Mailman 3 November 2009 - yt-users

Hop vs HaloProfiler
by Agarwal, Shankar 03 Dec '09

03 Dec '09

Hi, I am a little confused as to how to use hop_circles. I tried this but it fails... from yt.mods import * fn = "RedshiftOutput0002" pf = load(fn) halos = HaloFinder(pf) halos.modify["hop_circles"](self, hop_output, max_number=None, annotate=False, min_size=20, max_size=10000000, font_size=8, print_halo_size=False, print_halo_mass=False, width=None) halos.write_out("HopAnalysis.out") Also, I tried HaloProfiler using http://yt.enzotools.org/doc/cookbook/recipes.html#cookbook-run-halo-profiler. It generated the radial_profiles/ directory with Halo_xxxx_profile.dat files. I am printing here the first few lines from Halo_0000_profile.dat... # ActualOverdensity CellVolume Density RadiusMpc Temperature TotalMassMsun myweight 2.796608e+03 9.422900e+72 1.407563e-27 1.086579e+00 4.551426e+07 3.320010e+13 3.334302e+12 1.587191e+03 1.884580e+73 3.247510e-28 1.121908e+00 3.392715e+07 3.768487e+13 7.692859e+11 1.213350e+03 3.298015e+73 8.512354e-28 1.158386e+00 3.176131e+07 5.041525e+13 2.016447e+12 9.092253e+02 5.182595e+73 7.672296e-28 1.196051e+00 3.692482e+07 5.936658e+13 1.817450e+12 Is Halo_0000_profile.dat related to the first Halo listed in HopAnalysis.out file ? What is # ? What is the meaning of ActualOverdensity ? And units ? What is the meaning of CellVolume? And units ? What is Density referring to ? And units ? What is mywieght ? I also got the projection/ directory. But I got errors... yt.lagos INFO 2009-11-24 16:57:52,561 Writing filtered halo list to /usr/rmt_share/scratch95/a/agarwa23/0eV/512/box200/sim1/RD0002/FilteredQuantities.out. yt INFO 2009-11-24 16:57:53,873 Created plot collection with default plot-center = [0.5, 0.5, 0.5] yt.lagos INFO 2009-11-24 16:57:53,873 Projecting halo 0000 in region: [0.154949, 0.130009, 0.810277] to [0.183709, 0.158769, 0.839037]. yt INFO 2009-11-24 16:57:53,875 Generating overlap masks for level 0 Reading and masking grids 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt INFO 2009-11-24 16:57:53,875 Finished calculating overlap. Projecting level 0 / 0 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:01 Combining level 0 / 0 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt INFO 2009-11-24 16:57:55,640 Level 0 done: 256 final yt INFO 2009-11-24 16:57:55,896 Generating overlap masks for level 0 Reading and masking grids 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt INFO 2009-11-24 16:57:55,896 Finished calculating overlap. Projecting level 0 / 0 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:01 Combining level 0 / 0 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt INFO 2009-11-24 16:57:57,381 Level 0 done: 256 final yt INFO 2009-11-24 16:57:57,527 Generating overlap masks for level 0 Reading and masking grids 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt INFO 2009-11-24 16:57:57,527 Finished calculating overlap. Traceback (most recent call last): | ETA: --:--:-- File "run_halo_profiler.py", line 37, in <module> halo_list='filtered',axes=[0,1,2]) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/extensions/HaloProfiler.py", line 474, in make_projections serialize=False, **kwargs) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/raven/PlotCollection.py", line 262, in add_projection return self._add_projection(PlotTypes.ProjectionPlot, *args, **kwargs) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/raven/PlotCollection.py", line 285, in _add_projection center=center, **kwargs) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 951, in __init__ self._refresh_data() File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 190, in _refresh_data self.get_data() File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 1137, in get_data my_coords, my_dx, my_fields = self.__project_level(level, fields) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 1029, in __project_level g_coords, g_fields = self._project_grid(grid, fields, zero_out) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 1182, in _project_grid for field in fields] File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 40, in save_state tr = func(self, grid, field) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 1222, in _get_data_from_grid return grid[field] * bad_points File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 199, in __getitem__ self.get_data(key) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseGridType.py", line 96, in get_data self._generate_field(field) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseGridType.py", line 54, in _generate_field self.pf.field_info[field].check_available(self) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/FieldInfoContainer.py", line 244, in check_available validator(data) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/FieldInfoContainer.py", line 337, in __call__ raise NeedsDataField(doesnt_have) yt.lagos.FieldInfoContainer.NeedsDataField: (['Metal_Density']) shankar

