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Subject: Re: [OMPI users] configure options
From: Zhigang Wei (daniel.wei_at_[hidden])
Date: 2010-07-08 11:25:56


Thank you Gus, your answer is very helpful.

I use a CFD opensource called OpenFOAM, from official build suggestions, I found something like "--with-sge",
but I just don't know if it make sense in my school 's hpc setting.

The basic question is, if simply "./configure --prefix=blahblah" works (as you have said the modern openmpi will AUTOMATICALLY detect the hard and software system configuaration), then, why should people around try to build it with "--with-sge", etc. That make those dummies like me really confused.

Thanks and best Regards,



Zhigang Wei
------------
NatHaz Modeling Laboratory
University of Notre Dame
112J FitzPatrick Hall
Notre Dame, IN 46556



2010-07-08



发件人: Gus Correa
发送时间: 2010-07-08 11:17:26
收件人: Open MPI Users
抄送:
主题: Re: [OMPI users] configure options
 
Hi Zhigang
So, did setting the LD_LIBRARY_PATH work?
**
I don't add many options to the OpenMPI configure,
besides --prefix.
OpenMPI does a very good job searching and checking
for everything that is available and that it needs in the system.
It will build with support for nearly everything it finds
and that works.
Since you are using OpenMPI in your university HPC computer,
you may want to piggy back support from its resource manager/queue
system (e.g. Torque/PBS, --with-tm, or SGE, or SLURM).
This makes mpiexec work in cooperation with the resource manager (RM),
automatically using the nodes that were allocated by the the RM
to your job.
That is not essential, but it helps.
The same is true if there is specific hardware
(e.g. Infinband --with-openib, NUMA, --with-libnuma, etc).
You may need to point configure to the directories where these libraries
are, if they are not in standard locations, it depends on your system.
Do ./configure --help for a list of options.
Also, consult the OpenMPI FAQ, which is the best resource to answer
many of your questions:
http://www.open-mpi.org/faq/
One way to check what configuration options OpenMPI is really using,
is to redirect the configure output to a file, and inspect it to see if
everything you want is there.
I hope this helps,
Gus Correa
---------------------------------------------------------------------
Gustavo Correa
Lamont-Doherty Earth Observatory - Columbia University
Palisades, NY, 10964-8000 - USA
---------------------------------------------------------------------
Zhigang Wei wrote:
> Hi, thanks, the LD_LIBRARY_PATH has been set, and I checked again, and I
> don't think there is a confict.
>
> May I ask you a question, how do you normally configure your openmpi?
>
> I guess you will not use simply "./configure --prefix=blahblah", pls
> correct me if I am wrong.
>
> So, what is your procedure to check your system hardware and software
> background, so as to make openmpi correctly built.
>
> That's my question.
>
> And Thank you, Gus
>
>
>
> Zhigang Wei
> ------------
> NatHaz Modeling Laboratory
> University of Notre Dame
> 112J FitzPatrick Hall
> Notre Dame, IN 46556
> ------------------------------------------------------------------------
> 2010-07-08
> ------------------------------------------------------------------------
> *发件人:* Gus Correa
> *发送时间:* 2010-07-08 10:07:13
> *收件人:* Open MPI Users
> *抄送:*
> *主题:* Re: [OMPI users] configure options
> Hi Zhigang
> Are you talking about a run time failure?
> If you are, I think what is missing is just to set the PATH and the
> LD_LIBRARY_PATH environment variables to point to the OpenMPI directories.
> This can be done in your .[t]cshrc / .profile / .bashrc
> file in your home directory (assuming it is accessible by all computers
> that you're using to run the program).
> Hopefully it will override the default OpenMPI 1.3.2 in your HPC.
> See this FAQ:
> http://www.open-mpi.org/faq/?category=running#adding-ompi-to-path
> There are other ways to do it, which you can find with
> "man $MY_OWN_DIR/share/man/man1/mpiexec".
> (You could also set MANPATH to get the right man pages.)
> I hope this helps,
> Gus Correa
> ---------------------------------------------------------------------
> Gustavo Correa
> Lamont-Doherty Earth Observatory - Columbia University
> Palisades, NY, 10964-8000 - USA
> ---------------------------------------------------------------------
> Zhigang Wei wrote:
> > Dear all,
> >
> > How can I decide the configure options? I am greatly confused.
> >
> > I am using school's high performance computer.
> > But the openmpi there is version 1.3.2, old, so I want to build the new one.
> >
> > I am new to openmpi, I have built the openmpi and it doesn't work, I
> > built and installed it to my own directory.
> > I use the following configure options,
> >
> > ./configure --with-sge --prefix=$MY_OWN_DIR --with-psm
> >
> > but it won't work and failed with somelines like
> > ......lib/openmpi/mca_ess_hnp: file not found (ignored)
> > in the output file.
> >
> > I guess my configure is wrong, could you tell me the meaning of
> > --with-psm, --with-sge, do I need to add other options? I guess the
> > computing nodes are using infiniband, but how to build with that? If I
> > don't have the su right, can I build it? What should I pay attettion if
> > I want to build and use my own openmpi?
> >
> > You see, in a personal multicore computer, building is so easy and
> > mpirun the program without any problems. But in school's hpc, it fails
> > all the time.
> >
> > Please help. Thank you all.
> >
> >
> > Zhigang Wei
> > ------------
> > NatHaz Modeling Laboratory
> > University of Notre Dame
> > 112J FitzPatrick Hall
> > Notre Dame, IN 46556
> > ------------------------------------------------------------------------
> > 2010-07-07
> >
> >
> > ------------------------------------------------------------------------
> >
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