~$ ls -l $(whereis mpirun) ls: cannot access mpirun:: No such file or directory lrwxrwxrwx 1 root root 24 Jul 14 2015 /usr/bin/mpirun -> /etc/alternatives/mpirun lrwxrwxrwx 1 root root 7 Dec 28 2013 /usr/bin/mpirun.openmpi -> orterun lrwxrwxrwx 1 root root 24 Jul 14 2015 /usr/bin/X11/mpirun -> /etc/alternatives/mpirun lrwxrwxrwx 1 root root 7 Dec 28 2013 /usr/bin/X11/mpirun.openmpi -> orterun lrwxrwxrwx 1 root root 29 Jul 14 2015 /usr/share/man/man1/mpirun.1.gz -> /etc/alternatives/mpirun.1.gz
~$ md5sum $(whereis mpirun) md5sum: mpirun:: No such file or directory 0595c8c001bce2417965ac9bb407264b /usr/bin/mpirun.openmpi 0595c8c001bce2417965ac9bb407264b /usr/bin/mpirun 0595c8c001bce2417965ac9bb407264b /usr/bin/X11/mpirun.openmpi 0595c8c001bce2417965ac9bb407264b /usr/bin/X11/mpirun 7c2207f7d0092b983d0b48e7ab46d894 /usr/share/man/man1/mpirun.1.gz I think the problem might have been that I followed the standard petsc installation and used --download-mpich, which seemed to have installed mpich somewhere that petsc would use it but that wouldn't show up with 'whereis'. I ended up getting Example 4 to work by specifying --with-mpi-dir in both my petsc and libmesh configurations and recompiling. Thanks all for the help! -Harriet On Fri, Apr 8, 2016 at 9:15 AM, Roy Stogner <[email protected]> wrote: > > On Thu, 7 Apr 2016, Harriet Li wrote: > > The only MPI's I could find are: >> >> $ whereis mpirun >> mpirun: /usr/bin/mpirun.openmpi /usr/bin/mpirun >> /usr/bin/X11/mpirun.openmpi >> /usr/bin/X11/mpirun /usr/share/man/man1/mpirun.1.gz >> >> $ whereis mpicxx >> mpicxx: /usr/bin/mpicxx /usr/bin/mpicxx.openmpi /usr/bin/X11/mpicxx >> /usr/bin/X11/mpicxx.openmpi /usr/share/man/man1/mpicxx.1.gz >> >> $ whereis mpicc >> mpicc: /usr/bin/mpicc /usr/bin/mpicc.openmpi /usr/bin/X11/mpicc >> /usr/bin/X11/mpicc.openmpi /usr/share/man/man1/mpicc.1.gz >> >> Not sure if this counts as multiple MPIs... >> > > Me neither. They could be symlinks to the same target. What does > "ls -l $(whereis mpirun)" say? How about "md5sum $(whereis mpirun)"? > > > It's also important that no multiple versions got in during compiling > or linking. To check for the most glaring errors: If you're using > libtool to build yourapplication-devel then in the build directory > you'd run "ldd .libs/yourapplication-devel | grep mpi"; if you're in > the install directory or not using libtool you'd just run "ldd > yourapplication-devel | grep mpi" > > > What distribution are you using? This looks like the > Debian/Ubuntu/etc way of setting up mpich-vs-openmpi; is it possible > that you previously compiled with mpich but didn't start running until > changing the libraries underneath you? > > > What happens if you build and run > http://mpitutorial.com/tutorials/mpi-hello-world/ > > Try it first by hand, then with $(libmesh-config --cxx) etc. > --- > Roy > ------------------------------------------------------------------------------ Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/ gampad/clk?id=1444514301&iu=/ca-pub-7940484522588532 _______________________________________________ Libmesh-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
