gbrowse internal server error: no mod_fcgid socket

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gbrowse internal server error: no mod_fcgid socket

Kenlee Nakasugi-2
Hi Scott,

Our Gbrowse can't be accessed and the resulting error was:

###
"make_path" is not exported by the File::Path module
Can't continue after import errors at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 13
BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 13.
Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
Compilation failed in require at (eval 48) line 3.
        ...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
[Sat Oct 19 09:55:45 2013] [warn] (104)Connection reset by peer: mod_fcgid: read data from fastcgi server error.
[Sat Oct 19 09:55:45 2013] [error] [client 10.37.80.24] Premature end of script headers: gbrowse, referer: http://sydney.edu.au/science/molecular_bioscience/sites/benthamiana/
[Sat Oct 19 09:55:50 2013] [notice] mod_fcgid: process /var/www/cgi-bin/gb2/gbrowse(19302) exit(communication error), terminated by calling exit(), return code: 9
##################


We've had this error before, and the admin said it was due to a socket missing in /var/run/mod_fcgid/ .

I checked under that dir, and indeed there was no socket. Previously it was as such:

$ file /var/run/mod_fcgid/28064.0
/var/run/mod_fcgid/28064.0: socket


Now there is nothing there.

It's the weekend and I'm not sure how to recreate this socket.
Could you advice what I should do as I've never tackled this error before.

cheers,
Ken


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Re: gbrowse internal server error: no mod_fcgid socket

Michael Dondrup-3
Hi,
we had the same error. It is caused by an outdated version (1.x) of File::Path which doesn't export
the "make_path" function. Some old redhat and centos dirstributions seem to still contain this module.

You can check this with

perl -MFile::Path -e 'print $File::Path::VERSION,"\n"'
2.08_01
version 2 is working if you get 1.something, then you can install a recent version of File::Path from cpan.

Best
Michael


On Oct 19, 2013, at 1:08 AM, Kenlee Nakasugi wrote:

> Hi Scott,
>
> Our Gbrowse can't be accessed and the resulting error was:
>
> ###
> "make_path" is not exported by the File::Path module
> Can't continue after import errors at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 13
> BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 13.
> Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> Compilation failed in require at (eval 48) line 3.
>         ...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
> BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
> Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
> BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Sat Oct 19 09:55:45 2013] [warn] (104)Connection reset by peer: mod_fcgid: read data from fastcgi server error.
> [Sat Oct 19 09:55:45 2013] [error] [client 10.37.80.24] Premature end of script headers: gbrowse, referer: http://sydney.edu.au/science/molecular_bioscience/sites/benthamiana/
> [Sat Oct 19 09:55:50 2013] [notice] mod_fcgid: process /var/www/cgi-bin/gb2/gbrowse(19302) exit(communication error), terminated by calling exit(), return code: 9
> ##################
>
>
> We've had this error before, and the admin said it was due to a socket missing in /var/run/mod_fcgid/ .
>
> I checked under that dir, and indeed there was no socket. Previously it was as such:
>
> $ file /var/run/mod_fcgid/28064.0
> /var/run/mod_fcgid/28064.0: socket
>
> Now there is nothing there.
>
> It's the weekend and I'm not sure how to recreate this socket.
> Could you advice what I should do as I've never tackled this error before.
>
> cheers,
> Ken
>
> ------------------------------------------------------------------------------
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------------
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Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
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Re: gbrowse internal server error: no mod_fcgid socket

Kenlee Nakasugi-2
Thanks Michael, I upgraded to 2.09 and it worked.
Best
Ken


On 19/10/2013, at 9:12 PM, "Michael Dondrup" <[hidden email]> wrote:

> Hi,
> we had the same error. It is caused by an outdated version (1.x) of File::Path which doesn't export
> the "make_path" function. Some old redhat and centos dirstributions seem to still contain this module.
>
> You can check this with
>
> perl -MFile::Path -e 'print $File::Path::VERSION,"\n"'
> 2.08_01
> version 2 is working if you get 1.something, then you can install a recent version of File::Path from cpan.
>
> Best
> Michael
>
>
> On Oct 19, 2013, at 1:08 AM, Kenlee Nakasugi wrote:
>
>> Hi Scott,
>>
>> Our Gbrowse can't be accessed and the resulting error was:
>>
>> ###
>> "make_path" is not exported by the File::Path module
>> Can't continue after import errors at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 13
>> BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 13.
>> Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> Compilation failed in require at (eval 48) line 3.
>>        ...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Sat Oct 19 09:55:45 2013] [warn] (104)Connection reset by peer: mod_fcgid: read data from fastcgi server error.
>> [Sat Oct 19 09:55:45 2013] [error] [client 10.37.80.24] Premature end of script headers: gbrowse, referer: http://sydney.edu.au/science/molecular_bioscience/sites/benthamiana/
>> [Sat Oct 19 09:55:50 2013] [notice] mod_fcgid: process /var/www/cgi-bin/gb2/gbrowse(19302) exit(communication error), terminated by calling exit(), return code: 9
>> ##################
>>
>>
>> We've had this error before, and the admin said it was due to a socket missing in /var/run/mod_fcgid/ .
>>
>> I checked under that dir, and indeed there was no socket. Previously it was as such:
>>
>> $ file /var/run/mod_fcgid/28064.0
>> /var/run/mod_fcgid/28064.0: socket
>>
>> Now there is nothing there.
>>
>> It's the weekend and I'm not sure how to recreate this socket.
>> Could you advice what I should do as I've never tackled this error before.
>>
>> cheers,
>> Ken
>>
>> ------------------------------------------------------------------------------
>> October Webinars: Code for Performance
>> Free Intel webinars can help you accelerate application performance.
>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
>> the latest Intel processors and coprocessors. See abstracts and register >
>> http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk_______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

------------------------------------------------------------------------------
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
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