[yt-users] Problems with rockstar halo finding
Jullian Santos
jullianhbsantos at gmail.com
Mon Jun 13 11:19:08 PDT 2016
Hi,
I tried with python 2 and I received:
File
"/home/jullian/.local/lib/python2.7/site-packages/yt-3.2.3-py2.7-linux-x86_64.egg/yt/__init__.py",
line 108, in <module>
from yt.fields.api import \
File
"/home/jullian/.local/lib/python2.7/site-packages/yt-3.2.3-py2.7-linux-x86_64.egg/yt/fields/api.py",
line 19, in <module>
from . import angular_momentum
File
"/home/jullian/.local/lib/python2.7/site-packages/yt-3.2.3-py2.7-linux-x86_64.egg/yt/fields/angular_momentum.py",
line 31, in <module>
from .vector_operations import \
File
"/home/jullian/.local/lib/python2.7/site-packages/yt-3.2.3-py2.7-linux-x86_64.egg/yt/fields/vector_operations.py",
line 31, in <module>
from yt.utilities.lib.misc_utilities import obtain_rv_vec
ImportError:
/home/jullian/.local/lib/python2.7/site-packages/yt-3.2.3-py2.7-linux-x86_64.egg/yt/utilities/lib/misc_utilities.so:
undefined symbol: PyUnicodeUCS4_DecodeUTF8
Traceback (most recent call last):
File "/home/jullian/ABinitio/Out/DD0050/halo_rockstar.py", line 12, in
<module>
import yt
File
"/home/jullian/.local/lib/python2.7/site-packages/yt-3.2.3-py2.7-linux-x86_64.egg/yt/__init__.py",
line 108, in <module>
from yt.fields.api import \
File
"/home/jullian/.local/lib/python2.7/site-packages/yt-3.2.3-py2.7-linux-x86_64.egg/yt/fields/api.py",
line 19, in <module>
from . import angular_momentum
File
"/home/jullian/.local/lib/python2.7/site-packages/yt-3.2.3-py2.7-linux-x86_64.egg/yt/fields/angular_momentum.py",
line 31, in <module>
from .vector_operations import \
File
"/home/jullian/.local/lib/python2.7/site-packages/yt-3.2.3-py2.7-linux-x86_64.egg/yt/fields/vector_operations.py",
line 31, in <module>
from yt.utilities.lib.misc_utilities import obtain_rv_vec
ImportError:
/home/jullian/.local/lib/python2.7/site-packages/yt-3.2.3-py2.7-linux-x86_64.egg/yt/utilities/lib/misc_utilities.so:
undefined symbol: PyUnicodeUCS4_DecodeUTF8
I installed yt-x86-64 by the All-in-One Installation Script and I don't
know how to change PyUnicode and rebuild. Do you have some guess to me?
Thanks
2016-06-09 12:02 GMT-03:00 Matthew Turk <matthewturk at gmail.com>:
> Hi Jullian,
>
> My guess from reading is that there's a python3 incompatibility
> specifically in the Rockstar code interface that yt provides. I
> believe that it should be fixable, but right now I don't have the
> setup to check it. If you file a bug we will mark it as a blocker and
> then return to it before the impending 3.3 release of yt; I'm sorry to
> not have better news right now. It should work on Python2, but for
> Python3 there is some location where the unicode/non-unicode decoding
> needs to happen to move between python strings and char*.
>
> -Matt
>
> On Tue, Jun 7, 2016 at 11:35 AM, Jullian Santos
> <jullianhbsantos at gmail.com> wrote:
> > Hello,
> > My name is Jullian Santos, I am a Ph.D. student of the University of São
> > Paulo, Brazil, and I am having some troubles with the Rockstar halo
> finding
> > function.
> >
> >
> > I tried to run a test analyses given by yt-project page (the link is
> below,
> > I only modified the file to be opened) but the job always finish in
> error. I
> > submitted the job in my own machine with the command:
> >
> >
> > #PBS -S /bin/bash
> > #PBS -l nodes=4
> > #PBS -e /sto/home/jullian/M2.e.txt
> > #PBS -o /sto/home/jullian/M2.o.txt
> > #PBS -V
> >
> >
> > mpirun -n 4 $PBS_NODEFILE python3
> > "/home/jullian/ABinitio/Out/DD0050/halo_rockstar.py"
> >
> > and the program returned:
> >
> > writers
> > P001 yt : [WARNING ] 2016-06-07 14:46:19,708 Total Particle Count:
> > 1.125e+06
> > File "/home/jullian/ABinitio/Out/DD0050/halo_rockstar.py", line 62, in
> > <module>
> > hc.create()
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",
> > line 293, in create
> > self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
> > line 305, in barrierize
> > retval = func(*args, **kwargs)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",
> > line 362, in _run
> > self.halos_ds = self.finder_method(self.data_ds)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py",
> > line 46, in __call__
> > return self.function(ds, *self.args, **self.kwargs)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py",
> > line 79, in _rockstar_method
> > rh.run()
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py",
> > line 348, in run
> > min_halo_size = self.min_halo_size)
> > File
> "yt/analysis_modules/halo_finding/rockstar/rockstar_interface.pyx",
> > line 254, in
> >
> yt.analysis_modules.halo_finding.rockstar.rockstar_interface.RockstarInterface.setup_rockstar
> > (yt/analysis_modules/halo_finding/rockstar/rockstar_interface.c:3785)
> > P002 yt : [ERROR ] 2016-06-07 14:46:19,758 TypeError: expected bytes,
> str
> > found
> > File "/home/jullian/ABinitio/Out/DD0050/halo_rockstar.py", line 62, in
> > <module>
> > hc.create()
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",
> > line 293, in create
> > self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
> > line 305, in barrierize
> > retval = func(*args, **kwargs)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",
> > line 362, in _run
> > self.halos_ds = self.finder_method(self.data_ds)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py",
> > line 46, in __call__
> > return self.function(ds, *self.args, **self.kwargs)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py",
> > line 79, in _rockstar_method
> > rh.run()
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py",
> > line 348, in run
> > min_halo_size = self.min_halo_size)
> > File
> "yt/analysis_modules/halo_finding/rockstar/rockstar_interface.pyx",
> > line 254, in
> >
> yt.analysis_modules.halo_finding.rockstar.rockstar_interface.RockstarInterface.setup_rockstar
> > (yt/analysis_modules/halo_finding/rockstar/rockstar_interface.c:3785)
> > P003 yt : [ERROR ] 2016-06-07 14:46:19,758 TypeError: expected bytes,
> str
> > found
> > P002 yt : [ERROR ] 2016-06-07 14:46:19,759 Error occured on rank 0.
