[ome-users] Help with OME installation on Fedora Core 6, (mod_perl not configured error...)

Ilya Goldberg igg at nih.gov
Wed Jan 23 17:25:18 GMT 2008 

On Jan 23, 2008, at 4:41 AM, Jerome Avondo wrote:

>
> hi,
>
> Thanks for the reply.
>
> I tried rerunnig the installation script, but it still produces the  
> same error. Im a bit stuck as out of ideas for what it could be...
> Ive copied the contents of my /var/tmp/ OME/install/ 
> ApacheConfigTask.log logfile at the end of this message. Had a look  
> at it but to be honest couldnt spot anything....


Nope nothing very informative there.  Your server is generating a  
server error when running that script (response is not "200 OK").
If you paste that script (as it appears in the logfile) into a file  
called /OME/perl2/mod_perl_test.pl, then go to
  http://localhost/perl2/mod_perl_test.pl
in a browser, then everything runs OK?
If so, potentially the OME user-agent (based on libcurl) is not  
configured correctly, but that normally gives an entirely different  
error earlier in the process.

Perhaps there's something funky about your httpd.conf file?  Can you  
send that to me as well as all the files in /OME/conf/ ?
Probably we should take this off-list.

Sorry for your troubles.  Honestly, we have a dozen boxes running FC  
6 with nary a hiccup...
-I


>
> j.
>
> --------------------------------------
> ApacheConfigTask.log
> --------------------------------------
>
> Apache setup
> Apache binary: /usr/sbin/httpd
> apachectl binary: /usr/sbin/apachectl
> httpd root: /etc/httpd
> httpd conf: /etc/httpd/conf/httpd.conf
> httpd version: 2
> Apache configuration:
>         Configure Apache?: yes
>   Developer configuration: no
>           Server restart?: yes
> Install OME servers:
>            Images (omeis): yes
>              Data (omeds): yes
>                       Web: yes
> Apache directories:
>              httpd binary: /usr/sbin/httpd
>          apachectl binary: /usr/sbin/apachectl
>              DocumentRoot: /var/www/html
>                   cgi-bin: /var/www/cgi-bin
> Web-UI HTML Templates:
>   Developer configuration: no
> Configuring Apache
> httpd.conf is /etc/httpd/conf/httpd.conf
> Installing OMEIS
> Copying src/C/omeis/omeis to /var/www/cgi-bin/omeis
> chmod 0755 /var/www/cgi-bin/omeis
> chown /var/www/cgi-bin/omeis to uid: 48 gid: 501
> Set APACHE_OMEIS_INCLUDE to Include /OME/conf/httpd2.omeis.conf
> Forking a process to upgrade OMEIS
> Installing OMEDS
> Set APACHE_OMEDS_INCLUDE to Include /OME/conf/httpd2.omeds.conf
> Installing WEB
> Copying src/perl2/serve.pl to /OME/perl2/serve.pl
> chmod 0755 /OME/perl2/serve.pl
> chown /OME/perl2/serve.pl to uid: 48 gid: 501
> Copying src/html/index.html to /var/www/html/index.html
> chmod 0644 /var/www/html/index.html
> chmod 0644 /var/www/html/favicon.ico
> Set APACHE_WEB_INCLUDE to Include /OME/conf/httpd2.web.conf
> Installing DAE web by copying NonblockingSlaveWorkerCGI
> Copying src/perl2/OME/Analysis/Engine/NonblockingSlaveWorkerCGI.pl  
> to /OME/perl2/NonblockingSlaveWorkerCGI.pl
> chmod 0755 /OME/perl2/NonblockingSlaveWorkerCGI.pl
> chown /OME/perl2/NonblockingSlaveWorkerCGI.pl to uid: 48 gid: 501
> Installing OME-startup.pl
> Copying src/perl2/OME-startup.pl to /OME/conf/OME-startup.pl
