Hi Mathew, segmentation faults are hard to track, lets try our best.
Following my experience with these, I would say to check couple of
things...
CASE 1:
If you build mod_perl and php in the same binary, you might get
Segmentation fault followed by this error:
exit signal Segmentation fault (11)
CASE 2:
Could you edit your martview.PLS and then rerun the configure script and
apache restart.
Add
shift @_;
just above the following line:
my $CGI = $ENV{MOD_PERL} ? CGI->new(shift @_) : CGI->new();
Also, could you please write to me what comes up in the browser when you
navigate to http://YOURSERVER:PORT/biomart/martview
thanks for your patience.
Cheers
Syed
On Fri, 2007-07-13 at 07:23 +1000, Matthew Hobbs wrote:
> Thanks for helping me!
>
>
> Syed Haider wrote:
> > Hi Mathew,
> > what goes into your erorr_log when this message comes up ?
>
> server starts:
>
> [Fri Jul 13 07:08:39 2007] [warn] pid file
> /usr/local/BioMart-0.6/biomart-perl/logs/httpd.pid overwritten --
> Unclean shutdown of previous Apache run?
> [Fri Jul 13 07:08:39 2007] [notice] Apache/2.2.4 (Unix) mod_perl/2.0.3
> Perl/v5.8.0 configured -- resuming normal operations
>
> request for /biomart/martview:
>
> ==> /usr/local/BioMart-0.6/biomart-perl/logs/access_log <==
> 144.134.235.139 - - [13/Jul/2007:07:11:27 +1000] "GET /biomart/martview
> HTTP/1.1" 200 138
>
> request for /biomart/martview/f747eb4b9bbf1f6523e267bf68da7df8 (the url
> specified in the previous response) :
>
> ==> /usr/local/BioMart-0.6/biomart-perl/logs/error_log <==
> [Fri Jul 13 07:13:17 2007] [notice] child pid 25443 exit signal
> Segmentation fault (11)
>
>
>
> > In addition can I have a look at your httpd.conf + settings.conf, please
> > mail me these files.
>
> attached
>
> you will notice one non-standard detail is that the apache binary is
> called 'httpd_biomart2' - this is simply a symlink to 'httpd'. I don't
> think this is the problem however as I get the same results if I use
> httpd in settings.conf and when starting the server.
>
>
> Matthew
> plain text document attachment (httpd.conf)
> User apache
> PidFile logs/httpd.pid
> Timeout 300
> KeepAlive On
> MaxKeepAliveRequests 100
> KeepAliveTimeout 15
> MinSpareServers 2
> MaxSpareServers 2
> StartServers 2
> MaxClients 50
> MaxRequestsPerChild 0
> Listen 80
>
> DirectoryIndex index.html
>
> TypesConfig conf/mime.types
> DefaultType text/plain
> AddType image/gif .gif
> AddType image/png .png
> AddType image/jpeg .jpg .jpeg
> AddType text/css .css
> AddType text/html .html .htm
> AddType text/xml .xml
> AddType text/plain .asc .txt
> AddType application/pdf .pdf
> AddType application/x-gzip .gz .tgz
> AddType application/vnd.ms-excel .xls
>
> ErrorLog logs/error_log
> LogLevel warn
> LogFormat "%h %l %u %t \"%r\" %>s %b" combined
> CustomLog logs/access_log combined
>
> LoadModule perl_module
> /usr/local/BioMart-0.6/apache/modules/mod_perl.so
>
> <Perl>
>
> use lib
> '/usr/local/BioMart-0.6/biomart-perl/lib';
> require "BioMart/Configuration/Attribute.pm";
> require "BioMart/Configuration/AttributeCollection.pm";
> require "BioMart/Configuration/AttributeGroup.pm";
> require "BioMart/Configuration/AttributeList.pm";
> require "BioMart/Configuration/AttributeTree.pm";
> require "BioMart/Configuration/BaseFilter.pm";
> require "BioMart/Configuration/BooleanFilter.pm";
> require "BioMart/Configuration/ConfigurationTree.pm";
> require "BioMart/Configuration/DBLocation.pm";
> require "BioMart/Configuration/FilterCollection.pm";
> require "BioMart/Configuration/FilterGroup.pm";
> require "BioMart/Configuration/FilterList.pm";
> require "BioMart/Configuration/FilterTree.pm";
> require "BioMart/Configuration/Location.pm";
> require "BioMart/Configuration/MartDBLocation.pm";
> require "BioMart/Configuration/MartURLLocation.pm";
> require "BioMart/Configuration/Option.pm";
> require "BioMart/Configuration/PushAction.pm";
> require "BioMart/Configuration/RegistryDBPointer.pm";
> require "BioMart/Configuration/RegistryURLPointer.pm";
> require "BioMart/Configuration/URLLocation.pm";
> require "BioMart/Configuration/ValueFilter.pm";
> require "BioMart/Configuration/VirtualSchema.pm";
> require "BioMart/AttributeTable.pm";
> require "BioMart/Configurator.pm";
> require "BioMart/DatasetI.pm";
> require "BioMart/Exception.pm";
> require "BioMart/FormatterI.pm";
