Re: [yt-users] Volume Rendering and Memory usage

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 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 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 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 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 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

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