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@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
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