> chown /OME/conf/OME-startup.pl to uid: 48 gid: 501
> Fixing variables in conf/httpd.ome.*.conf
> Replacing %OME_DIST_BASE with /home/ut/Desktop/OME-2.6.1
> Replacing %OME_INSTALL_BASE with /OME
> Reading /OME/conf/httpd.ome.conf
> Writing /OME/conf/httpd.ome.conf
> Reading /OME/conf/httpd.omeds-dev.conf
> Writing /OME/conf/httpd.omeds-dev.conf
> Reading /OME/conf/httpd.omeds.conf
> Writing /OME/conf/httpd.omeds.conf
> Reading /OME/conf/httpd.omeis-dev.conf
> Writing /OME/conf/httpd.omeis-dev.conf
> Reading /OME/conf/httpd.omeis.conf
> Writing /OME/conf/httpd.omeis.conf
> Reading /OME/conf/httpd.web-dev.conf
> Writing /OME/conf/httpd.web-dev.conf
> Reading /OME/conf/httpd.web.conf
> Writing /OME/conf/httpd.web.conf
> Reading /OME/conf/httpd1.99.omeds-dev.conf
> Writing /OME/conf/httpd1.99.omeds-dev.conf
> Reading /OME/conf/httpd1.99.omeds.conf
> Writing /OME/conf/httpd1.99.omeds.conf
> Reading /OME/conf/httpd1.99.omeis-dev.conf
> Writing /OME/conf/httpd1.99.omeis-dev.conf
> Reading /OME/conf/httpd1.99.omeis.conf
> Writing /OME/conf/httpd1.99.omeis.conf
> Reading /OME/conf/httpd1.99.web-dev.conf
> Writing /OME/conf/httpd1.99.web-dev.conf
> Reading /OME/conf/httpd1.99.web.conf
> Writing /OME/conf/httpd1.99.web.conf
> Reading /OME/conf/httpd2.omeds-dev.conf
> Writing /OME/conf/httpd2.omeds-dev.conf
> Reading /OME/conf/httpd2.omeds.conf
> Writing /OME/conf/httpd2.omeds.conf
> Reading /OME/conf/httpd2.omeis-dev.conf
> Writing /OME/conf/httpd2.omeis-dev.conf
> Reading /OME/conf/httpd2.omeis.conf
> Writing /OME/conf/httpd2.omeis.conf
> Reading /OME/conf/httpd2.web-dev.conf
> Writing /OME/conf/httpd2.web-dev.conf
> Reading /OME/conf/httpd2.web.conf
> Writing /OME/conf/httpd2.web.conf
> Reading /OME/conf/httpd.ome.conf
> Writing /OME/conf/httpd.ome.conf
> Restarting Apache
> Executing /usr/sbin/apachectl restart
> Getting an OME::Util::cURL user agent
> Generated mod_perl test script:
> #!/usr/bin/perl -w
> use strict;
> use CGI qw/-no_xhtml/;
>
> my $CGI = CGI->new();
> print $CGI->header(-type => 'text/plain'),
>
>
> my ($key,$value);
> while ( ($key, $value) = each %ENV)
> {
>         print "$key = $value\n";
> }
>
>
> 1;
>
> Writing script to /OME/perl2/mod_perl_test.pl
> Getting response from http://localhost/perl2/mod_perl_test.pl
> Apache/mod_perl is not properly configured.  Did not get a response  
> from http://localhost/perl2/mod_perl_test.pl.
> ----------
>
>
> ----------------------------------------
>> CC: ome-users at lists.openmicroscopy.org.uk
>> From: igg at nih.gov
>> Subject: Re: [ome-users] Help with OME installation on Fedora Core  
>> 6, (mod_perl not configured error...)
>> Date: Tue, 22 Jan 2008 13:10:45 -0500
>> To: jeromeavondo at msn.com
>>
>> Hi Jerome
>> Fedora Core 6 is a supported platform and we use it for both of our
>> production servers (lab and department).  OS X is mainly used for
>> development.
>> It would be informative to look at the logfile in  /var/tmp/OME/
>> install/ApacheConfigTask.log
>>
>> Although somehow, you were able to run this manually,
>> http://localhost/perl2/mod_perl_test.pl
>>
>> When the installation script tried to run it, it produced an error
>> (i.e. the server responded with something other than a 200 response
>> code).  The logfile should have more details.
