[phenixbb] runtime error in phenix.refine

Eugene Valkov eugene.valkov at gmail.com
Mon Jun 11 13:50:48 PDT 2012


Hi Nat and Pavel,

Here is the output of "boost_adaptbx.show_platform_info". The inputs
and logs I will send off-list.

It's a reasonably large cell (119.84, 163.9, 178.39, 90, 94.2, 90)
with over 64,000 atoms. Refinement proceeds fine in REFMAC and BUSTER,
if that helps.

__FILE__ = /net/anaconda/scratch1/phenix/phenix-1.8-1069/cctbx_project/boost_adaptbx/meta_ext.cpp
__DATE__ = Jun  2 2012
__TIME__ = 07:34:31
__x86_64__
__linux
__GNUC__ = 3
__GNUC_MINOR__ = 4
__GNUC_PATCHLEVEL__ = 2
boost::python::cxxabi_cxa_demangle_is_broken(): false
__GXX_WEAK__ = 1
__LP64__ = 1
__VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3)
FE_INEXACT = 32
FE_DIVBYZERO = 4
FE_UNDERFLOW = 16
FE_OVERFLOW = 8
FE_INVALID = 1
FE_ALL_EXCEPT = 61
__SSE2__ = 1
BOOST_LIB_VERSION = 1_48
PY_VERSION = 2.7.2
PYTHON_API_VERSION = 1013
sizeof(bool) = 1
sizeof(short) = 2
sizeof(int) = 4
sizeof(long) = 8
sizeof(std::size_t) = 8
sizeof(void*) = 8
sizeof(long long) = 8
sizeof(float) = 4
sizeof(double) = 8
sizeof(long double) = 16
sizeof(boost::int32_t) = 4
sizeof(boost::uint32_t) = 4
sizeof(wchar_t) = 4
__PTRDIFF_TYPE__
Py_USING_UNICODE
sizeof(PY_UNICODE_TYPE) = 2
gnu libc version: 2.12
BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG
boost/TAG: 73458
os.name: posix
sys.platform: linux2
sys.byteorder: little
platform.platform():
Linux-2.6.32-220.13.1.el6.x86_64-x86_64-with-redhat-6.2-Santiago
platform.architecture(): ('64bit', 'ELF')
floating_point_exceptions.division_by_zero_trapped: False
floating_point_exceptions.invalid_trapped: False
floating_point_exceptions.overflow_trapped: False
number of processors: 24
Memory total:  203,085,643,776
Memory free:    54,516,293,632
import thread: OK
Division operator semantics: true division
"hello" = ['h', 'e', 'l', 'l', 'o']
u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00']
u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85']
LATIN CAPITAL LETTER A WITH RING ABOVE = Å
u+s,u,s: 0.14 0.10 0.04 micro-seconds/tick: 0.211

On 11 June 2012 20:05, Pavel Afonine <pafonine at lbl.gov> wrote:
> Hi Eugene,
>
> if you send me the necessary inputs (off-list) I'll try to reproduce the
> problem and see what generates it ...
>
> Pavel
>
>
>  On 6/11/12 11:44 AM, Nathaniel Echols wrote:
>>
>> On Sun, Jun 10, 2012 at 10:04 AM, Eugene Valkov<eugene.valkov at gmail.com>
>>  wrote:
>>>
>>> I'm encountering the following during the second macro-cycle in
>>> phenix.refine in latest 1.8-1069 dev build for Linux 64-bit:
>>>
>>> RuntimeError: Excessive number of cubicles:
>>>  This may be due to unreasonable parameters:
>>>    cubicle_edge=5
>>>    space_span=(8467.78,8440.85,8372.67)
>>>    n_cubicles=(1694,1689,1675)
>>>    max_number_of_bytes=101542821888
>>>
>>> Any thoughts/suggestions much appreciated.
>>
>> If I'm interpreting the code correctly, this means that the number of
>> cubicles will lead to an integer format overflow - which I find hard
>> to believe if you're using a 64-bit system.  Could you please send me
>> the rest of the error message, along with the output of the command
>> "boost_adaptbx.show_platform_info"?
>>
>> thanks,
>> Nat
>> _______________________________________________
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>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
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