gbrowse 2.08 behaviour

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gbrowse 2.08 behaviour

okeeffe
Hi Folks,
Just did (what I thought was going to be) a routine update from
Gbrowse2.05->2.08 today incl. a Bio::Graphics update to 2.09.
I'm getting the following in the error log - strange memory alloc errors
plus other strange stuff:
(Admittedly Bio-Samtools is 1.16 not 1.19)

Also getting a heck of a lot of compilation errors:
Can't load
'/home/okeeffe/lib/perl5/5.8.8/x86_64-linux/auto/File/Glob/Glob.so' for
module File::Glob:
/home/okeeffe/lib/perl5/5.8.8/x86_64-linux/auto/File/Glob/Glob.so:
failed to map segment from shared object: Cannot allocate memory at
/home/okeeffe/lib/perl5/5.8.8/x86_64-linux/XSLoader.pm line 70.,
referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]  at
/home/okeeffe/lib/perl5/5.8.8/x86_64-linux/File/Glob.pm line 96,
referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
failed in require at
/project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/FeatureFile.pm
line 478., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
failed--compilation aborted at
/project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/FeatureFile.pm
line 478., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
failed in require at (eval 2) line 3., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] \t...propagated
at /home/okeeffe/lib/perl5/5.8.8/base.pm line 85., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
failed--compilation aborted at
/project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
line 5., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
failed in require at (eval 1) line 3., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] \t...propagated
at /home/okeeffe/lib/perl5/5.8.8/base.pm line 85., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
failed--compilation aborted at
/project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2.pm
line 9., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
failed in require at
/project/gbrowse/httpd_internal/cgi-bin/gbrowse2/gbrowse line 9.,
referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
failed--compilation aborted at
/project/gbrowse/httpd_internal/cgi-bin/gbrowse2/gbrowse line 9.,
referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Premature end
of script headers: gbrowse, referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:37 2010] [error] [client 141.14.29.50] Can't load
'/project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/auto/Bio/DB/Sam/Sam.so'
for module Bio::DB::Sam:
/project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/auto/Bio/DB/Sam/Sam.so:
failed to map segment from shared object: Cannot allocate memory at
/home/okeeffe/lib/perl5/5.8.8/x86_64-linux/DynaLoader.pm line 230

Finally I did a top on the running processes and notice multiple
instances of gbrowse eating 100% of cpu and large shares of memory.
Can't say if these are related but I'd never seen processes like these
before.

Best,
Sean.


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Re: gbrowse 2.08 behaviour

Lincoln Stein
Something is wrong with Perl's dynamic library loader. Lots of these errors have nothing to do with well-established modules like File::Glob. There might be something lurking in the Apache environment, such as a PERL5LIB variable that is pointing to a previous Perl installation. Were you able to run GBrowse's tests from the command line ok?

Lincoln

On Thu, May 27, 2010 at 9:56 AM, Sean O'Keeffe <[hidden email]> wrote:
Hi Folks,
Just did (what I thought was going to be) a routine update from
Gbrowse2.05->2.08 today incl. a Bio::Graphics update to 2.09.
I'm getting the following in the error log - strange memory alloc errors
plus other strange stuff:
(Admittedly Bio-Samtools is 1.16 not 1.19)

Also getting a heck of a lot of compilation errors:
Can't load
'/home/okeeffe/lib/perl5/5.8.8/x86_64-linux/auto/File/Glob/Glob.so' for
module File::Glob:
/home/okeeffe/lib/perl5/5.8.8/x86_64-linux/auto/File/Glob/Glob.so:
failed to map segment from shared object: Cannot allocate memory at
/home/okeeffe/lib/perl5/5.8.8/x86_64-linux/XSLoader.pm line 70.,
referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]  at
/home/okeeffe/lib/perl5/5.8.8/x86_64-linux/File/Glob.pm line 96,
referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
failed in require at
/project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/FeatureFile.pm
line 478., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
failed--compilation aborted at
/project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/FeatureFile.pm
line 478., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
failed in require at (eval 2) line 3., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] \t...propagated
at /home/okeeffe/lib/perl5/5.8.8/base.pm line 85., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
failed--compilation aborted at
/project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
line 5., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
failed in require at (eval 1) line 3., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] \t...propagated
at /home/okeeffe/lib/perl5/5.8.8/base.pm line 85., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
failed--compilation aborted at
/project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2.pm
line 9., referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
failed in require at
/project/gbrowse/httpd_internal/cgi-bin/gbrowse2/gbrowse line 9.,
referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
failed--compilation aborted at
/project/gbrowse/httpd_internal/cgi-bin/gbrowse2/gbrowse line 9.,
referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Premature end
of script headers: gbrowse, referer:
http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
[Thu May 27 14:44:37 2010] [error] [client 141.14.29.50] Can't load
'/project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/auto/Bio/DB/Sam/Sam.so'
for module Bio::DB::Sam:
/project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/auto/Bio/DB/Sam/Sam.so:
failed to map segment from shared object: Cannot allocate memory at
/home/okeeffe/lib/perl5/5.8.8/x86_64-linux/DynaLoader.pm line 230

