October 2017 - firedrake - imperial.ac.uk

Firedrake installation on cluster
by Burns, Paul 02 Nov '17

02 Nov '17

Dear Sir/Madam, I am trying to get Firedrake up and running on the Isca cluster at Exeter. The standard install method (i.e., executing 'python3 firedrake-install') does not work, however, we have managed to install Firedrake by developing an install script that loads modules manually, that sets a number of petsc options, and that passes a number of extra options to firedrake-install. However, when I try and run a simulation on Gusto I get the following error: Traceback (most recent call last): File "./examples/boussinesq_2d_lab.py", line 1, in <module> from gusto import * File "/gpfs/ts0/home/pb412/firedrake-20171026/src/gusto/gusto/__init__.py", line 11, in <module> from gusto.state import * # noqa File "/gpfs/ts0/home/pb412/firedrake-20171026/src/gusto/gusto/state.py", line 3, in <module> from netCDF4 import Dataset File "/gpfs/ts0/home/pb412/firedrake-20171026/lib/python3.5/site-packages/netCDF4/__init__.py", line 3, in <module> from ._netCDF4 import * ImportError: /gpfs/ts0/home/pb412/firedrake-20171026/lib/python3.5/site-packages/netCDF4/_netCDF4.cpython-35m-x86_64-linux-gnu.so: undefined symbol: _PyThreadState_UncheckedGet So it looks like there is some problem with the netCDF4 library. Please advise. Regards, Paul

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Install failing on PETSc build
by William Booker [RPG] 01 Nov '17

01 Nov '17

Hi, The install script keeps failing for me whenever it tries to build PETSc, what should I do to fix this? Thanks Will

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FEniCS'18 Conference 21-23 March, University of Oxford
by Patrick Farrell 27 Oct '17

27 Oct '17

Dear Firedrake community, Registration and abstract submission are open for FEniCS 2018. The conference will take place on 21-23 March 2018, at the University of Oxford. For further details please see https://fenicsproject.org/fenics18/ . We are very much looking forward to seeing you in Oxford! Best regards, Patrick

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Profiling
by Floriane Gidel [RPG] 19 Oct '17

19 Oct '17

Dear all, How can I profile my firedrake script to known the allocation of the computational time? I tried python -m cProfile -o output.out my_script.py but the output file is not as expected (part of it is pasted below). Thank you, Floriane output.out: {(sG/Users/mmfg/firedrake/lib/python2.7/site-packages/sympy/core/numbers.pyi?t_eval_is_prime(iig???????>g?3??O?>{(sK/Users/mmfg/firedrake/lib/python2.7/site-packages/sympy/core/assumptions.pyi?t_ask(iig???????>g?3??O?>0(s2/Users/mmfg/firedrake/src/ufl/ufl/tensoralgebra.pyisCofactor(iig???????>g???????>{(s2/Users/mmfg/firedrake/src/ufl/ufl/tensoralgebra.pyi<module>(iig???????>g???????>0(sH/Users/mmfg/firedrake/lib/python2.7/site-packages/sympy/series/gruntz.pyivR(iig,C??6?gT?qs*9?{(sH/Users/mmfg/firedrake/lib/python2.7/site-packages/sympy/series/limits.pyiR(iig,C??6?gT?qs*9?0(sI/Users/mmfg/firedrake/lib/python2.7/site-packages/mpmath/ctx_mp_python.pyiHt _constant(iig?h㈵??>g?h㈵??>{(sI/Users/mmfg/firedrake/lib/python2.7/site-packages/mpmath/ctx_mp_python.pyiR(iig?h㈵??>g?h㈵??>0(s0/Users/mmfg/firedrake/src/PyOP2/pyop2/caching.pyi{t__new__(i/i6g1{?v?A?gV??6o???{(s-/Users/mmfg/firedrake/src/PyOP2/pyop2/base.pyi>tset(iigT?qs*?>g??̔???>(s-/Users/mmfg/firedrake/src/PyOP2/pyop2/base.pyi? __init__(iig?k$ ??gM0?k????(sB/Users/mmfg/firedrake/src/firedrake/firedrake/functionspaceimpl.pyi?texterior_facet_node_map(iig?h㈵??>g{?V???0?(s-/Users/mmfg/firedrake/src/PyOP2/pyop2/base.pyi8 ttoset(iig???????>g???????>(s9/Users/mmfg/firedrake/src/firedrake/firedrake/assemble.pyi?t _assemble(iig ?F??g"O???|??(sB/Users/mmfg/firedrake/src/firedrake/firedrake/functionspaceimpl.pyidof_dset(iig???????>gT?qs*?>(s5/Users/mmfg/firedrake/src/firedrake/firedrake/mesh.pyi?tlocal_facet_dat(iig?h㈵??>g?t><K??(s-/Users/mmfg/firedrake/src/PyOP2/pyop2/base.pyi?

