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Subject: Re: [OMPI users] python-mrmpi() failed
From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2012-09-06 08:05:30


On Sep 4, 2012, at 3:09 PM, mariana Vargas wrote:

> 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...

I think I know what's happening here.

It's a complicated linker issue that we've discussed before -- I'm not sure whether it was on this users list or the OMPI developers list.

The short version is that you should remove your prior Open MPI installation, and then rebuild Open MPI with the --disable-dlopen configure switch. See if that fixes the problem.

> 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)
>
>
>
>
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-- 
Jeff Squyres
jsquyres_at_[hidden]
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