[yt-users] Volume Rendering and Memory usage
Andrew Myers
atmyers at berkeley.edu
Wed Feb 2 10:03:49 PST 2011
Hi guys,
Actually, the code:
for g in pf.h.grids:
if na.any(na.isnan(na.log10(g["Density"]))): raise RuntimeError
does seem to proceed to completion without raising an exception.
Andrew M
On Wed, Feb 2, 2011 at 9:55 AM, Matthew Turk <matthewturk at gmail.com> wrote:
> Hi Andrew,
>
> This is I think a spurious issue -- it comes from the calculation of
> the radius when detecting which derived fields can be used by yt. I
> would actually guess that you see this whenever the hierarchy is
> instantiated:
>
> pf.h
>
> and not only when the PlotCollection goes out. I tried kind of hard
> to eliminate this issue but I couldn't figure out a way; I think it's
> cosmetic and unrelated, though. Can you have a go at the checking for
> NaNs code?
>
> -Matt
>
> On Wed, Feb 2, 2011 at 12:51 PM, Andrew Myers <atmyers at berkeley.edu>
> wrote:
> > Actually, and I probably should have mentioned this earlier, but I
> remember
> > now that once I upgraded to yt-2.0 I started seeing warning messages
> like:
> >
> > Warning: invalid value encountered in sqrt
> >
> > when I create a plot collection from this dataset, which supports the
> > negative value theory. I assume that these values were always there, but
> > yt-2.0 started warning me about them. Probably the center of the domain
> does
> > not include the bad value(s), so it only chokes the volume renderer if I
> > make the domain large enough. Thanks for the help, both of you!
> >
> > ~Andrew
> >
> > On Wed, Feb 2, 2011 at 9:42 AM, Matthew Turk <matthewturk at gmail.com>
> wrote:
> >>
> >> Jeff, you are absolutely right. Maybe a better solution would be:
> >>
> >> for g in pf.h.grids:
> >> if na.any(na.isnan.na.log10(grid["Density"]))): raise RuntimeError
> >>
> >> That should be a more true-to-life method.
> >>
> >> -Matt
> >>
> >> On Wed, Feb 2, 2011 at 12:40 PM, j s oishi <jsoishi at gmail.com> wrote:
> >> > Hi Matt,
> >> >
> >> > Could it not also be from a negative value that has had its log()
> taken?
> >> >
> >> > j
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > On Wed, Feb 2, 2011 at 9:38 AM, Matthew Turk <matthewturk at gmail.com>
> >> > wrote:
> >> >> Hi Andrew,
> >> >>
> >> >> Okay, I have seen this before. I think it is related to a bad data
> >> >> value that it's trying to traverse. In the past this has been caused
> >> >> by NaNs, usually from a zero value that has been logged, as I believe
> >> >> other values should be handled correctly. Can you try this code for
> >> >> me?
> >> >>
> >> >> for g in pf.h.grids:
> >> >> if na.any(grid["Density"] == 0): raise RuntimeError
> >> >>
> >> >> and see if it proceeds to completion? I will see if I can think of a
> >> >> good way to handle NaNs; obviously a segfault is a pretty poor
> >> >> strategy.
> >> >>
> >> >> -Matt
> >> >>
> >> >> On Wed, Feb 2, 2011 at 12:32 PM, Andrew Myers <atmyers at berkeley.edu>
> >> >> wrote:
> >> >>> Hi Matt,
> >> >>>
> >> >>> Thanks for the help. This is the outcome of the "bt" command in gdb:
> >> >>>
> >> >>> (gdb) bt
> >> >>> #0 __pyx_f_2yt_9utilities_9amr_utils_FIT_get_value
> >> >>> (__pyx_v_self=0x87ab9c0,
> >> >>> __pyx_v_dt=0.00024472523295100413, __pyx_v_dvs=0x50e9d670,
> >> >>> __pyx_v_rgba=0x7fffd8a94f60,
> >> >>> __pyx_v_grad=<value optimized out>) at
> >> >>> yt/utilities/amr_utils.c:13705
> >> >>> #1
> >> >>>
> __pyx_f_2yt_9utilities_9amr_utils_21TransferFunctionProxy_eval_transfer
> >> >>> (__pyx_v_self=0x87ab9c0, __pyx_v_dt=0.00024472523295100413,