Finally I did a top on the running processes and notice multiple
instances of gbrowse eating 100% of cpu and large shares of memory.
Can't say if these are related but I'd never seen processes like these
before.

Best,
Sean.


------------------------------------------------------------------------------

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--
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 <[hidden email]>

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Re: gbrowse 2.08 behaviour

okeeffe
Lincoln Stein wrote:

> Something is wrong with Perl's dynamic library loader. Lots of these
> errors have nothing to do with well-established modules like
> File::Glob. There might be something lurking in the Apache
> environment, such as a PERL5LIB variable that is pointing to a
> previous Perl installation. Were you able to run GBrowse's tests from
> the command line ok?
>
> Lincoln
>
> On Thu, May 27, 2010 at 9:56 AM, Sean O'Keeffe <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi Folks,
>     Just did (what I thought was going to be) a routine update from
>     Gbrowse2.05->2.08 today incl. a Bio::Graphics update to 2.09.
>     I'm getting the following in the error log - strange memory alloc
>     errors
>     plus other strange stuff:
>     (Admittedly Bio-Samtools is 1.16 not 1.19)
>
>     Also getting a heck of a lot of compilation errors:
>     Can't load
>     '/home/okeeffe/lib/perl5/5.8.8/x86_64-linux/auto/File/Glob/Glob.so'
>     for
>     module File::Glob:
>     /home/okeeffe/lib/perl5/5.8.8/x86_64-linux/auto/File/Glob/Glob.so:
>     failed to map segment from shared object: Cannot allocate memory at
>     /home/okeeffe/lib/perl5/5.8.8/x86_64-linux/XSLoader.pm line 70.,
>     referer:
>     http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>     [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]  at
>     /home/okeeffe/lib/perl5/5.8.8/x86_64-linux/File/Glob.pm line 96,
>     referer:
>     http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>     [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
>     failed in require at
>     /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/FeatureFile.pm
>     line 478., referer:
>     http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>     [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
>     failed--compilation aborted at
>     /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/FeatureFile.pm
>     line 478., referer:
>     http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>     [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
>     failed in require at (eval 2) line 3., referer:
>     http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>     [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]
>     \t...propagated
>     at /home/okeeffe/lib/perl5/5.8.8/base.pm <http://base.pm> line
>     85., referer:
>     http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>     [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
>     failed--compilation aborted at
>     /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
>     line 5., referer:
>     http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>     [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
>     failed in require at (eval 1) line 3., referer:
>     http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>     [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]
>     \t...propagated
>     at /home/okeeffe/lib/perl5/5.8.8/base.pm <http://base.pm> line
>     85., referer:
>     http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>     [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
>     failed--compilation aborted at
>     /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2.pm
>     line 9., referer:
>     http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>     [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
>     failed in require at
>     /project/gbrowse/httpd_internal/cgi-bin/gbrowse2/gbrowse line 9.,
>     referer:
>     http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>     [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
>     failed--compilation aborted at
>     /project/gbrowse/httpd_internal/cgi-bin/gbrowse2/gbrowse line 9.,
>     referer:
>     http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>     [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Premature end
>     of script headers: gbrowse, referer:
>     http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>     [Thu May 27 14:44:37 2010] [error] [client 141.14.29.50] Can't load
>     '/project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/auto/Bio/DB/Sam/Sam.so'
>     for module Bio::DB::Sam:
>     /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/auto/Bio/DB/Sam/Sam.so:
>     failed to map segment from shared object: Cannot allocate memory at
>     /home/okeeffe/lib/perl5/5.8.8/x86_64-linux/DynaLoader.pm line 230
>
>     Finally I did a top on the running processes and notice multiple
>     instances of gbrowse eating 100% of cpu and large shares of memory.
>     Can't say if these are related but I'd never seen processes like these
>     before.
>
>     Best,
>     Sean.
>
>
>     ------------------------------------------------------------------------------
>
>     _______________________________________________
>     Gmod-gbrowse mailing list
>     [hidden email]
>     <mailto:[hidden email]>
>     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 <[hidden email]
> <mailto:[hidden email]>>
Seems OK, Lincoln.

