[petsc-users] make test freeze

[Patrick Begou]

Hi Matthew,

Launching manualy ex19 shows only one process consuming cpu time, after 952mn 
I've killed the job this morning.

[begou at 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 at 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....

Patrick

Matthew Knepley a écrit :
> On Thu, Jan 5, 2017 at 6:31 AM, Patrick Begou 
> <Patrick.Begou at legi.grenoble-inp.fr> 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:Patrick.Begou at grenoble-inp.fr
>     <mailto:Patrick.Begou at grenoble-inp.fr> |
>     |  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:Patrick.Begou at grenoble-inp.fr  |
|  LEGI                    |                                      |
|  BP 53 X                 | Tel 04 76 82 51 35                   |
|  38041 GRENOBLE CEDEX    | Fax 04 76 82 52 71                   |
===================================================================

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