OpenMPI issues, no response in two attempts to subscribe to list

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OpenMPI issues, no response in two attempts to subscribe to list

mathog
Greetings,

I'm trying to run maker 2.31.9 with OpenMPI on a Centos 6.7 system.  It
just won't start.  OpenMPI works fine with a small test program, it just
doesn't work with maker.  It fails in exactly the same way on a second
Centos system with minor software differences (Centos 6.9 and perl 5.20
compiled without thread support, the perl on the first machine had
thread support.) The gory details were posted already in a Centos forum
so rather than repeat it all here, this is a link to that thread:

    https://www.centos.org/forums/viewtopic.php?f=14&t=64099

maker was unpacked from the maker-2.31.9.tgz a second time (after moving
the original) after setting up the "module add openmpi-x86_64" to my
.bash_profile
and logging in cleanly.  It was rebuilt.  The build messages were
identical to the previous ones and when a run was attempted it also
failed in exactly the same way.

I also tried to subscribe to the list here

   
https://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

once yesterday, and once today, but no email ever came back.  Hopefully
this message gets through!

Regards,

David Mathog
[hidden email]
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Re: OpenMPI issues, no response in two attempts to subscribe to list

Carson Holt-2
Mi David,

First thing. MAKER binds shared C libraries using Perl, so you have to tell MAKER where to find the needed files before you install it. Then it compiles the bindings and saves them for MAKER to use. If you have two MPI installation, you may have MAKER setup to use one of the installations then you are trying to call it with the other one. That would break the compiles bindings.

Also make sure you did the following (info from the …/maker/INSTALL instructions file) —>

"make sure to set LD_PRELOAD to the location of libmpi.so before even trying to install MAKER. It must also be set before running MAKER (or any program that binds OpenMPI's shared libraries), so it's best just to add it to your ~/.bash_profile. (i.e. export LD_PRELOAD=/usr/local/openmpi/lib/libmpi.so)."

Remember to replace '/usr/local/openmpi/lib/libmpi.so’ with the actual location of the file.

Second once you can get maker to start under OpenMPI, you may get freezes or failures part way into a run because OpenFabrics libraries use registered memory in a weird way that can cause system calls in a program to fail with a snowballing error effect. Adding this to the mpiexec options can stop this from occurring —> '-mca btl ^openib'

That option has the side effect of disabling infiniband and using the ethernet adapter instead. However if you need to use the infiniband adapter, you can use this flag instead '--mca btl vader,tcp,self --mca btl_tcp_if_include ib0'

That command will use IP over infiniband rather than the native infiniband which will have the same effect of diabling the OpenFabrics libraries.

Thanks,
Carson



> On Sep 13, 2017, at 12:01 PM, mathog <[hidden email]> wrote:
>
> Greetings,
>
> I'm trying to run maker 2.31.9 with OpenMPI on a Centos 6.7 system.  It just won't start.  OpenMPI works fine with a small test program, it just doesn't work with maker.  It fails in exactly the same way on a second Centos system with minor software differences (Centos 6.9 and perl 5.20 compiled without thread support, the perl on the first machine had thread support.) The gory details were posted already in a Centos forum so rather than repeat it all here, this is a link to that thread:
>
>   https://www.centos.org/forums/viewtopic.php?f=14&t=64099
>
> maker was unpacked from the maker-2.31.9.tgz a second time (after moving the original) after setting up the "module add openmpi-x86_64" to my .bash_profile
> and logging in cleanly.  It was rebuilt.  The build messages were identical to the previous ones and when a run was attempted it also failed in exactly the same way.
>
> I also tried to subscribe to the list here
>
>  https://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> once yesterday, and once today, but no email ever came back.  Hopefully this message gets through!
>
> Regards,
>
> David Mathog
> [hidden email]
> Manager, Sequence Analysis Facility, Biology Division, Caltech
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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