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Subject: [OMPI users] python-mrmpi() failed
From: mariana Vargas (mmarianav_at_[hidden])
Date: 2012-09-04 15:09:00


Hi

I 'am new in this, I have some codes that use mpi for python and I
just installed (openmpi, mrmpi, mpi4py) in my home (from a cluster
account) without apparent errors and I tried to perform this simple
test in python and I get the following error related with openmpi,
could you help to figure out what is going on? I attach as many
informations as possible...

Thanks.

Mariana

 From a python console
>>> from mrmpi import mrmpi
>>> mr=mrmpi()
[ferrari:23417] mca: base: component_find: unable to open /home/
mvargas/lib/openmpi/mca_paffinity_hwloc: /home/mvargas/lib/openmpi/
mca_paffinity_hwloc.so: undefined symbol: opal_hwloc_topology (ignored)
[ferrari:23417] mca: base: component_find: unable to open /home/
mvargas/lib/openmpi/mca_carto_auto_detect: /home/mvargas/lib/openmpi/
mca_carto_auto_detect.so: undefined symbol:
opal_carto_base_graph_get_host_graph_fn (ignored)
[ferrari:23417] mca: base: component_find: unable to open /home/
mvargas/lib/openmpi/mca_carto_file: /home/mvargas/lib/openmpi/
mca_carto_file.so: undefined symbol:
opal_carto_base_graph_get_host_graph_fn (ignored)
[ferrari:23417] mca: base: component_find: unable to open /home/
mvargas/lib/openmpi/mca_shmem_mmap: /home/mvargas/lib/openmpi/
mca_shmem_mmap.so: undefined symbol: opal_show_help (ignored)
[ferrari:23417] mca: base: component_find: unable to open /home/
mvargas/lib/openmpi/mca_shmem_posix: /home/mvargas/lib/openmpi/
mca_shmem_posix.so: undefined symbol: opal_show_help (ignored)
[ferrari:23417] mca: base: component_find: unable to open /home/
mvargas/lib/openmpi/mca_shmem_sysv: /home/mvargas/lib/openmpi/
mca_shmem_sysv.so: undefined symbol: opal_show_help (ignored)
--------------------------------------------------------------------------
It looks like opal_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during opal_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  opal_shmem_base_select failed
  --> Returned value -1 instead of OPAL_SUCCESS
--------------------------------------------------------------------------
[ferrari:23417] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file
runtime/orte_init.c at line 79
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or
environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):

  ompi_mpi_init: orte_init failed
  --> Returned "Error" (-1) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL: your MPI job will now abort
[ferrari:23417] Local abort before MPI_INIT completed successfully;
not able to aggregate error messages, and not able to guarantee that
all other processes were killed!

echo $PATH

/home/mvargas/idl/pro/LibsSDSSS/idlutilsv5_4_15/bin:/usr/local/itt/
idl70/bin:/opt/local/bin:/home/mvargas/bin:/home/mvargas/lib:/home/
mvargas/lib/openmpi/:/home/mvargas:/home/vargas/bin/:/home/mvargas/idl/
pro/LibsSDSSS/idlutilsv5_4_15/bin:/usr/local/itt/idl70/bin:/opt/local/
bin:/home/mvargas/bin:/home/mvargas/lib:/home/mvargas/lib/openmpi/:/
home/mvargas:/home/vargas/bin/:/usr/lib64/qt3.3/bin:/usr/kerberos/bin:/
usr/local/bin:/bin:/usr/bin:/opt/pbs/bin:/opt/pbs/lib/xpbs/bin:/opt/
envswitcher/bin:/opt/pvm3/lib:/opt/pvm3/lib/LINUX64:/opt/pvm3/bin/
LINUX64:/opt/c3-4/

echo $LD_LIBRARY_PATH
/usr/local/mpich2/lib:/home/mvargas/lib:/home/mvargas/:/home/mvargas/
lib64:/home/mvargas/lib/openmpi/:/usr/lib64/openmpi/1.4-gcc/lib/:/user/
local/:/usr/local/mpich2/lib:/home/mvargas/lib:/home/mvargas/:/home/
mvargas/lib64:/home/mvargas/lib/openmpi/:/usr/lib64/openmpi/1.4-gcc/
lib/:/user/local/:

Version: openmpi-1.6


mpirun --bynode --tag-output ompi_info -v ompi full --parsable
[1,0]<stdout>:package:Open MPI mvargas_at_ferrari Distribution
[1,0]<stdout>:ompi:version:full:1.6
[1,0]<stdout>:ompi:version:svn:r26429
[1,0]<stdout>:ompi:version:release_date:May 10, 2012
[1,0]<stdout>:orte:version:full:1.6
[1,0]<stdout>:orte:version:svn:r26429
[1,0]<stdout>:orte:version:release_date:May 10, 2012
[1,0]<stdout>:opal:version:full:1.6
[1,0]<stdout>:opal:version:svn:r26429
[1,0]<stdout>:opal:version:release_date:May 10, 2012
[1,0]<stdout>:mpi-api:version:full:2.1
[1,0]<stdout>:ident:1.6

eth0 Link encap:Ethernet HWaddr 00:30:48:95:99:CC
         inet addr:192.168.2.1 Bcast:192.168.2.255 Mask:255.255.255.0
         inet6 addr: fe80::230:48ff:fe95:99cc/64 Scope:Link
         UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1
         RX packets:4739875255 errors:0 dropped:1636 overruns:0 frame:0
         TX packets:5196871012 errors:0 dropped:0 overruns:0 carrier:0
         collisions:0 txqueuelen:1000
         RX bytes:4959384349297 (4.5 TiB) TX bytes:3933641883577 (3.5
TiB)
         Memory:ef300000-ef320000

eth1 Link encap:Ethernet HWaddr 00:30:48:95:99:CD
         inet addr:128.2.116.104 Bcast:128.2.119.255 Mask:
255.255.248.0
         inet6 addr: fe80::230:48ff:fe95:99cd/64 Scope:Link
         UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1
         RX packets:2645952109 errors:0 dropped:13353 overruns:0 frame:0
         TX packets:2974763570 errors:0 dropped:0 overruns:0 carrier:0
         collisions:0 txqueuelen:1000
         RX bytes:2024044043824 (1.8 TiB) TX bytes:3390935387820 (3.0
TiB)
         Memory:ef400000-ef420000

lo Link encap:Local Loopback
         inet addr:127.0.0.1 Mask:255.0.0.0
         inet6 addr: ::1/128 Scope:Host
         UP LOOPBACK RUNNING MTU:16436 Metric:1
         RX packets:143359307 errors:0 dropped:0 overruns:0 frame:0
         TX packets:143359307 errors:0 dropped:0 overruns:0 carrier:0
         collisions:0 txqueuelen:0
         RX bytes:80413513464 (74.8 GiB) TX bytes:80413513464 (74.8
GiB)