Sorry, if I execute mpirun in a *really *bare terminal, without X
Server running it works! but with an error message :
Invalid MIT-MAGIC-COOKIE-1 key
So the problem is related to X, but I have still no solution
Jorge
Le 14/11/2020 à 12:33, Jorge Silva via users a écrit :
Hello,
In spite of the delay, I was not able to solve my problem. Thanks to
Joseph and Prentice for their interesting suggestions.
I uninstalled AppAmor (SElinux is not installed ) as suggested by
Prentice but there were no changes, mpirun sttill hangs.
The result of gdb stack trace is the following:
$ sudo gdb -batch -ex "thread apply all bt" -p $(ps -C mpirun -o pid=
| head -n 1)
[Thread debugging using libthread_db enabled]
Using host libthread_db library
"/lib/x86_64-linux-gnu/libthread_db.so.1".
0x00007f9289544307 in __libc_connect (fd=9, addr=..., len=16) at
../sysdeps/unix/sysv/linux/connect.c:26
26 ../sysdeps/unix/sysv/linux/connect.c: Aucun fichier ou dossier
de ce type.
Thread 1 (Thread 0x7f92891f4e80 (LWP 4948)):
#0 0x00007f9289544307 in __libc_connect (fd=9, addr=..., len=16) at
../sysdeps/unix/sysv/linux/connect.c:26
#1 0x00007f9288fff59d in ?? () from /lib/x86_64-linux-gnu/libxcb.so.1
#2 0x00007f9288fffc49 in xcb_connect_to_display_with_auth_info ()
from /lib/x86_64-linux-gnu/libxcb.so.1
#3 0x00007f928906cb7a in _XConnectXCB () from
/lib/x86_64-linux-gnu/libX11.so.6
#4 0x00007f928905d319 in XOpenDisplay () from
/lib/x86_64-linux-gnu/libX11.so.6
#5 0x00007f92897de4fb in ?? () from
/usr/lib/x86_64-linux-gnu/hwloc/hwloc_gl.so
#6 0x00007f92893b901e in ?? () from /lib/x86_64-linux-gnu/libhwloc.so.15
#7 0x00007f92893c13a0 in hwloc_topology_load () from
/lib/x86_64-linux-gnu/libhwloc.so.15
#8 0x00007f92896df564 in opal_hwloc_base_get_topology () from
/lib/x86_64-linux-gnu/libopen-pal.so.40
#9 0x00007f92891da6be in ?? () from
/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_hnp.so
#10 0x00007f92897a22fc in orte_init () from
/lib/x86_64-linux-gnu/libopen-rte.so.40
#11 0x00007f92897a6c86 in orte_submit_init () from
/lib/x86_64-linux-gnu/libopen-rte.so.40
#12 0x000055819fd0b3a3 in ?? ()
#13 0x00007f92894480b3 in __libc_start_main (main=0x55819fd0b1c0,
argc=1, argv=0x7fff5334fe48, init=<optimized out>, fini=<optimized
out>, rtld_fini=<optimized out>, stack_end=0x7fff5334fe38) at
../csu/libc-start.c:308
#14 0x000055819fd0b1fe in ?? ()
[Inferior 1 (process 4948) detached]
So it seems to be a problem in the connection via libxcb (socket ?)
but this is out of my system computer skills.. Is there any
authorization needed?
As is libX11 at the origin of the call I tried to execute in a bare
terminal (ctrl-alt-f2 and via ssh) but the message is the same. I
tried to recompile/install the hole package and have the same result.
Thank you for your help.
Jorge
Le 22/10/2020 à 12:16, Joseph Schuchart via users a écrit :
Hi Jorge,
Can you try to get a stack trace of mpirun using the following
command in a separate terminal?
sudo gdb -batch -ex "thread apply all bt" -p $(ps -C mpirun -o pid= |
head -n 1)
Maybe that will give some insight where mpirun is hanging.
Cheers,
Joseph
On 10/21/20 9:58 PM, Jorge SILVA via users wrote:
Hello Jeff,
The program is not executed, seems waits for something to connect
with (why twice ctrl-C ?)
jorge@gcp26:~/MPIRUN$ mpirun -np 1 touch /tmp/foo
^C^C
jorge@gcp26:~/MPIRUN$ ls -l /tmp/foo
ls: impossible d'accéder à '/tmp/foo': Aucun fichier ou dossier de
ce type
no file is created..
