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@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@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
>
>
>
> _______________________________________________
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> yt-users@lists.spacepope.org
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>
>
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