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