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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: Tomislav Maric (tomislav.maric_at_[hidden])
Date: 2009-08-02 10:09:52


Dominik Táborský wrote:
> Hi Tomislav,
>
> I also had this issue. When you try to trace it, you'll find out that
> when you manually connect to a machine and immediately execute a
> command, it will inherit your environment, not the environment of the
> node. See:
> $ ssh node1 && echo $PATH
>
> This will echo the PATH on your computer, the master one, not the node.
> But if you do this:
> $ ssh node1
> node1$ echo $PATH
>
> it will echo the PATH on your node.

I've tried it:

$ ssh node1 && echo $PATH

at first does nothing, leaving me loged in on the node, but when I exit,
it writes out the $PATH on the master node.

ssh node1

slax_at_node1$ echo $PATH

gives me the path on the slave node1

and

slax_at_master$ ssh node1 'echo $PATH'

gives me the reduced path on the slave node. I think that the problem is
exactly the same as the last line - when I execute a bash script, it is
envoked in a non-interactive mode (login mode, because of the ssh), and
maybe some other config file is read instead of .bash_profile or
.bashrc? This reduced PATH and LD_LIBRARY_PATH cause problems for mpirun
to find the right libraries and binaries.

> Solution to this is to write the path to the executables and path to
> libraries to the variables you have set on your own computer, tha
> master.

The master computer already has everything set, because the Live DVD is
configured properly (i ran a test case on dual core - mpirun runs fine
locally), I'm not sure I understand, could you please explain a bit more
- this is all new to me.

Thank you very much for your advice and time!

Best regards,

Tomislav

>
> Let me know how that works for you!
>
> Dr. Eddy
>
>
> Tomislav Maric píše v Ne 02. 08. 2009 v 13:09 +0200:
>> Prasadcse Perera wrote:
>>> Hi,
>>> One workaround is you can define PATH and LD_LIBRARY_PATH in your common
>>> .bashrc and have a resembling paths of installation in two nodes. This
>>> works for me nicely with my three node installation :).
>>>
>> Thank you very much for the advice. Actually I'm running OpenFOAM (read:
>> a program parallelized to run with Open MPI) from SLAX Live DVD, so the
>> installation paths are identical, as well as everything else.
>>
>> I've added commands that set enviromental variables in .bashrc on both
>> nodes, but you mention "common .bashrc". Common in what way? I'm sorry
>> for newbish question, again, I'm supposed to be a Mechanical Engineer.
>> :))))
>>
>> OpenFOAM toolkit carries a separate directory for third-party support
>> software. In this directory there are programs for postprocessing
>> simulation results and analyze data and Open MPI. Therefore, in my case,
>> Open MPI is built in a separate directory and the build is automated.
>>
>> After the build of both programs, there is a special bashrc located in
>>
>> some/path/OpenFOAM/OpenFOAM-1.5-dev/etc/
>>
>> that sets all the variables needed to use Open FOAM, such as
>> FOAM_TUTORIALS (where are the tutorials), FOAM_RUN (where is the working
>> dir), WM_COMPILER (what compiler to use), etc. This bashrc also sets
>> LD_LIBRARY_PATH and PATH so that locally installed Open MPI can be found.
>>
>> I've tried this installation on the Live DVD on my laptop with two
>> cores, decomposed the case and ran the simulation in parallel without a
>> problem.
>>
>> I hope this information is more helpful.
>>
>> Best regards,
>> Tomislav
>>
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