NOTE: Run ./Build reconfig to change existing configuration.
Writing config notes to blib/lib/GBrowse/ConfigData.pm
Performing variable substitutions in blib/conf/detail_select_menu.conf
Performing variable substitutions in blib/conf/enzymes.txt
Performing variable substitutions in blib/conf/GBrowse.conf
Performing variable substitutions in blib/conf/log4perl.conf
Performing variable substitutions in blib/conf/MobyServices/moby.conf
Performing variable substitutions in blib/conf/pop_demo.conf
Performing variable substitutions in blib/conf/slave_preload.conf
Performing variable substitutions in blib/conf/submitter_plugin.conf
Performing variable substitutions in blib/conf/synteny/rice_synteny.conf
Performing variable substitutions in
blib/conf/synteny/wild_rice_synteny.conf
Performing variable substitutions in blib/conf/themes/solid_gray_colors
Performing variable substitutions in blib/conf/themes/transparent_colors
Performing variable substitutions in blib/conf/themes/warm_colors
Performing variable substitutions in blib/conf/yeast_chr1+2.conf
Performing variable substitutions in blib/conf/yeast_renderfarm.conf
Performing variable substitutions in blib/conf/yeast_simple.conf
Performing variable substitutions in blib/htdocs/annotation_help.html
Performing variable substitutions in blib/htdocs/gbrowse_karyotype_help.html
Performing variable substitutions in blib/htdocs/gbrowse_syn_help.html
Performing variable substitutions in blib/htdocs/general_help.html
Performing variable substitutions in blib/htdocs/index.html
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/elegans_core.conf
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/elegans_extra.conf
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/HEADER.html
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/volvox.conf
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/volvox_final.conf
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/volvox_halfway.conf
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/volvox_Phylo.conf
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/volvox_quarter.conf
Performing variable substitutions in
blib/htdocs/tutorial/conf_files/volvox_refactored.conf
Performing variable substitutions in
blib/htdocs/tutorial/data_files/HEADER.html
Performing variable substitutions in blib/htdocs/tutorial/tutorial.html
Performing variable substitutions in
blib/htdocs/tutorial/tutorial.phyTreeEdit.html
t/01yeast...................ok
t/02.rearchitecture.........ok
t/03.render.................21/138 Use of uninitialized value in
concatenation (.) or string at (eval 345) line 15.
Use of uninitialized value in concatenation (.) or string at (eval 345)
line 15.
t/03.render.................108/138 Subroutine
Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
/home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
 at
/project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm
line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined at
/home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
 at
/project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm
line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at
/home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
 at
/project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm
line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE redefined
at /home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
 at
/project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm
line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW redefined
at /home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
 at
/project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm
line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at
/home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
 at
/project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm
line 10
t/03.render.................ok
t/04.remoteserver...........ok
t/05.deferredrendering......ok
t/06.featuresearch..........ok
t/07.karyotype..............ok
t/08.calign.................ok
All tests successful.
Files=8, Tests=332, 37 wallclock secs ( 0.08 usr  0.02 sys +  8.96 cusr  
5.38 csys = 14.44 CPU)
Result: PASS


------------------------------------------------------------------------------

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Re: gbrowse 2.08 behaviour

Lincoln Stein
In reply to this post by okeeffe
I didn't notice your comments on top. It is expected for each request to launch multiple gbrowse instances (up to four at a time, I think), but they shouldn't chew up a lot of memory or CPU (except very transiently). If you are seeing these problems when viewing BAM tracks, it is possible that you have run into a bug in Bio::Samtools which tries to reindex BAM files even when they don't need it. You can fix this by either "touch"ing all your .bai files so that their modification dates are more recent than the .bam files, or by upgrading to the more recent Bio::Samtools.

