<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Fri, Jan 6, 2017 at 2:39 AM, Patrick Begou <span dir="ltr"><<a href="mailto:Patrick.Begou@legi.grenoble-inp.fr" target="_blank">Patrick.Begou@legi.grenoble-inp.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<tt>Hi Matthew,<br>
<br>
Launching manualy ex19 shows only one process consuming cpu time,
after 952mn I've killed the job this morning.<br>
<br>
[begou@kareline tutorials]$ make ex19<br>
mpicc -o ex19.o -c -Wall -Wwrite-strings -Wno-strict-aliasing
-Wno-unknown-pragmas -fvisibility=hidden -g3
-I/kareline/data/begou/YALES2_<wbr>1.0.0/PREREQUIS/petsc-git/<wbr>include
-I/kareline/data/begou/YALES2_<wbr>1.0.0/PREREQUIS/petsc-git/<wbr>GCC48/include
`pwd`/ex19.c<br>
mpicc -Wall -Wwrite-strings -Wno-strict-aliasing
-Wno-unknown-pragmas -fvisibility=hidden -g3 -o ex19 ex19.o
-L/kareline/data/begou/YALES2_<wbr>1.0.0/PREREQUIS/petsc-git/<wbr>GCC48/lib
-lpetsc -llapack -lblas -lX11 -lhwloc -lssl -lcrypto
-L/opt/openmpi173-GCC48-node/<wbr>lib
-L/opt/GCC48c/lib/gcc/x86_64-<wbr>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/<wbr>lib
-L/opt/GCC48c/lib/gcc/x86_64-<wbr>unknown-linux-gnu/4.8.1
-L/opt/GCC48c/lib64 -L/opt/GCC48c/lib -ldl -lmpi -lgcc_s -lpthread
-ldl <br>
/bin/rm -f ex19.o<br>
[begou@kareline tutorials]$ mpiexec -n 2 ./ex19 -snes_monitor<br>
<br>
top command shows:<br>
<br>
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+
COMMAND <br>
32184 begou 20 0 249m 7152 5132 R 99.8 0.0 952:15.97
ex19 <br>
32183 begou 20 0 71676 3508 2264 S 0.0 0.0 0:00.04
mpiexec <br>
32185 begou 20 0 185m 7132 5124 S 0.0 0.0 0:00.04
ex19 <br>
<br>
looks like the first process waiting for something that never
occur in MPI communication....<br></tt></div></blockquote><div><br></div><div>1000s of people run this every day, so I am skeptical of that explanation.</div><div><br></div><div>However, this could happen if the 'mpiexec' in your path does not match the MPI libraries that PETSc is linked to.</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div text="#000000" bgcolor="#FFFFFF"><tt>
Patrick<br>
</tt><tt><br>
Matthew Knepley a écrit :
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Thu, Jan 5, 2017 at 6:31 AM,
Patrick Begou <span dir="ltr"><<a class="m_5136712065869368947moz-txt-link-abbreviated" href="mailto:Patrick.Begou@legi.grenoble-inp.fr" target="_blank"></a><a class="m_5136712065869368947moz-txt-link-abbreviated" href="mailto:Patrick.Begou@legi.grenoble-inp.fr" target="_blank">Patrick.Begou@legi.grenoble-<wbr>inp.fr</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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<br>
<br>
sshd---bash-+-gedit<br>
`-make---sh-+-gmake---sh---gma<wbr>ke---sh---mpiexec---ex19<br>
`-tee<br>
I've tested petsc-3.7.5.tar.gz and the latest sources
on the Git repository.<br>
</blockquote>
<div><br>
</div>
<div>All make is doing is running ex19, which you can do
by hand. What do you get for</div>
<div><br>
</div>
<div> cd $PETSC_DIR</div>
<div> cd src/snes/examples/tutorials</div>
<div> make ex19</div>
<div> mpiexec -n 2 ./ex19 -snes_monitor</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Setup
from the Git repo:<br>
./configure --prefix=/kareline/data/begou/<wbr>YALES2_1.0.0/PREREQUIS/petsc-g<wbr>it-binaries
\<br>
--PETSC_ARCH=GCC48 \<br>
--PETSC_DIR=/kareline/data/beg<wbr>ou/YALES2_1.0.0/PREREQUIS/pets<wbr>c-git
\<br>
--with-shared-libraries=0 \<br>
--with-fortran-interfaces=1 \<br>
--with-fortran-kernels=1 \<br>
--with-cc=mpicc \<br>
--with-fc=mpif90 \<br>
--with-cxx=mpicxx<br>
<br>
make PETSC_DIR=/kareline/data/begou<wbr>/YALES2_1.0.0/PREREQUIS/petsc-<wbr>git
PETSC_ARCH=GCC48 all<br>
<br>
make PETSC_DIR=/kareline/data/begou<wbr>/YALES2_1.0.0/PREREQUIS/petsc-<wbr>git
PETSC_ARCH=GCC48 install<br>
<br>
make PETSC_DIR=/kareline/data/begou<wbr>/YALES2_1.0.0/PREREQUIS/petsc-<wbr>git-binaries
PETSC_ARCH="" test<br>
<br>
<br>
In the log file I've just:<br>
<br>
Running test examples to verify correct installation<br>
Using PETSC_DIR=/kareline/data/begou<wbr>/YALES2_1.0.0/PREREQUIS/petsc-<wbr>git-binaries
and PETSC_ARCH=<br>
<br>
I'm using:<br>
gcc version 4.8.1<br>
Open MPI: 1.7.3 (build with gcc 4.8.1)<br>
(This environment is in production for a while for many
local software and works fine)<br>
<br>
Any suggestion is welcome<span class="m_5136712065869368947HOEnZb"><font color="#888888"><br>
<br>
Patrick<br>
<br>
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| Patrick BEGOU | mailto:<a href="mailto:Patrick.Begou@grenoble-inp.fr" target="_blank">Patrick.Begou@grenoble-<wbr>inp.fr</a>
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<br>
</font></span></blockquote>
</div>
<br>
<br clear="all"><span class="HOEnZb"><font color="#888888">
<div><br>
</div>
-- <br>
<div class="m_5136712065869368947gmail_signature" data-smartmail="gmail_signature">What most experimenters
take for granted before they begin their experiments is
infinitely more interesting than any results to which
their experiments lead.<br>
-- Norbert Wiener</div>
</font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></blockquote><span class="HOEnZb"><font color="#888888">
<br>
<br>
</font></span></tt><span class="HOEnZb"><font color="#888888">
<pre class="m_5136712065869368947moz-signature" cols="80">--
==============================<wbr>==============================<wbr>=======
| Equipe M.O.S.T. | |
| Patrick BEGOU | <a class="m_5136712065869368947moz-txt-link-freetext" href="mailto:Patrick.Begou@grenoble-inp.fr" target="_blank">mailto:Patrick.Begou@grenoble-<wbr>inp.fr</a> |
| LEGI | |
| BP 53 X | Tel 04 76 82 51 35 |
| 38041 GRENOBLE CEDEX | Fax 04 76 82 52 71 |
==============================<wbr>==============================<wbr>=======
</pre>
</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div>
</div></div>