Dear All, First, thank you for the previous help that I got from the ML. Now I have another issue. Traceback (most recent call last): File "/astro/py/halo_finder.py", line 14, in <module> hp = HP.HaloProfiler(fn, halo_list_file='HopAnalysis.out') File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 310, in __init__ self._load_halo_data() File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 967, in _load_halo_data self._run_hop(hop_file) File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 1124, in _run_hop **self.halo_finder_kwargs) File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/halo_objects.py", line 2268, in __init__ premerge=premerge, tree=self.tree) File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/halo_objects.py", line 1639, in - Ignored: __init__ HaloList.__init__(self, data_source, dm_only) File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/halo_objects.py", line 1067, in __init__ self._run_finder() File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/halo_objects.py", line 1667, in _run_finder tree=self.tree) File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py", line 73, in __init__ self._chain_hop() File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py", line 1536, in _chain_hop self._init_kd_tree() File "/astro/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py", line 351, in _init_kd_tree fKD.dens = na.zeros(self.size, dtype='float64', order='F') NameError: global name 'fKD' is not defined I tried to install Fortran kD Tree Setup http://yt-project.org/doc/analysis_modules/running_halofinder.html?highlight... But I got the follow error. Using Forthon () Forthon -F gfortran --compile_first fKD_source --no2underscores --with-numpy --fopt "-O3" fKD fKD_source.f90 Usage: Forthon [options] pkgname [extra Fortran or C files to be compiled or objects to link] [options for distutils] Forthon: error: no such option: --with-numpy make: *** [fKD] Error 2 X-Riesco-Francia:kdtree friesco$ sudo make Using Forthon () Forthon -F gfortran --compile_first fKD_source --no2underscores --with-numpy --fopt "-O3" fKD fKD_source.f90 Usage: Forthon [options] pkgname [extra Fortran or C files to be compiled or objects to link] [options for distutils] Forthon: error: no such option: --with-numpy make: *** [fKD] Error 2 I am using Mac IOS Lion 10.7.4 and the latest YT build Thank in Advance
For me, what works is using an older version of Forthon at: http://hifweb.lbl.gov/Forthon/Forthon-0.8.7.tgz I just copied the download link from the official site and changed the 0.8.10 to 0.8.7. I believe Stephen has asked the Forthon author to fix the installation issue but I have not attempted to use the latest. From G.S. On Wed, Aug 29, 2012 at 10:05 AM, Francia F. Riesco <ff2214@columbia.edu>wrote:
Dear All, First, thank you for the previous help that I got from the ML. Now I have another issue. Traceback (most recent call last): File "/astro/py/halo_finder.py", line 14, in <module> hp = HP.HaloProfiler(fn, halo_list_file='HopAnalysis.**out') File "/astro/yt/yt-x86_64/src/yt-**hg/yt/analysis_modules/halo_** profiler/multi_halo_profiler.**py", line 310, in __init__ self._load_halo_data() File "/astro/yt/yt-x86_64/src/yt-**hg/yt/analysis_modules/halo_** profiler/multi_halo_profiler.**py", line 967, in _load_halo_data self._run_hop(hop_file) File "/astro/yt/yt-x86_64/src/yt-**hg/yt/analysis_modules/halo_** profiler/multi_halo_profiler.**py", line 1124, in _run_hop **self.halo_finder_kwargs) File "/astro/yt/yt-x86_64/src/yt-**hg/yt/analysis_modules/halo_**finding/halo_objects.py", line 2268, in __init__ premerge=premerge, tree=self.tree) File "/astro/yt/yt-x86_64/src/yt-**hg/yt/analysis_modules/halo_**finding/halo_objects.py", line 1639, in
- Ignored: __init__ HaloList.__init__(self, data_source, dm_only) File "/astro/yt/yt-x86_64/src/yt-**hg/yt/analysis_modules/halo_**finding/halo_objects.py", line 1067, in __init__ self._run_finder() File "/astro/yt/yt-x86_64/src/yt-**hg/yt/analysis_modules/halo_**finding/halo_objects.py", line 1667, in _run_finder tree=self.tree) File "/astro/yt/yt-x86_64/src/yt-**hg/yt/analysis_modules/halo_** finding/parallel_hop/parallel_**hop_interface.py", line 73, in __init__ self._chain_hop() File "/astro/yt/yt-x86_64/src/yt-**hg/yt/analysis_modules/halo_** finding/parallel_hop/parallel_**hop_interface.py", line 1536, in _chain_hop self._init_kd_tree() File "/astro/yt/yt-x86_64/src/yt-**hg/yt/analysis_modules/halo_** finding/parallel_hop/parallel_**hop_interface.py", line 351, in _init_kd_tree fKD.dens = na.zeros(self.size, dtype='float64', order='F') NameError: global name 'fKD' is not defined
I tried to install Fortran kD Tree Setup http://yt-project.org/doc/**analysis_modules/running_** halofinder.html?highlight=**friend%20friend<http://yt-project.org/doc/analysis_modules/running_halofinder.html?highlight...>
But I got the follow error. Using Forthon () Forthon -F gfortran --compile_first fKD_source --no2underscores --with-numpy --fopt "-O3" fKD fKD_source.f90 Usage: Forthon [options] pkgname [extra Fortran or C files to be compiled or objects to link] [options for distutils]
Forthon: error: no such option: --with-numpy make: *** [fKD] Error 2 X-Riesco-Francia:kdtree friesco$ sudo make Using Forthon () Forthon -F gfortran --compile_first fKD_source --no2underscores --with-numpy --fopt "-O3" fKD fKD_source.f90 Usage: Forthon [options] pkgname [extra Fortran or C files to be compiled or objects to link] [options for distutils]
Forthon: error: no such option: --with-numpy make: *** [fKD] Error 2
I am using Mac IOS Lion 10.7.4 and the latest YT build Thank in Advance ______________________________**_________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/**listinfo.cgi/yt-users-**spacepope.org<http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
Hi Francia,
Forthon: error: no such option: --with-numpy
This "--with-numpy" issue is fixed in the current development tip of yt, so if you are using the development version of yt, updating your install ("yt update") should fix this error when attempting to build the fortran kdtree module. Geoffrey's suggestion of using a slightly older version of Forthon should work as well. Good luck, and write back if you have more problems. -- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice)
participants (3)
-
Francia F. Riesco -
Geoffrey So -
Stephen Skory