> require "BioMart/Initializer.pm";
> require "BioMart/Links.pm";
> require "BioMart/Query.pm";
> require "BioMart/QueryRunner.pm";
> require "BioMart/Registry.pm";
> require "BioMart/ResultTable.pm";
> require "BioMart/Root.pm";
> require "BioMart/RootI.pm";
> require "BioMart/Web.pm";
> require
> "BioMart/Dataset/GenomicSequence/DNAAdaptor.pm";
> require "BioMart/Dataset/GenomicAlign.pm";
> require "BioMart/Dataset/GenomicMAlign.pm";
> require "BioMart/Dataset/GenomicSequence.pm";
> require "BioMart/Dataset/GenomicSequenceMod.pm";
> require "BioMart/Dataset/TableSet.pm";
> require "BioMart/Formatter/AXTPLUS.pm";
> require "BioMart/Formatter/ADF.pm";
> require "BioMart/Formatter/AXT.pm";
> require "BioMart/Formatter/FASTA.pm";
> require "BioMart/Formatter/CSV.pm";
> require "BioMart/Formatter/FASTAA.pm";
> require "BioMart/Formatter/FASTACDNA.pm";
> require "BioMart/Formatter/FASTAH.pm";
> require "BioMart/Formatter/GFF.pm";
> require "BioMart/Formatter/HTML.pm";
> require "BioMart/Formatter/MAF.pm";
> require "BioMart/Formatter/MAF_NOPREVIEW.pm";
> require "BioMart/Formatter/MAF_RESTRICTED.pm";
> require "BioMart/Formatter/MFA.pm";
> require "BioMart/Formatter/MFASTA.pm";
> require "BioMart/Formatter/TSV.pm";
> require "BioMart/Formatter/TXT.pm";
> require "BioMart/Formatter/XLS.pm";
> require "BioMart/Web/CGIXSLT.pm";
> require "BioMart/Web/PageStub.pm";
> require "BioMart/Web/SiteDefs.pm";
> require "BioMart/Web/TemplateBuilder.pm";
> require "BioMart/Web/Zlib.pm";
> #warn "MartView:: Initializing master Mart registry";
> eval { my $init = BioMart::Initializer->new(registryFile =>
> '/usr/local/BioMart-0.6/biomart-perl/conf/martURLLocation.xml');
> $main::BIOMART_REGISTRY = $init->getRegistry() || die "Can't
> get registry from initializer";
> };
> </Perl>
>
> DocumentRoot "/usr/local/BioMart-0.6/biomart-perl/htdocs"
> <Location />
> Options Indexes FollowSymLinks MultiViews
> AllowOverride None
> Order allow,deny
> Allow from all
> </Location>
>
> ScriptAlias /biomart/martview
> "/usr/local/BioMart-0.6/biomart-perl/cgi-bin/martview"
> <Location /biomart/martview>
>
> AllowOverride None
> Options None
> Order allow,deny
> Allow from all
>
> <IfModule mod_deflate.c>
> ## zip both input and output
> SetOutputFilter DEFLATE
> SetInputFilter DEFLATE
> ## donot zip already zipped files
> SetEnvIfNoCase Request_URI
> \.(?:exe|t?gz|zip|bz2|sit|rar)$ no-gzip dont-vary
> </IfModule>
> SetHandler perl-script
> PerlResponseHandler ModPerl::Registry
> Options +ExecCGI
> </Location>
>
> ScriptAlias /biomart/martservice
> "/usr/local/BioMart-0.6/biomart-perl/cgi-bin/martservice"
> <Location /biomart/martservice>
> AllowOverride None
> Options None
> Order allow,deny
> Allow from all
> SetHandler perl-script
> PerlResponseHandler ModPerl::Registry
> Options +ExecCGI
> </Location>
>
> ScriptAlias /biomart/martresults
> "/usr/local/BioMart-0.6/biomart-perl/cgi-bin/martresults"
> <Location /biomart/martresults>
> AllowOverride None
> Options None
> Order allow,deny
> Allow from all
> SetHandler perl-script
> PerlResponseHandler ModPerl::Registry
> Options +ExecCGI
> </Location>
>
> <Location /biomart/perl-status>
> SetHandler perl-script
> PerlHandler Apache2::Status
> </Location>
>
> ScriptAlias /biomart/das/dsn
> "/usr/local/BioMart-0.6/biomart-perl/cgi-bin/dsn"
> <Location /biomart/das/dsn>
> AllowOverride None
> Options None
> Order allow,deny
> Allow from all
> SetHandler perl-script
> PerlResponseHandler ModPerl::Registry
> Options +ExecCGI
> </Location>
>
> plain text document attachment (settings.conf)
> #########################################################
> ################ httpd.conf settings ####################
>
> [httpdSettings]
> #apacheBinary=/usr/sbin/httpd
> #apacheBinary=/usr/sbin/httpd_biomart2
> #apacheBinary=/EnsMart/apache/bin/httpd_biomart2
> apacheBinary=/usr/local/BioMart-0.6/apache/bin/httpd_biomart2
> #serverHost=test.biomart.org
> serverHost=localhost
> #port=9002
> port=80
> # to use proxying set the proxy port below (even if its 80) and set
> serverHost as your proxy host
> #proxy=localhost:443
> proxy=
> location=biomart
>
>
> # Colours settings for MARTVIEW
> # A good online tool help with picking a palette is;
> # http://slayeroffice.com/tools/color_palette/
> [cssSettings]
>
> # The default theme, based on a 6-level grey scale from black to white.
