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It is not the first time I have this problem and my aim was now to
try to solve it instead of ignoring tests. The environment seams
coherent (see below).<br>
I'll try to run in debug mode to investigate where the code hangs.<br>
<br>
Patrick<br>
<br>
<tt>[begou@kareline tutorials]$ make ex19</tt><tt><br>
</tt><tt><b>mpicc</b> -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</tt><tt><br>
</tt><tt>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 </tt><tt><br>
</tt><tt>/bin/rm -f ex19.o</tt><tt><br>
<br>
</tt><tt>[begou@kareline tutorials]$ <b>which mpiexec</b></tt><b><tt><br>
</tt></b><b><tt>/opt/openmpi173-GCC48-node/bin/mpiexec</tt></b><tt><br>
<br>
</tt><tt>[begou@kareline tutorials]$ <b>mpicc --showme</b></tt><b><tt><br>
</tt></b><b><tt>gcc -I/opt/openmpi173-GCC48-node/include -pthread
-L/opt/openmpi173-GCC48-node/lib -lmpi</tt></b><tt><br>
<br>
</tt><tt>[begou@kareline tutorials]$ <b>ldd ./ex19</b></tt><tt><br>
</tt><tt> linux-vdso.so.1 => (0x00007ffe771ea000)</tt><tt><br>
</tt><tt> liblapack.so.3 => /usr/lib64/atlas/liblapack.so.3
(0x00007f5ac8596000)</tt><tt><br>
</tt><tt> libblas.so.3 => /usr/lib64/libblas.so.3
(0x00007f5ac833e000)</tt><tt><br>
</tt><tt> libX11.so.6 => /usr/lib64/libX11.so.6
(0x0000003c66600000)</tt><tt><br>
</tt><tt> libhwloc.so.5 => /usr/lib64/libhwloc.so.5
(0x0000003dde600000)</tt><tt><br>
</tt><tt> libssl.so.10 => /usr/lib64/libssl.so.10
(0x0000003c71600000)</tt><tt><br>
</tt><tt> libcrypto.so.10 => /usr/lib64/libcrypto.so.10
(0x0000003c69a00000)</tt><tt><br>
</tt><tt> libmpi_usempi.so.1 => <b>/opt/openmpi173-GCC48-node/lib/libmpi_usempi.so.1</b>
(0x00007f5ac80a4000)</tt><tt><br>
</tt><tt> libmpi_mpifh.so.2 => <b>/opt/openmpi173-GCC48-node/lib/libmpi_mpifh.so.2</b>
(0x00007f5ac7e5a000)</tt><tt><br>
</tt><tt> libgfortran.so.3 =>
/opt/GCC48c/lib64/libgfortran.so.3 (0x00007f5ac7b43000)</tt><tt><br>
</tt><tt> libm.so.6 => /lib64/libm.so.6 (0x0000003c63200000)</tt><tt><br>
</tt><tt> libquadmath.so.0 =>
/opt/GCC48c/lib64/libquadmath.so.0 (0x00007f5ac7907000)</tt><tt><br>
</tt><tt> libmpi_cxx.so.1 => <b>/opt/openmpi173-GCC48-node/lib/libmpi_cxx.so.1</b>
(0x00007f5ac76ed000)</tt><tt><br>
</tt><tt> libstdc++.so.6 => /opt/GCC48c/lib64/libstdc++.so.6
(0x00007f5ac73e4000)</tt><tt><br>
</tt><tt> libdl.so.2 => /lib64/libdl.so.2 (0x0000003c63a00000)</tt><tt><br>
</tt><tt> libmpi.so.1 => <b>/opt/openmpi173-GCC48-node/lib/libmpi.so.1</b>
(0x00007f5ac7115000)</tt><tt><br>
</tt><tt> libgcc_s.so.1 => /opt/GCC48c/lib64/libgcc_s.so.1
(0x00007f5ac6eff000)</tt><tt><br>
</tt><tt> libpthread.so.0 => /lib64/libpthread.so.0
(0x0000003c63600000)</tt><tt><br>
</tt><tt> libc.so.6 => /lib64/libc.so.6 (0x0000003c62e00000)</tt><tt><br>
</tt><tt> libf77blas.so.3 => /usr/lib64/atlas/libf77blas.so.3
(0x00007f5ac6cdf000)</tt><tt><br>
</tt><tt> libcblas.so.3 => /usr/lib64/atlas/libcblas.so.3
(0x00007f5ac6abe000)</tt><tt><br>
</tt><tt> libxcb.so.1 => /usr/lib64/libxcb.so.1
(0x0000003c66200000)</tt><tt><br>
</tt><tt> libnuma.so.1 => /usr/lib64/libnuma.so.1
(0x0000003ddee00000)</tt><tt><br>
</tt><tt> libpci.so.3 => /lib64/libpci.so.3
