[Users] Error in exe/cactus_sim

Rishank Diwan rishank2610 at gmail.com
Mon Apr 27 07:05:28 CDT 2020


Hello Roland and Ian,

I removed the  mpich-doc mpich mpich-doc libmpich-dev libmpich12 and other
dependencies as you suggested and got the updated version of mpi file I
sent you.

ii  compiz
1:0.9.13.1+18.04.20180302-0ubuntu1                  all          OpenGL
window and compositing manager
ii  compiz-core
 1:0.9.13.1+18.04.20180302-0ubuntu1                  amd64        OpenGL
window and compositing manager
ii  compiz-gnome
1:0.9.13.1+18.04.20180302-0ubuntu1                  amd64        OpenGL
window and compositing manager - GNOME window decorator
ii  compiz-plugins-default:amd64
1:0.9.13.1+18.04.20180302-0ubuntu1                  amd64        OpenGL
window and compositing manager - default plugins
ii  libcompizconfig0:amd64
1:0.9.13.1+18.04.20180302-0ubuntu1                  amd64        Settings
library for plugins - OpenCompositing Project
ii  libdecoration0:amd64
1:0.9.13.1+18.04.20180302-0ubuntu1                  amd64        Compiz
window decoration library
ii  libexempi3:amd64                           2.4.5-2
                        amd64        library to parse XMP metadata (Library)
ii  libhdf5-openmpi-100:amd64                  1.10.0-patch1+docs-4
                       amd64        Hierarchical Data Format 5 (HDF5) -
runtime files - OpenMPI version
ii  libhdf5-openmpi-dev                        1.10.0-patch1+docs-4
                       amd64        Hierarchical Data Format 5 (HDF5) -
development files - OpenMPI version
ii  libopenmpi-dev                             2.1.1-8
                        amd64        high performance message passing
library -- header files
ii  libopenmpi2:amd64                          2.1.1-8
                        amd64        high performance message passing
library -- shared library
ii  make                                       4.1-9.1ubuntu1
                       amd64        utility for directing compilation
ii  openmpi-bin                                2.1.1-8
                        amd64        high performance message passing
library -- binaries
ii  openmpi-common                             2.1.1-8
                        all          high performance message passing
library -- common files

I don't see any mpich dependencies now. I also tried
installing einsteintoolkit again and it happens to be working fine.

Thank you very much for your help.

Yours Sincerely,
Rishank Diwan


On Sun, 26 Apr 2020 at 21:24, Roland Haas <rhaas at illinois.edu> wrote:

