Re: [OMPI users] MCA version error

[Jeff Squyres (jsquyres)]

Yes, it looks like you are mixing multiple versions of Open MPI.

It looks like you have installed Open MPI v1.10.0 via RPM in the system 
defaults location (perhaps in /usr/bin and /usr/lib and the like?), and then 
installed Open MPI v2.1.1 via building from source under your home directory 
(/home/user/EMAN2/bin and /home/user/EMAN2/lib and the like).

Your statement about your program working fine with MCA 2.0 is a little 
suspicious -- your should first clear up your PATH issues, recompile your 
application, and try running again.  If that fails, please provide all the 
information listed in https://www.open-mpi.org/community/help/.



> On Oct 13, 2017, at 11:41 AM, abhisek Mondal  wrote:
> 
> Hi,
> 
> I'm bit confused now.
> When I supply ompi_info, it gives:
> [user@localhost openmpi-x86_64]$ ompi_info 
> [localhost.localdomain:11068] Error: Unable to get the current working 
> directory
>  Package: Open MPI root@3fecdf07461e Distribution
> Open MPI: 2.1.1
>   Open MPI repo revision: v2.1.0-100-ga2fdb5b
>Open MPI release date: May 10, 2017
> Open RTE: 2.1.1
>   Open RTE repo revision: v2.1.0-100-ga2fdb5b
>Open RTE release date: May 10, 2017
> OPAL: 2.1.1
>   OPAL repo revision: v2.1.0-100-ga2fdb5b
>OPAL release date: May 10, 2017
>  MPI API: 3.1.0
> Ident string: 2.1.1
>   Prefix: /home/user/EMAN2
>  Configured architecture: x86_64-unknown-linux-gnu
> 
> Form the Bold line, I assume it is sourcing this version and loading 2.1.1 by 
> default.
> 
> But when I provide: rpm -qf /usr/lib64/openmpi/lib/openmpi/mca_shmem_mmap.so
> It gives me: openmpi-1.10.0-10.el7.x86_64
> 
> So, I think I'm having some sort of path issue. Is that right ? The program I 
> wish to run will go fine with MCA 2.0. 
> 
> On Fri, Oct 13, 2017 at 3:06 PM, Jeff Squyres (jsquyres)  
> wrote:
> From the output you supplied, it looks like you are running Open MPI v2.1.x.
> 
> Did you install Open MPI v2.1.x from source, and install it into the same 
> directory that you had previously installed Open MPI v2.0.x?
> 
> If so, the warnings you are seeing (not errors) are likely the fact that 
> there are some Open MPI v2.0.x plugins left over in the Open MPI v2.1.x 
> installation tree (installing version B of Open MPI over a previous 
> installation of Open MPI version A does *not* remove all of version A's 
> files).
> 
> You should probably get a clean install of Open MPI v2.1.x, and the warnings 
> will disappear.
> 
> See https://www.open-mpi.org/faq/?category=building#install-overwrite for 
> more details.
> 
> 
> 
> > On Oct 13, 2017, at 10:02 AM, Gilles Gouaillardet 
> >  wrote:
> >
> > one more thing,
> > can you run
> > rpm -qf /usr/lib64/openmpi/lib/openmpi/mca_shmem_mmap.so
> > and make sure this comes from the openmpi rpm ?
> >
> > if not, you can remove the openmpi rpm, rm -rf
> > /usr/lib64/openmpi/lib/openmpi and then re-install the rpm
> >
> > Cheers,
> >
> > Gilles
> >
> > On Fri, Oct 13, 2017 at 10:49 PM, Gilles Gouaillardet
> >  wrote:
> >> can you run ldd on your binary ?
> >> i suspect it might not use the right Open MPI library
> >>
> >> Cheers,
> >>
> >> Gilles
> >>
> >> On Fri, Oct 13, 2017 at 10:41 PM, abhisek Mondal  
> >> wrote:
> >>> Hello,
> >>>
> >>> I'm getting this following error:
> >>> [localhost.localdomain:00307] mca_base_component_repository_open: shmem
> >>> "/usr/lib64/openmpi/lib/openmpi/mca_shmem_mmap" uses an MCA interface that
> >>> is not recognized (component MCA v2.0.0 != supported MCA v2.1.0) -- 
> >>> ignored
> >>> [localhost.localdomain:00307] mca_base_component_repository_open: unable 
> >>> to
> >>> open mca_shmem_posix: /usr/lib64/openmpi/lib/openmpi/mca_shmem_posix.so:
> >>> undefined symbol: opal_shmem_base_output (ignored)
> >>> [localhost.localdomain:00307] mca_base_component_repository_open: shmem
> >>> "/usr/lib64/openmpi/lib/openmpi/mca_shmem_sysv" uses an MCA interface that
> >>> is not recognized (component MCA v2.0.0 != supported MCA v2.1.0) -- 
> >>> ignored
> >>>
> >>> I had installed it using yum command: yum install openmpi-1.10.0-10.el7
> >>>
> >>> My current MCA version is showing 2.1.0.
> >>>
> >>> On Fri, Oct 13, 2017 at 1:24 PM, Gilles Gouaillardet
> >>>  wrote:
> 
>  Hi,
> 
>  let's take one or two steps back.
> 
>  which version of Open MPI did you use in order to build your program ?
> 
>  what does "not working under MCA2.1" mean ?
>  link error ? unresolved symbols ? runtime crash ?
> 
>  please detail your environment and post all relevant error messages
> 
>  Cheers,
> 
>  Gilles
> 
>  On Fri, Oct 13, 2017 at 10:17 PM, abhisek Mondal 
>  wrote:
> >
> > Hi,
> >
> 

Re: [OMPI users] MCA version error

[Jeff Squyres (jsquyres)]

I think you're mixing a few versions there:

- You mention installing Open MPI v1.10
- But you say that running ompi_info shows MCA v2.1 (which probably means Open 
MPI v2.1)
- And you say that running your code with MCA v2.0 (which probably means Open 
MPI v2.0) works

You might want to de-snaggle which version of Open MPI you are actually using, 
and verify that you are using that version on all nodes in your job.

After that, describe what the problem is with your code.  You may have an 
actual bug that just happens to work on Open MPI v2.0 but fails with Open MPI 
v2.1.


> On Oct 13, 2017, at 9:18 AM, abhisek Mondal  wrote:
> 
> Hi,
> 
> I have installed an openmpi using following command:
> yum install openmpi-1.10.0-10.el7
> 
> When I put ompi_info command it shows me that it is using MCAv.2.1. Is there 
> any way I can use MCA2.0 ?
> 
> My program is not working under MCA2.1.
> Please help me out here.
> 
> Thank you
> 
> -- 
> Abhisek Mondal
> Senior Research Fellow
> Structural Biology and Bioinformatics Division
> CSIR-Indian Institute of Chemical Biology
> Kolkata 700032
> INDIA
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-- 
Jeff Squyres
jsquy...@cisco.com

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