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[ESPResSo-users] A few questions on building Espresso


From: Michael Winokur
Subject: [ESPResSo-users] A few questions on building Espresso
Date: Fri, 18 Nov 2016 13:29:48 -0600

Hello,

I'm building Espresso, 3.3 and 3.4-dev, on a Debian testing platform with a recent kernel. 

If I try to compile these out of the box I get error messages:

In file included from cells.cpp:30:0:
utils.hpp:150:16: error: ‘std::pmalloc’ has not been declared
 #define malloc pmalloc
                ^
utils.hpp:147:17: error: ‘std::prealloc’ has not been declared
 #define realloc prealloc

However in 3.3, if I comment out these lines the package builds and passes the tests.

In 3.4-dev I get the same error message but, after removal of these two lines, I see

Error compiling Cython file:
------------------------------------------------------------
...
  def __cinit__(self, _id):
#    utils.init_intlist(self.particleData.el)
    utils.init_intlist(&(self.particleData.bl))
    self.id=_id

  cdef int updateParticleData(self) except -1:
      ^
------------------------------------------------------------

particle_data.pyx:32:7: Signature not compatible with previous declaration

Error compiling Cython file:
------------------------------------------------------------
...

cdef class ParticleHandle(object):
  cdef public int id
  cdef bint valid
  cdef Particle particleData
  cdef int updateParticleData(self)
                            ^
------------------------------------------------------------

particle_data.pxd:186:29: Previous declaration is here
warning: particle_data.pyx:164:47: local variable 'x' referenced before assignment
warning: particle_data.pyx:165:16: local variable 'x' referenced before assignment
warning: particle_data.pyx:198:53: local variable 'o' referenced before assignment
warning: particle_data.pyx:199:26: local variable 'o' referenced before assignment
warning: particle_data.pyx:199:31: local variable 'o' referenced before assignment
warning: particle_data.pyx:199:36: local variable 'o' referenced before assignment
warning: particle_data.pyx:231:46: local variable 'x' referenced before assignment
warning: particle_data.pyx:232:26: local variable 'x' referenced before assignment
warning: particle_data.pyx:232:31: local variable 'x' referenced before assignment
warning: particle_data.pyx:232:36: local variable 'x' referenced before assignment
warning: particle_data.pyx:232:41: local variable 'x' referenced before assignment
warning: particle_data.pyx:248:47: local variable 'x' referenced before assignment
warning: particle_data.pyx:249:26: local variable 'x' referenced before assignment
warning: particle_data.pyx:249:31: local variable 'x' referenced before assignment
warning: particle_data.pyx:249:36: local variable 'x' referenced before assignment
Makefile:748: recipe for target 'particle_data.cpp' failed
make[4]: *** [particle_data.cpp] Error 1

Q1: With the 1st error what the proper fix?
Q2: With the 2nd error, is there a straightforward fix?

Q3: What is the status of the python interface?  I have both python 2.7 and 3.5

Thanks!

Michael

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