> >> >>> __pyx_v_dvs=0x50e9d670,
> >> >>> __pyx_v_rgba=0x7fffd8a94f60, __pyx_v_grad=<value optimized out>)
> >> >>> at
> >> >>> yt/utilities/amr_utils.c:14285
> >> >>> #2 0x00002b5e0a62c464 in
> >> >>> __pyx_f_2yt_9utilities_9amr_utils_15PartitionedGrid_sample_values
> >> >>> (__pyx_v_self=0x50e9d610, __pyx_v_v_pos=<value optimized out>,
> >> >>> __pyx_v_v_dir=<value optimized out>,
> >> >>> __pyx_v_enter_t=23.346866210722702,
> >> >>> __pyx_v_exit_t=<value optimized out>, __pyx_v_ci=<value optimized
> >> >>> out>,
> >> >>> __pyx_v_rgba=0x7fffd8a94f60, __pyx_v_tf=0x87ab9c0) at
> >> >>> yt/utilities/amr_utils.c:17719
> >> >>> #3 0x00002b5e0a62ce16 in
> >> >>> __pyx_f_2yt_9utilities_9amr_utils_15PartitionedGrid_integrate_ray
> >> >>> (__pyx_v_self=0x50e9d610, __pyx_v_v_pos=0x7fffd8a94fd0,
> >> >>> __pyx_v_v_dir=0x45457d0, __pyx_v_rgba=0x7fffd8a94f60,
> >> >>> __pyx_v_tf=0x87ab9c0) at yt/utilities/amr_utils.c:17386
> >> >>> #4 0x00002b5e0a624876 in
> >> >>> __pyx_pf_2yt_9utilities_9amr_utils_15PartitionedGrid_2cast_plane
> >> >>> (__pyx_v_self=0x50e9d610, __pyx_args=<value optimized out>,
> >> >>> __pyx_kwds=<value optimized out>) at
> >> >>> yt/utilities/amr_utils.c:16199
> >> >>> #5 0x0000000000495124 in call_function (f=0x5a7ce490,
> >> >>> throwflag=<value
> >> >>> optimized out>) at Python/ceval.c:3706
> >> >>> #6 PyEval_EvalFrameEx (f=0x5a7ce490, throwflag=<value optimized
> out>)
> >> >>> at
> >> >>> Python/ceval.c:2389
> >> >>> #7 0x00000000004943ff in call_function (f=0x87aa260,
> throwflag=<value
> >> >>> optimized out>) at Python/ceval.c:3792
> >> >>> #8 PyEval_EvalFrameEx (f=0x87aa260, throwflag=<value optimized
> out>)
> >> >>> at
> >> >>> Python/ceval.c:2389
> >> >>> #9 0x0000000000495d6d in PyEval_EvalCodeEx (co=0x24286c0,
> >> >>> globals=<value
> >> >>> optimized out>, locals=<value optimized out>, args=0xb62c38,
> >> >>> argcount=2,
> >> >>> kws=0xb62c48,
> >> >>> kwcount=0, defs=0x242a2a8, defcount=1, closure=0x0) at
> >> >>> Python/ceval.c:2968
> >> >>> #10 0x0000000000493c79 in call_function (f=0xb62ac0,
> throwflag=<value
> >> >>> optimized out>) at Python/ceval.c:3802
> >> >>> #11 PyEval_EvalFrameEx (f=0xb62ac0, throwflag=<value optimized out>)
> >> >>> at
> >> >>> Python/ceval.c:2389
> >> >>> #12 0x0000000000495d6d in PyEval_EvalCodeEx (co=0x2b5e01aed288,
> >> >>> globals=<value optimized out>, locals=<value optimized out>,
> args=0x0,
> >> >>> argcount=0, kws=0x0, kwcount=0,
> >> >>> defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:2968
> >> >>> #13 0x0000000000495db2 in PyEval_EvalCode (co=0x87ab9c0,
> >> >>> globals=0x50e9d670,
> >> >>> locals=0x72f1270) at Python/ceval.c:522
> >> >>> #14 0x00000000004b7ee1 in run_mod (fp=0xb54ed0,
> >> >>> filename=0x7fffd8a965a4
> >> >>> "vr.py", start=<value optimized out>, globals=0xb03190,
> >> >>> locals=0xb03190,
> >> >>> closeit=1,
> >> >>> flags=0x7fffd8a958d0) at Python/pythonrun.c:1335
> >> >>> #15 PyRun_FileExFlags (fp=0xb54ed0, filename=0x7fffd8a965a4 "vr.py",
> >> >>> start=<value optimized out>, globals=0xb03190, locals=0xb03190,
> >> >>> closeit=1,
> >> >>> flags=0x7fffd8a958d0)
> >> >>> at Python/pythonrun.c:1321
> >> >>> #16 0x00000000004b8198 in PyRun_SimpleFileExFlags (fp=<value
> optimized
> >> >>> out>,
> >> >>> filename=0x7fffd8a965a4 "vr.py", closeit=1, flags=0x7fffd8a958d0) at
> >> >>> Python/pythonrun.c:931
> >> >>> #17 0x0000000000413e4f in Py_Main (argc=<value optimized out>,
> >> >>> argv=0x7fffd8a959f8) at Modules/main.c:599
> >> >>> #18 0x00002b5e0259a994 in __libc_start_main () from /lib64/libc.so.6
