Wonderful! Thanks so much for all of your help! Kai
On Fri, Jul 25, 2014 at 3:50 PM, Barry Smith <[email protected]> wrote: > > Well it is running. It is just producing annoying warning messages. You > need to talk to your local MPI expert on that system for how to get rid of > the problem. > > Barry > > On Jul 25, 2014, at 3:23 PM, Kai Song <[email protected]> wrote: > > > Hi Barry, > > > > I indeed deleted some of the OpenMPI related warning messages, it should > be irrelevant. Here is the full output: > > ====================== > > [kaisong@n0009 petsc-3.5.0]$ sh petsc-3.5.0-gcc.sh > > Running test examples to verify correct installation > > Using PETSC_DIR=/clusterfs/voltaire/home/software/modules/petsc/3.5.0 > and PETSC_ARCH=arch-linux2-c-debug > > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI > process > > See http://www.mcs.anl.gov/petsc/documentation/faq.html > > > -------------------------------------------------------------------------- > > WARNING: There is at least non-excluded one OpenFabrics device found, > > but there are no active ports detected (or Open MPI was unable to use > > them). This is most certainly not what you wanted. Check your > > cables, subnet manager configuration, etc. The openib BTL will be > > ignored for this job. > > > > Local host: n0009.scs00 > > > -------------------------------------------------------------------------- > > lid velocity = 0.0016, prandtl # = 1, grashof # = 1 > > Number of SNES iterations = 2 > > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 MPI > processes > > See http://www.mcs.anl.gov/petsc/documentation/faq.html > > > -------------------------------------------------------------------------- > > WARNING: There is at least non-excluded one OpenFabrics device found, > > but there are no active ports detected (or Open MPI was unable to use > > them). This is most certainly not what you wanted. Check your > > cables, subnet manager configuration, etc. The openib BTL will be > > ignored for this job. > > > > Local host: n0009.scs00 > > > -------------------------------------------------------------------------- > > lid velocity = 0.0016, prandtl # = 1, grashof # = 1 > > Number of SNES iterations = 2 > > [n0009.scs00:07638] 1 more process has sent help message > help-mpi-btl-openib.txt / no active ports found > > [n0009.scs00:07638] Set MCA parameter "orte_base_help_aggregate" to 0 to > see all help / error messages > > Possible error running Fortran example src/snes/examples/tutorials/ex5f > with 1 MPI process > > See http://www.mcs.anl.gov/petsc/documentation/faq.html > > > -------------------------------------------------------------------------- > > WARNING: There is at least non-excluded one OpenFabrics device found, > > but there are no active ports detected (or Open MPI was unable to use > > them). This is most certainly not what you wanted. Check your > > cables, subnet manager configuration, etc. The openib BTL will be > > ignored for this job. > > > > Local host: n0009.scs00 > > > -------------------------------------------------------------------------- > > Number of SNES iterations = 4 > > Completed test examples > > ========================================= > > Now to evaluate the computer systems you plan use - do: > > make PETSC_DIR=/clusterfs/voltaire/home/software/modules/petsc/3.5.0 > PETSC_ARCH=arch-linux2-c-debug streams NPMAX=<number of MPI processes you > intend to use> > > ====================== > > > > I also followed your suggestion and built ex19 separately, and made sure > using the same compiler that built petsc. Here is the complete output: > > ====================== > > [kaisong@n0009 tutorials]$ mpiexec -n 2 ./ex19 > > > -------------------------------------------------------------------------- > > WARNING: There is at least non-excluded one OpenFabrics device found, > > but there are no active ports detected (or Open MPI was unable to use > > them). This is most certainly not what you wanted. Check your > > cables, subnet manager configuration, etc. The openib BTL will be > > ignored for this job. > > > > Local host: n0009.scs00 > > > -------------------------------------------------------------------------- > > lid velocity = 0.0625, prandtl # = 1, grashof # = 1 > > Number of SNES iterations = 2 > > [n0009.scs00:09124] 1 more process has sent help message > help-mpi-btl-openib.txt / no active ports found > > [n0009.scs00:09124] Set MCA parameter "orte_base_help_aggregate" to 0 to > see all help / error messages > > ====================== > > > > Thanks, > > > > Kai > > > > > > > > On Fri, Jul 25, 2014 at 1:32 PM, Barry Smith <[email protected]> wrote: > > > > On Jul 25, 2014, at 12:23 PM, Kai Song <[email protected]> wrote: > > > > > Hi All, > > > > > > Thanks for all the suggestions! I took Satish's advice, removed the > source, and did a fresh built. > > > > > > It got through the test compiling, but the tests failed as follow: > > > ================== > > > Running test examples to verify correct installation > > > Using PETSC_DIR=/clusterfs/voltaire/home/software/modules/petsc/3.5.0 > and PETSC_ARCH=arch-linux2-c-debug > > > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 > MPI process > > > See http://www.mcs.anl.gov/petsc/documentation/faq.html > > > lid velocity = 0.0016, prandtl # = 1, grashof # = 1 > > > Number of SNES iterations = 2 > > > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 > MPI processes > > > See http://www.mcs.anl.gov/petsc/documentation/faq.html > > > … > > > > Surely it did not print … here? What was the complete message? > > > > Usually this happens due to an incompatible mpiexec being used > because it appears earlier in the path. > > > > What happens if you do > > > > cd src/snes/examples/tutorials > > make ex19 > > mpiexec -n 2 ./ex19 > > > > for mpiexec use the one associated with the MPI that you built PETSc with > > > > Barry > > > > > ================== > > > > > > I tried to go into src/snes/examples/tutorials/ex19, but didn't find > any logs. Is this error for the test Okay? > > > > > > Thanks, > > > > > > Kai > > > > > > > > > > > > On Fri, Jul 25, 2014 at 11:06 AM, Satish Balay <[email protected]> > wrote: > > > Its probably best to do a fresh build with the latest petsc-3.5.1 > tarball and see > > > if the problem is reproduceable [with --with-shared-libraries=0] > > > > > > Satish > > > > > > On Fri, 25 Jul 2014, Jed Brown wrote: > > > > > > > Matthew Knepley <[email protected]> writes: > > > > > > > > > On Thu, Jul 24, 2014 at 5:33 PM, Kai Song <[email protected]> wrote: > > > > > > > > > >> Hi Satish, > > > > >> > > > > >> Thanks for the quick response. I attached the make.log in this > email, and > > > > >> a quick glance, I didn't see any obvious errors. > > > > >> > > > > > > > > > > This never built the MUMPS directory, even though you have > PETSC_HAVE_MUMPS > > > > > defined. I can see two > > > > > possible reasons for this: > > > > > > > > > > 1) You distribution as missing files > > > > > > > > > > 2) You have two copies of PETSc fighting each other here (old > PETSC_DIR?) > > > > > > > > > > Can you make sure you have the file mumps.c in > > > > > > > > > > src/mat/impls/aij/mpi/mumps > > > > > > > > > > Jed, how do we check what make is doing here? > > > > > > > > mumps.c should be listed in $PETSC_ARCH/conf/files after the code > > > > generator runs. Possibly a file system problem or tinkering caused > it > > > > to appear up-to-date after reconfiguring? (Just speculating because > we > > > > haven't seen this problem before.) > > > > > > > > > > > > > > > > > > > -- > > > Kai Song > > > <[email protected]> 1.510.495.2180 > > > 1 Cyclotron Rd. Berkeley, CA94720, MS-50B 3209 > > > High Performance Computing Services (HPCS) > > > Lawrence Berkeley National Laboratory - http://scs.lbl.gov > > > > > > > > > > -- > > Kai Song > > <[email protected]> 1.510.495.2180 > > 1 Cyclotron Rd. Berkeley, CA94720, MS-50B 3209 > > High Performance Computing Services (HPCS) > > Lawrence Berkeley National Laboratory - http://scs.lbl.gov > > -- Kai Song <[email protected]> 1.510.495.2180 1 Cyclotron Rd. Berkeley, CA94720, MS-50B 3209 High Performance Computing Services (HPCS) Lawrence Berkeley National Laboratory - http://scs.lbl.gov
