Hi Matt,<br><br>Thanks for the help. This is the outcome of the "bt" command in gdb:<br><br><div style="margin-left: 40px;">(gdb) bt<br>#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, <br>
__pyx_v_grad=<value optimized out>) at yt/utilities/amr_utils.c:13705<br>#1 __pyx_f_2yt_9utilities_9amr_utils_21TransferFunctionProxy_eval_transfer (__pyx_v_self=0x87ab9c0, __pyx_v_dt=0.00024472523295100413, __pyx_v_dvs=0x50e9d670, <br>
__pyx_v_rgba=0x7fffd8a94f60, __pyx_v_grad=<value optimized out>) at yt/utilities/amr_utils.c:14285<br>#2 0x00002b5e0a62c464 in __pyx_f_2yt_9utilities_9amr_utils_15PartitionedGrid_sample_values (__pyx_v_self=0x50e9d610, __pyx_v_v_pos=<value optimized out>, <br>
__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>, <br> __pyx_v_rgba=0x7fffd8a94f60, __pyx_v_tf=0x87ab9c0) at yt/utilities/amr_utils.c:17719<br>
#3 0x00002b5e0a62ce16 in __pyx_f_2yt_9utilities_9amr_utils_15PartitionedGrid_integrate_ray (__pyx_v_self=0x50e9d610, __pyx_v_v_pos=0x7fffd8a94fd0, <br> __pyx_v_v_dir=0x45457d0, __pyx_v_rgba=0x7fffd8a94f60, __pyx_v_tf=0x87ab9c0) at yt/utilities/amr_utils.c:17386<br>
#4 0x00002b5e0a624876 in __pyx_pf_2yt_9utilities_9amr_utils_15PartitionedGrid_2cast_plane (__pyx_v_self=0x50e9d610, __pyx_args=<value optimized out>, <br> __pyx_kwds=<value optimized out>) at yt/utilities/amr_utils.c:16199<br>
#5 0x0000000000495124 in call_function (f=0x5a7ce490, throwflag=<value optimized out>) at Python/ceval.c:3706<br>#6 PyEval_EvalFrameEx (f=0x5a7ce490, throwflag=<value optimized out>) at Python/ceval.c:2389<br>
#7 0x00000000004943ff in call_function (f=0x87aa260, throwflag=<value optimized out>) at Python/ceval.c:3792<br>#8 PyEval_EvalFrameEx (f=0x87aa260, throwflag=<value optimized out>) at Python/ceval.c:2389<br>
#9 0x0000000000495d6d in PyEval_EvalCodeEx (co=0x24286c0, globals=<value optimized out>, locals=<value optimized out>, args=0xb62c38, argcount=2, kws=0xb62c48, <br> kwcount=0, defs=0x242a2a8, defcount=1, closure=0x0) at Python/ceval.c:2968<br>
#10 0x0000000000493c79 in call_function (f=0xb62ac0, throwflag=<value optimized out>) at Python/ceval.c:3802<br>#11 PyEval_EvalFrameEx (f=0xb62ac0, throwflag=<value optimized out>) at Python/ceval.c:2389<br>#12 0x0000000000495d6d in PyEval_EvalCodeEx (co=0x2b5e01aed288, globals=<value optimized out>, locals=<value optimized out>, args=0x0, argcount=0, kws=0x0, kwcount=0, <br>
defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:2968<br>#13 0x0000000000495db2 in PyEval_EvalCode (co=0x87ab9c0, globals=0x50e9d670, locals=0x72f1270) at Python/ceval.c:522<br>#14 0x00000000004b7ee1 in run_mod (fp=0xb54ed0, filename=0x7fffd8a965a4 "vr.py", start=<value optimized out>, globals=0xb03190, locals=0xb03190, closeit=1, <br>
flags=0x7fffd8a958d0) at Python/pythonrun.c:1335<br>#15 PyRun_FileExFlags (fp=0xb54ed0, filename=0x7fffd8a965a4 "vr.py", start=<value optimized out>, globals=0xb03190, locals=0xb03190, closeit=1, flags=0x7fffd8a958d0)<br>