> >> >>> #19 0x00000000004130b9 in _start ()
> >> >>>
> >> >>> Thanks,
> >> >>> Andrew
> >> >>>
> >> >>>
> >> >>> On Wed, Feb 2, 2011 at 5:25 AM, Matthew Turk <matthewturk at gmail.com
> >
> >> >>> wrote:
> >> >>>>
> >> >>>> Hi Andrew,
> >> >>>>
> >> >>>> That's an odd bug! Do you think you could get a backtrace from the
> >> >>>> segfault? You might do this by setting your core dump ulimit to
> >> >>>> unlimited:
> >> >>>>
> >> >>>> [in base]
> >> >>>>
> >> >>>> ulimit -c unlimited
> >> >>>>
> >> >>>> [in csh]
> >> >>>>
> >> >>>> limit coredumpsize unlimited
> >> >>>>
> >> >>>> and then running again. When the core dump gets spit out,
> >> >>>>
> >> >>>> gdb python2.6 -c that_core_file
> >> >>>> bt
> >> >>>>
> >> >>>> should tell us where in the code it died. Sam Skillman should have
> a
> >> >>>> better idea about any possible memory issues, but the segfault to
> me
> >> >>>> feels like maybe there's a roundoff that's putting it outside a
> grid
> >> >>>> data array space or something.
> >> >>>>
> >> >>>> Sorry for the trouble,
> >> >>>>
> >> >>>> Matt
> >> >>>>
> >> >>>> On Tue, Feb 1, 2011 at 11:13 PM, Andrew Myers <
> atmyers at berkeley.edu>
> >> >>>> wrote:
> >> >>>> > Hello yt users,
> >> >>>> >
> >> >>>> > I'm trying to volume render an Orion simulation with about 6,000
> >> >>>> > grids
> >> >>>> > and
> >> >>>> > 100 million cells, and I think I'm running out of memory. I don't
> >> >>>> > know
> >> >>>> > if
> >> >>>> > this is large compared to other simulations people have volume
> >> >>>> > rendered
> >> >>>> > before, but if I set the width of my field of view to be 0.02 pc
> >> >>>> > (20
> >> >>>> > times
> >> >>>> > smaller than the entire domain), the following code works fine.
> If
> >> >>>> > I set
> >> >>>> > it
> >> >>>> > to 0.04 pc or anything larger, the code segfaults, which I assume
> >> >>>> > means
> >> >>>> > I'm
> >> >>>> > running out of memory. This happens no matter how many cores I
> run
> >> >>>> > on -
> >> >>>> > running in parallel seems to be speed up the calculation, but not
> >> >>>> > increase
> >> >>>> > the size of the domain I can render. Am I doing something wrong?
> Or
> >> >>>> > do I
> >> >>>> > just need to find a machine with more memory to do this on? The
> one
> >> >>>> > I'm
> >> >>>> > using now has 3 gigs per core, which strikes me as pretty solid.
> >> >>>> > I'm
> >> >>>> > using
> >> >>>> > the trunk version of yt-2.0. Here's the script for reference:
> >> >>>> >
> >> >>>> > from yt.mods import *
> >> >>>> >
> >> >>>> > pf = load("plt01120")
> >> >>>> >
> >> >>>> > dd = pf.h.all_data()
> >> >>>> > mi, ma = na.log10(dd.quantities["Extrema"]("Density")[0])
> >> >>>> > mi -= 0.1 ; ma += 0.1 # To allow a bit of room at the
> >> >>>> > edges
> >> >>>> >
> >> >>>> > tf = ColorTransferFunction((mi, ma))
> >> >>>> > tf.add_layers(8, w=0.01)
> >> >>>> > c = na.array([0.0,0.0,0.0])
> >> >>>> > L = na.array([1.0, 1.0, 1.0])
> >> >>>> > W = 6.17e+16 # 0.02
> >> >>>> > pc
> >> >>>> >
> >> >>>> > N = 512
> >> >>>> >
> >> >>>> > cam = Camera(c, L, W, (N,N), tf, pf=pf)
> >> >>>> > fn = "%s_image.png" % pf
> >> >>>> >
> >> >>>> > cam.snapshot(fn)
> >> >>>> >
> >> >>>> > Thanks,
> >> >>>> > Andrew Myers
> >> >>>> >
> >> >>>> >
> >> >>>> >
> >> >>>> > _______________________________________________
> >> >>>> > yt-users mailing list
> >> >>>> > yt-users at lists.spacepope.org
> >> >>>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >>>> >
> >> >>>> >
> >> >>>> _______________________________________________
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