[yt-users] Problems with rockstar halo finding
Jullian Santos
jullianhbsantos at gmail.com
Tue Jun 7 11:35:20 PDT 2016
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
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