gbrowse 2 and renderfarm
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gbrowse 2 and renderfarm
by Baptiste Brault
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Hi all,
I tried gbrowse2 with mod perl + renderfarm. Everything is okay for GFF, Mysql, Bio::SeqFeature::Store. I also try with Postgresql/ Chado. I get this error message : Magic number checking on storable string failed at ../../lib/Storable.pm (autosplit into ../../lib/auto/Storable/thaw.al) line 363, at /home/projects/gpi/ggb/Generic-Genome-Browser-2.00-beta/lib/perl5/sun4-solaris-thread-multi-64/Bio/Graphics/Browser/RenderPanels.pm line 653, referer: http://localhost:1671/gb2/gbrowse/Botrytis/?name=bt4ctg_0111%3A3858..6529 So, tracks aren't displayed. My configuration works without mod perl + renderfarm, mod perl only. Could you please help me ? Thanks, Baptiste -- Baptiste Brault INRA URGI/BIOGER, Bat 18 Route de Saint Cyr 78026 Versailles baptiste.brault@... tel:+33 1 30 83 37 70 ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: gbrowse 2 and renderfarm
by Scott Cain-4
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Hi Baptiste,
That is really interesting, and I have no idea what might be going on. If anybody else has any suggestions, I'd like to hear about them. In the meantime, I'll set up a system with modperl to see if I can reproduce it. Scott On Sep 2, 2009, at 12:09 PM, Baptiste Brault wrote: > Hi all, > > I tried gbrowse2 with mod perl + renderfarm. Everything is okay for > GFF, > Mysql, Bio::SeqFeature::Store. > > I also try with Postgresql/ Chado. I get this error message : > > Magic number checking on storable string failed at ../../lib/ > Storable.pm > (autosplit into ../../lib/auto/Storable/thaw.al) line 363, at > /home/projects/gpi/ggb/Generic-Genome-Browser-2.00-beta/lib/perl5/ > sun4-solaris-thread-multi-64/Bio/Graphics/Browser/RenderPanels.pm > line 653, referer: > http://localhost:1671/gb2/gbrowse/Botrytis/?name=bt4ctg_0111%3A3858..6529 > > So, tracks aren't displayed. > My configuration works without mod perl + renderfarm, mod perl only. > > Could you please help me ? > > > Thanks, > > Baptiste > > -- > Baptiste Brault > INRA URGI/BIOGER, Bat 18 > Route de Saint Cyr 78026 Versailles > baptiste.brault@... > tel:+33 1 30 83 37 70 > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse ----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: gbrowse 2 and renderfarm
by Lincoln Stein-3
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Hi Baptiste, Scott,
This message happens when the object is corrupted for any reason. Is the error occurring on the slave or the master? My guess is that the slave is missing some library needed for the Chado connection and is throwing an error and returning a partial object to the master. Check the slave error logs. Lincoln On Wed, Sep 2, 2009 at 1:11 PM, Scott Cain <scott@...> wrote: Hi Baptiste, -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: gbrowse 2 and renderfarm
by Scott Cain-4
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Ah, OK. Baptiste let me know if you find anything out. I did set up
a simple system (no renderfarm so far) and found that as you wrote, it works fine (although very much faster than without. That was incredibly easy to set up--Thanks, Lincoln). Scott On Sep 2, 2009, at 2:14 PM, Lincoln Stein wrote: > Hi Baptiste, Scott, > > This message happens when the object is corrupted for any reason. Is > the error occurring on the slave or the master? My guess is that the > slave is missing some library needed for the Chado connection and is > throwing an error and returning a partial object to the master. > Check the slave error logs. > > Lincoln > > On Wed, Sep 2, 2009 at 1:11 PM, Scott Cain <scott@...> > wrote: > Hi Baptiste, > > That is really interesting, and I have no idea what might be going > on. If anybody else has any suggestions, I'd like to hear about them. > > In the meantime, I'll set up a system with modperl to see if I can > reproduce it. > > Scott > > > On Sep 2, 2009, at 12:09 PM, Baptiste Brault wrote: > > > Hi all, > > > > I tried gbrowse2 with mod perl + renderfarm. Everything is okay for > > GFF, > > Mysql, Bio::SeqFeature::Store. > > > > I also try with Postgresql/ Chado. I get this error message : > > > > Magic number checking on storable string failed at ../../lib/ > > Storable.pm > > (autosplit into ../../lib/auto/Storable/thaw.al) line 363, at > > /home/projects/gpi/ggb/Generic-Genome-Browser-2.00-beta/lib/perl5/ > > sun4-solaris-thread-multi-64/Bio/Graphics/Browser/RenderPanels.pm > > line 653, referer: > > http://localhost:1671/gb2/gbrowse/Botrytis/?name=bt4ctg_0111%3A3858..6529 > > > > So, tracks aren't displayed. > > My configuration works without mod perl + renderfarm, mod perl only. > > > > Could you please help me ? > > > > > > Thanks, > > > > Baptiste > > > > -- > > Baptiste Brault > > INRA URGI/BIOGER, Bat 18 > > Route de Saint Cyr 78026 Versailles > > baptiste.brault@... > > tel:+33 1 30 83 37 70 > > > > > > > ------------------------------------------------------------------------------ > > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > > 30-Day > > trial. Simplify your report design, integration and deployment - and > > focus on > > what you do best, core application coding. Discover what's new with > > Crystal Reports now. http://p.sf.net/sfu/bobj-july > > _______________________________________________ > > Gmod-gbrowse mailing list > > Gmod-gbrowse@... > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > ----------------------------------------------------------------------- > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > > > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > > -- > Lincoln D. Stein > Director, Informatics and Biocomputing Platform > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa <Renata.Musa@...> ----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: gbrowse 2 and renderfarm
by Baptiste Brault
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Hi Scott, Lincoln,
when I checked the slave error logs. I see Can't locate Bio/DB/Das/Chado.pm So I add in /etc/default/gbrowse_slave the path of Bio::DB::Das::Chado and now it's work Thanks, Baptiste Scott Cain wrote: > Ah, OK. Baptiste let me know if you find anything out. I did set up > a simple system (no renderfarm so far) and found that as you wrote, it > works fine (although very much faster than without. That was > incredibly easy to set up--Thanks, Lincoln). > > Scott > > > On Sep 2, 2009, at 2:14 PM, Lincoln Stein wrote: > >> Hi Baptiste, Scott, >> >> This message happens when the object is corrupted for any reason. Is >> the error occurring on the slave or the master? My guess is that the >> slave is missing some library needed for the Chado connection and is >> throwing an error and returning a partial object to the master. Check >> the slave error logs. >> >> Lincoln >> >> On Wed, Sep 2, 2009 at 1:11 PM, Scott Cain <scott@...> wrote: >> Hi Baptiste, >> >> That is really interesting, and I have no idea what might be going >> on. If anybody else has any suggestions, I'd like to hear about them. >> >> In the meantime, I'll set up a system with modperl to see if I can >> reproduce it. >> >> Scott >> >> >> On Sep 2, 2009, at 12:09 PM, Baptiste Brault wrote: >> >> > Hi all, >> > >> > I tried gbrowse2 with mod perl + renderfarm. Everything is okay for >> > GFF, >> > Mysql, Bio::SeqFeature::Store. >> > >> > I also try with Postgresql/ Chado. I get this error message : >> > >> > Magic number checking on storable string failed at ../../lib/ >> > Storable.pm >> > (autosplit into ../../lib/auto/Storable/thaw.al) line 363, at >> > /home/projects/gpi/ggb/Generic-Genome-Browser-2.00-beta/lib/perl5/ >> > sun4-solaris-thread-multi-64/Bio/Graphics/Browser/RenderPanels.pm >> > line 653, referer: >> > >> http://localhost:1671/gb2/gbrowse/Botrytis/?name=bt4ctg_0111%3A3858..6529 >> >> > >> > So, tracks aren't displayed. >> > My configuration works without mod perl + renderfarm, mod perl only. >> > >> > Could you please help me ? >> > >> > >> > Thanks, >> > >> > Baptiste >> > >> > -- >> > Baptiste Brault >> > INRA URGI/BIOGER, Bat 18 >> > Route de Saint Cyr 78026 Versailles >> > baptiste.brault@... >> > tel:+33 1 30 83 37 70 >> > >> > >> > >> ------------------------------------------------------------------------------ >> >> > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >> > 30-Day >> > trial. Simplify your report design, integration and deployment - and >> > focus on >> > what you do best, core application coding. Discover what's new with >> > Crystal Reports now. http://p.sf.net/sfu/bobj-july >> > _______________________________________________ >> > Gmod-gbrowse mailing list >> > Gmod-gbrowse@... >> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> ----------------------------------------------------------------------- >> Scott Cain, Ph. D. scott at scottcain dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >> 30-Day >> trial. Simplify your report design, integration and deployment - and >> focus on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> >> >> -- >> Lincoln D. Stein >> Director, Informatics and Biocomputing Platform >> Ontario Institute for Cancer Research >> 101 College St., Suite 800 >> Toronto, ON, Canada M5G0A3 >> 416 673-8514 >> Assistant: Renata Musa <Renata.Musa@...> > > ----------------------------------------------------------------------- > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > > > -- Baptiste Brault INRA URGI/BIOGER, Bat 18 Route de Saint Cyr 78026 Versailles baptiste.brault@... tel:+33 1 30 83 37 70 ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: gbrowse 2 and renderfarm
by Lincoln Stein-3
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Hi Brault,
Ok, I'm very happy to hear this. Lincoln On Thu, Sep 3, 2009 at 4:56 AM, Baptiste Brault <baptiste.brault@...> wrote: Hi Scott, Lincoln, -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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