[Users] Error in exe/cactus_sim
Roland Haas
rhaas at illinois.edu
Sun Apr 26 10:54:16 CDT 2020
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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