[yt-users] Still having issues with parallel yt on STAMPEDE
Rick Sarmento
rsarment at asu.edu
Tue Jan 20 21:26:22 PST 2015
Hello all,
I still can’t get parallel yt running… please pass along any ideas…
I’ve got the ipcluster running ok … yt 3.1 going — but I’m still getting "AttributeError: 'module' object has no attribute ‘utilities’” when trying to load a RAMSES output file…
Here’s the cluster running..
11:14:02 earnric /home1/02744/earnric $ ipcluster start --engines=MPI
…
2015-01-20 23:14:10.653 [IPClusterStart] Starting 16 Engines with MPI
2015-01-20 23:14:40.657 [IPClusterStart] Engines appear to have started successfully
Here are the modules loaded:
11:21:47 earnric /home1/02744/earnric $ module list
Currently Loaded Modules:
1) TACC-paths 3) cluster-paths 5) cluster 7) intel/14.0.1.106 9) python/2.7.6
2) Linux 4) xalt/0.4.6 6) TACC 8) mvapich2/2.0b 10) hdf5/1.8.13
and my ENVs:
11:22:13 earnric /home1/02744/earnric $ echo $PYTHONPATH
/home1/02744/earnric/.local/lib/python2.7/site-packages/:/opt/apps/intel14/mvapich2_2_0/python/2.7.6/lib/python2.7/site-packages:
11:22:23 earnric /home1/02744/earnric $ echo $PATH
/home1/02744/earnric/.local/bin:/home1/02744/earnric/bin:/opt/apps/intel14/hdf5/1.8.13/x86_64/bin:/opt/apps/intel14/mvapich2_2_0/python/2.7.6/bin:/opt/apps/intel14/mvapich2/2.0b/bin:/opt/apps/intel/13/vtune_amplifier_xe_2013/bin64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/mpirt/bin/intel64:/opt/intel/sep/bin:/opt/apps/xalt/0.4.6/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/opt/ofed/bin:/opt/ofed/sbin:.:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/bin/intel64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/bin/intel64_mic:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/debugger/gui/intel64
11:22:31 earnric /home1/02744/earnric $ echo $LD_LIBRARY_PATH
/opt/apps/intel14/mvapich2_2_0/python/2.7.6/lib:/opt/apps/intel14/mvapich2/2.0b/lib:/opt/apps/intel14/mvapich2/2.0b/lib/shared:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/tbb/lib/intel64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/compiler/lib/intel64:/opt/intel/mic/coi/host-linux-release/lib:/opt/intel/mic/myo/lib:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/mpirt/lib/intel64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/ipp/../compiler/lib/intel64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/ipp/lib/intel64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/compiler/lib/intel64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/mkl/lib/intel64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/tbb/lib/intel64
Here’s what I’m seeing — if you have any ideas I’d appreciate it:
In [1]:
from IPython.parallel import Client
rc = Client()
In [2]:
rc.ids
Out[2]:
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]
In [3]:
%autopx
%autopx enabled
In [4]:
from mpi4py import MPI
MPI.COMM_WORLD.Get_rank()
Out[0:1]: 8
Out[1:1]: 12
Out[2:1]: 9
Out[3:1]: 6
Out[4:1]: 10
Out[5:1]: 1
Out[6:1]: 2
Out[7:1]: 11
Out[8:1]: 13
Out[9:1]: 5
Out[10:1]: 3
Out[11:1]: 14
Out[12:1]: 7
Out[13:1]: 0
Out[14:1]: 15
Out[15:1]: 4
In [7]:
import yt
yt.enable_parallelism()
import numpy as np
import os
import shutil
import h5py
import gc
import glob
[0:execute]:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)<ipython-input-4-34dfdffceb1e> in <module>()
----> 1 import yt
2 yt.enable_parallelism()
3 import numpy as np
4 import os
5 import shutil
/home1/02744/earnric/.local/lib/python2.7/site-packages/yt-3.1dev-py2.7-linux-x86_64.egg/yt/__init__.py in <module>()
97 from yt.utilities.logger import ytLogger as mylog
98
---> 99 import yt.utilities.physical_constants as physical_constants
100 import yt.units as units
101 from yt.units.yt_array import \
AttributeError: 'module' object has no attribute 'utilities'
[1:execute]:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)<ipython-input-4-34dfdffceb1e> in <module>()
----> 1 import yt
2 yt.enable_parallelism()
3 import numpy as np
4 import os
5 import shutil
/home1/02744/earnric/.local/lib/python2.7/site-packages/yt-3.1dev-py2.7-linux-x86_64.egg/yt/__init__.py in <module>()
97 from yt.utilities.logger import ytLogger as mylog
98
---> 99 import yt.utilities.physical_constants as physical_constants
100 import yt.units as units
101 from yt.units.yt_array import \
AttributeError: 'module' object has no attribute 'utilities'
[2:execute]:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)<ipython-input-4-34dfdffceb1e> in <module>()
----> 1 import yt
2 yt.enable_parallelism()
3 import numpy as np
4 import os
5 import shutil
/home1/02744/earnric/.local/lib/python2.7/site-packages/yt-3.1dev-py2.7-linux-x86_64.egg/yt/__init__.py in <module>()
97 from yt.utilities.logger import ytLogger as mylog
98
---> 99 import yt.utilities.physical_constants as physical_constants
100 import yt.units as units
101 from yt.units.yt_array import \
AttributeError: 'module' object has no attribute 'utilities'
[3:execute]:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)<ipython-input-4-34dfdffceb1e> in <module>()
----> 1 import yt
2 yt.enable_parallelism()
3 import numpy as np
4 import os
5 import shutil
/home1/02744/earnric/.local/lib/python2.7/site-packages/yt-3.1dev-py2.7-linux-x86_64.egg/yt/__init__.py in <module>()
97 from yt.utilities.logger import ytLogger as mylog
98
---> 99 import yt.utilities.physical_constants as physical_constants
100 import yt.units as units
101 from yt.units.yt_array import \
AttributeError: 'module' object has no attribute 'utilities'
... 12 more exceptions ...
Cheers!
Rick Sarmento
SESE Astronomy/Astrophysics Grad Student
rsarment at asu.edu
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