Lincoln

On Thu, May 27, 2010 at 12:36 PM, Sean O'Keeffe <[hidden email]> wrote:
[hidden email] wrote:
If the tests work, then GBrowse should work. Have you changed anything in Apache's environment that might cause the CGI script to find a different version of Perl and/or its libraries?

Lincoln

On May 27, 2010 11:43am, Sean O'Keeffe <[hidden email]> wrote:
> Lincoln Stein wrote:
>
>
> Something is wrong with Perl's dynamic library loader. Lots of these errors have nothing to do with well-established modules like File::Glob. There might be something lurking in the Apache environment, such as a PERL5LIB variable that is pointing to a previous Perl installation. Were you able to run GBrowse's tests from the command line ok?
>
>
>
> Lincoln
>
>
>
> On Thu, May 27, 2010 at 9:56 AM, Sean O'Keeffe [hidden email] [hidden email]>> wrote:
>
>
>
>    Hi Folks,
>
>    Just did (what I thought was going to be) a routine update from
>
>    Gbrowse2.05->2.08 today incl. a Bio::Graphics update to 2.09.
>
>    I'm getting the following in the error log - strange memory alloc
>
>    errors
>
>    plus other strange stuff:
>
>    (Admittedly Bio-Samtools is 1.16 not 1.19)
>
>
>
>    Also getting a heck of a lot of compilation errors:
>
>    Can't load
>
>    '/home/okeeffe/lib/perl5/5.8.8/x86_64-linux/auto/File/Glob/Glob.so'
>
>    for
>
>    module File::Glob:
>
>    /home/okeeffe/lib/perl5/5.8.8/x86_64-linux/auto/File/Glob/Glob.so:
>
>    failed to map segment from shared object: Cannot allocate memory at
>
>    /home/okeeffe/lib/perl5/5.8.8/x86_64-linux/XSLoader.pm line 70.,
>
>    referer:
>
>    http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>
>    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]  at
>
>    /home/okeeffe/lib/perl5/5.8.8/x86_64-linux/File/Glob.pm line 96,
>
>    referer:
>
>    http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>
>    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
>
>    failed in require at
>
>    /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/FeatureFile.pm
>
>    line 478., referer:
>
>    http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>
>    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
>
>    failed--compilation aborted at
>
>    /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/FeatureFile.pm
>
>    line 478., referer:
>
>    http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>
>    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
>
>    failed in require at (eval 2) line 3., referer:
>
>    http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>
>    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]
>
>    \t...propagated
>
>    at /home/okeeffe/lib/perl5/5.8.8/base.pm http://base.pm> line
>
>    85., referer:
>
>    http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>
>    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
>
>    failed--compilation aborted at
>
>    /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
>
>    line 5., referer:
>
>    http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>
>    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
>
>    failed in require at (eval 1) line 3., referer:
>
>    http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>
>    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]
>
>    \t...propagated
>
>    at /home/okeeffe/lib/perl5/5.8.8/base.pm http://base.pm> line
>
>    85., referer:
>
>    http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>
>    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
>
>    failed--compilation aborted at
>
>    /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2.pm
>
>    line 9., referer:
>
>    http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>
>    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Compilation
>
>    failed in require at
>
>    /project/gbrowse/httpd_internal/cgi-bin/gbrowse2/gbrowse line 9.,
>
>    referer:
>
>    http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>
>    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] BEGIN
>
>    failed--compilation aborted at
>
>    /project/gbrowse/httpd_internal/cgi-bin/gbrowse2/gbrowse line 9.,
>
>    referer:
>
>    http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>
>    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50] Premature end
>
>    of script headers: gbrowse, referer:
>
>    http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>
>    [Thu May 27 14:44:37 2010] [error] [client 141.14.29.50] Can't load
>
>    '/project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/auto/Bio/DB/Sam/Sam.so'
>
>    for module Bio::DB::Sam:
>
>    /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/auto/Bio/DB/Sam/Sam.so:
>
>    failed to map segment from shared object: Cannot allocate memory at
>
>    /home/okeeffe/lib/perl5/5.8.8/x86_64-linux/DynaLoader.pm line 230
>
>
>
>    Finally I did a top on the running processes and notice multiple
