<div dir="ltr"><div>Hello, <br>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.<br><br><br></div><div>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:<br><br><br>#PBS -S /bin/bash<br>#PBS -l nodes=4<br>#PBS -e /sto/home/jullian/M2.e.txt<br>#PBS -o /sto/home/jullian/M2.o.txt<br>#PBS -V<br><br><br>mpirun -n 4 $PBS_NODEFILE python3 "/home/jullian/ABinitio/Out/DD0050/halo_rockstar.py" <br><br></div><div>and the program returned:<br><br>writers<br>P001 yt : [WARNING ] 2016-06-07 14:46:19,708 Total Particle Count: 1.125e+06<br> File "/home/jullian/ABinitio/Out/DD0050/halo_rockstar.py", line 62, in <module><br> hc.create()<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py", line 293, in create<br> self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 305, in barrierize<br> retval = func(*args, **kwargs)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py", line 362, in _run<br> self.halos_ds = self.finder_method(self.data_ds)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py", line 46, in __call__<br> return self.function(ds, *self.args, **self.kwargs)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py", line 79, in _rockstar_method<br> rh.run()<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 348, in run<br> min_halo_size = self.min_halo_size)<br> 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)<br>P002 yt : [ERROR ] 2016-06-07 14:46:19,758 TypeError: expected bytes, str found<br> File "/home/jullian/ABinitio/Out/DD0050/halo_rockstar.py", line 62, in <module><br> hc.create()<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py", line 293, in create<br> self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 305, in barrierize<br> retval = func(*args, **kwargs)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py", line 362, in _run<br> self.halos_ds = self.finder_method(self.data_ds)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py", line 46, in __call__<br> return self.function(ds, *self.args, **self.kwargs)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py", line 79, in _rockstar_method<br> rh.run()<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 348, in run<br> min_halo_size = self.min_halo_size)<br> 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)<br>P003 yt : [ERROR ] 2016-06-07 14:46:19,758 TypeError: expected bytes, str found<br>P002 yt : [ERROR ] 2016-06-07 14:46:19,759 Error occured on rank 0.<br>application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2<br>P003 yt : [ERROR ] 2016-06-07 14:46:19,759 Error occured on rank 1.<br>application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3<br> File "/home/jullian/ABinitio/Out/DD0050/halo_rockstar.py", line 62, in <module><br> hc.create()<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py", line 293, in create<br> self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 305, in barrierize<br> retval = func(*args, **kwargs)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py", line 362, in _run<br> self.halos_ds = self.finder_method(self.data_ds)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py", line 46, in __call__<br> return self.function(ds, *self.args, **self.kwargs)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py", line 79, in _rockstar_method<br> rh.run()<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 348, in run<br> min_halo_size = self.min_halo_size)<br> 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)<br>P000 yt : [ERROR ] 2016-06-07 14:46:19,761 TypeError: expected bytes, str found<br>application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0<br> File "/home/jullian/ABinitio/Out/DD0050/halo_rockstar.py", line 62, in <module><br> hc.create()<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py", line 293, in create<br> self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 305, in barrierize<br> retval = func(*args, **kwargs)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py", line 362, in _run<br> self.halos_ds = self.finder_method(self.data_ds)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py", line 46, in __call__<br> return self.function(ds, *self.args, **self.kwargs)<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_finding_methods.py", line 79, in _rockstar_method<br> rh.run()<br> File "/home/jullian/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 348, in run<br> min_halo_size = self.min_halo_size)<br> 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)<br>P001 yt : [ERROR ] 2016-06-07 14:46:19,761 TypeError: expected bytes, str found<br>application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1<br><br>===================================================================================<br>= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES<br>= EXIT CODE: 1<br>= CLEANING UP REMAINING PROCESSES<br>= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES<br>===================================================================================<br><br>===================================================================================<br>= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES<br>= EXIT CODE: 1<br>= CLEANING UP REMAINING PROCESSES<br>= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES<br>===================================================================================<br><br><br><br></div><div>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:<br><br>[mpiexec@julian-ubuntu] match_arg (./utils/args/args.c:160): unrecognized argument mca<br>[mpiexec@julian-ubuntu] HYDU_parse_array (./utils/args/args.c:175): argument matching returned error<br>[mpiexec@julian-ubuntu] parse_args (./ui/mpich/utils.c:1609): error parsing input array<br>[mpiexec@julian-ubuntu] HYD_uii_mpx_get_parameters (./ui/mpich/utils.c:1660): unable to parse user arguments<br>[mpiexec@julian-ubuntu] main (./ui/mpich/mpiexec.c:153): error parsing parameters<br><br></div><div> How could I fix this problem? Do I have to launch the script in some remote machine? Do I have to use the IPython?<br></div><div><br><br></div><div>Thanks by the attention,<br><br></div><div>Best Regards,<br><br></div><div>Jullian<br></div><br><br>Script link:<br><a href="http://yt-project.org/doc/cookbook/cosmological_analysis.html#running-rockstar-to-find-halos-on-multi-resolution-particle-datasets" target="_blank">http://yt-project.org/doc/cookbook/cosmological_analysis.html#running-rockstar-to-find-halos-on-multi-resolution-particle-datasets</a></div>