Mailman 3 August 2010 - yt-users

simple calculation question
by Robert Thompson Aug. 17, 2010

Aug. 17, 2010

Hi yt users, I'm still very new at python syntax so please forgive me =) I've ran a few n-body simulations and I'd like to simply calculate the pairwise velocity between the halo pairs. I simply need to read in the x,y,z positions & vx,vy,vz velocities from the halo finder output, do some calculations, and output the result. I've done this in C but I'd love to learn how to do this in yt. Here's my calculation in C: for(i=0; i<NUM; i++) { for(j=i+1; j<NUM; j++) { dXctr = periodic(Xctr[i] - Xctr[j]) / 1000.; /* in Mpc/h */ dYctr = periodic(Yctr[i] - Yctr[j]) / 1000.; dZctr = periodic(Zctr[i] - Zctr[j]) / 1000.; d = sqrt(dXctr*dXctr + dYctr*dYctr + dZctr*dZctr); /* in Mpc/h */ if(d < 10.) /* less than 10 Mpc/h */ { dvx = vx[i] - vx[j]; dvy = vy[i] - vy[j]; dvz = vz[i] - vz[j]; vrel = sqrt(dvx*dvx + dvy*dvy + dvz*dvz); } } How would I go about doing this in yt given the halo finder outputs. Thanks for the assistance! -Robert Thompson

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questions about halo profiling
by Irina Dvorkin Aug. 15, 2010

Aug. 15, 2010

Hello All, After reading the halo profiler python files, I got the impression that it reads the position of the halo center and then approximates the halo to a sphere with this center, and so includes some mass that is actually not in the halo (for example if the halo is an ellipsoid). My knowledge of python, however, is rather poor, so it would help me a lot if you could tell me whether my understanding is correct. Also, I noticed that both the halo profiler and the halo finder use a non-standard definition of the virial radius: usually it is defined as the radius that encompasses a region that is, say, 200 (or other number) times denser than the *critical* density at that redshift. The definition in the halo profiler is 200 (or other number) times the density of *matter*. So I would suggest to specifically mention this definition in the manual because it can cause confusion. Thanks, Irina

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h5py execution time
by Jean-Claude Passy Aug. 13, 2010

Aug. 13, 2010

Hi all, I have a unigrid 256^3 simulation that run on 64 processors. I need to copy/modify some data: I want to set the velocity of all cells having a density higher than a certain threshold to a fixed value, the others to 0. I wrote a little script using h5py. I have shortened it below: ################################################### for grid in glob.glob('%s/*.cpu*' %(folderIN+NameIN)): file1 = H.File(...,'r') file2 = H.File(..., 'w') for group in file1.keys(): mygroup = file1[group] subgroup = file2.create_group(group) *density = file1[group]['Density']* for field in mygroup.keys(): print 'Field:', field, ' in ', mygroup mydset = mygroup[field] shape = mydset.shape where = '/'+group+'/'+field # Setting up the gas velocity if (field == 'x-velocity'): tmp = N.zeros(file1[group][field].shape) size = file1[group][field].shape for k1 in range(0,size[0],1): for k2 in range(0,size[1],1): for k3 in range(0,size[2],1): * if (density[k1,k2,k3] > Threshold):* tmp[k1,k2,k3] = SomeValue else: tmp[k1,k2,k3] = 0.0 print 'Setting up Vx = ', SomeValue, 'if rho >', Threshold dset = subgroup.create_dataset(field,shape,data=tmp) ################################################### The issue is that this script needs more than 40 minutes to complete !!!! In the meantime, if I replace the test : ################################ *if (density[k1,k2,k3] > Threshold):* ################################ by a static test like: ################################ *if (10 > Threshold):* ################################ then the execution lasts only a few seconds ! So the problem comes from the test involving the field density. I don't really understand what is going on since I declared the variable density outside every loop. Could it be a memory issue ? I would really appreciate if someone could help solve that problem. Thanks a lot, JC

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projection a rectangular region
by Christine Simpson Aug. 9, 2010

Aug. 9, 2010

Hi all, This is a pretty simple question but one I've been trying to figure out for a while now. I'd like to make some projections of a region that is not a perfect cube. For instance, a case where the axis along which I'm projecting is shorter than the two axes parallel to the face of the projected image. This functionality exists in the projection option built into enzo, but I'm trying to move away from this and do all my analysis in yt. Is this really simple and obvious? Thanks for your help. Christine

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x-velocity
by Jean-Claude Passy Aug. 8, 2010

Aug. 8, 2010

Hi all, there is something regarding the x-velocity field I don't really understand. When I analyze a file with yt, I find: ###################################################################### In [1]: filen = 'DD0001/CommonEnvelope0001' In [2]: pf = load(filen) In [3]: region = pf.h.region([0.5, 0.5, 0.5], [0.0, 0.0, 0.0], [1.0,1.0, 1.0]) yt INFO 2010-08-08 14:29:57,375 Getting the binary hierarchy yt INFO 2010-08-08 14:29:57,389 Finished with binary hierarchy reading In [4]: vx = region["x-velocity"] yt INFO 2010-08-08 14:30:06,647 Getting field x-velocity from 1 In [5]: max(vx) Out[5]: 232812.74801568719 ###################################################################### with the latest results being in cm.s-1 However, when I make a slice and plot the x-velocity field, I end up with the figure enclosed, saying that the max velocity is around 1.6e-4 cm.s-1 ! I don't quite understand. Where am I wrong ? Thanks for yoru help, JC

