I have a Perl script which reads three files and writes new files after reading each one of them. Everything is one thread.
In this script, I open and work with three text files and store the contents in a hash. The files are large (close to 3 MB).
I am using a loop to go through each of the files (open -> read -> Do some action (hash table) -> close)
I am noticing that the whenever I am scanning through the first file, the Perl terminal window in my Cygwin shell gets stuck. The moment I hit the enter key I can see the script process the rest of the files without any issues.
It's very odd as there is no read from STDIN in my script. Moreover, the same logic applies to all the three files as everything is in the same loop.
Has anyone here faced a similar issue? Does this usually happen when dealing with large files or big hashes?
I can't post the script here, but there is not much in it to post anyway.
Could this just be a problem in my Cygwin shell?
If this problem does not go away, how can I circumvent it? Like providing the enter input when the script is in progress? More importantly, how can I debug such a problem?
sub read_set
{
#lines_in_set = ();
push #lines_in_set , $_[0];
while (<INPUT_FILE>)
{ $line = $_;
chomp($line);
if ($line=~ /ENDNEWTYPE/i or $line =~ /ENDSYNTYPE/ or eof())
{
push #lines_in_set , $line;
last;
}
else
{
push #lines_in_set , $line;
}
}
return #lines_in_set;
}
--------> I think i found the problem :- or eof() call was ensuring that the script would be stuck !! Somehow happening only at the first time. I have no idea why though
The eof() call is the problem. See perldoc -f eof.
eof with empty parentheses refers to the pseudo file accessed via while (<>), which consists of either all the files named in #ARGV, or to STDIN if there are none.
And in particular:
Note that this function actually reads a character and then "ungetc"s it, so isn't useful in an interactive context.
But your loop reads from another handle, one called INPUT_FILE.
It would make more sense to call eof(INPUT_FILE). But even that probably isn't necessary; your outer loop will terminate when it reaches the end of INPUT_FILE.
Some more suggestions, not related to the symptoms you're seeing:
Add
use strict;
use warnings;
near the top of your script, and correct any error messages this produces (perl -cw script-name does a compile-only check). You'll need to declare your variables using my (perldoc -f my). And use consistent indentation; I recommend the same style you'll find in most Perl documentation.
Related
Was debugging a perl script for the first time in my life and came over this:
$my_temp_file = File::Temp->tmpnam();
system("cmd $blah | cmd2 > $my_temp_file");
open(FIL, "$my_temp_file");
...
unlink $my_temp_file;
This works pretty much like I want, except the obvious race conditions in lines 1-3. Even if using proper tempfile() there is no way (I can think of) to ensure that the file streamed to at line 2 is the same opened at line 3. One solution might be pipes, but the errors during cmd might occur late because of limited pipe buffering, and that would complicate my error handling (I think).
How do I:
Write all output from cmd $blah | cmd2 into a tempfile opened file handle?
Read the output without re-opening the file (risking race condition)?
You can open a pipe to a command and read its contents directly with no intermediate file:
open my $fh, '-|', 'cmd', $blah;
while( <$fh> ) {
...
}
With short output, backticks might do the job, although in this case you have to be more careful to scrub the inputs so they aren't misinterpreted by the shell:
my $output = `cmd $blah`;
There are various modules on CPAN that handle this sort of thing, too.
Some comments on temporary files
The comments mentioned race conditions, so I thought I'd write a few things for those wondering what people are talking about.
In the original code, Andreas uses File::Temp, a module from the Perl Standard Library. However, they use the tmpnam POSIX-like call, which has this caveat in the docs:
Implementations of mktemp(), tmpnam(), and tempnam() are provided, but should be used with caution since they return only a filename that was valid when function was called, so cannot guarantee that the file will not exist by the time the caller opens the filename.
This is discouraged and was removed for Perl v5.22's POSIX.
That is, you get back the name of a file that does not exist yet. After you get the name, you don't know if that filename was made by another program. And, that unlink later can cause problems for one of the programs.
The "race condition" comes in when two programs that probably don't know about each other try to do the same thing as roughly the same time. Your program tries to make a temporary file named "foo", and so does some other program. They both might see at the same time that a file named "foo" does not exist, then try to create it. They both might succeed, and as they both write to it, they might interleave or overwrite the other's output. Then, one of those programs think it is done and calls unlink. Now the other program wonders what happened.
In the malicious exploit case, some bad actor knows a temporary file will show up, so it recognizes a new file and gets in there to read or write data.
