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Subject: Re: [OMPI users] Open MPI and env. variables (LD_LIBRARY_PATH and PATH) - complete and utter Open MPI / Linux noob
From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2009-08-06 14:06:32


Sorry for not replying earlier -- travel to the MPI Forum last week
put me waaaay behind on my INBOX. :-(

I don't think you want to "printenv > ~/.ssh/environment" -- you don't/
can't know for sure that the remote environment should be exactly the
same as your local environment.

Instead, you might want to use OMPI's built-in "set the PATH /
LD_LIBRARY_PATH remotely" functionality. Use the full path name to
mpirun, like:

/opt/openmpi/bin/mpirun ...

And that should tell mpirun to set the PATH and LD_LIBRARY_PATH
remotely. Note that this functionality assumes that Open MPI is
installed in exactly the same filesystem location on the node where
mpirun is invoked and the back-end compute nodes.

FWIW, you can also use the --prefix argument to mpirun; the "/opt/
openmpi/bin/mpirun ..." behavior is a shortcut for that same behavior
(we emulated the idea of using the full pathname to mpirun from HP MPI).

Additionally, you can force Open MPI to use the --prefix behavior by
default if you configure/build Open MPI with the --enable-mpirun-
prefix-by-default configure switch.

Hope that helps!

On Aug 3, 2009, at 7:35 AM, Tomislav Maric wrote:

> Thank you Dominik for all your help!!
>
> I've solved the problem: execute : printenv > ~/.ssh/environment
>
> edit /etc/ssh/sshd_config and set PermitUserEnvironment to "yes" and
> check that UseLogin is set to "no"
>
> scp hostname ~/.ssh/environment user_at_hostname:~/.ssh/environment
>
> edit sshd_config on the other host and set the same things.
>
> Works like a charm!
>
> Tomislav
>
> Dominik Táborský wrote:
>> I'm sorry, I can't help you with NFS. I have never had it on my
>> network.
>>
>> Good luck anyway... :)
>>
>>
>> Tomislav Maric píše v Ne 02. 08. 2009 v 20:18 +0200:
>>> Dominik Táborský wrote:
>>>> Okay, now it's getting more confusing since I just found out that
>>>> it
>>>> somehow stopped working for me!
>>>>
>>>> Anyway, let's find a solution.
>>>> I found out that there is difference between
>>>> ssh node1 echo $PATH
>>>> and
>>>> ssh node1 'echo $PATH'
>>>> These command give you different output. 'man ssh' states that it
>>>> sets
>>>> its own PATH variable right before the user logs in but after the
>>>> connection is established. This variable is set during compilation.
>>>>
>>>> I am using dropbear as SSH2 server so I won't be able to guide
>>>> you if
>>>> you're using OpenSSH as a server, but the manpages should be
>>>> sufficient.
>>>> Look into man ssh and man ssh_config. You should create files
>>>> ~/.ssh/rc
>>>> OR ~/.ssh/config OR ~/.ssh/environment. Setting it up in one of
>>>> these
>>>> files should be enough.
>>>>
>>>> I will probably recompile dropbear with new default PATH.
>>>>
>>>> Anyway, I am sure it used to work for me and I have no idea why it
>>>> stopped.
>>>>
>>>> If you'd need more help, just ask :-)
>>>>
>>>> Dr. Eddy
>>>>
>>> Thank you very much!! I'm also finding out about those files and I'm
>>> using OpenSSH. I'll try and configure it to work. The weirdest
>>> thing is
>>> that people who use Ubuntu on OpenFOAM forum just had to comment a
>>> line
>>> in .bashrc that returns if the bash is run in non-interactive mode.
>>>
>>> I just don't get it. Let me ask you just one thing, before the
>>> next 5-6
>>> hours of fighting with config files:
>>>
>>> what about NFS?
>>>
>>> What if I export the directory? On OMPI pages is written that nfs
>>> simplifies things. I'm noob in networking so I don't know if this
>>> would
>>> benefit me.
>>>
>>> If I edit ~/.ssh/environment then I have to manually set
>>> VARIABLE=VALUE,
>>> and there are dozens of variables to set. I think I'll try the rc
>>> file
>>> first.
>>>
>>> Thank you again!
>>>
>>> Best regards,
>>> Tomislav
>>> _______________________________________________
>>> users mailing list
>>> users_at_[hidden]
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
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-- 
Jeff Squyres
jsquyres_at_[hidden]