Hi, Thanks for this guys. I think I might have two MPI implementations installed because 'locate mpirun' gives (see bold lines) : ----------------------------------------- /etc/alternatives/mpirun /etc/alternatives/mpirun.1.gz */home/djordje/Build_WRF/LIBRARIES/mpich/bin/mpirun* /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/intel/ 4.1.1.036/linux-x86_64/bin/mpirun /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/intel/ 4.1.1.036/linux-x86_64/bin64/mpirun /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/intel/ 4.1.1.036/linux-x86_64/ia32/bin/mpirun /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/intel/ 4.1.1.036/linux-x86_64/intel64/bin/mpirun /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/openmpi/1.4.3/linux-x86_64-2.3.4/gnu4.5/bin/mpirun /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/openmpi/1.4.3/linux-x86_64-2.3.4/gnu4.5/share/man/man1/mpirun.1 /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/openmpi/1.6.4/linux-x86_64-2.3.4/gnu4.6/bin/mpirun /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/openmpi/1.6.4/linux-x86_64-2.3.4/gnu4.6/share/man/man1/mpirun.1 /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.2.0.0/linux64_2.6-x86-glibc_2.3.4/bin/mpirun /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.2.0.0/linux64_2.6-x86-glibc_2.3.4/bin/mpirun.mpich /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.2.0.0/linux64_2.6-x86-glibc_2.3.4/bin/mpirun.mpich2 /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.2.0.0/linux64_2.6-x86-glibc_2.3.4/ia32/bin/mpirun /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.2.0.0/linux64_2.6-x86-glibc_2.3.4/ia32/bin/mpirun.mpich /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.2.0.0/linux64_2.6-x86-glibc_2.3.4/ia32/bin/mpirun.mpich2 /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.2.0.0/linux64_2.6-x86-glibc_2.3.4/ia32/lib/linux_amd64/libmpirun.so /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.2.0.0/linux64_2.6-x86-glibc_2.3.4/ia32/lib/linux_ia32/libmpirun.so /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.2.0.0/linux64_2.6-x86-glibc_2.3.4/lib/linux_amd64/libmpirun.so /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.2.0.0/linux64_2.6-x86-glibc_2.3.4/lib/linux_ia32/libmpirun.so /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.2.0.0/linux64_2.6-x86-glibc_2.3.4/share/man/man1/mpirun.1.gz /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.3.0.2/linux64_2.6-x86-glibc_2.3.4/bin/mpirun /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.3.0.2/linux64_2.6-x86-glibc_2.3.4/bin/mpirun.mpich /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.3.0.2/linux64_2.6-x86-glibc_2.3.4/bin/mpirun.mpich2 /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.3.0.2/linux64_2.6-x86-glibc_2.3.4/ia32/bin/mpirun /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.3.0.2/linux64_2.6-x86-glibc_2.3.4/ia32/bin/mpirun.mpich /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.3.0.2/linux64_2.6-x86-glibc_2.3.4/ia32/bin/mpirun.mpich2 /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.3.0.2/linux64_2.6-x86-glibc_2.3.4/ia32/lib/linux_amd64/libmpirun.so /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.3.0.2/linux64_2.6-x86-glibc_2.3.4/ia32/lib/linux_ia32/libmpirun.so /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.3.0.2/linux64_2.6-x86-glibc_2.3.4/lib/linux_amd64/libmpirun.so /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.3.0.2/linux64_2.6-x86-glibc_2.3.4/lib/linux_ia32/libmpirun.so /home/djordje/StarCCM/Install/STAR-CCM+8.06.007/mpi/platform/ 8.3.0.2/linux64_2.6-x86-glibc_2.3.4/share/man/man1/mpirun.1.gz */usr/bin/mpirun* /usr/bin/mpirun.openmpi /usr/lib/openmpi/include/openmpi/ompi/runtime/mpiruntime.h /usr/share/man/man1/mpirun.1.gz /usr/share/man/man1/mpirun.openmpi.1.gz /var/lib/dpkg/alternatives/mpirun ----------------------------------------- This is a single machine. I actually just got it... another user used it for 1-2 years.
Is this a possible cause of the problem? Regards, Djordje On Mon, Apr 14, 2014 at 7:06 PM, Gus Correa <g...@ldeo.columbia.edu> wrote: > 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.el...@intel.com> 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-boun...@open-mpi.org] 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 <g...@ldeo.columbia.edu> >>> 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 <djord...@gmail.com >>> <mailto:djord...@gmail.com>> wrote: >>> >>> Yes, but I was hoping to get. :) >>> >>> >>> On Mon, Apr 14, 2014 at 3:02 PM, Jeff Squyres (jsquyres) >>> <jsquy...@cisco.com <mailto:jsquy...@cisco.com>> 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 < >>> djord...@gmail.com >>> <mailto:djord...@gmail.com>> wrote: >>> >>> > I didn't use OpenMPI. >>> > >>> > >>> > On Mon, Apr 14, 2014 at 2:37 PM, Jeff Squyres (jsquyres) >>> <jsquy...@cisco.com <mailto:jsquy...@cisco.com>> 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 >>> <djord...@gmail.com <mailto:djord...@gmail.com>> 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) >>> <dgood...@cisco.com <mailto:dgood...@cisco.com>> wrote: >>> > > On Apr 14, 2014, at 12:15 PM, Djordje Romanic >>> <djord...@gmail.com <mailto:djord...@gmail.com>> 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 >>> > > >>> > > _______________________________________________ >>> > > users mailing list >>> > > us...@open-mpi.org <mailto:us...@open-mpi.org> >>> >>> > > http://www.open-mpi.org/mailman/listinfo.cgi/users >>> > > >>> > > <configure.wrf>_______________ >>> ________________________________ >>> > > users mailing list >>> > > us...@open-mpi.org <mailto:us...@open-mpi.org> >>> >>> > > http://www.open-mpi.org/mailman/listinfo.cgi/users >>> > >>> > >>> > -- >>> > Jeff Squyres >>> > jsquy...@cisco.com <mailto:jsquy...@cisco.com> >>> >>> > For corporate legal information go to: >>> http://www.cisco.com/web/about/doing_business/legal/cri/ >>> > >>> > _______________________________________________ >>> > users mailing list >>> > us...@open-mpi.org <mailto:us...@open-mpi.org> >>> >>> > http://www.open-mpi.org/mailman/listinfo.cgi/users >>> > >>> > _______________________________________________ >>> > users mailing list >>> > us...@open-mpi.org <mailto:us...@open-mpi.org> >>> >>> > http://www.open-mpi.org/mailman/listinfo.cgi/users >>> >>> >>> -- >>> Jeff Squyres >>> jsquy...@cisco.com <mailto:jsquy...@cisco.com> >>> >>> For corporate legal information go to: >>> http://www.cisco.com/web/about/doing_business/legal/cri/ >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org <mailto:us...@open-mpi.org> >>> >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>> >>> >>> >>> >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>> >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>> >> >> >> > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users >