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Re: [yt-users] IYT gives problem after updation of system
by Matthew Turk Aug. 8, 2010

Aug. 8, 2010

Hi Abhijit, Setting HDF5_DISABLE_VERSION_CHECK to 2 should be okay in this case. Let us know if it acts up, though! -Matt On Aug 7, 2010 2:22 PM, "Dr. ABHIJIT BHATTACHARYYA" <b_abhijit2k(a)yahoo.co.in> wrote: Hi I upgraded my system to OpenSUSE 11.3. I kept 'iyt' and 'enzo' in '/usr/local' while I only upgraded '/' while '/' and '/usr/local' are two different partitions. Now Enzo is working while iyt gives following error. $> iyt Warning! ***HDF5 library version mismatched error*** The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this application is linked. Data corruption or segmentation faults may occur if the application continues. This can happen when an application was compiled by one version of HDF5 but linked with a different version of static or shared HDF5 library. You should recompile the application or check your shared library related settings such as 'LD_LIBRARY_PATH'. You can, at your own risk, disable this warning by setting the environment variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. Setting it to 2 or higher will suppress the warning messages totally. Headers are 1.8.5, library is 1.8.4 SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ------------------- HDF5 Version: 1.8.4-patch1 Configured on: Sat May 29 02:41:00 IST 2010 Configured by: root@Pakudidi Configure mode: production Host system: x86_64-unknown-linux-gnu Uname information: Linux Pakudidi 2.6.31-rc9-7-default #1 SMP 2009-09-08 18:49:15 +0200 x86_64 x86_64 x86_64 GNU/Linux Byte sex: little-endian Libraries: Installation point: /usr/local Compiling Options: ------------------ Compilation Mode: production C Compiler: /usr/bin/gcc (gcc-4.4.1) CFLAGS: H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -O0 -fomit-frame-pointer -finline-functions AM_CFLAGS: CPPFLAGS: H5_CPPFLAGS: -D_POSIX_SOURCE -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_BSD_SOURCE Shared Libraries: yes Static Libraries: yes Statically Linked Executables: no LDFLAGS: AM_LDFLAGS: Extra libraries: -lz -lm Archiver: ar Ranlib: ranlib Debugged Packages: API Tracing: no Languages: ---------- Fortran: yes Fortran Compiler: ifort Fortran Flags: H5 Fortran Flags: -O3 AM Fortran Flags: -fPIC C++: yes C++ Compiler: g++ C++ Flags: H5 C++ Flags: AM C++ Flags: Features: --------- Parallel HDF5: no High Level library: yes Threadsafety: no Default API Mapping: v18 With Deprecated Public Symbols: yes I/O filters (external): deflate(zlib) I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset MPE: no Direct VFD: no dmalloc: no Clear file buffers before write: yes Using memory checker: no Function Stack Tracing: no GPFS: no Strict File Format Checks: no Optimization Instrumentation: no Linux Large File Support (LFS): yes Bye... Abort $> Can you help me how to proceed? Thanks and Regs Abhijit _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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IYT gives problem after updation of system
by Dr. ABHIJIT BHATTACHARYYA Aug. 7, 2010

Aug. 7, 2010

Hi I upgraded my system to OpenSUSE 11.3. I kept 'iyt' and 'enzo' in '/usr/local' while I only upgraded '/' while '/' and '/usr/local' are two different partitions. Now Enzo is working while iyt gives following error. $> iyt Warning! ***HDF5 library version mismatched error*** The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this application is linked. Data corruption or segmentation faults may occur if the application continues. This can happen when an application was compiled by one version of HDF5 but linked with a different version of static or shared HDF5 library. You should recompile the application or check your shared library related settings such as 'LD_LIBRARY_PATH'. You can, at your own risk, disable this warning by setting the environment variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. Setting it to 2 or higher will suppress the warning messages totally. Headers are 1.8.5, library is 1.8.4 SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ------------------- HDF5 Version: 1.8.4-patch1 Configured on: Sat May 29 02:41:00 IST 2010 Configured by: root@Pakudidi Configure mode: production Host system: x86_64-unknown-linux-gnu Uname information: Linux Pakudidi 2.6.31-rc9-7-default #1 SMP 2009-09-08 18:49:15 +0200 x86_64 x86_64 x86_64 GNU/Linux Byte sex: little-endian Libraries: Installation point: /usr/local Compiling Options: ------------------ Compilation Mode: production C Compiler: /usr/bin/gcc (gcc-4.4.1) CFLAGS: H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -O0 -fomit-frame-pointer -finline-functions AM_CFLAGS: CPPFLAGS: H5_CPPFLAGS: -D_POSIX_SOURCE -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_BSD_SOURCE Shared Libraries: yes Static Libraries: yes Statically Linked Executables: no LDFLAGS: AM_LDFLAGS: Extra libraries: -lz -lm Archiver: ar Ranlib: ranlib Debugged Packages: API Tracing: no Languages: ---------- Fortran: yes Fortran Compiler: ifort Fortran Flags: H5 Fortran Flags: -O3 AM Fortran Flags: -fPIC C++: yes C++ Compiler: g++ C++ Flags: H5 C++ Flags: AM C++ Flags: Features: --------- Parallel HDF5: no High Level library: yes Threadsafety: no Default API Mapping: v18 With Deprecated Public Symbols: yes I/O filters (external): deflate(zlib) I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset MPE: no Direct VFD: no dmalloc: no Clear file buffers before write: yes Using memory checker: no Function Stack Tracing: no GPFS: no Strict File Format Checks: no Optimization Instrumentation: no Linux Large File Support (LFS): yes Bye... Abort $> Can you help me how to proceed? Thanks and Regs Abhijit

