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Subject: Re: [OMPI users] mpirun runs in serial even I set np to several processors
From: Gus Correa (gus_at_[hidden])
Date: 2014-04-14 19:06:52


Apologies for stirring even more the confusion by mispelling
"Open MPI" as "OpenMPI".
"OMPI" doesn't help either, because all OpenMP environment
variables and directives start with "OMP".
Maybe associating the names to
"message passing" vs. "threads" would help?

Djordje:

'which mpif90' etc show everything in /usr/bin.
So, very likely they were installed from packages
(yum, apt-get, rpm ...),right?
Have you tried something like
"yum list |grep mpi"
to see what you have?

As Dave, Jeff and Tom said, this may be a mixup of different
MPI implementations at compilation (mpicc mpif90) and runtime (mpirun).
That is common, you may have different MPI implementations installed.

Other possibilities that may tell what MPI you have:

mpirun --version
mpif90 --show
mpicc --show

Yet another:

locate mpirun
locate mpif90
locate mpicc

The ldd didn't show any MPI libraries, maybe they are static libraries.

An alternative is to install Open MPI from source,
and put it in a non-system directory
(not /usr/bin, not /usr/local/bin, etc).

Is this a single machine or a cluster?
Or perhaps a set of PCs that you have access to?
If it is a cluster, do you have access to a filesystem that is
shared across the cluster?
On clusters typically /home is shared, often via NFS.