>
>    instances of gbrowse eating 100% of cpu and large shares of memory.
>
>    Can't say if these are related but I'd never seen processes like these
>
>    before.
>
>
>
>    Best,
>
>    Sean.
>
>
>
>
>
>    ------------------------------------------------------------------------------
>
>
>
>    _______________________________________________
>
>    Gmod-gbrowse mailing list
>
>    [hidden email]
>
>    [hidden email]>
>
>    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 [hidden email] [hidden email]>>
>
>
> Seems OK, Lincoln.
>
>
>
> NOTE: Run ./Build reconfig to change existing configuration.
>
> Writing config notes to blib/lib/GBrowse/ConfigData.pm
>
> Performing variable substitutions in blib/conf/detail_select_menu.conf
>
> Performing variable substitutions in blib/conf/enzymes.txt
>
> Performing variable substitutions in blib/conf/GBrowse.conf
>
> Performing variable substitutions in blib/conf/log4perl.conf
>
> Performing variable substitutions in blib/conf/MobyServices/moby.conf
>
> Performing variable substitutions in blib/conf/pop_demo.conf
>
> Performing variable substitutions in blib/conf/slave_preload.conf
>
> Performing variable substitutions in blib/conf/submitter_plugin.conf
>
> Performing variable substitutions in blib/conf/synteny/rice_synteny.conf
>
> Performing variable substitutions in blib/conf/synteny/wild_rice_synteny.conf
>
> Performing variable substitutions in blib/conf/themes/solid_gray_colors
>
> Performing variable substitutions in blib/conf/themes/transparent_colors
>
> Performing variable substitutions in blib/conf/themes/warm_colors
>
> Performing variable substitutions in blib/conf/yeast_chr1+2.conf
>
> Performing variable substitutions in blib/conf/yeast_renderfarm.conf
>
> Performing variable substitutions in blib/conf/yeast_simple.conf
>
> Performing variable substitutions in blib/htdocs/annotation_help.html
>
> Performing variable substitutions in blib/htdocs/gbrowse_karyotype_help.html
>
> Performing variable substitutions in blib/htdocs/gbrowse_syn_help.html
>
> Performing variable substitutions in blib/htdocs/general_help.html
>
> Performing variable substitutions in blib/htdocs/index.html
>
> Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_core.conf
>
> Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_extra.conf
>
> Performing variable substitutions in blib/htdocs/tutorial/conf_files/HEADER.html
>
> Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox.conf
>
> Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final.conf
>
> Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf
>
> Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_halfway.conf
>
> Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_Phylo.conf
>
> Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_quarter.conf
>
> Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_refactored.conf
>
> Performing variable substitutions in blib/htdocs/tutorial/data_files/HEADER.html
>
> Performing variable substitutions in blib/htdocs/tutorial/tutorial.html
>
> Performing variable substitutions in blib/htdocs/tutorial/tutorial.phyTreeEdit.html
>
> t/01yeast...................ok
>
> t/02.rearchitecture.........ok
>
> t/03.render.................21/138 Use of uninitialized value in concatenation (.) or string at (eval 345) line 15.
>
> Use of uninitialized value in concatenation (.) or string at (eval 345) line 15.
>
> t/03.render.................108/138 Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at /home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
>
> at /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined at /home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
>
> at /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at /home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
>
> at /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE redefined at /home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
>
> at /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW redefined at /home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
>
> at /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at /home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
>
> at /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
>
> t/03.render.................ok
>
> t/04.remoteserver...........ok
>
> t/05.deferredrendering......ok
>
> t/06.featuresearch..........ok
>
> t/07.karyotype..............ok
>
> t/08.calign.................ok
>
> All tests successful.
>
> Files=8, Tests=332, 37 wallclock secs ( 0.08 usr  0.02 sys +  8.96 cusr  5.38 csys = 14.44 CPU)
>
> Result: PASS
>
>
>
Probably. I'll figure it out somehow, lincoln.
It's the multiple processes running when issuing the top on the server that really confuses me - don't know if you saw that at the bottom of the original mail.
Anyways I've gone back to the previous version and will look into it some more later.