>> You might just try running the installer again - possibly there were
>> some things that didn't "take" the first time.  The fact that you
>> were able to run the test script manually indicates that the system
>> was configured correctly.
>>
>> We've had very little trouble installing this on "stock" Fedora Core
>> OSes.
>> If re-running the installer doesn't work, please send the /var/tmp/
>> OME/install/ApacheConfigTask.log logfile.
>>
>> Also, you should change the server name to something other than
>> localhost.  This will cause your OME system to work only locally
>> (i.e. the images, etc will not appear on any other client).
>>
>> -Ilya
>>
>>
>>
>>
>> On Jan 22, 2008, at 5:12 AM, Jerome Avondo wrote:
>>
>>>
>>> hi,
>>>
>>> Dont know if this helps but tried running the following below
>>> manually, once apache is started, and the script "seems" to work.
>>>
>>> http://localhost/perl2/mod_perl_test.pl
>>>
>>> I get the following output:
>>>
>>> ----------------------------------------------------------------
>>> SCRIPT_NAME = /perl2/mod_perl_test.pl
>>> SERVER_NAME = localhost
>>> SERVER_ADMIN = root at localhost
>>> HTTP_ACCEPT_ENCODING = gzip,deflate
>>> HTTP_CONNECTION = keep-alive
>>> REQUEST_METHOD = GET
>>> HTTP_ACCEPT = text/xml,application/xml,application/xhtml+xml,text/
>>> html;q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5
>>> SCRIPT_FILENAME = /OME/perl2/mod_perl_test.pl
>>> SERVER_SOFTWARE = Apache/2.2.6 (Fedora)
>>> HTTP_ACCEPT_CHARSET = ISO-8859-1,utf-8;q=0.7,*;q=0.7
>>> QUERY_STRING =
>>> REMOTE_PORT = 59930
>>> HTTP_USER_AGENT = Mozilla/5.0 (X11; U; Linux i686; en-US; rv:
>>> 1.8.0.7) Gecko/20061011 Fedora/1.5.0.7-7.fc6 Firefox/1.5.0.7
>>> SERVER_PORT = 80
>>> SERVER_SIGNATURE = Apache/2.2.6 (Fedora) Server at localhost Port 80
>>>
>>> HTTP_ACCEPT_LANGUAGE = en-us,en;q=0.5
>>> REMOTE_ADDR = 127.0.0.1
>>> HTTP_KEEP_ALIVE = 300
>>> SERVER_PROTOCOL = HTTP/1.1
>>> PATH = /usr/bin/:/usr/local/bin/:/sw/bin/
>>> MOD_PERL_API_VERSION = 2
>>> REQUEST_URI = /perl2/mod_perl_test.pl
>>> GATEWAY_INTERFACE = CGI/1.1
>>> SERVER_ADDR = 127.0.0.1
>>> DOCUMENT_ROOT = /var/www/html
>>> HTTP_HOST = localhost
>>> MOD_PERL = mod_perl/2.0.2
>>> ----------------------------------------------------------------
>>>
>>> Also when I try and start/restart apache I get the following
>>> warning message:
>>> " [warn] The ScriptAlias directive in /OME/conf/httpd2.omeis.conf
>>> at line 2 will probably never match because it overlaps an earlier
>>> ScriptAlias."
>>>
>>> Also found a previous OME-USERS thread with similar symptoms too
>>> but wasnt much help, as it seems the user was running an old
>>> install.pl script... http://lists.openmicroscopy.org.uk/pipermail/
>>> ome-users/2005-July/000068.html
>>>
>>> Well Im a bit stuck, if any expert has any suggestions/pointers,
>>> would be very greatful...
>>> Regards,
>>>
>>> J.