But this can also happen within the same program. Two or more versions of the same program run at the same time and try to do the same thing. With randomized filenames, it is probably exceedingly rare that two running programs will choose the same name at the same time. However, we don't care how rare something is; we care how devastating the consequences are should it happen. And, rare is much more frequent than never.
File::Temp
Knowing all that, File::Temp handles the details of ensuring that you get a filehandle:
my( $fh, $name ) = File::Temp->tempfile;
This uses a default template to create the name. When the filehandle goes out of scope, File::Temp also cleans up the mess.
{
my( $fh, $name ) = File::Temp->tempfile;
print $fh ...;
...;
} # file cleaned up
Some systems might automatically clean up temp files, although I haven't care about that in years. Typically is was a batch thing (say once a week).
I often go one step further by giving my temporary filenames a template, where the Xs are literal characters the module recognizes and fills in with randomized characters:
my( $name, $fh ) = File::Temp->tempfile(
sprintf "$0-%d-XXXXXX", time );
I'm often doing this while I'm developing things so I can watch the program make the files (and in which order) and see what's in them. In production I probably want to obscure the source program name ($0) and the time; I don't want to make it easier to guess who's making which file.
A scratchpad
I can also open a temporary file with open by not giving it a filename. This is useful when you want to collect outside the program. Opening it read-write means you can output some stuff then move around that file (we show a fixed-length record example in Learning Perl):
open(my $tmp, "+>", undef) or die ...
print $tmp "Some stuff\n";
seek $tmp, 0, 0;
my $line = <$tmp>;
File::Temp opens the temp file in O_RDWR mode so all you have to do is use that one file handle for both reading and writing, even from external programs. The returned file handle is overloaded so that it stringifies to the temp file name so you can pass that to the external program. If that is dangerous for your purpose you can get the fileno() and redirect to /dev/fd/<fileno> instead.
All you have to do is mind your seeks and tells. :-) Just remember to always set autoflush!
use File::Temp;
use Data::Dump;
$fh = File::Temp->new;
$fh->autoflush;
system "ls /tmp/*.txt >> $fh" and die $!;
#lines = <$fh>;
printf "%s\n\n", Data::Dump::pp(\#lines);
print $fh "How now brown cow\n";
seek $fh, 0, 0 or die $!;
#lines2 = <$fh>;
printf "%s\n", Data::Dump::pp(\#lines2);
Which prints
[
"/tmp/cpan_htmlconvert_DPzx.txt\n",
"/tmp/cpan_htmlconvert_DunL.txt\n",
"/tmp/cpan_install_HfUe.txt\n",
"/tmp/cpan_install_XbD6.txt\n",
"/tmp/cpan_install_yzs9.txt\n",
]
[
"/tmp/cpan_htmlconvert_DPzx.txt\n",
"/tmp/cpan_htmlconvert_DunL.txt\n",
"/tmp/cpan_install_HfUe.txt\n",
"/tmp/cpan_install_XbD6.txt\n",
"/tmp/cpan_install_yzs9.txt\n",
"How now brown cow\n",
]
HTH
I have a Perl script that I, well, mostly pieced together from questions on this site. I've read the documentation on some parts to better understand it. Anyway, here it is:
#!/usr/bin/perl
use File::Find;
my $dir = '/home/jdoe';
my $string = "hard-coded pattern to match";
find(\&printFile, $dir);
sub printFile
{
my $element = $_;
if(-f $element && $element =~ /\.txt$/)
{
open my $in, "<", $element or die $!;
while(<$in>)
{
if (/\Q$string\E/)
{
print "$File::Find::name\n";
last; # stops looking after match is found
}
}
}
}
This is a simple script that, similar to grep, will look down recursively through directories for a matching string. It will then print the location of the file that contains the string. It works, but only if the file is located in my home directory. If I change the hard-coded search to look in a different directory (that I have permissions in), for example /admin/programs, the script no longer seems to do anything: No output is displayed, even when I know it should be matching at least one file (tested by making a file in admin/programs with the hard-coded pattern. Why am I experiencing this behavior?
Also, might as well disclaim that this isn't a really useful script (heck, this would be so easy with grep or awk!), but understanding how to do this in Perl is important to me right now. Thanks
EDIT: Found the problem. A simple oversight in that the files in the directory I was looking for did not have .txt as extension. Thanks for helping me find that.
I was able to get the desired output using the code you pasted by making few changes like:
use strict;
use warnings;
You should always use them as they notify of various errors in your code which you may not get hold of.
Next I changed the line :
my $dir = './home/jdoe'; ##'./admin/programs'
The . signifies current directory. Also if you face problems still try using the absolute path(from source) instead of relative path. Do let me know if this solves your problem.