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Bad object header error
by Jean-Claude Passy Aug. 4, 2010

Aug. 4, 2010

Hi all, I have slightly modified some output data from Enzo. I edited the datasets in the .cpu**** files, the .boundary files, the restart file, etc... So far, I was using only a unigrid and I was able to restart Enzo with this 'edited' data and to manipulate it without any problem. Now, I am tried to do the same thing on a data with several grids and the following error occurred: ########################################################################################### [17:22:23] osprey:$ python error_header.py --paste Traceback (most recent call last): File "error_header.py", line 6, in <module> pf.h.print_stats() File "/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/OutputTypes.py", line 150, in _get_hierarchy self.__hierarchy = self._hierarchy_class(self, data_style=self.data_style) File "/rpod2/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/HierarchyType.py", line 359, in __init__ harray_fp = h5py.File(harray_fn) File "/rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/h5py-1.2.0-py2.6-linux-x86_64.egg/h5py/highlevel.py", line 642, in __init__ Group.__init__(self, self, '/') File "/rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/h5py-1.2.0-py2.6-linux-x86_64.egg/h5py/highlevel.py", line 232, in __init__ self.id = h5g.open(parent_object.id, name) File "/rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/h5py-1.2.0-py2.6-linux-x86_64.egg/h5py/_sync.py", line 88, in wrap return func(*args, **kwds) File "h5g.pyx", line 125, in h5py.h5g.open (h5py/h5g.c:1470) h5py.h5e.ObjectHeaderError: Bad object header version number (Object header layer: Wrong version number) Traceback pasted to http://paste.enzotools.org/show/n4Oufpec7uJVOh80RzkX ################################################################################################## I have included the script. I can upload the data in a drop.io is necessary. Does anyone have an idea how to solve this problem ? Thanks for your help, JC

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halo mass function question
by Robert Thompson Aug. 4, 2010

Aug. 4, 2010

I'm running through different cookbook tutorials and I've ran into a snag when trying to form the halo mass function. ( http://yt.enzotools.org/doc/howto/hmf_howto.html#hmf-howto) I can run the halo finder, but the halo profiler is where I run into the issue. I've been unsuccessful with both N-body only and N-body+gas runs of different sizes. It seems that the filter the tutorial employs filters out all of my halos and I get this for every halo: yt.lagos ERROR 2010-08-04 12:34:35,198 Skipping halo with r_max / r_min = 0.153458. yt.lagos ERROR 2010-08-04 12:34:35,198 Skipping halo with r_max / r_min = 0.167703. yt.lagos ERROR 2010-08-04 12:34:35,199 Skipping halo with r_max / r_min = 0.209952. yt.lagos ERROR 2010-08-04 12:34:35,199 Skipping halo with r_max / r_min = 0.184501. yt.lagos ERROR 2010-08-04 12:34:35,199 No halos in filtered list. Now if I change any of the parameters such as must_be_virialized=False, or reduce the overdensity_field, or reduce the total mass filter to a lower mass I get the same result. By simply removing the filter: hp.add_halo_filter(HP.VirialFilter,must_be_virialized=True, overdensity_field='ActualOverdensity', virial_overdensity=200, virial_filters=[['TotalMassMsun','>=','1e8']], virial_quantities=['TotalMassMsun','RadiusMpc']) it goes through and profiles all of the halos, but doesn't output the TotalMassMsun that I'm looking for. I've tried simply removing the filter and adding: hp.add_profile('TotalMassMsun', weight_field=None, accumulation=False) just before hp.make_profile() and it just returns yt.lagos ERROR no halos in filtered list once again. Am I missing something simple? Thanks~ -Robert Thompson

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Particles in volume rendering
by Stella Offner Aug. 2, 2010

Aug. 2, 2010

Hi, Does anyone know an easy way to include particles positions (i.e. as small spheres) in a volume rendering? It occurred to me that I could add high values to the locations of the particles within the field that is being rendered and then define the transfer function in order to pick them out. However, I'm not sure how to modify the field data to do this. Any suggestions? Thanks! Stella

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