[maker-devel] regarding mpich

[Carson Holt]

Some files it can reuse, but not all. So, exporting finished contigs with
GFF3 pass-through is an option.

--Carson


From:  Daniel Hughes <dsth at ebi.ac.uk>
Date:  Monday, 4 March, 2013 3:57 PM
To:  Kenlee Nakasugi <kenlee.nakasugi at sydney.edu.au>
Cc:  "maker-devel at yandell-lab.org List" <maker-devel at yandell-lab.org>,
Carson Holt <carsonhh at gmail.com>
Subject:  Re: [maker-devel] regarding mpich


Unlikely. Probably safer to export what has finished as gff and run it as
re-annotation if you don't want to waste what was alteady processed for
running additional iterations.

Dan

from me phone...

On Mar 4, 2013 8:52 PM, "Kenlee Nakasugi" <kenlee.nakasugi at sydney.edu.au>
wrote:
> Thanks Carson. Will Maker 2.27 be able to continue analysis on Maker 2.1 files
> that stopped halfway?
> Thanks
> Ken
> 
> 
> 
> On 05/03/2013, at 1:44 AM, "Carson Holt" <carsonhh at gmail.com> wrote:
> 
>> Use the last MPICH2 version, as MPICH3 is very different (it's the first
>> attempt to implement the new MPI3 protocol set, and not just a version
>> update).  Alternatively you can use OpenMPI.  Also use maker version 2.27
>> instead for MPI.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> From: Kenlee Nakasugi <kenlee.nakasugi at sydney.edu.au>
>> Date: Sunday, 3 March, 2013 6:44 PM
>> To: "maker-devel at yandell-lab.org List" <maker-devel at yandell-lab.org>
>> Subject: [maker-devel] regarding mpich
>> 
>> Hi, 
>> 
>> I'm trying to install mpi_maker (Maker 2.1) on a new system (intel ix x86_64)
>> which has mpich v3.0.2 installed, but I can't seem to get maker Build.PL to
>> recognize it. I tried editing the Build.pm file to point to it, but with no
>> success. 
>> All dependencies have been installed and successfully recognized, it is just
>> MPI support that is not.
>> 
>> Is there anything I could modify in the install scripts to make it recognize
>> this? Currently, the directly path to where the mpicc and mpiexec are is
>> /apps/mpich/3.0.2/bin
>> I don't have sys admin rights for the machine, and I'm not sure if this
>> version of mpich was installed for shared libraries as per the GMOD tutorial.
>> But I have previously circumvented this with an earlier version of mpich by
>> modifying the Build.pm module with success. I'm wondering if mpichv3.02 is
>> not compatible? 
>> 
>> 
>> Cheers, 
>> Ken
>> 
>> -- 
>> Kenlee Nakasugi | Research Fellow
>> School of Molecular Bioscience
>> Level 8, SMB Building (G08)| The University of Sydney | NSW | 2006
>> T: +61 2 9114 1321 <tel:%2B61%202%209114%201321>
>> E: kenlee.nakasugi at sydney.edu.au
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> 
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