Dear all,

We are still struggling with the installation of firedrake on a linux machine (running Centos).

The only person with access rights on the machine is an IT who just told me that he cannot install using the installation script because it crashes immediately. As a first step, I asked him to run

firedrake-install --no-package-manager

but I am also asking for your help if you identify which dependency is missing by the error below.

Thank you,

Anna.

---------------------

Traceback (most recent call last):
File "nozzle_nsch.py", line 164, in <module>
    solve(F_u == 0, u, bcs = [bc0,bc2,bc3,bc4, phi_bc, mu_bc],solver_parameters={'pc_type': 'lu', 'pc_factor_mat_solver_package': 'mumps'} ) #
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/solving.py", line 118, in solve
    _solve_varproblem(*args, **kwargs)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/solving.py", line 160, in _solve_varproblem
    options_prefix=options_prefix)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/variational_solver.py", line 125, in __init__
    ctx = solving_utils._SNESContext(problem)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/solving_utils.py", line 106, in __init__
    for problem in problems)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/solving_utils.py", line 106, in <genexpr>
    for problem in problems)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/assemble.py", line 66, in assemble
    inverse=inverse, nest=nest)
File "<decorator-gen-295>", line 2, in _assemble
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/utils.py", line 62, in wrapper
    return f(*args, **kwargs)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/assemble.py", line 100, in _assemble
    inverse=inverse)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/tsfc_interface.py", line 243, in compile_form
    number_map).kernels
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", line 203, in __new__
    obj = make_obj()
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", line 193, in make_obj
    obj.__init__(*args, **kwargs)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/tsfc_interface.py", line 174, in __init__
    kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts),
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/backends.py", line 118, in __call__
    return t(*args, **kwargs)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", line 203, in __new__
    obj = make_obj()
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", line 193, in make_obj
    obj.__init__(*args, **kwargs)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/base.py", line 3848, in __init__
    self._code = self._ast_to_c(self._ast, self._opts)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/host.py", line 60, in _ast_to_c
    ast_handler.plan_cpu(self._opts)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/plan.py", line 184, in plan_cpu
    _generate_cpu_code(self, kernel, **params)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/plan.py", line 110, in _generate_cpu_code
    loop_opt.eliminate_zeros()
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/optimizer.py", line 167, in eliminate_zeros
    self.nz_syms = zls.reschedule(self.header)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/scheduler.py", line 852, in reschedule
    nz_syms, nz_info = self._reschedule_itspace(root, candidates)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/scheduler.py", line 728, in _reschedule_itspace
    dim_size = tuple(((0, dict(i)[l.dim][0]), l.dim) for l in loops)
File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/scheduler.py", line 728, in <genexpr>
    dim_size = tuple(((0, dict(i)[l.dim][0]), l.dim) for l in loops)
KeyError: 'k'
Exception AttributeError: "'NonlinearVariationalSolver' object has no attribute '_parameters'" in <bound method NonlinearVariationalSolver.__del__ of <firedrake.variational_solver.NonlinearVariationalSolver object at 0x7f2dc6cfc510>> ignored

On 24/05/16 06:45, Homolya, Miklós wrote:

It seems that the new COFFEE dependency GLPK is not found, which should be installed automatically by the update script.

Can you verify that your installation is in virtualenv, not global?

Can you run firedrake-update again and send its output?

Get Outlook for Android

From: Fryderyk Wilczynski
Sent: Tuesday, 24 May, 06:25
Subject: [firedrake] Failed update
To: firedrake

Dear Firedrakes,

we suspect some mistake has been made when we tried updating Firedrake yesterday. I tried running some sample scripts from the documentation page and get the following exception

mat-lin4123.leeds.ac.uk% (19) python benney_luke.py

COFFEE finished in 0.0112019 seconds (flops: 0 -> 0)

COFFEE finished in 0.00383806 seconds (flops: 0 -> 0)

compute_form_data finished in 0.057472 seconds.

compile_integral finished in 0.0535629 seconds.

TSFC finished in 0.111062 seconds.

Traceback (most recent call last):

File "benney_luke.py", line 133, in <module>

phi_solver_h = NonlinearVariationalSolver(phi_problem_h)

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/variational_solver.py", line 125, in __init__

ctx = solving_utils._SNESContext(problem)

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/solving_utils.py", line 106, in __init__

for problem in problems)

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/solving_utils.py", line 106, in <genexpr>

for problem in problems)

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/assemble.py", line 66, in assemble

inverse=inverse, nest=nest)

File "<decorator-gen-295>", line 2, in _assemble

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/utils.py", line 62, in wrapper

return f(*args, **kwargs)

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/assemble.py", line 100, in _assemble

inverse=inverse)

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/tsfc_interface.py", line 243, in compile_form

number_map).kernels

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", line 203, in __new__

obj = make_obj()

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", line 193, in make_obj

obj.__init__(*args, **kwargs)

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/tsfc_interface.py", line 174, in __init__

kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts),

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/backends.py", line 118, in __call__

return t(*args, **kwargs)

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", line 203, in __new__

obj = make_obj()

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", line 193, in make_obj

obj.__init__(*args, **kwargs)

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/base.py", line 3848, in __init__

self._code = self._ast_to_c(self._ast, self._opts)

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/host.py", line 60, in _ast_to_c

ast_handler.plan_cpu(self._opts)

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/plan.py", line 184, in plan_cpu

_generate_cpu_code(self, kernel, **params)

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/plan.py", line 106, in _generate_cpu_code

loop_opt.rewrite(rewrite)

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/optimizer.py", line 120, in rewrite

ew.SGrewrite()

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/rewriter.py", line 497, in SGrewrite

prob.solve(ilp.GLPK(msg=0))

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/pulp/pulp.py", line 1643, in solve

status = solver.actualSolve(self, **kwargs)

File "/opt/firedrake/1605.1/lib/python2.7/site-packages/pulp/solvers.py", line 346, in actualSolve

raise PulpSolverError("PuLP: cannot execute "+self.path)

pulp.solvers.PulpSolverError: PuLP: cannot execute glpsol

Exception AttributeError: "'NonlinearVariationalSolver' object has no attribute '_parameters'" in <bound method NonlinearVariationalSolver.__del__ of <firedrake.variational_solver.NonlinearVariationalSolver object at 0x7f3e2ea40710>> ignored

Would you be able to help us identify what is going wrong and how to fix it?

Thanks,

Fryderyk
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