at Python/pythonrun.c:1321<br>#16 0x00000000004b8198 in PyRun_SimpleFileExFlags (fp=<value optimized out>, filename=0x7fffd8a965a4 "vr.py", closeit=1, flags=0x7fffd8a958d0) at Python/pythonrun.c:931<br>
#17 0x0000000000413e4f in Py_Main (argc=<value optimized out>, argv=0x7fffd8a959f8) at Modules/main.c:599<br>#18 0x00002b5e0259a994 in __libc_start_main () from /lib64/libc.so.6<br>#19 0x00000000004130b9 in _start ()<br>
<br></div>Thanks,<br>Andrew <br><br><br><div class="gmail_quote">On Wed, Feb 2, 2011 at 5:25 AM, Matthew Turk <span dir="ltr"><<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Andrew,<br>
<br>
That's an odd bug! Do you think you could get a backtrace from the<br>
segfault? You might do this by setting your core dump ulimit to<br>
unlimited:<br>
<br>
[in base]<br>
<br>
ulimit -c unlimited<br>
<br>
[in csh]<br>
<br>
limit coredumpsize unlimited<br>
<br>
and then running again. When the core dump gets spit out,<br>
<br>
gdb python2.6 -c that_core_file<br>
bt<br>
<br>
should tell us where in the code it died. Sam Skillman should have a<br>
better idea about any possible memory issues, but the segfault to me<br>
feels like maybe there's a roundoff that's putting it outside a grid<br>
data array space or something.<br>
<br>
Sorry for the trouble,<br>
<br>
Matt<br>
<div><div></div><div class="h5"><br>
On Tue, Feb 1, 2011 at 11:13 PM, Andrew Myers <<a href="mailto:atmyers@berkeley.edu">atmyers@berkeley.edu</a>> wrote:<br>
> Hello yt users,<br>
><br>
> I'm trying to volume render an Orion simulation with about 6,000 grids and<br>
> 100 million cells, and I think I'm running out of memory. I don't know if<br>
> this is large compared to other simulations people have volume rendered<br>
> before, but if I set the width of my field of view to be 0.02 pc (20 times<br>
> smaller than the entire domain), the following code works fine. If I set it<br>
> to 0.04 pc or anything larger, the code segfaults, which I assume means I'm<br>
> running out of memory. This happens no matter how many cores I run on -<br>
> running in parallel seems to be speed up the calculation, but not increase<br>
> the size of the domain I can render. Am I doing something wrong? Or do I<br>
> just need to find a machine with more memory to do this on? The one I'm<br>
> using now has 3 gigs per core, which strikes me as pretty solid. I'm using<br>
> the trunk version of yt-2.0. Here's the script for reference:<br>
><br>
> from yt.mods import *<br>
><br>
> pf = load("plt01120")<br>
><br>
> dd = pf.h.all_data()<br>
> mi, ma = na.log10(dd.quantities["Extrema"]("Density")[0])<br>
> mi -= 0.1 ; ma += 0.1 # To allow a bit of room at the<br>
> edges<br>
><br>
> tf = ColorTransferFunction((mi, ma))<br>
> tf.add_layers(8, w=0.01)<br>
> c = na.array([0.0,0.0,0.0])<br>
> L = na.array([1.0, 1.0, 1.0])<br>
> W = 6.17e+16 # 0.02<br>
> pc<br>
><br>
> N = 512<br>
><br>
> cam = Camera(c, L, W, (N,N), tf, pf=pf)<br>
> fn = "%s_image.png" % pf<br>
><br>
> cam.snapshot(fn)<br>
><br>
> Thanks,<br>
> Andrew Myers<br>
><br>
><br>
><br>
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