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Problem with PyOP2 on KNL machine
by Justin Chang 19 Oct '17

19 Oct '17

Hi everyone, I installed firedrake onto our local KNL box which runs on CentOS 7.4, so I managed to install all the necessary requirements using --no-package-manager. The installation returns no error but I am seeing this error: (firedrake) [root@caamhpc ~]# python -c "from firedrake import *" Traceback (most recent call last): File "<string>", line 1, in <module> File "/root/Software/firedrake/src/firedrake/firedrake/__init__.py", line 29, in <module> from pyop2 import op2 # noqa File "/root/Software/firedrake/src/PyOP2/pyop2/__init__.py", line 4, in <module> from pyop2.op2 import * # noqa File "/root/Software/firedrake/src/PyOP2/pyop2/op2.py", line 42, in <module> from pyop2.base import i # noqa: F401 File "/root/Software/firedrake/src/PyOP2/pyop2/base.py", line 57, in <module> from pyop2.sparsity import build_sparsity ImportError: /root/Software/firedrake/src/PyOP2/pyop2/ sparsity.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _intel_fast_memset I have never seen this before. Here's some information that may be helpful: (firedrake) [root@caamhpc ~]# ldd /root/Software/firedrake/src/PyOP2/pyop2/ sparsity.cpython-36m-x86_64-linux-gnu.so linux-vdso.so.1 => (0x00007fffc8f54000) libpetsc.so.3.07 => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libpetsc.so.3.07 (0x00007fbf5e1f0000) libpython3.6m.so.1.0 => /usr/local/lib/libpython3.6m.so.1.0 (0x00007fbf5dcb9000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fbf5da86000) libc.so.6 => /lib64/libc.so.6 (0x00007fbf5d6c2000) liblapack.so.3 => /lib64/liblapack.so.3 (0x00007fbf5cf64000) libblas.so.3 => /lib64/libblas.so.3 (0x00007fbf5cd0b000) libparmetis.so => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libparmetis.so (0x00007fbf5cacf000) libmetis.so => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libmetis.so (0x00007fbf5c858000) libhdf5hl_fortran.so.10 => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libhdf5hl_fortran.so.10 (0x00007fbf5c645000) libhdf5_fortran.so.10 => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libhdf5_fortran.so.10 (0x00007fbf5c409000) libhdf5_hl.so.10 => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libhdf5_hl.so.10 (0x00007fbf5c1e7000) libhdf5.so.10 => /root/Software/firedrake/lib/python3.6/site-packages/petsc/lib/libhdf5.so.10 (0x00007fbf5bd08000) libm.so.6 => /lib64/libm.so.6 (0x00007fbf5ba06000) libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007fbf5b6e3000) libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007fbf5b4a7000) libmpicxx.so.12 => /opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/lib/libmpicxx.so.12 (0x00007fbf5b287000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fbf5af7e000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fbf5ad7a000) libmpifort.so.12 => /opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/lib/libmpifort.so.12 (0x00007fbf5a9dc000) libmpi.so.12 => /opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/lib/libmpi.so.12 (0x00007fbf5a20c000) librt.so.1 => /lib64/librt.so.1 (0x00007fbf5a004000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fbf59dee000) libutil.so.1 => /lib64/libutil.so.1 (0x00007fbf59bea000) /lib64/ld-linux-x86-64.so.2 (0x00007fbf5f8b9000) (firedrake) [root@caamhpc ~]# which mpicc /opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/bin/mpicc (firedrake) [root@caamhpc ~]# mpicc --version gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) Copyright (C) 2015 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. This system wants to use intel compilers but I told it to use GNU compilers. I suspect this error has something to do with intel. I can try and provide more information as necessary. Thanks, Justin

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where is firedrake...
by Kara, Erdi 12 Oct '17

12 Oct '17

Hi I have recently installed Firedrake to my Ubuntu 16 and made all tests successfully. However it doest show up in any of Python3 directories. Therefore, the command " from firedrake import * " never works. If you have any suggestion, I would really appreciate. Have a good day.

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CG2 giving me 4th order L2 convergence
by Justin Chang 05 Oct '17

05 Oct '17

CG2 for poisson equation should be 3rd order L2 convergence but for some reason I am getting near 4th order convergence. If I use DG2 elements, I get the 3rd order convergence as theory suggests. Why is this happening? Below is the snippet of my code mesh = UnitSquareMesh(20,20,quadrilateral=False) Q = FunctionSpace(mesh,CG,2) ... x = SpatialCoordinate(Q.mesh()) u_exact = interpolate(sin(2*x[0]**2*math.pi)*sin(2*x[1]**2*math.pi),Q) f = interpolate( 16*math.pi**2*sin(2*math.pi*x[0]**2)*sin(2*math.pi*x[1]**2 )*(x[0]**2+x[1]**2) - 4*math.pi*(cos(2*math.pi*x[0]**2)*sin(2*math.pi*x[1]**2) + sin(2 *math.pi*x[0]**2)*cos(2*math.pi*x[1]**2)),Q) ... L2_error = errornorm(u_exact,u_h) I never had this "problem" earlier this year when I ran CG2 experiments (though I didn't use the UFL format, but I don't think that's the problem here). Justin

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