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Overplotting particles
by Agarwal, Shankar 30 Nov '09

30 Nov '09

Hi, I wanted to know what the simulation volume and the number of particles are for the following 2 plots.. http://yt.enzotools.org/attachment/wiki/Screenshots/s_projection_z_density.… http://yt.enzotools.org/doc/cookbook/recipes.html#overplot-particles For the first one, what is the command to plot hop-particles inside the circles ? I am using hop_circles, But it only plots circles. regards shankar

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HaloProfiler vs sum_mass_in_sphere.py
by Agarwal, Shankar 30 Nov '09

30 Nov '09

Hi, I ran HaloProfiler on HaloAnalysis.out and here is the data for the first halo... # id center[0] center[1] center[2] RadiusMpc TotalMassMsun 0000 0.169329105 0.144388856 0.8246570556 3.1986507886 1.07530961369e+15 Then I ran sum_mass_in_sphere.py with the above center and radius ... from yt.mods import * fn = "RedshiftOutput0002" pf = load(fn) sp = pf.h.sphere([0.169329105,0.144388856,0.8246570556],3.1986507886/pf["mpc"]) baryon_mass, particle_mass = sp.quantities["TotalQuantity"]( ["CellMassMsun", "ParticleMassMsun"], lazy_reader=True) print "Total mass in sphere is %0.5e (gas = %0.5e / particles = %0.5e)" % \ (baryon_mass + particle_mass, baryon_mass, particle_mass) And got... Total mass in sphere is 1.27226e+15 (gas = 2.06890e+14 / particles = 1.06537e+15) Let me know if the TotalMassMsun should match. Because they don't. regards shankar KU Cosmology

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Halos on slices
by Agarwal, Shankar 30 Nov '09

30 Nov '09

Hi, a couple of questions.. 1. I did pc.add_slice("Density",0). Now, I want to plot the halos just for that slice. Is it possible to plot the Halos (from HaloAnalysis.out) slice wise ? 2. I added the Density contours on the slice like... p.modify["contour"]("Density",ncont=4,take_log=False,clim=(1e-28,1e-30)) Here, if I am correct, the (1e-28,1e-30) range is divided into 4 equal intervals. So, would the contours be (1e-28,7.525e-29,5.05e-29, 2.575e-29, 1e-30) ? And which of these 5 will get plotted (the first 4? or the last 4?) In any case, I have the plot here... http://drop.io/hop_circles . And it does not show any contour with 1e-29. regards shankar

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Is pc.add_projection("Density", ax) a valid statement ?
by Agarwal, Shankar 28 Nov '09

28 Nov '09

Hi, In the following code, I am getting an error when I use pc.add_projection("Density", ax). But If I specifically use pc.add_projection("Density", 0) then it runs fine. Any idea ? Code... from yt.mods import * pf = load("RedshiftOutput0002") pc = PlotCollection(pf) for ax in range(3): p = pc.add_projection("Density", ax) p.modify["hop_circles"](halos, max_number=None, annotate=True, min_size=0, max_size=100000000, font_size=8, print_halo_size=True, print_halo_mass=True, width=None) pc.save() Error.... Traceback (most recent call last): File "hop_yt.py", line 20, in <module> p = pc.add_projection("Density", ax) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/raven/PlotCollection.py", line 262, in add_projection return self._add_projection(PlotTypes.ProjectionPlot, *args, **kwargs) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/raven/PlotCollection.py", line 285, in _add_projection center=center, **kwargs) Shankar KU cosmology

