[maker-devel] maker-2.23

Thu Feb 23 10:08:12 MST 2012

Does it indicate at any level what the compilation error is?

Could you pack up your job and send it to me?  I'll just try it on a couple
of system types.  A malloc error with perl would normally happen at the C
level, so it's a matter of identifying what module is being called.

Thanks,
Carson

From:  Rodolfo Aramayo <raramayo at tamu.edu>
Date:  Thu, 23 Feb 2012 11:00:37 -0600
To:  Carson Holt <carsonhh at gmail.com>
Cc:  MAKER <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] maker-2.23

Carson,

Reinstalled storable, forks and forks::shared
Re-compiled maker
Same problem

Change from forks/forks::shared to threads/threads::shared in the compiled
executable and
Running maker gives me:

"Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to
compilation errors."

Ideas?

Thanks

--R

On Thu, Feb 23, 2012 at 09:26, Carson Holt <carsonhh at gmail.com> wrote:
> All MAKER versions after 2.2 use the CPAN forks.pm <http://forks.pm>  module
> rather than threads.pm <http://threads.pm> .  forks.pm <http://forks.pm>  is
> just a drop in replacement for threads.pm <http://threads.pm>  so you can use
> the same syntax for forks as you do with threads.  Even if you have perl
> compiled with threads MAKER still uses forks.pm <http://forks.pm>  (I am
> referring to the about the module forks.pm <http://forks.pm>  and not forks
> themselves).  The place where you get the error suggests the problem is at the
> C level, so the forks.pm <http://forks.pm>  module from CPAN and Storable.pm
> are the  two most likely culprits.  Reinstalling both of those would be the
> first thing to do.  If you have threaded perl you can just change the 'use'
> statement at the start of MAKER, but if you don't have threaded perl, just
> reinstall forks.pm <http://forks.pm> .  Don't worry about changing the perl
> installation.
> 
> Thanks,
> Carson
> 
> From:  Rodolfo Aramayo <raramayo at tamu.edu>
> Date:  Thu, 23 Feb 2012 09:17:36 -0600
> To:  Carson Holt <carsonhh at gmail.com>
> Cc:  MAKER <maker-devel at yandell-lab.org>
> Subject:  Re: [maker-devel] maker-2.23
> 
> Thanks Carson...please see below
> 
> On Thu, Feb 23, 2012 at 08:56, Carson Holt <carsonhh at gmail.com> wrote:
>> Try two things for me.  Install/Re-install the latest version of the CPAN
>> Storable module.  Install/Re-install forks and forks::shared from CPAN.
>> Alternatively change 'use forks' to 'use threads' and 'use forks::shared' to
>> 'use threads::shared' in the MAKER executable.  Those modules are supposed to
>> be drop in replacements for each other.
> 
> which modules? I assume threads will be dropped, right?
> and if this is the case what are the advantages/disadvantages of using Perl 5,
> version 12, subversion 3 (v5.12.3) built for darwin-thread-multi-2level
> should I change to non-threads version?? or it does not matter
> 
> Thanks
> 
> --R
> 
>> 
>> Thanks,
>> Carson
>> 
>> From:  Rodolfo Aramayo <raramayo at tamu.edu>
>> Date:  Thu, 23 Feb 2012 08:47:32 -0600
>> To:  MAKER <maker-devel at yandell-lab.org>
>> Subject:  [maker-devel] maker-2.23
>> 
>> I am running into an unusual problem
>> If I run Maker in the maker01 directory, say "/Volumes/g0006/maker/maker01"
>> things go well no problem so far...but if I start a second maker inside the
>> maker02 directory:  "/Volumes/g0006/maker/maker02"
>> the second maker quits with a: "[3]+  Abort trap              nohup maker"
>> and in the nohup file I see the following:
>> 
>> #############################################################################
>> #############################
>> ...
>> ...
>> ...
>> ...
>> #-------------------------------#
>> re reading genemark report.
>> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_f
>> inal_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastore/
>> C6/70/NODE_2_length_2929_cov_50.101059//theVoid.NODE_2_length_2929_cov_50.101
>> 059/NODE_2_length_2929_cov_50%2E101059.all.Ralstonia_solanacearum%2Emod.genem
>> ark
>> running  genemark.
>> #--------- command -------------#
>> Widget::genemark:
>> /opt/local/bin/perl
>> /usr/local/bioinfosoft/maker-2.23/bin/../lib/Widget/genemark/gmhmm_wrap -m
>> /Volumes/a0003/bioinfodata/genemark/hmm/Ralstonia_solanacearum_plasmid_pGMI10
>> 00MP.mod -g /usr/local/bioinfosoft/genemark/gmhmmp -p
>> /usr/local/bioinfosoft/genemark/probuild -o
>> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_f
>> inal_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastore/
>> C6/70/NODE_2_length_2929_cov_50.101059//theVoid.NODE_2_length_2929_cov_50.101
>> 059/NODE_2_length_2929_cov_50%2E101059.all.Ralstonia_solanacearum_plasmid_pGM
>> I1000MP%2Emod.genemark
>> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_f
>> inal_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastore/
>> C6/70/NODE_2_length_2929_cov_50.101059//theVoid.NODE_2_length_2929_cov_50.101
>> 059/query.fasta
>> #-------------------------------#
>> formating database...
>> #--------- command -------------#
>> Widget::formater:
>> /usr/local/bin/makeblastdb -dbtype prot -in
>> /tmp/maker_hZ_8Uc/uniprot_sprot%2Efasta.mpi.10.0
>> #-------------------------------#
>> running  blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/local/bin/blastx -db /tmp/maker_hZ_8Uc/uniprot_sprot%2Efasta.mpi.10.0
>> -query /tmp/maker_hZ_8Uc/rank0/NODE_2_length_2929_cov_50%2E101059.0
>> -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300
>> -searchsp 20000000 -num_threads 7 -seg yes -soft_masking true -lcase_masking
>> -show_gis -out 
>> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_f
>> inal_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastore/
>> C6/70/NODE_2_length_2929_cov_50.101059//theVoid.NODE_2_length_2929_cov_50.101
>> 059/NODE_2_length_2929_cov_50%2E101059.0.uniprot_sprot%2Efasta.blastx.temp_di
>> r/uniprot_sprot%2Efasta.mpi.10.0.blastx
>> #-------------------------------#
>> deleted:97 hits
>> perl(12478) malloc: *** error for object 0x1033bada0: pointer being freed was
>> not allocated
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
>> freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
>> freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
>> freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
>> freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
>> freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
>> freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
>> freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum for
>> freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>> 
>> #############################################################################
>> #############################
>> 
>> I am using Maker 2.23
>> 
>> I see this problem in Maker with and without mpich2 compilation
>> I am using:
>> 
>> Perl 5, version 12, subversion 3 (v5.12.3) built for
>> darwin-thread-multi-2level
>> 
>> 
>> Any ideas?
>> 
>> Thanks
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma
>> ker-devel_yandell-lab.org
> 

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