Hello,
I just installed PyFR 0.8.0.
The 2d euler vortex example is working perfectly with Intel MPI 15, but I
am having issues trying to run it with OpenMPI. (I tried with
OpenMPI 1.8.5 and 1.8.1).
This is the error I am getting:
bash-4.2$ pyfr import euler_vortex_2d.msh euler_vortex_2d.pyfrm
bash-4.2$ pyfr partition 2 euler_vortex_2d.pyfrm .
bash-4.2$ mpirun -n 2 pyfr run -p euler_vortex_2d.pyfrm euler_vortex_2d.ini
Traceback (most recent call last):
File "/ssd/apps/python-3.4.3/bin/pyfr", line 9, in <module>
load_entry_point('pyfr==0.8.0', 'console_scripts', 'pyfr')()
File
"/ssd/apps/python-3.4.3/lib/python3.4/site-packages/mpmath/ctx_mp.py", line
1301, in g
return f(*args, **kwargs)
File
"/ssd/apps/python-3.4.3/lib/python3.4/site-packages/pyfr-0.8.0-py3.4.egg/pyfr/scripts/main.py",
line 126, in main
File
"/ssd/apps/python-3.4.3/lib/python3.4/site-packages/pyfr-0.8.0-py3.4.egg/pyfr/scripts/main.py",
line 247, in process_run
File
"/ssd/apps/python-3.4.3/lib/python3.4/site-packages/pyfr-0.8.0-py3.4.egg/pyfr/scripts/main.py",
line 228, in _process_common
File
"/ssd/apps/python-3.4.3/lib/python3.4/site-packages/pyfr-0.8.0-py3.4.egg/pyfr/rank_allocator.py",
line 14, in get_rank_allocation
File
"/ssd/apps/python-3.4.3/lib/python3.4/site-packages/pyfr-0.8.0-py3.4.egg/pyfr/rank_allocator.py",
line 32, in __init__
RuntimeError: Mesh has 2 partitions but running with 1 MPI ranks
Traceback (most recent call last):
File "/ssd/apps/python-3.4.3/bin/pyfr", line 9, in <module>
load_entry_point('pyfr==0.8.0', 'console_scripts', 'pyfr')()
File
"/ssd/apps/python-3.4.3/lib/python3.4/site-packages/mpmath/ctx_mp.py", line
1301, in g
return f(*args, **kwargs)
File
"/ssd/apps/python-3.4.3/lib/python3.4/site-packages/pyfr-0.8.0-py3.4.egg/pyfr/scripts/main.py",
line 126, in main
File
"/ssd/apps/python-3.4.3/lib/python3.4/site-packages/pyfr-0.8.0-py3.4.egg/pyfr/scripts/main.py",
line 247, in process_run
File
"/ssd/apps/python-3.4.3/lib/python3.4/site-packages/pyfr-0.8.0-py3.4.egg/pyfr/scripts/main.py",
line 228, in _process_common
File
"/ssd/apps/python-3.4.3/lib/python3.4/site-packages/pyfr-0.8.0-py3.4.egg/pyfr/rank_allocator.py",
line 14, in get_rank_allocation
File
"/ssd/apps/python-3.4.3/lib/python3.4/site-packages/pyfr-0.8.0-py3.4.egg/pyfr/rank_allocator.py",
line 32, in __init__
RuntimeError: Mesh has 2 partitions but running with 1 MPI ranks
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status,
thus causing
the job to be terminated. The first process to do so was:
Process name: [[41831,1],0]
Exit code: 1
--------------------------------------------------------------------------
It is weird it says it is "running with 1 MPI ranks". These are the
variables defined when mpirun happens:
declare -x MPIHOME="/ssd/apps/openmpi-1.8.1-intel15"
declare -x OMPI_APP_CTX_NUM_PROCS="2"
declare -x OMPI_COMMAND="test.sh"
declare -x OMPI_COMM_WORLD_LOCAL_RANK="0"
declare -x OMPI_COMM_WORLD_LOCAL_SIZE="2"
declare -x OMPI_COMM_WORLD_NODE_RANK="0"
declare -x OMPI_COMM_WORLD_RANK="0"
