Hey,
me again...obviously I like to collect install problems so I ran over an
already known one, highlighted in this previous message :
http://www.mail-archive.com/[email protected]/msg00892.html
However, I had a look and did not find a second boost install on my machine and
linking seems to be correct (I tested the .so files of $RDBASE/bin using ldd).
So I tried a gdb on python importing rdkit.Chem, which yields this :
[r...@eris ~]# gdb python
GNU gdb Red Hat Linux (6.5-37.el5rh)
Copyright (C) 2006 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu"...Using host libthread_db
library "/lib64/libthread_db.so.1".
(gdb) run
Starting program: /usr/local/bin/python
[Thread debugging using libthread_db enabled]
Python 2.7 (r27:82500, Jul 21 2010, 15:22:18)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
[New Thread 47389131751648 (LWP 22182)]
>>> import rdkit.Chem as Chem
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 47389131751648 (LWP 22182)]
0x0000000000000000 in ?? ()
(gdb) where
#0 0x0000000000000000 in ?? ()
#1 0x00002b19a88cb864 in std::vector<std::pair<char const*, char const*>,
std::allocator<std::pair<char const*, char const*> > >::_M_insert_aux ()
from /root/pool/lib/libboost_python.so.1.41.0
#2 0x00002b19a88cbb46 in boost::python::objects::enum_base::enum_base$base ()
from /root/pool/lib/libboost_python.so.1.41.0
#3 0x00002b19a91b424c in discreteValVec_wrapper::wrap ()
from /usr/local/RDKit_Q22010_1/rdkit/DataStructs/cDataStructs.so
#4 0x00002b19a91b029a in init_module_cDataStructs ()
from /usr/local/RDKit_Q22010_1/rdkit/DataStructs/cDataStructs.so
#5 0x00002b19a88daa08 in boost::python::detail::exception_handler::operator()
() from /root/pool/lib/libboost_python.so.1.41.0
#6 0x00002b19a81ef710 in
boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool,
boost::python::detail::translate_exception<ValueErrorException, void
(*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>,
boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >,
bool, boost::python::detail::exception_handler const&, boost::function0<void>
const&>::invoke () from /usr/local/RDKit_Q22010_1/rdkit/rdBase.so
#7 0x00002b19a88da98b in boost::python::detail::exception_handler::operator()
() from /root/pool/lib/libboost_python.so.1.41.0
#8 0x00002b19a81ef780 in
boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool,
boost::python::detail::translate_exception<IndexErrorException, void
(*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>,
boost:---Type <return> to continue, or q <return> to quit---
:arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool,
boost::python::detail::exception_handler const&, boost::function0<void>
const&>::invoke () from /usr/local/RDKit_Q22010_1/rdkit/rdBase.so
#9 0x00002b19a88da5e3 in boost::python::handle_exception_impl ()
from /root/pool/lib/libboost_python.so.1.41.0
#10 0x00002b19a88db678 in boost::python::handle_exception<void (*)()> ()
from /root/pool/lib/libboost_python.so.1.41.0
#11 0x00002b19a88db455 in boost::python::detail::init_module ()
from /root/pool/lib/libboost_python.so.1.41.0
#12 0x00002b19a42f8ce2 in _PyImport_LoadDynamicModule (
name=0x7fff068aad00 "rdkit.DataStructs.cDataStructs",
pathname=0x7fff068a9c40
"/usr/local/RDKit_Q22010_1/rdkit/DataStructs/cDataStructs.so", fp=<value
optimized out>) at ./Python/importdl.c:53
#13 0x00002b19a42f6b10 in import_submodule (mod=0x2b19a46e90f8,
subname=0x7fff068aad12 "cDataStructs",
fullname=0x7fff068aad00 "rdkit.DataStructs.cDataStructs")
at Python/import.c:2596
#14 0x00002b19a42f6fe2 in load_next (mod=0x2b19a46e90f8,
altmod=0x2b19a4586c30, p_name=<value optimized out>,
buf=0x7fff068aad00 "rdkit.DataStructs.cDataStructs",
p_buflen=0x7fff068abd10) at Python/import.c:2416
#15 0x00002b19a42f7278 in PyImport_ImportModuleLevel (
name=<value optimized out>, globals=0x99f2d50,
---Type <return> to continue, or q <return> to quit---q
locals=<value optimized out>,Quit
) at Python/import.c:2137
#16 0x00002b19a42d78dd in builtin___import__ (self=<value optimized out>,
args=<value optimized out>, kwds=<value optimized out>)
at Python/bltinmodule.c:49
#17 0x00002b19a42396b8 in PyObject_Call (func=0x2b19a45fedd0,
arg=0x2b19a46cbc00, kw=0x0) at Objects/abstract.c:2522
#18 0x00002b19a42d7f26 in PyEval_CallObjectWithKeywords (func=0x2b19a45fedd0,
arg=0x2b19a46cbc00, kw=0x0) at Python/ceval.c:3881
#19 0x00002b19a42dc4ac in PyEval_EvalFrameEx (f=0x99f28c0,