Gus Correa

On 04/14/2014 05:15 PM, Jeff Squyres (jsquyres) wrote:
> Maybe we should rename OpenMP to be something less confusing --
> perhaps something totally unrelated, perhaps even non-sensical.
> That'll end lots of confusion!
>
> My vote: OpenMP --> SharkBook
>
> It's got a ring to it, doesn't it? And it sounds fearsome!
>
>
>
> On Apr 14, 2014, at 5:04 PM, "Elken, Tom" <tom.elken_at_[hidden]> wrote:
>
>> That’s OK. Many of us make that mistake, though often as a typo.
>> One thing that helps is that the correct spelling of Open MPI has a space in it,
but OpenMP does not.
>> If not aware what OpenMP is, here is a link: http://openmp.org/wp/
>>
>> What makes it more confusing is that more and more apps.
offer the option of running in a hybrid mode, such as WRF,
with OpenMP threads running over MPI ranks with the same executable.
And sometimes that MPI is Open MPI.
>>
>> Cheers,
>> -Tom
>>
>> From: users [mailto:users-bounces_at_[hidden]] On Behalf Of Djordje Romanic
>> Sent: Monday, April 14, 2014 1:28 PM
>> To: Open MPI Users
>> Subject: Re: [OMPI users] mpirun runs in serial even I set np to several processors
>>
>> OK guys... Thanks for all this info. Frankly, I didn't know these diferences between OpenMP and OpenMPI. The commands:
>> which mpirun
>> which mpif90
>> which mpicc
>> give,
>> /usr/bin/mpirun
>> /usr/bin/mpif90
>> /usr/bin/mpicc
>> respectively.
>>
>> A tutorial on how to compile WRF (http://www.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php) provides a test program to test MPI. I ran the program and it gave me the output of successful run, which is:
>> ---------------------------------------------
>> C function called by Fortran
>> Values are xx = 2.00 and ii = 1
>> status = 2
>> SUCCESS test 2 fortran + c + netcdf + mpi
>> ---------------------------------------------
>> It uses mpif90 and mpicc for compiling. Below is the output of 'ldd ./wrf.exe':
>>
>>
>> linux-vdso.so.1 => (0x00007fff584e7000)
>> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f4d160ab000)
>> libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007f4d15d94000)
>> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f4d15a97000)
>> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f4d15881000)
>> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f4d154c1000)
>> /lib64/ld-linux-x86-64.so.2 (0x00007f4d162e8000)
>> libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f4d1528a000)
>>
>>
>>
>> On Mon, Apr 14, 2014 at 4:09 PM, Gus Correa <gus_at_[hidden]> wrote:
>> Djordje
>>
>> Your WRF configure file seems to use mpif90 and mpicc (line 115 & following).
>> In addition, it also seems to have DISABLED OpenMP (NO TRAILING "I")
>> (lines 109-111, where OpenMP stuff is commented out).
>> So, it looks like to me your intent was to compile with MPI.
>>
>> Whether it is THIS MPI (OpenMPI) or another MPI (say MPICH, or MVAPICH,
>> or Intel MPI, or Cray, or ...) only your environment can tell.
>>
>> What do you get from these commands:
>>
>> which mpirun
>> which mpif90
>> which mpicc
>>
>> I never built WRF here (but other people here use it).
>> Which input do you provide to the command that generates the configure
>> script that you sent before?
>> Maybe the full command line will shed some light on the problem.
>>
>>
>> I hope this helps,
>> Gus Correa
>>
>>
>> On 04/14/2014 03:11 PM, Djordje Romanic wrote:
>> to get help :)
>>
>>
>>
>> On Mon, Apr 14, 2014 at 3:11 PM, Djordje Romanic <djordje8_at_[hidden]
>> <mailto:djordje8_at_[hidden]>> wrote:
>>
>> Yes, but I was hoping to get. :)
>>
>>
>> On Mon, Apr 14, 2014 at 3:02 PM, Jeff Squyres (jsquyres)
>> <jsquyres_at_[hidden] <mailto:jsquyres_at_[hidden]>> wrote:
>>
>> If you didn't use Open MPI, then this is the wrong mailing list
>> for you. :-)
>>
>> (this is the Open MPI users' support mailing list)
>>
>>
>> On Apr 14, 2014, at 2:58 PM, Djordje Romanic <djordje8_at_[hidden]
>> <mailto:djordje8_at_[hidden]>> wrote:
>>
>> > I didn't use OpenMPI.
>> >
>> >
>> > On Mon, Apr 14, 2014 at 2:37 PM, Jeff Squyres (jsquyres)
>> <jsquyres_at_[hidden] <mailto:jsquyres_at_[hidden]>> wrote:
>> > This can also happen when you compile your application with
>> one MPI implementation (e.g., Open MPI), but then mistakenly use
>> the "mpirun" (or "mpiexec") from a different MPI implementation
>> (e.g., MPICH).
>> >
>> >
>> > On Apr 14, 2014, at 2:32 PM, Djordje Romanic
>> <djordje8_at_[hidden] <mailto:djordje8_at_[hidden]>> wrote:
>> >
>> > > I compiled it with: x86_64 Linux, gfortran compiler with
>> gcc (dmpar). dmpar - distributed memory option.
>> > >
>> > > Attached is the self-generated configuration file. The
>> architecture specification settings start at line 107. I didn't
>> use Open MPI (shared memory option).
>> > >
>> > >
>> > > On Mon, Apr 14, 2014 at 1:23 PM, Dave Goodell (dgoodell)
>> <dgoodell_at_[hidden] <mailto:dgoodell_at_[hidden]>> wrote:
>> > > On Apr 14, 2014, at 12:15 PM, Djordje Romanic
>> <djordje8_at_[hidden] <mailto:djordje8_at_[hidden]>> wrote:
>> > >
>> > > > When I start wrf with mpirun -np 4 ./wrf.exe, I get this:
>> > > > -------------------------------------------------
>> > > > starting wrf task 0 of 1
>> > > > starting wrf task 0 of 1
>> > > > starting wrf task 0 of 1
>> > > > starting wrf task 0 of 1
>> > > > -------------------------------------------------
>> > > > This indicates that it is not using 4 processors, but 1.
>> > > >
>> > > > Any idea what might be the problem?
>> > >
>> > > It could be that you compiled WRF with a different MPI
>> implementation than you are using to run it (e.g., MPICH vs.
>> Open MPI).
>> > >
>> > > -Dave
>> > >
>> > > _______________________________________________
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>>
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>> > >
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>> >
>> >
>> > --
>> > Jeff Squyres
>> > jsquyres_at_[hidden] <mailto:jsquyres_at_[hidden]>
>>
>> > For corporate legal information go to:
>> http://www.cisco.com/web/about/doing_business/legal/cri/
>> >
>> > _______________________________________________
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>> > users_at_[hidden] <mailto:users_at_[hidden]>
>>
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>> >
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>> > users_at_[hidden] <mailto:users_at_[hidden]>
>>
>> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>> --
>> Jeff Squyres
>> jsquyres_at_[hidden] <mailto:jsquyres_at_[hidden]>
>>
>> For corporate legal information go to:
>> http://www.cisco.com/web/about/doing_business/legal/cri/
>>
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>> users mailing list
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>>
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>>
>>
>>
>>
>>
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>
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