This script works fine without any issue. One thing hidden from this script to us is the pattern. you can share the pattern and let us know what you are expecting from that pattern, so that we can validate that.
You could also run your program in debug mode i.e.,
perl -d your_program.
That should take you to debug mode and there are lot of options available to inspect through the flow. type 'n' on the debug prompt to step in to the code flow to understand how your code flows. Typing 'n' will print the code execution point and its result
In my script I am dealing with opening files and writing to files. I found that there is some thing wrong with a file I try to open, the file exists, it is not empty and I am passing the right path to file handle.
I know that my question might sounds weird but while I was debugging my code I put the following command in my script to check some files
system ("ls");
Then my script worked well, when it's removed it does not work correctly anymore.
my #unique = ("test1","test2");
open(unique_fh,">orfs");
print unique_fh #unique ;
open(ORF,"orfs")or die ("file doesnot exist");
system ("ls");
while(<ORF>){
split ;
}
#neworfs=#_ ;
print #neworfs ;
Perl buffers the output when you print to a file. In other words, it doesn't actually write to the file every time you say print; it saves up a bunch of data and writes it all at once. This is faster.
In your case, you couldn't see anything you had written to the file, because Perl hadn't written anything yet. Adding the system("ls") call, however, caused Perl to write your output first (the interpreter is smart enough to do this, because it thinks you might want to use the system() call to do something with the file you just created).
How do you get around this? You can close the file before you open it again to read it, as choroba suggested. Or you can disable buffering for that file. Put this code just after you open the file:
my $fh = select (unique_fh);
$|=1;
select ($fh);
Then anytime you print to the file, it will get written immediately ($| is a special variable that sets the output buffering behavior).
Closing the file first is probably a better idea, although it is possible to have a filehandle for reading and writing open at the same time.
You did not close the filehandle before trying to read from the same file.
There is a system() call in a Perl script with multiple pipes, using a single scalar argument. The call looks more or less like this:
system("zcat /foo.gz | grep '^.{6}X|Y|Z' | awk '{print $2,$3,$4,$6}' | bzip2 > /foo.processed.bz2");
The file in question (foo.gz) is quite large, about 2GB compressed in size. I guess that's why it was originally done via a system call.
Questions:
The problem now is, that this system call always seem to return 0, whether one of the system commands fail or not. I assume this is because it gets invoked via sh -c '...'. Is that correct?
Is there a way to check if a system() call was successful if only a single scalar argument is passed?
Is there a better way to process a large file like this, in a way thats equally or more efficient (in terms of speed mainly)?
Thanks for any hints as I am not really familiar with Perl.
Two things:
When you do a system call, the value returned is the last value in the pipeline. Thus, you're getting the status code of the bzip2 command.
The reason the program is doing this is because the people who wrote the program probably didn't know any better. I've seen Perl programs use system calls for finding the basename of the file, doing a find, and even doing a copy/rename/move. These are all things that can be done faster and easier inside the Perl program. And, you don't have the whole Windows/Unix compatibility issues.
You're always better off using Perl modules for things like this. In this case, I bet the Perl modules will be even faster than the shell pipeline, and you'll have more control over the entire operation.
There's a set called IO::Compress that can handle both Zip and BZip2.
I use Archive::Zip which is a great module, but you want to use the Bzip2 compression algorithm, and Archive::Zip can't handle that.
system() returns what the /bin/sh shell returns. When multiple commands are pipelined, the shell forks a new process for each of them and the status code of the last command in the chain is returned, in this case bzip2.
Based on your comments and answers, I'd do it like that now:
$infile =~ s/(.*\.gz)\s*$/gzip -dc < $1|/;
open(OUTFH, "| /bin/bzip > $outfile") or die "Can't open $outfile: $!";
open(INFH, $infile) or die "Can't open $infile: $!";
while (my $line = <INFH>) {
if ($line =~ /^.{6}X|Y|Z) {
# TODO: the awk part...
print OUTFH $line;
}
}
close(INFH);
close(OUTFH);
Please feel free to comment and vote up/down.
You'd be better doing the text processing from within perl itself - that's what perl's for :)
system() only ever returns 0 or 1. To capture actual output, try calling it via backticks: `command` rather than system('command')
The following snippet of code is used to find the PID of a user's terminal, by using ptree and grabbing the third PID from the results it returns. All terminal PID's are stored in a hash with the user's login as the key.