throwflag=<value optimized out>) at Python/ceval.c:2332
#20 0x00002b19a42e0959 in PyEval_EvalCodeEx (co=0x2b19a46d76b0,
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:3252
#21 0x00002b19a42e09d2 in PyEval_EvalCode (co=0x9a0f030,
globals=0x2b19a47005a8, locals=0x0) at Python/ceval.c:666
#22 0x00002b19a42f3ca2 in PyImport_ExecCodeModuleEx (
name=0x7fff068af3c0 "rdkit.DataStructs", co=0x2b19a46d76b0,
pathname=0x7fff068ac190
"/usr/local/RDKit_Q22010_1/rdkit/DataStructs/__init__.pyc") at
Python/import.c:681
#23 0x00002b19a42f636e in load_source_module (
name=0x7fff068af3c0 "rdkit.DataStructs",
pathname=0x7fff068ac190
"/usr/local/RDKit_Q22010_1/rdkit/DataStructs/__init_---Type <return> to
continue, or q <return> to quit---q
Quit
) at Python/import.c:1021
#24 0x00002b19a42f80bd in load_package (
name=0x7fff068af3c0 "rdkit.DataStructs", pathname=<value optimized out>)
at Python/import.c:1077
#25 0x00002b19a42f6b10 in import_submodule (mod=0x2b19a46e09b8,
subname=0x2b19a46e30e4 "DataStructs",
fullname=0x7fff068af3c0 "rdkit.DataStructs") at Python/import.c:2596
#26 0x00002b19a42f6db1 in ensure_fromlist (mod=0x2b19a46e09b8,
fromlist=0x2b19a46d9c90, buf=0x7fff068af3c0 "rdkit.DataStructs", buflen=5,
recursive=0) at Python/import.c:2507
#27 0x00002b19a42f741e in PyImport_ImportModuleLevel (
name=<value optimized out>, globals=0x99d0200,
locals=<value optimized out>, fromlist=0x2b19a46d9c90,
level=<value optimized out>) at Python/import.c:2175
#28 0x00002b19a42d78dd in builtin___import__ (self=<value optimized out>,
args=<value optimized out>, kwds=<value optimized out>)
at Python/bltinmodule.c:49
#29 0x00002b19a42396b8 in PyObject_Call (func=0x2b19a45fedd0,
arg=0x2b19a46cb2b8, kw=0x0) at Objects/abstract.c:2522
#30 0x00002b19a42d7f26 in PyEval_CallObjectWithKeywords (func=0x2b19a45fedd0,
arg=0x2b19a46cb2b8, kw=0x0) at Python/ceval.c:3881
#31 0x00002b19a42dc4ac in PyEval_EvalFrameEx (f=0x99d1640,
throwflag=<value optimized out>) at Python/ceval.c:2332
---Type <return> to continue, or q <return> to quit---q
I installed cmake2.8 and recompiled the whole rdkit again and now it works like
a charm (only two tests fail instead of 40%).
Just as you weren't sure if Kirks problem was due to linking or cmake...my
problem seems (IMO) linked to cmake...
Thanks again for your hints.
Peter
PS : rdkit seems to work OK on python 2.7
On 26/07/2010, at 15:47, Greg Landrum wrote:
> Dear Peter,
>
> On Mon, Jul 26, 2010 at 3:19 PM, Peter Schmidtke <[email protected]> wrote:
>> Hey Greg,
>> I already compiled boost using the instructions from the rdkit wiki. Anyway,
>> recompiling rdkit completely solves this problem.
>> But that wasn't easy enough. Next error :
>> [ 84%] Built target rdSLNParse
>> [ 85%] Building CXX object
> ... snip ...
>> /root/pool/include/boost/type_traits/detail/cv_traits_impl.hpp:37: internal
>> compiler error: in make_rtl_for_nonlocal_decl, at cp/decl.c:5067
>> Please submit a full bug report,
>> with preprocessed source if appropriate.
>> See <URL:http://bugzilla.redhat.com/bugzilla> for instructions.
>> Preprocessed source stored into /tmp/ccgSaXge.out file, please attach this
>> to your bugreport.
>> make[2]: *** [Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o]
>> Error 1
>> make[1]: *** [Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all] Error 2
>> make: *** [all] Error 2
>>
>>
>> I saw this error online also, and people suggested to add
>> the BOOST_PYTHON_NO_PY_SIGNATURES
>> flag, and recompile boost, which is what I did, but no effect on this
>> error.
>
> Ah... it's not boost that you need to recompile. Add the following to
> the top of $RDBASE/Code/GraphMol/Wrap/EditableMol.cpp:
> #define BOOST_PYTHON_NO_PY_SIGNATURES
>
> (related post:
> http://www.mail-archive.com/[email protected]/msg01178.html)
>
>> Someone has an idea? Are there plans to come around these boost dependencies
>> in rdkit...it's a real showstopper on older systems...real pain to get it
>> installed :(
>
> No plans to stop using boost, sorry. The fact that the RDKit uses such
> a high-quality, well-documented library (that is maintained by someone
> else) is actually one of the strengths of the project. The problem you
> describe above is a bug in gcc, not a problem with boost.
>
> -greg
Peter Schmidtke
-----------------
PhD Student
Department of Physical Chemistry
School of Pharmacy
University of Barcelona
Barcelona, Spain
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