Epilogue: I was able to complete the configuration and compilation using an interactive session in one compute node. Certainly, there was no need for the --with-batch option.
However, at run time, the SGI MPT's mpiexec_mpt (required by the job scheduler in this cluster) throws a cryptic error: Cannot find executable: -f It seems not petsc specific, though, as other mpi programs also fail. In any case I would like to thank you all for the prompt help! Santiago On Mon, Dec 18, 2017 at 1:03 AM, Smith, Barry F. <bsm...@mcs.anl.gov> wrote: > > Configure runs fine. When it runs fine absolutely no reason to run it > with --with-batch. > > Make test fails because it cannot launch parallel jobs directly using > the mpiexec it is using. > > You need to determine how to submit jobs on this system and then you > are ready to go. > > Barry > > > > On Dec 17, 2017, at 4:55 PM, Santiago Andres Triana <rep...@gmail.com> > wrote: > > > > Thanks for your quick responses! > > > > Attached is the configure.log obtained without using the --with-batch > option. Configures without errors but fails at the 'make test' stage. A > snippet of the output with the error (which I attributed to the job > manager) is: > > > > > > > > > Local host: hpca-login > > > Registerable memory: 32768 MiB > > > Total memory: 65427 MiB > > > > > > Your MPI job will continue, but may be behave poorly and/or hang. > > > ------------------------------------------------------------ > -------------- > > 3c25 > > < 0 KSP Residual norm 0.239155 > > --- > > > 0 KSP Residual norm 0.235858 > > 6c28 > > < 0 KSP Residual norm 6.81968e-05 > > --- > > > 0 KSP Residual norm 2.30906e-05 > > 9a32,33 > > > [hpca-login:38557] 1 more process has sent help message > help-mpi-btl-openib.txt / reg mem limit low > > > [hpca-login:38557] Set MCA parameter "orte_base_help_aggregate" to 0 > to see all help / error messages > > /home/trianas/petsc-3.8.3/src/snes/examples/tutorials > > Possible problem with ex19_fieldsplit_fieldsplit_mumps, diffs above > > ========================================= > > 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: It appears that your OpenFabrics subsystem is configured to only > > allow registering part of your physical memory. This can cause MPI jobs > to > > run with erratic performance, hang, and/or crash. > > > > This may be caused by your OpenFabrics vendor limiting the amount of > > physical memory that can be registered. You should investigate the > > relevant Linux kernel module parameters that control how much physical > > memory can be registered, and increase them to allow registering all > > physical memory on your machine. > > > > See this Open MPI FAQ item for more information on these Linux kernel > module > > parameters: > > > > http://www.open-mpi.org/faq/?category=openfabrics#ib-locked-pages > > > > Local host: hpca-login > > Registerable memory: 32768 MiB > > Total memory: 65427 MiB > > > > Your MPI job will continue, but may be behave poorly and/or hang. > > ------------------------------------------------------------ > -------------- > > Number of SNES iterations = 4 > > Completed test examples > > ========================================= > > Now to evaluate the computer systems you plan use - do: > > make PETSC_DIR=/home/trianas/petsc-3.8.3 PETSC_ARCH=arch-linux2-c-debug > streams > > > > > > > > > > On Sun, Dec 17, 2017 at 11:32 PM, Matthew Knepley <knep...@gmail.com> > wrote: > > On Sun, Dec 17, 2017 at 3:29 PM, Santiago Andres Triana < > rep...@gmail.com> wrote: > > Dear petsc-users, > > > > I'm trying to install petsc in a cluster that uses a job manager. This > is the configure command I use: > > > > ./configure --known-mpi-shared-libraries=1 --with-scalar-type=complex > --with-mumps=1 --download-mumps --download-parmetis > --with-blaslapack-dir=/sw/sdev/intel/psxe2015u3/composer_xe_2015.3.187/mkl > --download-metis --with-scalapack=1 --download-scalapack --with-batch > > > > This fails when including the option --with-batch together with > --download-scalapack: > > > > We need configure.log > > > > ============================================================ > =================== > > Configuring PETSc to compile on your system > > ============================================================ > =================== > > TESTING: check from config.libraries(config/ > BuildSystem/config/libraries.py:158) > ************************************************************ > ******************* > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log > for details): > > ------------------------------------------------------------ > ------------------- > > Unable to find scalapack in default locations! > > Perhaps you can specify with --with-scalapack-dir=<directory> > > If you do not want scalapack, then give --with-scalapack=0 > > You might also consider using --download-scalapack instead > > ************************************************************ > ******************* > > > > > > However, if I omit the --with-batch option, the configure script manages > to succeed (it downloads and compiles scalapack; the install fails later at > the make debug because of the job manager). > > > > Can you send this failure as well? > > > > Thanks, > > > > Matt > > > > Any help or suggestion is highly appreciated. Thanks in advance! > > > > Andres > > > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > > > <configure.log> > >