Re: [OMPI users] users Digest, Vol 1000, Issue 1

[Jeff Squyres]

On Sep 9, 2008, at 3:05 PM, Christopher Tanner wrote:

I think I've found the problem / solution. With Ubuntu, there's a  
program called 'ldconfig' that updates the dynamic linker run-time  
bindings. Since Open MPI was compiled to use dynamic linking, these  
have to be updated. Thus, these commands have to be run on all of  
the nodes


$ sudo ldconfig -v /usr/local/lib
$ sudo ldconfig -v /usr/local/lib/openmpi


Note that you shouldn't need the 2nd of those -- the only things that  
should be in /usr/local/lib/openmpi should be plugins.


FWIW, I do not believe that this is a side effect of the Open MPI  
installation.  The libraries you cited are part of the Intel compiler  
suite, not Open MPI.  The above would work if the Intel libraries are  
also installed in /usr/local/lib.  More specifically, if you had OMPI  
and the Intel compilers installed in different directories, you'd  
either need to run ldconfig on both of them or adjust your  
LD_LIBRARY_PATH to include both.


--
Jeff Squyres
Cisco Systems

Re: [OMPI users] users Digest, Vol 1000, Issue 1

[Jeremy Stout]

On clusters where I'm using the Intel compilers and OpenMPI, I setup
the compiler directory (usually /opt/intel) as a NFS export. The
computation nodes then mount that export. Next, I add the following
lines to the ld.so.conf file and distribute it to the computation
nodes:
/opt/intel/cce/version_number/lib/em64t
/opt/intel/fce/version_number/lib/em64t

That will depend on the path and version of the compiler set you are
using. Do a '/sbin/ldconfig' on each node and you should be good to
go.

You can also try updating the library path in your submission file.

Jeremy Stout

On Tue, Sep 9, 2008 at 2:58 PM, Christopher Tanner
 wrote:
> Jeremy -
>
> Thanks for the help - this bit of advice came up quite a bit through
> internet searches. However, I made sure that the LD_LIBRARY_PATH was set and
> correct on all nodes -- and the error persists.
>
> Any other possible solutions? Thanks.
>
> ---
> Chris Tanner
> Space Systems Design Lab
> Georgia Institute of Technology
> christopher.tan...@gatech.edu
> ---
>
>
>
> On Sep 9, 2008, at 12:00 PM, users-requ...@open-mpi.org wrote:
>
>>
>> The library you specified in your post (libimf.so) is part of the
>> Intel Compiler Suite (fce and cce). You'll need to make those
>> libraries available to your computation nodes and update the
>> LD_LIBRARY_PATH accordingly.
>>
>> Jeremy Stout
>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>

Re: [OMPI users] users Digest, Vol 1000, Issue 1

[Christopher Tanner]

Jeremy -

I think I've found the problem / solution. With Ubuntu, there's a  
program called 'ldconfig' that updates the dynamic linker run-time  
bindings. Since Open MPI was compiled to use dynamic linking, these  
have to be updated. Thus, these commands have to be run on all of the  
nodes


$ sudo ldconfig -v /usr/local/lib
$ sudo ldconfig -v /usr/local/lib/openmpi

When installing from an RPM (in RedHat) or installing for a dpkg (in  
Debain), this linking is done automatically at the end of the install.  
However, if you compile from source, you have to link it manually.


Now Open MPI runs fine. :)

---
Chris Tanner
Space Systems Design Lab
Georgia Institute of Technology
christopher.tan...@gatech.edu
---

The library you specified in your post (libimf.so) is part of the
Intel Compiler Suite (fce and cce). You'll need to make those
libraries available to your computation nodes and update the
LD_LIBRARY_PATH accordingly.

Jeremy Stout

Re: [OMPI users] users Digest, Vol 1000, Issue 1

[Jeff Squyres]

You might want to double check this; it's an easy thing to test  
incorrectly.


What you want to check is that the LD_LIBRARY_PATH is set properly for  
*non-interactive logins* (I assume you are using the rsh/ssh launcher  
for Open MPI, vs. using a resource manager such as SLURM, Torque,  
etc.).  For example, try this:


-
shell$ ssh othernode env | grep LD_LIBRARY_PATH
-

This runs "env" on the other node and will show you what the  
LD_LIBRARY_PATH is over there.   This is what you want to check  
includes the right paths for the Intel libraries.  Note that it is  
different than:


-
shell$ ssh othernode
othernode$ env | grep LD_LIBRARY_PATH
-

Because shell startup files may differentiate between interactive and  
non-interactive logins.  It depends on your local system setup.


Hope that helps.



On Sep 9, 2008, at 2:58 PM, Christopher Tanner wrote:


Jeremy -

Thanks for the help - this bit of advice came up quite a bit through  
internet searches. However, I made sure that the LD_LIBRARY_PATH was  
set and correct on all nodes -- and the error persists.


Any other possible solutions? Thanks.

---
Chris Tanner
Space Systems Design Lab
Georgia Institute of Technology
christopher.tan...@gatech.edu
---



On Sep 9, 2008, at 12:00 PM, users-requ...@open-mpi.org wrote:



The library you specified in your post (libimf.so) is part of the
Intel Compiler Suite (fce and cce). You'll need to make those
libraries available to your computation nodes and update the
LD_LIBRARY_PATH accordingly.

Jeremy Stout


___
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users



--
Jeff Squyres
Cisco Systems

Re: [OMPI users] users Digest, Vol 1000, Issue 1

[Christopher Tanner]

Jeremy -

Thanks for the help - this bit of advice came up quite a bit through  
internet searches. However, I made sure that the LD_LIBRARY_PATH was  
set and correct on all nodes -- and the error persists.


Any other possible solutions? Thanks.

---
Chris Tanner
Space Systems Design Lab
Georgia Institute of Technology
christopher.tan...@gatech.edu
---



On Sep 9, 2008, at 12:00 PM, users-requ...@open-mpi.org wrote:



The library you specified in your post (libimf.so) is part of the
Intel Compiler Suite (fce and cce). You'll need to make those
libraries available to your computation nodes and update the
LD_LIBRARY_PATH accordingly.

Jeremy Stout