> Hello Rishank Diwan,
>
> looking at you file "mpi" there are still bits and pieces of mpich
> installed. Namely:
>
> ii  mpich-doc                                  3.3~a2-4
>                         all          Documentation for MPICH
> ii  mpich                                      3.3~a2-4
>                         amd64        Implementation of the MPI Message
> Passing Interface standard
> ii  mpich-doc                                  3.3~a2-4
>                         all          Documentation for MPICH
> ii  libmpich-dev                               3.3~a2-4
>                         amd64        Development files for MPICH
> ii  libmpich-dev                               3.3~a2-4
>                         amd64        Development files for MPICH
> ii  libmpich12:amd64                           3.3~a2-4
>                         amd64        Shared libraries for MPICH
>
> as well as a lot of MPICH using libraries:
>
> ii  gromacs-mpich                              2018.1-1
>                         amd64        Molecular dynamics sim, binaries for
> MPICH parallelization
> ii  libhdf5-mpich-100:amd64                    1.10.0-patch1+docs-4
>                         amd64        Hierarchical Data Format 5 (HDF5) -
> runtime files - MPICH2 version
> ii  libhdf5-mpich-dev                          1.10.0-patch1+docs-4
>                         amd64        Hierarchical Data Format 5 (HDF5) -
> development files - MPICH version
> ii  libmeep-mpich2-8                           1.3-4build3
>                          amd64        library for using parallel (OpenMPI)
> version of meep
> ii  libmeep-mpich2-dev                         1.3-4build3
>                          amd64        development library for using
> parallel (OpenMPI) version of meep
> ii  libmpich12:amd64                           3.3~a2-4
>                         amd64        Shared libraries for MPICH
> ii  libscalapack-mpich-dev                     2.0.2-4
>                          amd64        Scalable Linear Algebra Package -
> Dev. files for MPICH
> ii  libscalapack-mpich2.0                      2.0.2-4
>                          amd64        Scalable Linear Algebra Package -
> Shared libs. for MPICH
> ii  libtachyon-mpich-0:amd64                   0.99~b6+dsx-8
>                          amd64        Parallel/Multiprocessor Ray Tracing
> Library - runtime - MPICH flavour
> ii  libtachyon-mpich-0-dev:amd64               0.99~b6+dsx-8
>                          amd64        Parallel/Multiprocessor Ray Tracing
> Library - development - MPICH flavour
> ii  meep-mpich2                                1.3-4build3
>                          amd64        software package for FDTD simulation,
> parallel (OpenMPI) version
> ii  netpipe-mpich2                             3.7.2-7.4build2
>                          amd64        Network performance tool using MPICH2
> MPI
> ii  yorick-mpy-mpich2                          2.2.04+dfsg1-9
>                         amd64        Message Passing Yorick (MPICH2 build)
> ii  libhdf5-mpich-100:amd64                    1.10.0-patch1+docs-4
>                         amd64        Hierarchical Data Format 5 (HDF5) -
> runtime files - MPICH2 version
> ii  libhdf5-mpich-dev                          1.10.0-patch1+docs-4
>                         amd64        Hierarchical Data Format 5 (HDF5) -
> development files - MPICH version
> ii  libmeep-mpich2-8                           1.3-4build3
>                          amd64        library for using parallel (OpenMPI)
> version of meep
> ii  libmeep-mpich2-dev                         1.3-4build3
>                          amd64        development library for using
> parallel (OpenMPI) version of meep
> ii  libscalapack-mpich-dev                     2.0.2-4
>                          amd64        Scalable Linear Algebra Package -
> Dev. files for MPICH
> ii  libscalapack-mpich2.0                      2.0.2-4
>                          amd64        Scalable Linear Algebra Package -
> Shared libs. for MPICH
> ii  libtachyon-mpich-0:amd64                   0.99~b6+dsx-8
>                          amd64        Parallel/Multiprocessor Ray Tracing
> Library - runtime - MPICH flavour
> ii  libtachyon-mpich-0-dev:amd64               0.99~b6+dsx-8
>                          amd64        Parallel/Multiprocessor Ray Tracing
> Library - development - MPICH flavour
>
> You will have to remove *all* the mpich pieces, namely:  mpich-doc
> mpich mpich-doc libmpich-dev libmpich12 to be sure to avoid any strange
> interference. Note that this will also remove the mpich using libraries.
>
> Yours,
> Roland
>
> > Hello Roland and Ian,
> >
> > I am attaching the build.log file. I have also tried running the
> simulation
> > after removing the MPICH with this I also attaching to file obtained from
> > "dpkg --list | grep -vi compile | grep -i mpi" command to compare from
> > previous one. I also did make changes in PATH and LD_Library_Path. The
> > current path are as follows:
> >
> > LD_LIBRARY_PATH=:/usr/lib/x86_64-linux-gnu/openmpi/lib/
> >
> >
> PATH=/home/rishank/miniconda2/bin:/home/rishank/anaconda2/bin:/home/rishank/anaconda2/condabin:/home/rishank/bin:/home/rishank/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/bin
> >
> > and the previous one were:
> >
> > LD_LIBRARY_PATH=:/home/rishank/.openmpi/lib/:/home/rishank/.openmpi/lib/
> >
> >
> PATH=/home/rishank/miniconda2/bin:/home/rishank/anaconda2/bin:/home/rishank/anaconda2/condabin:/home/rishank/bin:/home/rishank/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/rishank/.openmpi/bin:/home/rishank/.openmpi/bin
> >
> > Yours Sincerely,
> > Rishank Diwan
> >
> >
> >
> >
> > On Thu, 23 Apr 2020 at 00:19, Roland Haas <rhaas at illinois.edu> wrote:
> >
> > > Hello Rishank,
> > >
> > > > It's possible that you might have to uninstall mpich, but I'm not
> > > > sure.  There *shouldn't* be a fundamental reason why you can't have
> > > > both installed and just use one of them, but there might be technical
> > > > reasons why it doesn't work.
> > > It is possible to have both installed at the same time. However things
> > > then become fragile. Ubuntu will declare one as the "default" using
> > > either the "alternatives" system (which is why eg /usr/bin/mpi and
> > > /usr/bin/mpicc point to files in /etc/alternatives/). This however does
> > > not include things like eg hdf5 which come in flavor packages
> > > hdf5-openmpi, hdf5-mpich, hdf5-serial each of which has libraries
> > > libhdf5_{openmpi,mpich,serial}.so. Then there's always the possibility
> > > something being wrong in the package setup.
> > >
> > > Thus having multiple MPI stacks installed at the same time, while
> > > possible, is outside of the realm of cases easily supported by our
> > > automated setup and would likely require a hand-crafted option list
> > > similar to the ones used on clusters. Eg setting
> > >
> > > MPI_DIR = /usr/lib/x86_64-linux-gnu/openmpi
> > > MPI_INC_DIRS = /usr/lib/x86_64-linux-gnu/openmpi/include
> > > MPI_LIB_DIRS = /usr/lib/x86_64-linux-gnu/openmpi/lib
> > > MPI_LIBS = mpi
> > >
> > > *may* work (though see my note above about libraries that can use MPI).
> > > Note that this still assumes that the mpirun found in $PATH is the one
> > > that matches the used MPI stack, ie OpenMPI's so it may require changes
> > > to the run script as well.
> > >
> > > Thus the simplest solution is likely to make sure only one MPI stack
> > > (OpenMPI or MPICH) is installed and uninstall the other one.
> > >
> > > Yours,
> > > Roland
> > >
> > > --
> > > My email is as private as my paper mail. I therefore support encrypting
> > > and signing email messages. Get my PGP key from http://pgp.mit.edu .
> > >
>
>
> --
> My email is as private as my paper mail. I therefore support encrypting
> and signing email messages. Get my PGP key from http://pgp.mit.edu .
>
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