Yes to all these questions. The Eclipse IDE was vulnerable to this. It discussed in more detail here.
As with all software, you should avoid downloading and running anything from a source you do not trust. CPAN is generally trustworthy; although I am not aware of anyone intentionally releasing rogue code to CPAN, it's possible it has happened.
You can avoid running code during compile checks with the $^C flag, e.g.:
BEGIN { load_data_from_db() unless $^C; }
chromatic explains how a Perl program works.
Note that sometimes this is a feature. BEGIN blocks inside mod_perl modules are executed only once, when they are first loaded. So you have a simple syntax to do page-level initialization in the same script, and place it "near" the code that it assists.
Occasionally it's similarly useful for writing complicated initialization code that you don't want to put at the top of a script.
But mostly it's just there for thematic compatibility with awk.
Related
i have been working on a perl program to process large amounts of dna. It outputs exactly what i need however it takes much longer than i would like using NYTprof i have narrowed down the major problem areas to be the loop that adds my values together. would using inline::C to do the math make my program faster or should i accept the speed and move on? is there another way to improve the speed? here is my program and an input it would run as well as an executable with the default values entered already.
It's unlikely you'll get useful help here (this included). I can see various problems with your code, and none have to do with the choice of language.
use CPAN. If you're parsing genbank, then use some an appropriate module.
You're writing assembly in Perl, and neither Perl nor you are very good at that. It's near impossible to know what's going on when you don't pass parameters to subroutines, instead relying on globals all over the place. What do #X1, #X2, #Y1, #Y2 mean?
The following might be your problem: until ($ender - $starter > $tlength) { (line 153). According to your test case, these start by being 103, 1, and 200, and it's not clear when or if they change. Depending on what's in #te, it might or might not ever get out of the loop; I just can't tell from your code.
It would help if we knew, exactly, what are the parameters to add, the in-out invariants, and what it is returning.
That's all I got.
I second the recommendation of PDL made in a comment, if it's applicable. Or the use of a CPAN module tailored to your problem (again, if applicable).
I didn't see anything that looked unambiguously like "the loop that adds my values together" in that code; please, show just the code you are considering optimizing, ideally with just enough structure around it to actually run it.
So to answer your generic question generically, yes, Inline::C can be a useful tool for optimization if you are certain your performance problem is limited to what it actually can do for you. In using it, be aware that invoking your C code from Perl or vice versa is non-trivially expensive, so you have to have enough code translated to C to minimize the transitions.
I'm about to rewrite a large portion of a project that I have developed over the last 10years while learning perl. There is alot of optimisation that can be gained.
A key part of the code is a large if/elsif block that require xxx.cgi files depending on a POST value. Eg:
if($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.
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?
It is "common knowledge" that source filters are bad and should not be used in production code.
When answering a a similar, but more specific question I couldn't find any good references that explain clearly why filters are bad and when they can be safely used. I think now is time to create one.
Why are source filters bad?
When is it OK to use a source filter?
Why source filters are bad:
Nothing but perl can parse Perl. (Source filters are fragile.)
When a source filter breaks pretty much anything can happen. (They can introduce subtle and very hard to find bugs.)
Source filters can break tools that work with source code. (PPI, refactoring, static analysis, etc.)
Source filters are mutually exclusive. (You can't use more than one at a time -- unless you're psychotic).
When they're okay:
You're experimenting.
You're writing throw-away code.
Your name is Damian and you must be allowed to program in latin.
You're programming in Perl 6.
Only perl can parse Perl (see this example):
#result = (dothis $foo, $bar);
# Which of the following is it equivalent to?
#result = (dothis($foo), $bar);
#result = dothis($foo, $bar);
This kind of ambiguity makes it very hard to write source filters that always succeed and do the right thing. When things go wrong, debugging is awkward.
After crashing and burning a few times, I have developed the superstitious approach of never trying to write another source filter.
I do occasionally use Smart::Comments for debugging, though. When I do, I load the module on the command line:
$ perl -MSmart::Comments test.pl
so as to avoid any chance that it might remain enabled in production code.
See also: Perl Cannot Be Parsed: A Formal Proof
I don't like source filters because you can't tell what code is going to do just by reading it. Additionally, things that look like they aren't executable, such as comments, might magically be executable with the filter. You (or more likely your coworkers) could delete what you think isn't important and break things.
Having said that, if you are implementing your own little language that you want to turn into Perl, source filters might be the right tool. However, just don't call it Perl. :)
It's worth mentioning that Devel::Declare keywords (and starting with Perl 5.11.2, pluggable keywords) aren't source filters, and don't run afoul of the "only perl can parse Perl" problem. This is because they're run by the perl parser itself, they take what they need from the input, and then they return control to the very same parser.
For example, when you declare a method in MooseX::Declare like this:
method frob ($bubble, $bobble does coerce) {
... # complicated code
}
The word "method" invokes the method keyword parser, which uses its own grammar to get the method name and parse the method signature (which isn't Perl, but it doesn't need to be -- it just needs to be well-defined). Then it leaves perl to parse the method body as the body of a sub. Anything anywhere in your code that isn't between the word "method" and the end of a method signature doesn't get seen by the method parser at all, so it can't break your code, no matter how tricky you get.
The problem I see is the same problem you encounter with any C/C++ macro more complex than defining a constant: It degrades your ability to understand what the code is doing by looking at it, because you're not looking at the code that actually executes.
In theory, a source filter is no more dangerous than any other module, since you could easily write a module that redefines builtins or other constructs in "unexpected" ways. In practice however, it is quite hard to write a source filter in a way where you can prove that its not going to make a mistake. I tried my hand at writing a source filter that implements the perl6 feed operators in perl5 (Perl6::Feeds on cpan). You can take a look at the regular expressions to see the acrobatics required to simply figure out the boundaries of expression scope. While the filter works, and provides a test bed to experiment with feeds, I wouldn't consider using it in a production environment without many many more hours of testing.
Filter::Simple certainly comes in handy by dealing with 'the gory details of parsing quoted constructs', so I would be wary of any source filter that doesn't start there.
In all, it really depends on the filter you are using, and how broad a scope it tries to match against. If it is something simple like a c macro, then its "probably" ok, but if its something complicated then its a judgement call. I personally can't wait to play around with perl6's macro system. Finally lisp wont have anything on perl :-)
There is a nice example here that shows in what trouble you can get with source filters.
http://shadow.cat/blog/matt-s-trout/show-us-the-whole-code/
They used a module called Switch, which is based on source filters. And because of that, they were unable to find the source of an error message for days.
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.