Is there any connection between the installation problem on CentOS and the traceback below? (I struggle to see any.)

The traceback suggests a bug in COFFEE. If you're installation is up-to-date, please file a bug here: https://github.com/coneoproject/COFFEE/issues/new

(If not up-to-date, please update, the bug might have been fixed already.)

With regard to the installation on CentOS:

python firedrake-install --no-package-manager

is the right thing to do. Beforehand you should make sure that the following system packages are installed:

(Also printed by the install script.)

Please don't run firedrake-install as root.

If there are still any problems with the installation, please send us the log (you get that by adding the --log option to firedrake-install), otherwise we cannot possibly figure out what could have gone wrong.

Thanks,
Miklós

From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Anna Kalogirou <a.kalogirou@leeds.ac.uk>
Sent: 24 May 2016 18:02:32
To: firedrake
Subject: Re: [firedrake] Failed update

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

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

_______________________________________________
firedrake mailing list
firedrake@imperial.ac.uk
https://mailman.ic.ac.uk/mailman/listinfo/firedrake