S.



--
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 <[hidden email]>

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Re: gbrowse 2.08 behaviour

okeeffe
Lincoln Stein wrote:

> I didn't notice your comments on top. It is expected for each request
> to launch multiple gbrowse instances (up to four at a time, I think),
> but they shouldn't chew up a lot of memory or CPU (except very
> transiently). If you are seeing these problems when viewing BAM
> tracks, it is possible that you have run into a bug in Bio::Samtools
> which tries to reindex BAM files even when they don't need it. You can
> fix this by either "touch"ing all your .bai files so that their
> modification dates are more recent than the .bam files, or by
> upgrading to the more recent Bio::Samtools.
>
> Lincoln
>
> On Thu, May 27, 2010 at 12:36 PM, Sean O'Keeffe <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     [hidden email] <mailto:[hidden email]> wrote:
>
>         If the tests work, then GBrowse should work. Have you changed
>         anything in Apache's environment that might cause the CGI
>         script to find a different version of Perl and/or its libraries?
>
>         Lincoln
>
>         On May 27, 2010 11:43am, Sean O'Keeffe <[hidden email]
>         <mailto:[hidden email]>> wrote:
>         > Lincoln Stein wrote:
>         >
>         >
>         > Something is wrong with Perl's dynamic library loader. Lots
>         of these errors have nothing to do with well-established
>         modules like File::Glob. There might be something lurking in
>         the Apache environment, such as a PERL5LIB variable that is
>         pointing to a previous Perl installation. Were you able to run
>         GBrowse's tests from the command line ok?
>         >
>         >
>         >
>         > Lincoln
>         >
>         >
>         >
>         > On Thu, May 27, 2010 at 9:56 AM, Sean O'Keeffe
>         [hidden email] <mailto:[hidden email]>
>         [hidden email] <mailto:[hidden email]>>> wrote:
>         >
>         >
>         >
>         >    Hi Folks,
>         >
>         >    Just did (what I thought was going to be) a routine
>         update from
>         >
>         >    Gbrowse2.05->2.08 today incl. a Bio::Graphics update to 2.09.
>         >
>         >    I'm getting the following in the error log - strange
>         memory alloc
>         >
>         >    errors
>         >
>         >    plus other strange stuff:
>         >
>         >    (Admittedly Bio-Samtools is 1.16 not 1.19)
>         >
>         >
>         >
>         >    Also getting a heck of a lot of compilation errors:
>         >
>         >    Can't load
>         >
>         >  
>          '/home/okeeffe/lib/perl5/5.8.8/x86_64-linux/auto/File/Glob/Glob.so'
>         >
>         >    for
>         >
>         >    module File::Glob:
>         >
>         >  
>          /home/okeeffe/lib/perl5/5.8.8/x86_64-linux/auto/File/Glob/Glob.so:
>         >
>         >    failed to map segment from shared object: Cannot allocate
>         memory at
>         >
>         >    /home/okeeffe/lib/perl5/5.8.8/x86_64-linux/XSLoader.pm
>         line 70.,
>         >
>         >    referer:
>         >
>         >  
>          http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>         >
>         >    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]  at
>         >
>         >    /home/okeeffe/lib/perl5/5.8.8/x86_64-linux/File/Glob.pm
>         line 96,
>         >
>         >    referer:
>         >
>         >  
>          http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>         >
>         >    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]
>         Compilation
>         >
>         >    failed in require at
>         >
>         >  
>          /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/FeatureFile.pm
>         >
>         >    line 478., referer:
>         >
>         >  
>          http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>         >
>         >    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]
>         BEGIN
>         >
>         >    failed--compilation aborted at
>         >
>         >  
>          /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/Graphics/FeatureFile.pm
>         >
>         >    line 478., referer:
>         >
>         >  
>          http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>         >
>         >    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]
>         Compilation
>         >
>         >    failed in require at (eval 2) line 3., referer:
>         >
>         >  
>          http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>         >
>         >    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]
>         >
>         >    \t...propagated
>         >
>         >    at /home/okeeffe/lib/perl5/5.8.8/base.pm <http://base.pm>
>         http://base.pm> line
>         >
>         >    85., referer:
>         >
>         >  
>          http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>         >
>         >    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]
>         BEGIN
>         >
>         >    failed--compilation aborted at
>         >
>         >  
>          /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
>         >
>         >    line 5., referer:
>         >
>         >  
>          http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>         >
>         >    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]