> #colour_saturation0=black
> #colour_saturation20=black
> #colour_saturation40=#666666
> #colour_saturation60=#CCCCCC
> #colour_saturation80=#E5E5E5
> #colour_saturation100=white
>
> # The MH theme
> #colour_saturation0=black
> #colour_saturation20=#8294BA
> #colour_saturation40=#D5DBE8
> #colour_saturation60=red
> #colour_saturation80=blue
> #colour_saturation100=white
>
> # The blue theme used for WormMart
> colour_saturation0=black
> colour_saturation20=#5870A3
> colour_saturation40=#8294BA
> colour_saturation60=#D5DBE8
> colour_saturation80=#EFF1F6
> colour_saturation100=white
>
> # These settings relate to the text displayed in the interface drop downs
>
> [aliases]
> Schema=- CHOOSE SCHEMA -
> Database=- CHOOSE DATABASE -
> Dataset=- CHOOSE DATASET -
>
>
> # If an attribute URL is specified relatively such as '/geneview/?=%s'
> # then by default this will be used relative to the current host
> # However if you set exturl below then this will be prefixed
> # to these URLs
>
> [urlPrefixes]
> #exturl=http://www.ensembl.org
>
>
> # These settings are used to control how the background
> # results jobs are managed.
> #
> # Set resultsDirCount to the number of results directories
> # you want to use. Then, use resultsDir1, resultsDir2 etc.
> # to assign names for these directories, up to resultsDirN
> # where N is the value of resultsDirCount. Background jobs
> # will be assigned to each of these resultsDir locations
> # by a hash function which is intended to distribute them
> # evenly.
> #
> # Use resultsDir to specify where
> # files containing results from background jobs are stored.
> # This folder must (a) exist and (b) be writable by the
> # owner of the web server process.
> #
> # The enable setting should have a value of 'yes'
> # if you want background jobs to be available to the user.
> # Any other value, including non-lowercase versions of 'yes'
> # will turn background jobs off.
>
> [background]
> resultsDirCount=1
> resultsDir1=/ebi/www/biomart/test/files
> enable=no
>
> # Mail settings are used for informing users when their
> # background tasks are finished. The mailerType defines
> # the way in which mail is sent, as understood by
> # Mail::Mailer. For details of how to control this, see:
> #
> # http://search.cpan.org/dist/MailTools/Mail/Mailer.pm
> #
> # The from address is the address that messages will
> # appear to be from.
>
> [mailSettings]
> mailerType=sendmail
> subject=Your BioMart results are ready
> [EMAIL PROTECTED]
>
> # These settings relate to sessions.
> #
> # The expire setting relates to how long sessions will live
> # on disk for. If not accessed for a period of time longer than
> # this, then the session will be dropped. Aliases are:
> #
> # +-----------+---------------+
> # | alias | meaning |
> # +-----------+---------------+
> # | s | Second |
> # | m | Minute |
> # | h | Hour |
> # | d | Day |
> # | w | Week |
> # | M | Month |
> # | y | Year |
> # +-----------+---------------+
> #
> # Driver could have values based on where you want the session to be
> # stored. default or no value assigned is set to Berkeley DB implementation.
> # All possible values could be:
> # driver=
> # driver=default
> # driver=files
> # driver=mysql
> # driver=oracle
> # a database table must already exist with any name but with strict
> columnName/Types
> # EXAMPLES
> # ========== MySQL ============
> # first create the table as
> # CREATE TABLE sessions ( id CHAR(32) NOT NULL UNIQUE, a_session LONGTEXT NOT
> NULL ) ;
> # then the following settings should follow under [sessions]
> # driver=mysql
> # dsn=DBI:mysql:database=YOU_DATABASE_NAME;host=127.0.0.1;port=3306
> # user=root
> # pass=
> # ========== ORACLE ============
> # first create the table as
> # CREATE TABLE sessions ( id CHAR(32) NOT NULL UNIQUE, a_session CLOB NOT
> NULL ) ;
> # then the following settings should follow under [sessions]
> # driver=oracle
> # dsn=dbi:Oracle:host=172.22.70.89;sid=XE;port=1521
> # user=root
> # pass=
>
>
> [sessions]
> #expire=1d
> expire=5m
> #driver=default
> driver=mysql
> dsn=DBI:mysql:database=mart_sessions;host=localhost;port=3309
> user=mart_admin
> pass=
>
> # Web Service Logging options
> [webserviceLogging]
> mode=ON
> log_query=ON
> log_IP=ON
>
>
>
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