>>> ----------------------------------------
>>>> From: jeromeavondo at msn.com
>>>> To: ome-users at lists.openmicroscopy.org.uk
>>>> Date: Mon, 21 Jan 2008 16:32:19 +0000
>>>> Subject: Re: [ome-users] Help with OME installation on Fedora Core
>>>> 6, (mod_perl not configured error...)
>>>>
>>>>
>>>> Hello,
>>>>
>>>> Been trying to get the OME server up and running on a fresh Fedora
>>>> core 6 installation.
>>>> However I am having an error with the install.pl script at the
>>>> APACHE SETUP stage.
>>>>
>>>> You can find the complete install log at the end of this message.
>>>>
>>>> Basically it seems that its complaining about mod_perl not being
>>>> configured correctly.
>>>> The exact error message I get is: "Errors executing task: Apache/
>>>> mod_perl is not properly configured."
>>>>
>>>> when I run "yum list mod_perl" mod_perl is shown as installed and
>>>> the version number is 2.0.2-6.2.fc6
>>>>
>>>> Anybody have any suggestion about how to go about sorting this
>>>> problem? Do I have to do anything more to setup mod_perl correctly?
>>>>
>>>> many thanks,
>>>>
>>>> j.
>>>>
>>>> --------------------------------------
>>>> COMPLETE INSTALL LOG:
>>>> --------------------------------------
>>>>
>>>> [root at JIC4367 OME-2.6.1]# perl install.pl
>>>> ------------------
>>>>  Pre-Installation
>>>> ------------------
>>>>
>>>> Term::ReadKey - Version 2.30
>>>> Storable - Version 2.15
>>>>
>>>> ----------------------------
>>>>  C Library Dependency Setup
>>>> ----------------------------
>>>>
>>>> (All verbose information logged in /var/tmp/ome-lib-check/
>>>> LibraryTask.log)
>>>>
>>>> Checking libraries
>>>>   \_ libssl 0.9.8 [OK].
>>>>   \_ libpng 1.2.10 [OK].
>>>>   \_ libjpeg 62 [OK].
>>>>   \_ libcurl 7.15.5 [OK].
>>>>   \_ libtiff 3.8.2 [OK].
>>>>   \_ zlib 1.2.3 [OK].
>>>>   \_ libdb_B-Tree 3 [OK].
>>>>   \_ libxml2 2.6.26 [OK].
>>>>   \_ libxslt 1.1.17 [OK].
>>>>   \_ expat 1.95 [OK].
>>>>   \_ bzlib N/A [OK].
>>>>
>>>> -------------------
>>>>  Core System Setup
>>>> -------------------
>>>>
>>>> Dropping umask to "0002".
>>>>
>>>> This part of the OME install will collect the initial information
>>>> required.
>>>> Basic directory structure and system users will be created and the
>>>> install
>>>> environment setup. If you are unsure of a particular question,  
>>>> please
>>>> choose the default as that will be more than adequate for most
>>>> people.
>>>>
>>>>        Base OME directory: /OME
>>>>      Base OMEIS directory: /OME/OMESIS
>>>>  Base temporary directory: /var/tmp/OME
>>>>             OME groupname: ome
>>>>        OME Unix  username: ome
>>>>     Apache Unix  username: apache
>>>>  Postgres admin  username: postgres
>>>>  OME Unix admin  username: ut
>>>>
>>>> Are these values correct ? [y/n]: y
>>>>
>>>> Building the core system
>>>>   \_ Checking directory "/OME".
>>>>   \_   Checking child "/OME/xml".
>>>>   \_   Checking child "/OME/bin".
>>>>   \_   Checking child "/OME/perl2".
>>>>   \_   Checking child "/OME/cgi".
>>>>   \_   Checking child "/OME/crontab".
>>>>   \_   Checking child "/OME/matlab".
>>>>   \_   Checking child "/OME/Inline".
>>>>   \_   Checking child "/OME/lib".
>>>>   \_   Checking child "/OME/java".
>>>>   \_ Checking directory "/OME/OMESIS".
>>>>   \_   Checking child "/OME/OMESIS/Files".
>>>>   \_   Checking child "/OME/OMESIS/Pixels".
