[maker-devel] Maker2 on IBM PowerLinux?

[Carson Holt]

MAKER is written in perl, so it can work pretty much anywhere you have perl.
It is more an issue of the tools MAKER uses.  If you can get SNAP, BLAST,
exonerate, etc. to run then MAKER should be no problem.

You can let MAKER try and install and configure any missing perl libraries
as well as external tools for you (this is by far the easiest way).  You
will need an internet connection.

cd Š/maker/src/
perl Build.PL               #say 'Y' to local installation of libraries and
'N' to MPI for now
./Build installdeps     #grabs missing perl libraries from the ether, and
installs them in  the .../maker/perl/ directory
./Build installers        #grabs missing tools from the ether, installs, and
configures them in the .../maker/exe/ directory
./Build install              #just installs maker


If you want to run via MPI, I'd recommend OpenMPI, and you will need to
rerun the 'perl Build.PL' and './Build install' steps (say yes to MPI this
time around).

Here are some variables you will likly have to add to your .bash_profile to
get openmpi to run with MAKER (you must add these and source the profile
before attempting to install with OpenMPI), otherwise compilation will not
work correctly (OpenMPI shared library issue).

#you need to set $OMPIHOME to OpenMPI's location here -->
export LD_PRELOAD=$OMPIHOME/lib/libmpi.so:$LD_PRELOAD


#this one just suppresses a warning -->
export OMPI_MCA_mpi_warn_on_fork=0


And on some systems you have to add this  ' -mca btl ^openib' to the mpiexec
command when I run maker.
Example-->
mpiexec -mca btl ^openib -n 20 maker

Thanks,
Carson


From:  Mark Wisner <markwiz at us.ibm.com>
Date:  Wednesday, October 2, 2013 12:52 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker2 on IBM PowerLinux?

IBMs PowerLinux is tuned for Big Data workloads. We have had queries for
Maker2 on PowerLinux.
How do we work with Maker2 development to create a PowerLinux port.
Thanks,

Mark K. Wisner
Linux On Power ISV PM
IBM
3039 Cornwallis Rd
RTP, NC 27709
Cell 919-649-5813
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20131002/27d2c4bc/attachment-0003.html>