declare -x OMPI_COMM_WORLD_SIZE="2"
declare -x
OMPI_FILE_LOCATION="/tmp/openmpi-sessions-prestrepo@goethe-0_0/46108/1/0"
declare -x OMPI_FIRST_RANKS="0"
declare -x OMPI_MCA_db="^pmi"
declare -x OMPI_MCA_ess="env"
declare -x OMPI_MCA_ess_base_jobid="3021733889"
declare -x OMPI_MCA_ess_base_vpid="0"
declare -x OMPI_MCA_grpcomm="^pmi"
declare -x
OMPI_MCA_initial_wdir="/ssd/home/prestrepo/PyFR-0.8.0/examples/my-euler_vortex_2d"
declare -x OMPI_MCA_mpi_yield_when_idle="0"
declare -x OMPI_MCA_orte_app_num="0"
declare -x OMPI_MCA_orte_bound_at_launch="1"
declare -x OMPI_MCA_orte_ess_node_rank="0"
declare -x OMPI_MCA_orte_ess_num_procs="2"
declare -x
OMPI_MCA_orte_hnp_uri="3021733888.0;tcp://128.210.9.6,192.168.2.2:40127"
declare -x
OMPI_MCA_orte_local_daemon_uri="3021733888.0;tcp://128.210.9.6,192.168.2.2:40127"
declare -x OMPI_MCA_orte_num_nodes="1"
declare -x OMPI_MCA_orte_num_restarts="0"
declare -x OMPI_MCA_orte_peer_fini_barrier_id="2"
declare -x OMPI_MCA_orte_peer_init_barrier_id="1"
declare -x OMPI_MCA_orte_peer_modex_id="0"
declare -x
OMPI_MCA_orte_precondition_transports="6dc9667b72b7564c-f67f87f2f974c41a"
declare -x OMPI_MCA_orte_tmpdir_base="/tmp"
declare -x OMPI_MCA_pubsub="^pmi"
declare -x OMPI_MCA_shmem_RUNTIME_QUERY_hint="mmap"
declare -x OMPI_NUM_APP_CTX="1"
declare -x OMPI_UNIVERSE_SIZE="1"
declare -x MPIHOME="/ssd/apps/openmpi-1.8.1-intel15"
declare -x OMPI_APP_CTX_NUM_PROCS="2"
declare -x OMPI_COMMAND="test.sh"
declare -x OMPI_COMM_WORLD_LOCAL_RANK="1"
declare -x OMPI_COMM_WORLD_LOCAL_SIZE="2"
declare -x OMPI_COMM_WORLD_NODE_RANK="1"
declare -x OMPI_COMM_WORLD_RANK="1"
declare -x OMPI_COMM_WORLD_SIZE="2"
declare -x
OMPI_FILE_LOCATION="/tmp/openmpi-sessions-prestrepo@goethe-0_0/46108/1/1"
declare -x OMPI_FIRST_RANKS="0"
declare -x OMPI_MCA_db="^pmi"
declare -x OMPI_MCA_ess="env"
declare -x OMPI_MCA_ess_base_jobid="3021733889"
declare -x OMPI_MCA_ess_base_vpid="1"
declare -x OMPI_MCA_grpcomm="^pmi"
declare -x
OMPI_MCA_initial_wdir="/ssd/home/prestrepo/PyFR-0.8.0/examples/my-euler_vortex_2d"
declare -x OMPI_MCA_mpi_yield_when_idle="0"
declare -x OMPI_MCA_orte_app_num="0"
declare -x OMPI_MCA_orte_bound_at_launch="1"
declare -x OMPI_MCA_orte_ess_node_rank="1"
declare -x OMPI_MCA_orte_ess_num_procs="2"
declare -x
OMPI_MCA_orte_hnp_uri="3021733888.0;tcp://128.210.9.6,192.168.2.2:40127"
declare -x
OMPI_MCA_orte_local_daemon_uri="3021733888.0;tcp://128.210.9.6,192.168.2.2:40127"
declare -x OMPI_MCA_orte_num_nodes="1"
declare -x OMPI_MCA_orte_num_restarts="0"
declare -x OMPI_MCA_orte_peer_fini_barrier_id="2"
declare -x OMPI_MCA_orte_peer_init_barrier_id="1"
declare -x OMPI_MCA_orte_peer_modex_id="0"
declare -x
OMPI_MCA_orte_precondition_transports="6dc9667b72b7564c-f67f87f2f974c41a"
declare -x OMPI_MCA_orte_tmpdir_base="/tmp"
declare -x OMPI_MCA_pubsub="^pmi"
declare -x OMPI_MCA_shmem_RUNTIME_QUERY_hint="mmap"
declare -x OMPI_NUM_APP_CTX="1"
declare -x OMPI_UNIVERSE_SIZE="1"
Thank you in advance for your help.
Pablo Restrepo.
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