2016-05-24 19:16 GMT+02:00 Homolya, Miklós <m.homolya14@imperial.ac.uk>:
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.)
Also, please run firedrake-clean after the update. Thanks
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:
* A C and C++ compiler (for example gcc/g++ or clang), GNU make * A Fortran compiler (for PETSc) * MPI * Blas and Lapack * Git, Mercurial * Python version 2.7 * pip and the Python headers * autoconf, automake, libtool * CMake * zlib (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
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 <https://aka.ms/ghei36>
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 listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake