HiI '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 canfail 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
files.tar.gz
Description: GNU Zip compressed data
mpirun --bynode --tag-output ompi_info -v ompi full --parsable
[1,0]<stdout>:package:Open MPI mvargas@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)
