{"id":93,"date":"2009-12-21T13:24:00","date_gmt":"2009-12-21T13:24:00","guid":{"rendered":"https:\/\/sandrock.co.za\/carl\/2009\/12\/21\/pysundials-problems\/"},"modified":"2009-12-21T13:24:00","modified_gmt":"2009-12-21T13:24:00","slug":"pysundials-problems","status":"publish","type":"post","link":"https:\/\/sandrock.co.za\/carl\/2009\/12\/pysundials-problems\/","title":{"rendered":"PySUNDIALS problems"},"content":{"rendered":"

I’m still installing JModelica. I am now in the annoying “nothing broke during install, but somethings still fail when I use them” phase. I am using the instructions here<\/a>, and using the example to test if things are working because JModelica doesn’t seem to have a test suite. This is what is happening now:<\/p>\n

<\/div>\n
<\/p>\n

In [1]: import jmodelica.examples.cstr as cstr
\/Library\/Python\/2.6\/site-packages\/jpype\/_pykeywords.py:18: DeprecationWarning: the sets module is deprecated
import sets
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

\/Users\/alchemyst\/ in ()

\/usr\/local\/Python\/jmodelica\/examples\/cstr.py in ()
  9 from jmodelica.initialization.ipopt import NLPInitialization
 10 from jmodelica.initialization.ipopt import InitializationOptimizer
---> 11 from jmodelica.simulation.sundials import TrajectoryLinearInterpolation
 12 from jmodelica.simulation.sundials import SundialsDAESimulator
 13 from jmodelica.optimization import ipopt

\/usr\/local\/Python\/jmodelica\/simulation\/sundials.py in ()
 14
 15 try:
---> 16     from pysundials import cvodes
 17     from pysundials import ida
 18     from pysundials import nvecserial

\/Library\/Python\/2.6\/site-packages\/pysundials\/cvodes.py in ()
 39 import ctypes
 40 import sundials_core
---> 41 import nvecserial
 42
 43 realtype = nvecserial.realtype

\/Library\/Python\/2.6\/site-packages\/pysundials\/nvecserial.py in ()
 56 PVector = ctypes.POINTER(_NVector)
 57
---> 58 nvecserial.N_VNew_Serial.restype = PVector
 59
 60 nvecserial.N_VLinearSum_Serial.argtypes = [realtype, PVector, realtype, PVector, PVector]

\/System\/Library\/Frameworks\/Python.framework\/Versions\/2.6\/lib\/python2.6\/ctypes\/__init__.pyc in __getattr__(self, name)
356         if name.startswith('__') and name.endswith('__'):
357             raise AttributeError(name)
--> 358         func = self.__getitem__(name)
359         setattr(self, name, func)
360         return func

\/System\/Library\/Frameworks\/Python.framework\/Versions\/2.6\/lib\/python2.6\/ctypes\/__init__.pyc in __getitem__(self, name_or_ordinal)
361
362     def __getitem__(self, name_or_ordinal):
--> 363         func = self._FuncPtr((name_or_ordinal, self))
364         if not isinstance(name_or_ordinal, (int, long)):
365             func.__name__ = name_or_ordinal

AttributeError: dlsym(0x102e957d0, N_VNew_Serial): symbol not found
<\/pre>\n
It’s clear something is wrong with pysundials.  On closer inspection, it seems that the dynamic library isn’t loading correctly.  A part of the problem is explained by this:<\/p><\/div>\n
<\/p>\n

$ nm \/usr\/local\/lib\/libsundials*dylib

\/usr\/local\/lib\/libsundials_cvode.1.0.0.dylib:
0000000000000000 s __mh_dylib_header
              U dyld_stub_binder
<\/pre>\n
<\/div>\n
And many more like it.  It seems like the .dylib built by the sundials build process doesn’t include the correct names.  After much browsing and learning about how .dylibs work, I realise that this can be solved with a simple change to the configure script call (typical – it was actually documented: use –enable-shared in the build!):<\/div>\n
<\/div>\n
<\/p>\n
<\/p>\n

FFLAGS=\"-arch x86_64\" .\/configure --prefix=\/usr\/local --enable-examples --enable-shared
make
sudo make install
<\/pre>\n
Now nm shows the items in the dylib.<\/p>\n<\/div>\n
I know sundials is working right because the examples compile and run fine.  Now for pysundials:<\/div>\n
<\/div>\n
<\/p>\n

In [2]: from pysundials import cvode
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

\/Users\/alchemyst\/tmp\/pysundials-2.3.0-rc2\/examples\/cvode\/serial\/ in ()