>         Compilation
>         >
>         >    failed in require at (eval 1) line 3., referer:
>         >
>         >  
>          http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>         >
>         >    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]
>         >
>         >    \t...propagated
>         >
>         >    at /home/okeeffe/lib/perl5/5.8.8/base.pm <http://base.pm>
>         http://base.pm> line
>         >
>         >    85., referer:
>         >
>         >  
>          http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>         >
>         >    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]
>         BEGIN
>         >
>         >    failed--compilation aborted at
>         >
>         >  
>          /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/Bio/Graphics/Browser2.pm
>         >
>         >    line 9., referer:
>         >
>         >  
>          http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>         >
>         >    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]
>         Compilation
>         >
>         >    failed in require at
>         >
>         >    /project/gbrowse/httpd_internal/cgi-bin/gbrowse2/gbrowse
>         line 9.,
>         >
>         >    referer:
>         >
>         >  
>          http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>         >
>         >    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]
>         BEGIN
>         >
>         >    failed--compilation aborted at
>         >
>         >    /project/gbrowse/httpd_internal/cgi-bin/gbrowse2/gbrowse
>         line 9.,
>         >
>         >    referer:
>         >
>         >  
>          http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>         >
>         >    [Thu May 27 14:44:32 2010] [error] [client 141.14.29.50]
>         Premature end
>         >
>         >    of script headers: gbrowse, referer:
>         >
>         >  
>          http://genome.molgen.mpg.de/cgi-bin/gbrowse2/gbrowse/MeDIP_GRC37/?name=chr21%3A43337000..43424000
>         >
>         >    [Thu May 27 14:44:37 2010] [error] [client 141.14.29.50]
>         Can't load
>         >
>         >  
>          '/project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/auto/Bio/DB/Sam/Sam.so'
>         >
>         >    for module Bio::DB::Sam:
>         >
>         >  
>          /project/gbrowse/httpd_perllib_new/lib/perl5/x86_64-linux/auto/Bio/DB/Sam/Sam.so:
>         >
>         >    failed to map segment from shared object: Cannot allocate
>         memory at
>         >
>         >    /home/okeeffe/lib/perl5/5.8.8/x86_64-linux/DynaLoader.pm
>         line 230
>         >
>         >
>         >
>         >    Finally I did a top on the running processes and notice
>         multiple
>         >
>         >    instances of gbrowse eating 100% of cpu and large shares
>         of memory.
>         >
>         >    Can't say if these are related but I'd never seen
>         processes like these
>         >
>         >    before.
>         >
>         >
>         >
>         >    Best,
>         >
>         >    Sean.
>         >
>         >
>         >
>         >
>         >
>         >  
>          ------------------------------------------------------------------------------
>         >
>         >
>         >
>         >    _______________________________________________
>         >
>         >    Gmod-gbrowse mailing list
>         >
>         >    [hidden email]
>         <mailto:[hidden email]>
>         >
>         >    [hidden email]
>         <mailto:[hidden email]>>
>         >
>         >    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 [hidden email]
>         <mailto:[hidden email]> [hidden email]
>         <mailto:[hidden email]>>>
>         >
>         >
>         > Seems OK, Lincoln.
>         >
>         >
>         >
>         > NOTE: Run ./Build reconfig to change existing configuration.
>         >
>         > Writing config notes to blib/lib/GBrowse/ConfigData.pm
>         >
>         > Performing variable substitutions in
>         blib/conf/detail_select_menu.conf
>         >
>         > Performing variable substitutions in blib/conf/enzymes.txt
>         >
>         > Performing variable substitutions in blib/conf/GBrowse.conf
>         >
>         > Performing variable substitutions in blib/conf/log4perl.conf
>         >
>         > Performing variable substitutions in
>         blib/conf/MobyServices/moby.conf
>         >
>         > Performing variable substitutions in blib/conf/pop_demo.conf
>         >
>         > Performing variable substitutions in
>         blib/conf/slave_preload.conf
>         >
>         > Performing variable substitutions in
>         blib/conf/submitter_plugin.conf
>         >
>         > Performing variable substitutions in
>         blib/conf/synteny/rice_synteny.conf
>         >
>         > Performing variable substitutions in
>         blib/conf/synteny/wild_rice_synteny.conf
>         >
>         > Performing variable substitutions in
>         blib/conf/themes/solid_gray_colors
>         >
>         > Performing variable substitutions in
>         blib/conf/themes/transparent_colors
>         >
>         > Performing variable substitutions in
>         blib/conf/themes/warm_colors
>         >
>         > Performing variable substitutions in blib/conf/yeast_chr1+2.conf
>         >
>         > Performing variable substitutions in
>         blib/conf/yeast_renderfarm.conf
