Dedalus error after installation

[Kaylan J. Burleigh]

Dear Dedalus Support,

I am a third year grad student in astronomy at UC Berkeley, and Daniel got me up and running on dedalus! However, after successfully running the install script on my Mac and typing the appropriate "source ..." command, I get the following error running the "2d_ivp"  and "id_ivp" test problems. (errors below)

Any help would be excellent!, Thanks,

Kaylan

kay...@berkeley.edu

(480)862-4256

-----------

(dedalus)airbears2-10-142-26-200:1d_ivp kburleigh$ python3 kdv_burgers.py 

Traceback (most recent call last):

  File "/Users/kburleigh/dedalus/dedalus/lib/python3.4/site-packages/sympy/core/compatibility.py", line 385, in as_int

    result = int(n)

TypeError: int() argument must be a string or a number, not 'tuple'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

  File "kdv_burgers.py", line 28, in <module>

    problem.expand(domain)

  File "/Users/kburleigh/dedalus/dedalus/src/dedalus2/dedalus2/pde/problems.py", line 249, in expand

    self.eqn_set = self._expand_expressions(eqns, c_params, nc_params, zbasis, order)

  File "/Users/kburleigh/dedalus/dedalus/src/dedalus2/dedalus2/pde/problems.py", line 268, in _expand_expressions

    M0 = self._expand_matrix(M0, nc_params, zbasis, order)

  File "/Users/kburleigh/dedalus/dedalus/src/dedalus2/dedalus2/pde/problems.py", line 291, in _expand_matrix

    C_exp = [[sy.zeros(shape) for p in range(order)] for i in range(nsubs)]

  File "/Users/kburleigh/dedalus/dedalus/src/dedalus2/dedalus2/pde/problems.py", line 291, in <listcomp>

    C_exp = [[sy.zeros(shape) for p in range(order)] for i in range(nsubs)]

  File "/Users/kburleigh/dedalus/dedalus/src/dedalus2/dedalus2/pde/problems.py", line 291, in <listcomp>

    C_exp = [[sy.zeros(shape) for p in range(order)] for i in range(nsubs)]

  File "/Users/kburleigh/dedalus/dedalus/lib/python3.4/site-packages/sympy/matrices/dense.py", line 1229, in zeros

    return cls.zeros(r, c)

  File "/Users/kburleigh/dedalus/dedalus/lib/python3.4/site-packages/sympy/matrices/dense.py", line 513, in zeros

    r = as_int(r)

  File "/Users/kburleigh/dedalus/dedalus/lib/python3.4/site-packages/sympy/core/compatibility.py", line 389, in as_int

    raise ValueError('%s is not an integer' % n)

TypeError: not all arguments converted during string formatting

--------

[Daniel Lecoanet]

Hi all,

Sympy just released a new version yesterday, and it appears that the new version is incompatible with Dedalus.  We should change the install script to download version 0.7.5 which still works.

Daniel

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[Keaton Burns]

Hi all,

Thanks for catching and reporting this Kaylan, and thanks for tracking down the source Daniel.  Turned out the exact issue was a deprecated constructor in sympy that we had accidentally been using, and which they finally removed in 0.7.6.  I’ve pushed a patch to the repo that fixes this, so it should now work with at least the last few versions of sympy (including 0.7.4, 0.7.5, and 0.7.6).

Thanks!

-Keaton

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