File Access for child process

crunchi has asked for the wisdom of the Perl Monks concerning the following question:

I am trying to use fork to perform a rather long task. The problem I'm having is that the child process doesn't seem to be able to access files. At least I think that's the problem. I fork using this code. It's not mine, I just grabbed it from somewhere... (die statements shortened for clarity...)

$SIG{CHLD} = 'IGNORE'; 
defined (my $kid = fork) or die "Cannot fork: $!\n"; 
if($kid) { # do nothing... } 
else 
{
    chdir '/webRoot/cgi-bin' or die ...
    open STDIN, '/dev/null' or die ...
    open STDOUT, '>/dev/null' or die ...
    open STDERR, '>/tmp/log' or die ...
    setsid or die ...
    my $oldfh = select STDERR; 
    local $| = 1; 
    select $oldfh; 
    my $run = "perl /webRoot/apps/startPipe.pl -f $dest_file -j $job_ 
++ID -c $created -t $job_type $adv_opts"; `$run`;
    CORE::exit(0); # terminate the process 
}
[download]

Then in the file startPipe.pl...

for my $i (1 .. 1) 
{ 
    $arab_string .= "my \@arab$i = ("; 
    $blast_run = "blastn ATH1_chr$i.1con.01222004 $seq_file_name - +wa
+rnings"; 
    warn "$blast_run\n"; 
    $blast_output = `$blast_run`; 
    warn "Error: $!\n";
    ...
[download]

and finally in the file /tmp/log

blastn ATH1_chr1.1con.01222004 /webRoot/cgi-bin/jobs/15-12-2007/WZuFQe
+ +miR8sSigXB3vFjLiuix/WZuFQemiR8sSigXB3vFjLiuix -warnings 

Error: No such file or directory
[download]

and if i copy the the string generated by $blast_run and paste it into bash it will work, the files are in the right places. I have chmodded everything to 777 to make sure that it's not permissions. I'm probably missing something very simple... Thanks.

Comment on File Access for child process Select or Download Code

Replies are listed 'Best First'.
Re: File Access for child process by Anonymous Monk on Dec 21, 2007 at 02:02 UTC
`my $oldfh = select STDERR; local $\| = 1; select $oldfh;` [download] This is superfluous as the STDERR stream is unbuffered. my $run = "perl /webRoot/apps/startPipe.pl -f $dest_file -j $job_ ++ID -c $created -t $job_type $adv_opts"; `$run`; [download] You have forked a new process and now you are using backticks in void context which forks another process and starts a shell to run your command and returns the STDOUT of that command. Just use exec: `exec 'perl', '/webRoot/apps/startPipe.pl', '-f', $dest_file, '-j', + $job_', '+ID', '-c', $created, '-t', $job_type, $adv_opts;` [download]	[reply] [d/l] [select]
Re: File Access for child process by almut (Canon) on Dec 20, 2007 at 23:49 UTC
I would try specifying the full path to `blastn` — your webserver (although you're not explicitly talking of one, the 'webRoot' and 'cgi-bin' make me figure you're using one) might have a different search path configured as your interactive shell... Just an idea.	[reply] [d/l]
Re: File Access for child process by dwm042 (Priest) on Dec 21, 2007 at 16:16 UTC
I have to agree with almut. If the code works fine entered manually, but not in a script, it's often a difference in the PATH environment variable. You can check this explicitly. Type: `echo $PATH` [download] in your BASH shell and also add the line: `print $ENV{"PATH"}, "\n";` [download] in your script just before the backticks.	[reply] [d/l] [select]
Re^2: File Access for child process by crunchi (Initiate) on Dec 22, 2007 at 04:13 UTC
Thanks guys. I probably should have worked that one out myself. But I had been working on this baby for about 19 hours straight. I think I fried my brain...	[reply]