[Catalyst] Running system commands under FastCGI with IPC::Cmd / IPC::Run

[Stuart Watt]

You may want to check your version of FCGI. There are previous reports =

of related issues, which seem to be an interaction between IPC::*  =

modules expectations of standard input/output/error, and FCGI, which =

fakes them. See =

http://www.mail-archive.com/ports@openbsd.org/msg16948.html for an =

example. In my FCGI, the FILENO method is present, but this appears to =

have been added in version 0.67_01 on 20 Dec 2009 - this is pretty =

recent and your Perl may not include it.

--S

Stuart Watt
ARM Product Developer
Information Balance


On 10/21/2010 2:43 PM, Ian Sillitoe wrote:
>
> I have a Catalyst model that runs a system command as part of a search =

> facility. The system call only takes a fraction of a second so is =

> processed inline and this all works fine when tested outside of =

> Catalyst and when called under the Catalyst standalone server. =

> However, when I deploy it to my FastCGI environment I have problems - =

> everything seems to work fine apart from the results of the system call.
>
> The system call is (give or take):
>
>     IPC::Cmd::run(
>             command =3D> [qw/ blastall -d sequences.db -i input.fa -o =

> output.results /],
>             verbose =3D> 0,
>             timeout =3D> 10,
>         );
>
> When run under the test server the file 'output.results' contains the =

> results of the search:
>
> gi|5524211|gb|AAD441661|        pdb|3cx5C00     45.26   285     =

> 154     1       1       283     91      375     4e-73    267
> gi|5524211|gb|AAD441661|        pdb|2e74A00     33.33   99      =

> 65      1       21      118     117     215     9e-16   77.0
> gi|5524211|gb|AAD441661|        pdb|2ih2A01     34.78   23      =

> 15      0       115     137     85      107     4.0     25.0
> ...
>
> When the same application is being run under FastCGI the file is =

> created but is empty.
>
> The system call was originally being wrapped with IPC::Cmd (via =

> MooseX::Role::Cmd). I checked what happened when I explicitly used =

> IPC::Run
>
>     my ($in, $out, $err);
>     my $success =3D IPC::Run::run [qw/ blastall -d sequences.db -i =

> input.fa -o output.results /], \$in, \$out, \$err, IPC::Run::timeout( =

> 10 );
>
> This works under the test server, but throws the following error under =

> FastCGI:
>
> |"Can't locate object method "FILENO" via package "FCGI::Stream" at /home=
/ian/perl5/lib/perl5/IPC/Run.pm line 1115.
>
> |
>
> If I bypass IPC::* and run the system command with backticks then it =

> seems to work fine under both the test server and FastCGI. However the =

> system call is happening a long way away from Catalyst - I don't =

> really want to hard code this with backticks just to get it working =

> under FastCGI.
>
> There seems to be a few different things going on here - I'm not sure =

> exactly where the problem lies or what might be a red herring - would =

> be grateful if anyone can help point me in the right direction.
>
> Cheers,
>
> Ian
>
>
>
>
> Running FastCGI server on my desktop on port 3001:
>
>   script/my_app_fastcgi.pl <http://my_app_fastcgi.pl> -l bsmlx53:3001 =

> -n 3 -p my-app.pid -d
>
> Forwarding requests there from external facing server with the =

> following config:
>
> <VirtualHost *:80>
>     ServerName test.foo.com <http://test.foo.com>
>     DocumentRoot    /home/ian/My-App/trunk/
>     ErrorLog        logs/test.foo.com-error_log
>
>     FastCgiExternalServer   /tmp/my-app.fcgi -host bsmlx53:3001
>
>     Alias           /static /home/ian/My-App/trunk/root/static
>     Alias           /       /tmp/my-app.fcgi/
> </VirtualHost>
>
> Modules:
>
>   Catalyst::Runtime (5.80029)
>   IPC::Run (0.89)
>   FCGI (0.67)
>
>
>
> -- =

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