## If process is a TEMINAL.
## The command ptree is used to get the terminal's process ID.
## The user can then use this ID to peek the user's terminal.
if ($PID =~ /(\w+)\s+(\d+) .+basic/) {
$user = $1;
if (open(PTREE, "ptree $2 |")) {
while ($PTREE = <PTREE>) {
if ($PTREE =~ /(\d+)\s+-pksh-ksh/) {
$terminals{$user} = $terminals{$user} . " $1";
last;
}
next;
}
close(PTREE);
}
next;
}
Below is a sample ptree execution:
ares./home_atenas/lmcgra> ptree 29064
485 /usr/lib/inet/inetd start
23054 /usr/sbin/in.telnetd
23131 -pksh-ksh
26107 -ksh
29058 -ksh
29064 /usr/ob/bin/basic s=61440 pgm=/usr/local/etc/logon -q -nr trans
412 sybsrvr
I'd like to know if there is a better way to code this. This is the part of the script that takes longest to run.
Note: this code, along with other snippets, are inside a loop and are executed a couple of times.
I think the main problem is that this code is in a loop. You don't need to run ptree and parse the results more than once! You need to figure out a way to run ptree once and put it into a data structure that you can use later. Probably be some kind of simple hash will suffice. You may even be able to just keep around your %terminals hash and keep reusing it.
Some nitpicks...
Both of your "next" statements seem
unnecessary to me... you should be
able to just remove them.
Replace
$terminals{$user} = $terminals{$user} . " $1";
with:
$terminals{$user} .= " $1";
Replace the bareword PTREE which you
are using as a filehandle with
$ptreeF or some such... using
barewords became unnecessary for
filehandles about 10 years ago :)
I don't know why your $PID variable
is all caps... it could be confusing
to readers of your code because it
looks like there is something
special about that variable, and
there isn't.
I think you'll get the best performance improvement by avoiding the overhead of repeatedly executing an external command (ptree, in this case). I'd look for a CPAN module that provides a direct interface to the data structures that ptree is reading. Check the Linux:: namespace, maybe? (I'm not sure if ptree is setuid; that may complicate things.)
The above advice aside, some additional style and robustness notes based on the posted snippet only (forgive me if the larger code invalidates them):
I'd start by using strict, at the very least. Lexical filehandles would also be a good idea.
You appear to be silently ignoring the case when you cannot open() the ptree command. That could happen for many reasons, some of which I can't imagine you wanting to ignore, such as…
You're not using the full path to the ptree command, but rather assuming it's in your path—and that the one in your path is the right one.
How many users are on the system? Can you invert this? List all -pksh-ksh processes in the system along with their EUIDs, and build the map from that - that might be only one execution of ps/ptree.
I was thinking of using ps to get the parents pid, but I would need to loop this to get the great-grandparent's pid. That's the one I need. Thanks. – lamcro
Sorry, there are many users and each can have up to three terminals open. The whole script is used to find those terminals that are using a file. I use fuser to find the processes that use a file. Then use ptree to find the terminal's pid. – lamcro
If you have (or can get) a list of PIDs using a file, and just need all of the grand-parents of that PID, there's an easier way, for sure.
#!perl
use warnings;
use strict;
#***** these PIDs are gotten with fuser or some other method *****
my($fpids) = [27538, 31812, 27541];
#***** get all processes, assuming linux PS *****
my($cmd) = "ps -ef";
open(PS, "$cmd |") || die qq([ERROR] Cannot open pipe from "$cmd" - $!\n);
my($processlist) = {};
while (<PS>) {
chomp;
my($user, $pid, $ppid, $rest) = split(/ +/, $_, 4);
$processlist->{$pid} = $ppid;
}
close PS;
#***** lookup grandparent *****
foreach my $fpid (#$fpids) {
my($parent) = $processlist->{$fpid} || 0;
my($grandparent) = $processlist->{$parent} || 0;
if ($grandparent) {
#----- do something here with grandparent's pid -----
print "PID:GRANDPID - $fpid:$grandparent\n";
}
else {
#----- some error condition -----
print "ERROR - Cannot determine GrandPID: $fpid ($parent)\n";
}
}
Which for me produces:
ERROR - Cannot determine GrandPID: 27538 (1)
PID:GRANDPID - 31812:2804
PID:GRANDPID - 27541:27538
Have you considered using 'who -u' to tell you which process is the login shell for a given tty instead of using ptree? This would simplify your search - irrespective of the other changes you should also make.
I just did some trivial timings here based on your script (calling "cat ptree.txt" instead of ptree itself) and confirmed my thoughts that all of your time is spent creating new sub-processes and running ptree itself. Unless you can factor away the need to call ptree (maybe there's a way to open up the connection once and reuse it, like with nslookup), you won't see any real gains.