(0x0000003ddea00000)</tt><tt><br>
</tt><tt> libxml2.so.2 => /usr/lib64/libxml2.so.2
(0x0000003c6e200000)</tt><tt><br>
</tt><tt> libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2
(0x0000003c70a00000)</tt><tt><br>
</tt><tt> libkrb5.so.3 => /lib64/libkrb5.so.3
(0x0000003c70e00000)</tt><tt><br>
</tt><tt> libcom_err.so.2 => /lib64/libcom_err.so.2
(0x0000003c69e00000)</tt><tt><br>
</tt><tt> libk5crypto.so.3 => /lib64/libk5crypto.so.3
(0x0000003c6f200000)</tt><tt><br>
</tt><tt> libz.so.1 => /lib64/libz.so.1 (0x0000003c64200000)</tt><tt><br>
</tt><tt> libopen-rte.so.6 => <b>/opt/openmpi173-GCC48-node/lib/libopen-rte.so.6</b>
(0x00007f5ac684a000)</tt><tt><br>
</tt><tt> libopen-pal.so.6 => <b>/opt/openmpi173-GCC48-node/lib/libopen-pal.so.6</b>
(0x00007f5ac6575000)</tt><tt><br>
</tt><tt> librt.so.1 => /lib64/librt.so.1 (0x0000003c63e00000)</tt><tt><br>
</tt><tt> libnsl.so.1 => /lib64/libnsl.so.1
(0x0000003c71a00000)</tt><tt><br>
</tt><tt> libutil.so.1 => /lib64/libutil.so.1
(0x0000003c6ba00000)</tt><tt><br>
</tt><tt> /lib64/ld-linux-x86-64.so.2 (0x0000003c62a00000)</tt><tt><br>
</tt><tt> libatlas.so.3 => /usr/lib64/atlas/libatlas.so.3
(0x00007f5ac5f18000)</tt><tt><br>
</tt><tt> libXau.so.6 => /usr/lib64/libXau.so.6
(0x0000003c66a00000)</tt><tt><br>
</tt><tt> libresolv.so.2 => /lib64/libresolv.so.2
(0x0000003c64e00000)</tt><tt><br>
</tt><tt> libkrb5support.so.0 => /lib64/libkrb5support.so.0
(0x0000003c6fe00000)</tt><tt><br>
</tt><tt> libkeyutils.so.1 => /lib64/libkeyutils.so.1
(0x0000003c6f600000)</tt><tt><br>
</tt><tt> libselinux.so.1 => /lib64/libselinux.so.1
(0x0000003c64600000)</tt><tt><br>
</tt><tt><br>
</tt><br>
Matthew Knepley a écrit :
<blockquote type="cite">
<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"><a class="moz-txt-link-abbreviated" href="mailto:Patrick.Begou@legi.grenoble-inp.fr">Patrick.Begou@legi.grenoble-inp.fr</a></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 class="moz-txt-link-abbreviated" href="mailto:Patrick.Begou@legi.grenoble">Patrick.Begou@legi.grenoble</a>-<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>
-- <br>
==============================<wbr>==============================<wbr>=======<br>
| Equipe M.O.S.T. |
|<br>
| Patrick BEGOU | mailto:<a
href="mailto:Patrick.Begou@grenoble-inp.fr"
target="_blank">Patrick.Begou@grenoble-<wbr>inp.fr</a>
|<br>
| LEGI |
|<br>
| BP 53 X | Tel 04 76
82 51 35 |<br>
| 38041 GRENOBLE CEDEX | Fax 04 76
82 52 71 |<br>
==============================<wbr>==============================<wbr>=======<br>
<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>
<div>
</div>--
<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.
-- Norbert Wiener</div>
</div></div>
</blockquote>
<pre class="moz-signature" cols="80">--
===================================================================
| Equipe M.O.S.T. | |
| Patrick BEGOU | <a class="moz-txt-link-freetext" href="mailto:Patrick.Begou@grenoble-inp.fr">mailto:Patrick.Begou@grenoble-inp.fr</a> |
| LEGI | |
| BP 53 X | Tel 04 76 82 51 35 |
| 38041 GRENOBLE CEDEX | Fax 04 76 82 52 71 |
===================================================================
</pre></body></html>