On Fri, Jan 6, 2017 at 2:39 AM, Patrick Begou < [email protected]> wrote:
> Hi Matthew, > > Launching manualy ex19 shows only one process consuming cpu time, after > 952mn I've killed the job this morning. > > [begou@kareline tutorials]$ make ex19 > mpicc -o ex19.o -c -Wall -Wwrite-strings -Wno-strict-aliasing > -Wno-unknown-pragmas -fvisibility=hidden -g3 > -I/kareline/data/begou/YALES2_1.0.0/PREREQUIS/petsc-git/include > -I/kareline/data/begou/YALES2_1.0.0/PREREQUIS/petsc-git/GCC48/include > `pwd`/ex19.c > mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > -fvisibility=hidden -g3 -o ex19 ex19.o -L/kareline/data/begou/YALES2_ > 1.0.0/PREREQUIS/petsc-git/GCC48/lib -lpetsc -llapack -lblas -lX11 > -lhwloc -lssl -lcrypto -L/opt/openmpi173-GCC48-node/lib > -L/opt/GCC48c/lib/gcc/x86_64-unknown-linux-gnu/4.8.1 -L/opt/GCC48c/lib64 > -L/opt/GCC48c/lib -lmpi_usempi -lmpi_mpifh -lgfortran -lm -lgfortran -lm > -lquadmath -lm -lmpi_cxx -lstdc++ -L/opt/openmpi173-GCC48-node/lib > -L/opt/GCC48c/lib/gcc/x86_64-unknown-linux-gnu/4.8.1 -L/opt/GCC48c/lib64 > -L/opt/GCC48c/lib -ldl -lmpi -lgcc_s -lpthread -ldl > /bin/rm -f ex19.o > [begou@kareline tutorials]$ mpiexec -n 2 ./ex19 -snes_monitor > > top command shows: > > PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ > COMMAND > 32184 begou 20 0 249m 7152 5132 R 99.8 0.0 952:15.97 > ex19 > 32183 begou 20 0 71676 3508 2264 S 0.0 0.0 0:00.04 > mpiexec > 32185 begou 20 0 185m 7132 5124 S 0.0 0.0 0:00.04 > ex19 > > looks like the first process waiting for something that never occur in MPI > communication.... > 1000s of people run this every day, so I am skeptical of that explanation. However, this could happen if the 'mpiexec' in your path does not match the MPI libraries that PETSc is linked to. Matt > Patrick > > Matthew Knepley a écrit : > > On Thu, Jan 5, 2017 at 6:31 AM, Patrick Begou < > <[email protected]>[email protected]> > wrote: > >> I am unable to run any test on petsc. It looks like if the ex19 run >> freeze on the server as it do not use any cpu time and pstree shows >> >> sshd---bash-+-gedit >> `-make---sh-+-gmake---sh---gmake---sh---mpiexec---ex19 >> `-tee >> I've tested petsc-3.7.5.tar.gz and the latest sources on the Git >> repository. >> > > All make is doing is running ex19, which you can do by hand. What do you > get for > > cd $PETSC_DIR > cd src/snes/examples/tutorials > make ex19 > mpiexec -n 2 ./ex19 -snes_monitor > > Thanks, > > Matt > > >> Setup from the Git repo: >> ./configure >> --prefix=/kareline/data/begou/YALES2_1.0.0/PREREQUIS/petsc-git-binaries >> \ >> --PETSC_ARCH=GCC48 \ >> --PETSC_DIR=/kareline/data/begou/YALES2_1.0.0/PREREQUIS/petsc-git \ >> --with-shared-libraries=0 \ >> --with-fortran-interfaces=1 \ >> --with-fortran-kernels=1 \ >> --with-cc=mpicc \ >> --with-fc=mpif90 \ >> --with-cxx=mpicxx >> >> make PETSC_DIR=/kareline/data/begou/YALES2_1.0.0/PREREQUIS/petsc-git >> PETSC_ARCH=GCC48 all >> >> make PETSC_DIR=/kareline/data/begou/YALES2_1.0.0/PREREQUIS/petsc-git >> PETSC_ARCH=GCC48 install >> >> make >> PETSC_DIR=/kareline/data/begou/YALES2_1.0.0/PREREQUIS/petsc-git-binaries >> PETSC_ARCH="" test >> >> >> In the log file I've just: >> >> Running test examples to verify correct installation >> Using >> PETSC_DIR=/kareline/data/begou/YALES2_1.0.0/PREREQUIS/petsc-git-binaries >> and PETSC_ARCH= >> >> I'm using: >> gcc version 4.8.1 >> Open MPI: 1.7.3 (build with gcc 4.8.1) >> (This environment is in production for a while for many local software >> and works fine) >> >> Any suggestion is welcome >> >> Patrick >> >> -- >> =================================================================== >> | Equipe M.O.S.T. | | >> | Patrick BEGOU | mailto:[email protected] | >> | LEGI | | >> | BP 53 X | Tel 04 76 82 51 35 | >> | 38041 GRENOBLE CEDEX | Fax 04 76 82 52 71 | >> =================================================================== >> >> > > > -- > 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 > > > > -- > =================================================================== > | Equipe M.O.S.T. | | > | Patrick BEGOU | mailto:[email protected] > <[email protected]> | > | LEGI | | > | BP 53 X | Tel 04 76 82 51 35 | > | 38041 GRENOBLE CEDEX | Fax 04 76 82 52 71 | > =================================================================== > > -- 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