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plotting questions
by Agarwal, Shankar 24 Nov '09

24 Nov '09

Hi, I was trying the following 2 methods... from yt.mods import * p = plots.get_slice("RedshiftOutput0002", "Density", 0) p.modify["grids"]() p.modify["contour"]("Density") p.save_image("plot1") from yt.mods import * pf = load("RedshiftOutput0002") pc = PlotCollection(pf) for ax in range(1): pc.add_slice("Density", ax).modify["grids"]() pc.save("plot2") I have the plots for them attached. My simulation box is 200 Mpc/h. I wanted to know what are the default span (length scales) for the 2 methods ? For plot 1, how can I control the spacing of contours ? And where is plot 1 centered at ? For plot 2, it is centered at the most dense point in the box. But how can I add density contours ? Also, how to control the spacing ? regards shankar KU Cosmology

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cookbook_hop_mass_sum.py
by Agarwal, Shankar 24 Nov '09

24 Nov '09

Hi, I ran cookbook_hop_mass_sum.py and it gives me this error... Traceback (most recent call last): File "cookbook_hop_mass_sum.py", line 19, in <module> sphere = halo.get_sphere() File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/HaloFinding.py", line 128, in get_sphere center, radius=radius) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 1800, in __init__ raise SyntaxError("Your radius is smaller than your finest cell!") SyntaxError: Your radius is smaller than your finest cell! How does it matter if halo radius is smaller than finest cell ? cookbook_hop_mass_sum.py should just spit the baryon mass, dark matter mass and total mass. # Group Mass # part max densx y z center-of-mass x y z vx vy vz max_r 0 1.009603589e+15 3202 6.803410660e+03 2.691574395e-01 1.892197430e-01 8.293117285e-01 2.701045173e-01 1.889703433e-01 8.276973165e-01 -6.232934392e+06 -2.872425257e+07 1.526929994e+06 1.886896417e-02 shankar

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HOP threshold
by Agarwal, Shankar 23 Nov '09

23 Nov '09

Hi, I am generating Halos using HOP (via yt). I see that the default overdensity is 160. I guess it means 160 particles per cell. But isn't cell size a function of the simulation box volume and the grid ? For example, if Box=200Mpc and Ngrid=512^3, then cell=(0.390625 Mpc)^3 Isn't 0.390625 Mpc too big for a galaxy ? What is the calculation behind 160 ? shankar KU Cosmology

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run_halo_profiler.py
by Agarwal, Shankar 23 Nov '09

23 Nov '09

Hi, Is there a syntax error in the piece below I took from run_halo_profiler.py ... """ This is a recipe for making radial profiles and projections of all of the halos within a cosmological simulation. See :ref:`halo_profiling` for full documentation of the HaloProfiler. """ import yt.extensions.HaloProfiler as HP # Instantiate HaloProfiler for this dataset. hp = HP.HaloProfiler("RD0002/RedshiftOutput0002") I get the following error... [agarwa23@tg-steele sim1]$ python run_halo_profiler.py yt.lagos INFO 2009-11-23 14:20:48,664 No HDF4 support /home/ba01/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/lib/python2.6/site-packages/IPython/Magic.py:38: DeprecationWarning: the sets module is deprecated from sets import Set Traceback (most recent call last): File "run_halo_profiler.py", line 7, in <module> import yt.extensions.HaloProfiler as HP File "/autohome/u118/agarwa23/enzo1/src/yt/yt/extensions/HaloProfiler.py", line 30, in <module> from HaloFilters import * ImportError: No module named HaloFilters shankar

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installing yt on Steele
by Agarwal, Shankar 22 Nov '09