>>>>   \_ Checking directory "/var/tmp/OME".
>>>>   \_   Checking child "/var/tmp/OME/lock".
>>>>   \_   Checking child "/var/tmp/OME/sessions".
>>>>   \_   Checking child "/var/tmp/OME/install".
>>>>
>>>> Copying stylesheets
>>>>   \_ src/xml/xslt/OME-CA2OME.xslt
>>>>   \_ src/xml/xslt/OME2OME-CA.xslt
>>>>
>>>> Copying IMAGE directories
>>>>   \_ images
>>>> Copying CONFIG directories
>>>>   \_ conf
>>>> Copying HTML directories
>>>>   \_ JavaScript
>>>>   \_ html
>>>>
>>>> -------------------
>>>>  Core Binary Setup
>>>> -------------------
>>>>
>>>> (All verbose information logged in /var/tmp/OME/install/
>>>> BinaryBuilds.log)
>>>>
>>>> OME can optionally be configured to work with BioFormats which  
>>>> is an
>>>> external Java library that can read 50+ common microscopy file
>>>> formats.
>>>> BioFormats requires Sun Java, but if you don't need BioFormats you
>>>> can
>>>> continue the install without Sun Java.
>>>>
>>>> Installing BioFormats
>>>>   \_ Checking for Sun Java [FOUND].
>>>>   \_ Checking for /OME/java/loci_tools.jar [FOUND].
>>>> Installing OMEIS
>>>>   \_ Configuring [SUCCESS].
>>>>   \_ Compiling [SUCCESS].
>>>>   \_ Installing [SUCCESS].
>>>> Installing omeis-http
>>>>   \_ Configuring [SUCCESS].
>>>>   \_ Compiling [SUCCESS].
>>>> Installing core binaries
>>>>   \_ Compiling [SUCCESS].
>>>>   \_ Installing [SUCCESS].
>>>>
>>>> ------------------------------
>>>>  Perl Module Dependency Setup
>>>> ------------------------------
>>>>
>>>> (All verbose information logged in /var/tmp/OME/install/
>>>> PerlModuleTask.log)
>>>>
>>>> Checking modules
>>>>   \_ Term::ReadKey 2.30 [OK].
>>>>   \_ Storable 2.15 [OK].
>>>>   \_ Carp::Assert 0.18 [OK].
>>>>   \_ Compress::Zlib 1.42 [OK].
>>>>   \_ DBI 1.52 [OK].
>>>>   \_ Digest::MD5 2.36 [OK].
>>>>   \_ MD5 [OK].
>>>>   \_ MIME::Base64 3.07 [OK].
>>>>   \_ Log::Agent 0.306 [OK].
>>>>   \_ Time::HiRes 1.86 [OK].
>>>>   \_ Date::Parse 2.27 [OK].
>>>>   \_ DBD::Pg 1.43 [OK].
>>>>   \_ Test::Harness 2.56 [OK].
>>>>   \_ Test::Simple 0.62 [OK].
>>>>   \_ HTML::Template 2.7 [OK].
>>>>   \_ IPC::Run 0.79 [OK].
>>>>   \_ Class::Accessor 0.19 [OK].
>>>>   \_ Class::Data::Inheritable 0.02 [OK].
>>>>   \_ File::Temp 0.16 [OK].
>>>>   \_ Exporter::Lite 0.01 [OK].
>>>>   \_ UNIVERSAL::exports 0.03 [OK].
>>>>   \_ URI 1.35 [OK].
>>>>   \_ HTML::Tagset 3.10 [OK].
>>>>   \_ HTML::Parser 3.55 [OK].
>>>>   \_ Parse::RecDescent 1.94 [OK].
>>>>   \_ Inline::C 0.44 [OK].
>>>>   \_ XML::NamespaceSupport 1.09 [OK].
>>>>   \_ XML::Sax 1.01 [OK].
>>>>   \_ XML::LibXML::Common 0.13 [OK].
>>>>   \_ XML::LibXML 1.62 [OK].
>>>>   \_ XML::Parser 2.34 [OK].
