On Thu, August 14, 2008 17:34, Anders Logg wrote:
On Thu, Aug 14, 2008 at 01:44:31PM +0200, Johan Hake wrote:
On Thursday 14 August 2008 09:46:00 Johannes Ring wrote:
On Thu, August 14, 2008 09:42, Anders Logg wrote:
On Thu, Aug 14, 2008 at 08:39:25AM +0100, Garth N. Wells wrote:
Johannes Ring wrote:
On Thu, August 14, 2008 08:52, Garth N. Wells wrote:
Anders Logg wrote:
On Wed, Aug 13, 2008 at 08:03:39PM +0100, Garth N. Wells wrote:
I'm experiencing a puzzling problem wth pyDOLFIN and MPI
again.
When I do
python file.py
where file.py is just
from dolfin import *
object = Function("/tmp/fileKFnQpl.xml")
plot(object)
interactive()
I see a plot as expected, and get
Plot active, press 'q' to continue.
After pressing 'q', I get
*** An error occurred in MPI_Attr_get
*** after MPI was finalized
*** MPI_ERRORS_ARE_FATAL (goodbye)
[gnw20pc:2277] Abort before MPI_INIT completed
successfully;
not
able to guarantee that all other processes were killed!
*** An error occurred in MPI_Comm_rank
*** after MPI was finalized
*** MPI_ERRORS_ARE_FATAL (goodbye)
*** An error occurred in MPI_Type_free
*** after MPI was finalized
*** MPI_ERRORS_ARE_FATAL (goodbye)
Segmentation fault
Somehow, Python appears to be calling MPI_Finalize before
DOLFIN
gets a
chance to finalise things correctly. Any ideas/experience on
how
Python
interacts with MPI? I've commented out MPI_Finalize() in
DOLFIN to
be
sure that DOLFIN is not calling it.
Garth
Would it help if we just call MPI_Finalized to check before
finalizing? We can add a wrapper for it just like for
MPI_Initialized.
I've added some annoying debug output to SubSystemsManager. Can
you
tell
me what you see when running
from dolfin import *
x = PETScVector(10)
When I run it, the first line of output is
MPI status in initPETSc() 1
which indicates that MPI_Initialize is saying that MPI has been
initialised before PETSc is initialised, but we haven't
initialise
it.
The same code in C++ gives
MPI status in initPETSc() 0
which is the expected result.
I get
from dolfin import *
x = PETScVector(10)
MPI status in initPETSc() 0
[simula-x61:17855] mca: base: component_find: unable to open osc
pt2pt:
file not found (ignored)
MPI status in initMPI() 1
Have you compiled Trilinos with MPI support? It seems to be the
same
problems I had with my Ubuntu packages for Trilinos on 64bit.
Turning
off
MPI support for Trilinos fixed the problem for me.
Yes, Trilinos with MPI support was the culprit, even though I
disabled
Trilinos (enableTrilinos=no). Trilinos must be placing some files
in
/usr/local/lib/ which cause a problem which is nasty. Just removing
Trilinos did the trick. Thanks!
Garth
What about the annoying
mca: base: component_find: unable to open osc pt2pt: file not
found
(ignored)
?
I'm not sure how to remove it.
I have a serial version of trilinos 8.0.7 compiled localy on my
computer,
which do not produce this output. See:
<http://www.fenics.org/pipermail/dolfin-dev/2008-June/008442.html>
I don't think this has anything to do with Trilinos. I had it long
time before I installed Trilinos.
Yes, me too, however, I have now found a way to remove the warning. Simply
add the following line to /etc/openmpi/openmpi-mca-params.conf:
mca_component_show_load_errors = 0
The default is 1. I'm not sure if it's safe, but the warning is at least
gone.
BTW: For those who get a similar warning as the one below, it can be
removed by uncommenting the following line in the same file:
btl = ^openib
Johannes
libibverbs: Fatal: couldn't read uverbs ABI version.
--------------------------------------------------------------------------
[0,0,0]: OpenIB on host simula-x61 was unable to find any HCAs.
Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
_______________________________________________
DOLFIN-dev mailing list
DOLFIN-dev@xxxxxxxxxx
http://www.fenics.org/mailman/listinfo/dolfin-dev