22 Nov '09

Hi, I am trying to install yt on Steele. When I do "bash install_script.sh", it crashes with H5 warnings and libz.a error. Any idea? shankar KU Cosmology Building dependencies for H5E.c H5E.c: in function `H5Eprint': H5E.c:467: warning: trace info was not inserted Building dependencies for H5F.c H5FDmulti.c: in function `H5Pset_fapl_split': H5FDmulti.c:291: warning: trace info was not inserted H5FDmulti.c: in function `H5Pset_fapl_multi': H5FDmulti.c:430: unable to parse `const char * const *memb_name' H5FDmulti.c: in function `H5Pget_fapl_multi': H5FDmulti.c:537: warning: trace info was not inserted H5FDmulti.c: in function `H5Pset_dxpl_multi': H5FDmulti.c:606: warning: trace info was not inserted H5FDmulti.c: in function `H5Pget_dxpl_multi': H5FDmulti.c:658: warning: trace info was not inserted Building dependencies for H5FDstdio.c H5FDstdio.c: in function `H5Pset_fapl_stdio': H5FDstdio.c:272: warning: trace info was not inserted make[1]: Leaving directory `/autohome/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/src/hdf5-1.6.8/src' make[1]: Entering directory `/autohome/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/src/hdf5-1.6.8/src' mkdir .libs mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5Dcontig.c -fPIC -DPIC -o .libs/H5Dcontig.lo H5Dcontig.c(497): warning #556: a value of type "const H5D_dxpl_cache_t *" cannot be assigned to an entity of type "H5D_dxpl_cache_t *" H5D_BUILD_IO_INFO(&io_info,dset,dxpl_cache,dxpl_id,store); ^ mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE - H5Dio.c(3208): warning #556: a value of type "const H5D_dxpl_cache_t *" cannot be assigned to an entity of type "H5D_dxpl_cache_t *" io_info->dxpl_cache=dxpl_cache; ^ mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5FD.c -fPIC -DPIC -o .libs/H5FD.lo H5FD.c(3670): warning #810: conversion from "void *" to "herr_t={int}" may lose significant bits HGOTO_ERROR(H5E_VFL, H5E_UNSUPPORTED, NULL, "file driver has no `get_vfd_handle' method"); ^ mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5FDmulti.c -fPIC -DPIC -o .libs/H5FDmulti.lo H5FDmulti.c(208): warning #266: function "strlen" declared implicitly if (NULL==(x=malloc(strlen(s)+1))) return NULL; ^ H5FDmulti.c(208): warning #167: argument of type "const char *" is incompatible with parameter of type "void *" if (NULL==(x=malloc(strlen(s)+1))) return NULL; ^ H5FDmulti.c(209): warning #266: function "strcpy" declared implicitly strcpy(x, s); ^ H5FDmulti.c(209): warning #167: argument of type "const char *" is incompatible with parameter of type "void *" strcpy(x, s); ^ H5FDmulti.c(1924): warning #266: function "memset" declared implicitly UNIQUE_MEMBERS(file->fa.memb_map, mt) { ^ mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5FDstdio.c -fPIC -DPIC -o .libs/H5FDstdio.lo H5FDstdio.c(774): warning #266: function "memset" declared implicitly memset(buf, 0, size); ^ H5FDstdio.c(800): warning #266: function "memset" declared implicitly memset((unsigned char *)buf + size - nbytes, 0, nbytes); ^ H5FDstdio.c(815): warning #266: function "memset" declared implicitly memset((unsigned char *)buf + n, 0, (size - n)); ^ mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5Gnode.c -fPIC -DPIC -o .libs/H5Gnode.lo H5Gnode.c(1671): warning #188: enumerated type mixed with another type udata->type = H5G_get_type(&(sn->entry[loc_idx]), dxpl_id); ^ mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5Gstab.c -fPIC -DPIC -o .libs/H5Gstab.lo mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5Obogus.c -fPIC -DPIC -o .libs/H5Obogus.lo mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5Spoint.c -fPIC -DPIC -o .libs/H5Spoint.lo H5Spoint.c(879): warning #167: argument of type "const hsize_t={unsigned long long} **" is incompatible with parameter of type "const hsize_t={unsigned long long} *" if((ret_value=H5S_select_elements(space,op,num_elem,(const hsize_t **)coord))<0) ^ mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5Spoint.c -o H5Spoint.o >/dev/null 2>&1 mv -f .libs/H5Spoint.lo H5Spoint.lo rm -f .libs/H5Sselect.lo mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5Sselec mv -f .libs/H5Zszip.lo H5Zszip.lo rm -fr .libs/libhdf5.la .libs/libhdf5.* .libs/libhdf5.* mpicc -shared H5.lo H5A.lo H5AC.lo H5B.lo H5Bcache.lo H5C.lo H5D.lo H5Dcontig.lo H5Dcompact.lo H5Defl.lo H5Dio.lo H5Distore.lo H5Dmpio.lo H5Dselect.lo H5Dtest.lo H5E.lo H5F.lo H5Fdbg.lo H5Fmount.lo H5Fsfile.lo H5Fsuper.lo H5FD.lo H5FDcore.lo H5FDfamily.lo H5FDlog.lo H5FDmpi.lo H5FDmpio.lo H5FDmpiposix.lo H5FDmulti.lo H5FDsec2.lo H5FDstdio.lo H5FL.lo H5FO.lo H5FS.lo H5G.lo H5Gent.lo H5Gname.lo H5Gnode.lo H5Gstab.lo H5Gtest.lo H5Gtraverse.lo H5HG.lo H5HGdbg.lo H5HL.lo H5HLdbg.lo H5HP.lo H5I.lo H5MF.lo H5MM.lo H5O.lo H5Oattr.lo H5Obogus.lo H5Ocache.lo H5Ocont.lo H5Odtype.lo H5Oefl.lo H5Ofill.lo H5Olayout.lo H5Omtime.lo H5Oname.lo H5Onull.lo H5Opline.lo H5Osdspace.lo H5Oshared.lo H5Ostab.lo H5P.lo H5Pdcpl.lo H5Pdxpl.lo H5Pfapl.lo H5Pfcpl.lo H5Ptest.lo H5R.lo H5RC.lo H5RS.lo H5S.lo H5Sall.lo H5Shyper.lo H5Smpio.lo H5Snone.lo H5Spoint.lo H5Sselect.lo H5Stest.lo H5SL.lo H5ST.lo H5T.lo H5Tarray.lo H5Tbit.lo H5Tcommit.lo H5Tcompound.lo H5Tconv.lo H5Tcset.lo H5Tenum.lo H5Tfields.lo H5Tfixed.lo H5Tfloat.lo H5Tinit.lo H5Tnative.lo H5Toffset.lo H5Topaque.lo H5Torder.lo H5Tpad.lo H5Tprecis.lo H5Tstrpad.lo H5Tvlen.lo H5TS.lo H5V.lo H5Z.lo H5Zdeflate.lo H5Zfletcher32.lo H5Zshuffle.lo H5Zszip.lo -Wl,--rpath -Wl,/home/ba01/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/lib64/ -Wl,--rpath -Wl,/home/ba01/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/lib/ -L/home/ba01/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/lib/ -L/home/ba01/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/lib64/ -lz -lm -Wl,-s -Wl,-soname -Wl,libhdf5.so.0 -o .libs/libhdf5.so.0.0.0 ld: /home/ba01/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/lib//libz.a(compress.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /home/ba01/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/lib//libz.a: could not read symbols: Bad value make[1]: *** [libhdf5.la] Error 1 make[1]: Leaving directory `/autohome/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/src/hdf5-1.6.8/src' make: *** [install] Error 1

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yt-users November 2009