>         >
>         > Performing variable substitutions in blib/conf/yeast_simple.conf
>         >
>         > Performing variable substitutions in
>         blib/htdocs/annotation_help.html
>         >
>         > Performing variable substitutions in
>         blib/htdocs/gbrowse_karyotype_help.html
>         >
>         > Performing variable substitutions in
>         blib/htdocs/gbrowse_syn_help.html
>         >
>         > Performing variable substitutions in
>         blib/htdocs/general_help.html
>         >
>         > Performing variable substitutions in blib/htdocs/index.html
>         >
>         > Performing variable substitutions in
>         blib/htdocs/tutorial/conf_files/elegans_core.conf
>         >
>         > Performing variable substitutions in
>         blib/htdocs/tutorial/conf_files/elegans_extra.conf
>         >
>         > Performing variable substitutions in
>         blib/htdocs/tutorial/conf_files/HEADER.html
>         >
>         > Performing variable substitutions in
>         blib/htdocs/tutorial/conf_files/volvox.conf
>         >
>         > Performing variable substitutions in
>         blib/htdocs/tutorial/conf_files/volvox_final.conf
>         >
>         > Performing variable substitutions in
>         blib/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf
>         >
>         > Performing variable substitutions in
>         blib/htdocs/tutorial/conf_files/volvox_halfway.conf
>         >
>         > Performing variable substitutions in
>         blib/htdocs/tutorial/conf_files/volvox_Phylo.conf
>         >
>         > Performing variable substitutions in
>         blib/htdocs/tutorial/conf_files/volvox_quarter.conf
>         >
>         > Performing variable substitutions in
>         blib/htdocs/tutorial/conf_files/volvox_refactored.conf
>         >
>         > Performing variable substitutions in
>         blib/htdocs/tutorial/data_files/HEADER.html
>         >
>         > Performing variable substitutions in
>         blib/htdocs/tutorial/tutorial.html
>         >
>         > Performing variable substitutions in
>         blib/htdocs/tutorial/tutorial.phyTreeEdit.html
>         >
>         > t/01yeast...................ok
>         >
>         > t/02.rearchitecture.........ok
>         >
>         > t/03.render.................21/138 Use of uninitialized
>         value in concatenation (.) or string at (eval 345) line 15.
>         >
>         > Use of uninitialized value in concatenation (.) or string at
>         (eval 345) line 15.
>         >
>         > t/03.render.................108/138 Subroutine
>         Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at
>         /home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
>         >
>         > at
>         /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm
>         <http://berkeleydb.pm> line 10
>         >
>         > Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT
>         redefined at /home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
>         >
>         > at
>         /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm
>         <http://berkeleydb.pm> line 10
>         >
>         > Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL
>         redefined at /home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
>         >
>         > at
>         /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm
>         <http://berkeleydb.pm> line 10
>         >
>         > Subroutine
>         Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE redefined
>         at /home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
>         >
>         > at
>         /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm
>         <http://berkeleydb.pm> line 10
>         >
>         > Subroutine
>         Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW redefined
>         at /home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
>         >
>         > at
>         /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm
>         <http://berkeleydb.pm> line 10
>         >
>         > Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR
>         redefined at /home/okeeffe/lib/perl5/5.8.8/Exporter.pm line 65.
>         >
>         > at
>         /project/gbrowse/httpd_perllib_new/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm
>         <http://berkeleydb.pm> line 10
>         >
>         > t/03.render.................ok
>         >
>         > t/04.remoteserver...........ok
>         >
>         > t/05.deferredrendering......ok
>         >
>         > t/06.featuresearch..........ok
>         >
>         > t/07.karyotype..............ok
>         >
>         > t/08.calign.................ok
>         >
>         > All tests successful.
>         >
>         > Files=8, Tests=332, 37 wallclock secs ( 0.08 usr  0.02 sys +
>          8.96 cusr  5.38 csys = 14.44 CPU)
>         >
>         > Result: PASS
>         >
>         >
>         >
>
>     Probably. I'll figure it out somehow, lincoln.
>     It's the multiple processes running when issuing the top on the
>     server that really confuses me - don't know if you saw that at the
>     bottom of the original mail.
>     Anyways I've gone back to the previous version and will look into
>     it some more later.
>
>     S.
>
>
>
>
> --
> 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 <[hidden email]
> <mailto:[hidden email]>>
Ok, good to know.
Thx again.

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