In fact, my question was if are there differences in mpirun usage
between these versions.. The
mpirun -help
gives a different output as expected, but I tried a lot of options
without any success.
Le 21/10/2020 à 21:16, Jeff Squyres (jsquyres) a écrit :
There's huge differences between Open MPI v2.1.1 and v4.0.3 (i.e.,
years of development effort); it would be very hard to categorize
them all; sorry!
What happens if you
mpirun -np 1 touch /tmp/foo
(Yes, you can run non-MPI apps through mpirun)
Is /tmp/foo created? (i.e., did the job run, and mpirun is somehow
not terminating)
On Oct 21, 2020, at 12:22 PM, Jorge SILVA via users
<users@lists.open-mpi.org <mailto:users@lists.open-mpi.org>> wrote:
Hello Gus,
Thank you for your answer.. Unfortunately my problem is much
more basic. I didn't try to run the program in both computers ,
but just to run something in one computer. I just installed the
new OS an openmpi in two different computers, in the standard way,
with the same result.
For example:
In kubuntu20.4.1 LTS with openmpi 4.0.3-0ubuntu
jorge@gcp26:~/MPIRUN$ cat hello.f90
print*,"Hello World!"
end
jorge@gcp26:~/MPIRUN$ mpif90 hello.f90 -o hello
jorge@gcp26:~/MPIRUN$ ./hello
Hello World!
jorge@gcp26:~/MPIRUN$ mpirun -np 1 hello <---here the program
hangs with no output
^C^Cjorge@gcp26:~/MPIRUN$
The mpirun task sleeps with no output, and only twice ctrl-C ends
the execution :
jorge 5540 0.1 0.0 44768 8472 pts/8 S+ 17:54 0:00
mpirun -np 1 hello
In kubuntu 18.04.5 LTS with openmpi 2.1.1, of course, the same
program gives
jorge@gcp30:~/MPIRUN$ cat hello.f90
print*, "Hello World!"
END
jorge@gcp30:~/MPIRUN$ mpif90 hello.f90 -o hello
jorge@gcp30:~/MPIRUN$ ./hello
Hello World!
jorge@gcp30:~/MPIRUN$ mpirun -np 1 hello
Hello World
jorge@gcp30:~/MPIRUN$
Even just typing mpirun hangs without the usual error message.
Are there any changes between the two versions of openmpi that I
miss? Some package lacking to mpirun ?
Thank you again for your help
Jorge
Le 21/10/2020 à 00:20, Gus Correa a écrit :
Hi Jorge
You may have an active firewall protecting either computer or both,
and preventing mpirun to start the connection.
Your /etc/hosts file may also not have the computer IP addresses.
You may also want to try the --hostfile option.
Likewise, the --verbose option may also help diagnose the problem.
It would help if you send the mpirun command line, the hostfile
(if any),
error message if any, etc.
These FAQs may help diagnose and solve the problem:
https://www.open-mpi.org/faq/?category=running#diagnose-multi-host-problems
https://www.open-mpi.org/faq/?category=running#mpirun-hostfile
https://www.open-mpi.org/faq/?category=running
I hope this helps,
Gus Correa
On Tue, Oct 20, 2020 at 4:47 PM Jorge SILVA via users
<users@lists.open-mpi.org <mailto:users@lists.open-mpi.org>> wrote:
Hello,
I installed kubuntu20.4.1 with openmpi 4.0.3-0ubuntu in two
different
computers in the standard way. Compiling with mpif90 works, but
mpirun
hangs with no output in both systems. Even mpirun command
without
parameters hangs and only twice ctrl-C typing can end the
sleeping
program. Only the command
mpirun --help
gives the usual output.
Seems that is something related to the terminal output, but the
command
worked well for Kubuntu 18.04. Is there a way to debug or fix
this
problem (without re-compiling from sources, etc)? Is it a known
problem?
Thanks,
Jorge
--
Jeff Squyres
jsquy...@cisco.com <mailto:jsquy...@cisco.com>