>>>>   \_ SOAP::Lite 0.60 [OK].
>>>>   \_ XML::LibXSLT 1.58 [OK].
>>>>   \_ OLE::Storage_Lite 0.14 [OK].
>>>>   \_ Spreadsheet::ParseExcel 0.2603 [OK].
>>>>
>>>> ------------------------
>>>>  Core Perl Module Setup
>>>> ------------------------
>>>>
>>>> (All verbose information logged in /var/tmp/OME/install/
>>>> PerlModuleTask.log)
>>>>
>>>> Installing modules
>>>>   \_ Configuring [SUCCESS].
>>>>   \_ Compiling [SUCCESS].
>>>>   \_ Installing [SUCCESS].
>>>> Use of uninitialized value in concatenation (.) or string at /home/
>>>> ut/Desktop/OME-2.6.1/src/perl2/OME/Install/ApacheConfigTask.pm
>>>> line 75.
>>>>
>>>> --------------
>>>>  Apache Setup
>>>> --------------
>>>>
>>>> (All verbose information logged in /var/tmp/OME/install/
>>>> ApacheConfigTask.log)
>>>>
>>>> OME Apache web server configuration is a critical part of your OME
>>>> install.
>>>> OME's web interface, remote clients and image server all use this
>>>> infrastructure to communicate. If you are unsure of a particular
>>>> question,
>>>> please choose the default as that will be more than adequate for  
>>>> most
>>>> people.
>>>>
>>>>
>>>> Apache configuration:
>>>>         Configure Apache?: yes
>>>>   Developer configuration: no
>>>>           Server restart?: yes
>>>> Install OME servers:
>>>>            Images (omeis): yes
>>>>              Data (omeds): yes
>>>>                       Web: yes
>>>> Apache directories:
>>>>              httpd binary: /usr/sbin/httpd
>>>>          apachectl binary: /usr/sbin/apachectl
>>>>              DocumentRoot: /var/www/html
>>>>                   cgi-bin: /var/www/cgi-bin/
>>>> Web-UI HTML Templates:
>>>>   Developer configuration: no
>>>>
>>>> Are these values correct ? [y/n]: y
>>>> [Mon Jan 21 16:14:00 2008] [warn] The ScriptAlias directive in /
>>>> OME/conf/httpd2.omeis.conf at line 2 will probably never match
>>>> because it overlaps an earlier ScriptAlias.
>>>> Testing Apache configuration
>>>>   \__ mod_perl [FAILURE].
>>>>
>>>>
>>>> Errors executing task: Apache/mod_perl is not properly
>>>> configured.  Got an error response from http://localhost/perl2/
>>>> mod_perl_test.pl:
>>>>
>>>> ERROR: The requested URL could not be retrieved
>>>>
>>>> ERROR
>>>> The requested URL could not be retrieved
>>>>
>>>>
>>>> While trying to retrieve the URL:
>>>> http://localhost/perl2/mod_perl_test.pl
>>>>
>>>> The following error was encountered:
>>>>
>>>>
>>>>
>>>> Connection Failed
>>>>
>>>>
>>>>
>>>>
>>>> The system returned:
>>>>     (111) Connection refused
>>>>
>>>>
>>>> The remote host or network may be down.  Please try the request
>>>> again.
>>>> Your cache administrator is webmstr at bbsrc.ac.uk.
>>>>
>>>>
>>>>
>>>>
>>>> Generated Mon, 21 Jan 2008 16:13:28 GMT by BBSRC-wwwcache-service
>>>> (squid/2.5.STABLE9)
>>>>
>>>>
>>>>
>>>> See /var/tmp/OME/install/ApacheConfigTask.log for more details. at
>>>> (eval 187) line 1
>>>>
>>>>  at install.pl line 82
>>>>         main::run_tasks() called at install.pl line 266
>>>> # Looks like your test died before it could output anything.
>>>>
>>>>
>>>> _________________________________________________________________
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>>>> http://www.searchgamesbox.com
>>>> _______________________________________________
>>>> ome-users mailing list
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>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
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>>
>
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