\/Library\/Python\/2.6\/site-packages\/pysundials\/cvode.py in ()
   350         if ret  352 cvode.CVodeSetFdata.argtypes = [ctypes.c_void_p, ctypes.c_void_p]
   353 cvode.CVodeSetFdata.restype = ctypes.c_int
   354

\/System\/Library\/Frameworks\/Python.framework\/Versions\/2.6\/lib\/python2.6\/ctypes\/__init__.pyc in __getattr__(self, name)
   356         if name.startswith('__') and name.endswith('__'):
   357             raise AttributeError(name)
--> 358         func = self.__getitem__(name)
   359         setattr(self, name, func)
   360         return func

\/System\/Library\/Frameworks\/Python.framework\/Versions\/2.6\/lib\/python2.6\/ctypes\/__init__.pyc in __getitem__(self, name_or_ordinal)
   361
   362     def __getitem__(self, name_or_ordinal):
--> 363         func = self._FuncPtr((name_or_ordinal, self))
   364         if not isinstance(name_or_ordinal, (int, long)):
   365             func.__name__ = name_or_ordinal

AttributeError: dlsym(0x1014d04f0, CVodeSetFdata): symbol not found

<\/pre>\n
And the original thing I was trying to do:<\/p>\n

In [1]: import jmodelica.examples.cstr as cstr
\/Library\/Python\/2.6\/site-packages\/jpype\/_pykeywords.py:18: DeprecationWarning: the sets module is deprecated
 import sets
---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)

\/Users\/alchemyst\/tmp\/pysundials-2.3.0-rc2\/examples\/cvode\/serial\/ in ()

\/usr\/local\/Python\/jmodelica\/examples\/cstr.py in ()
     9 from jmodelica.initialization.ipopt import NLPInitialization
    10 from jmodelica.initialization.ipopt import InitializationOptimizer
---> 11 from jmodelica.simulation.sundials import TrajectoryLinearInterpolation
    12 from jmodelica.simulation.sundials import SundialsDAESimulator
    13 from jmodelica.optimization import ipopt

\/usr\/local\/Python\/jmodelica\/simulation\/sundials.py in ()
    14
    15 try:
---> 16     from pysundials import cvodes
    17     from pysundials import ida
    18     from pysundials import nvecserial

\/Library\/Python\/2.6\/site-packages\/pysundials\/cvodes.py in ()
    44 NVector = nvecserial.NVector
    45
---> 46 cvodes = sundials_core.loadlib(\"cvodes\")
    47
    48 #Linear Multistep method constants


\/Library\/Python\/2.6\/site-packages\/pysundials\/sundials_core.pyc in loadlib(libname)
    62                 lib = ctypes.CDLL(libpaths[libname])
    63         except OSError, e:
---> 64                 raise OSError(\"%snCannot load shared library %s. Please check you config file and ensure the paths to the shared libraries are correct.\"%(e, libpaths[libname]))
    65         return lib
    66

OSError: dlopen(\/usr\/local\/libsundials_cvodes.dylib, 6): image not found
Cannot load shared library \/usr\/local\/libsundials_cvodes.dylib. Please check you config file and ensure the paths to the shared libraries are correct.

<\/pre>\n
So the error has changed to it not finding the library.  Something must be screwy with paths.  Frustrating afternoon.<\/p><\/div>\n","protected":false},"excerpt":{"rendered":"
I’m still installing JModelica. I am now in the annoying “nothing broke during install, but somethings still fail when I use them” phase. I am using the instructions here, and using the example to test if things are working because JModelica doesn’t seem to have a test suite. This is what is happening now: In […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_feature_clip_id":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_post_was_ever_published":false},"categories":[1],"tags":[],"class_list":["post-93","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"","_links":{"self":[{"href":"https:\/\/sandrock.co.za\/carl\/wp-json\/wp\/v2\/posts\/93","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sandrock.co.za\/carl\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/sandrock.co.za\/carl\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/sandrock.co.za\/carl\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/sandrock.co.za\/carl\/wp-json\/wp\/v2\/comments?post=93"}],"version-history":[{"count":0,"href":"https:\/\/sandrock.co.za\/carl\/wp-json\/wp\/v2\/posts\/93\/revisions"}],"wp:attachment":[{"href":"https:\/\/sandrock.co.za\/carl\/wp-json\/wp\/v2\/media?parent=93"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/sandrock.co.za\/carl\/wp-json\/wp\/v2\/categories?post=93"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/sandrock.co.za\/carl\/wp-json\/wp\/v2\/tags?post=93"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}