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
> > P003 yt : [ERROR ] 2016-06-07 14:46:19,759 Error occured on rank 1.
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
> > File "/home/jullian/ABinitio/Out/DD0050/halo_rockstar.py", line 62, in
> > <module>
> > hc.create()
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",
> > line 293, in create
> > self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
> > line 305, in barrierize
> > retval = func(*args, **kwargs)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",
> > line 362, in _run
> > self.halos_ds = self.finder_method(self.data_ds)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py",
> > line 46, in __call__
> > return self.function(ds, *self.args, **self.kwargs)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py",
> > line 79, in _rockstar_method
> > rh.run()
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py",
> > line 348, in run
> > min_halo_size = self.min_halo_size)
> > File
> "yt/analysis_modules/halo_finding/rockstar/rockstar_interface.pyx",
> > line 254, in
> >
> yt.analysis_modules.halo_finding.rockstar.rockstar_interface.RockstarInterface.setup_rockstar
> > (yt/analysis_modules/halo_finding/rockstar/rockstar_interface.c:3785)
> > P000 yt : [ERROR ] 2016-06-07 14:46:19,761 TypeError: expected bytes,
> str
> > found
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> > File "/home/jullian/ABinitio/Out/DD0050/halo_rockstar.py", line 62, in
> > <module>
> > hc.create()
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",
> > line 293, in create
> > self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
> > line 305, in barrierize
> > retval = func(*args, **kwargs)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",
> > line 362, in _run
> > self.halos_ds = self.finder_method(self.data_ds)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py",
> > line 46, in __call__
> > return self.function(ds, *self.args, **self.kwargs)
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py",
> > line 79, in _rockstar_method
> > rh.run()
> > File
> >
> "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py",
> > line 348, in run
> > min_halo_size = self.min_halo_size)
> > File
> "yt/analysis_modules/halo_finding/rockstar/rockstar_interface.pyx",
> > line 254, in
> >
> yt.analysis_modules.halo_finding.rockstar.rockstar_interface.RockstarInterface.setup_rockstar
> > (yt/analysis_modules/halo_finding/rockstar/rockstar_interface.c:3785)
> > P001 yt : [ERROR ] 2016-06-07 14:46:19,761 TypeError: expected bytes,
> str
> > found
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
> >
> >
> ===================================================================================
> > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> > = EXIT CODE: 1
> > = CLEANING UP REMAINING PROCESSES
> > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> >
> ===================================================================================
> >
> >
> ===================================================================================
> > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> > = EXIT CODE: 1
> > = CLEANING UP REMAINING PROCESSES
> > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> >
> ===================================================================================
> >
> >
> >
> > If I try to run with the command suggested in the yt page (mpirun -n 4
> > $PBS_NODEFILE --mca btl ^openib python3
> > "/home/jullian/ABinitio/Out/DD0050/halo_rockstar.py" --parallel) I get:
> >
> > [mpiexec at julian-ubuntu] match_arg (./utils/args/args.c:160):
> unrecognized
> > argument mca
> > [mpiexec at julian-ubuntu] HYDU_parse_array (./utils/args/args.c:175):
> argument
> > matching returned error
> > [mpiexec at julian-ubuntu] parse_args (./ui/mpich/utils.c:1609): error
> parsing
> > input array
> > [mpiexec at julian-ubuntu] HYD_uii_mpx_get_parameters
> > (./ui/mpich/utils.c:1660): unable to parse user arguments
> > [mpiexec at julian-ubuntu] main (./ui/mpich/mpiexec.c:153): error parsing
> > parameters
> >
> > How could I fix this problem? Do I have to launch the script in some
> remote
> > machine? Do I have to use the IPython?
> >
> >
> > Thanks by the attention,
> >
> > Best Regards,
> >
> > Jullian
> >
> >
> > Script link:
> >
> http://yt-project.org/doc/cookbook/cosmological_analysis.html#running-rockstar-to-find-halos-on-multi-resolution-particle-datasets
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
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