- firedrake - imperial.ac.uk

Reminder: early registration and abstract submission for Firedrake '19
by Lawrence Mitchell 29 Jul '19

29 Jul '19

Dear all, a reminder that the deadlines for abstract submission and early registration for the Firedrake meeting in Durham this September will soon be upon us. Both early registration (save £30!) and abstract submission close on Friday 16th August. For more details see: https://firedrakeproject.org/firedrake_19.html Look forward to seeing many of you in Durham in September. Cheers, Lawrence

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firedrake-update fail
by Francis Poulin 04 Jul '19

04 Jul '19

Hello, Today I installed firedrake on an ubuntu machine and that seemed to go well but then, when I tried to do an update, it had a core dump. I am including the output below. Any idea what is going wrong? Francis ------------------ Francis Poulin Professor Department of Applied Mathematics University of Waterloo email: fpoulin(a)uwaterloo.ca Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637 [X] (firedrake) mmstastn@boogaloo:~/software$ firedrake-update Running /home/mmstastn/software/firedrake/bin/firedrake-update Updating the git repository for firedrake Creating firedrake-update script. Running ../bin/firedrake-update --no-update-script Checking for presence of package build-essential... installed. Checking for presence of package autoconf... installed. Checking for presence of package automake... installed. Checking for presence of package cmake... installed. Checking for presence of package gfortran... installed. Checking for presence of package git... installed. Checking for presence of package libblas-dev... installed. Checking for presence of package liblapack-dev... installed. Checking for presence of package libmpich-dev... installed. Checking for presence of package libtool... installed. Checking for presence of package mercurial... installed. Checking for presence of package mpich... installed. Checking for presence of package python3-dev... installed. Checking for presence of package python3-pip... installed. Checking for presence of package python3-tk... installed. Checking for presence of package python3-venv... installed. Checking for presence of package zlib1g-dev... installed. Checking for presence of package libboost-dev... installed. Finding dependencies of PyOP2 Finding dependencies of firedrake Finding dependencies of gusto Updating the git repository for petsc Updating the git repository for petsc4py Updating the git repository for COFFEE Updating the git repository for loopy Updating the git repository for ufl Updating the git repository for fiat Updating the git repository for FInAT Updating the git repository for tsfc Updating the git repository for PyOP2 Updating the git repository for gusto Updating the git repository for firedrake Installing pip dependencies for COFFEE Installing pip dependencies for loopy Installing pip dependencies for ufl No dependencies found. Skipping. Installing pip dependencies for fiat No dependencies found. Skipping. Installing pip dependencies for FInAT Installing pip dependencies for tsfc Installing pip dependencies for PyOP2 Installing pip dependencies for gusto Installing pip dependencies for firedrake Installing h5py Updating the git repository for h5py No need to rebuild h5py Installing libspatialindex Updating the git repository for libspatialindex No need to rebuild libspatialindex Installing libsupermesh Updating the git repository for libsupermesh No need to rebuild libsupermesh Cleaning loopy Installing loopy/ Cleaning COFFEE Installing COFFEE/ Cleaning ufl Installing ufl/ Cleaning fiat Installing fiat/ Cleaning FInAT Installing FInAT/ Cleaning tsfc Installing tsfc/ Cleaning gusto Installing gusto/ Cleaning PyOP2 Installing PyOP2/ Cleaning firedrake Installing firedrake/ Configuration saved to configuration.json Clearing just in time compilation caches. Warning! ***HDF5 library version mismatched error*** The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this application is linked. Data corruption or segmentation faults may occur if the application continues. This can happen when an application was compiled by one version of HDF5 but linked with a different version of static or shared HDF5 library. You should recompile the application or check your shared library related settings such as 'LD_LIBRARY_PATH'. You can, at your own risk, disable this warning by setting the environment variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. Setting it to 2 or higher will suppress the warning messages totally. Headers are 1.8.18, library is 1.8.17 SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ------------------- HDF5 Version: 1.8.17 Configured on: Wed Sep 7 15:12:54 EDT 2016 Configured by: root@boogaloo Configure mode: production Host system: x86_64-unknown-linux-gnu Uname information: Linux boogaloo 3.13.0-95-generic #142-Ubuntu SMP Fri Aug 12 17:00:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Byte sex: little-endian Libraries: static, shared Installation point: /opt/hdf5-1.8.17/hdf5 Compiling Options: ------------------ Compilation Mode: production C Compiler: /usr/bin/mpicc ( Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.4-2ubuntu1~14.04.3' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-libmudflap --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu built with gcc version 4.8.4 (Ubuntu 4.8.4-2ubuntu1~14.04.3)) CFLAGS: H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -O3 AM_CFLAGS: CPPFLAGS: H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: -I/opt/zlib-1.2.8/zlib//include Shared C Library: yes Static C Library: yes Statically Linked Executables: no LDFLAGS: H5_LDFLAGS: AM_LDFLAGS: -L/opt/zlib-1.2.8/zlib//lib Extra libraries: -lz -ldl -lm Archiver: ar Ranlib: ranlib Debugged Packages: API Tracing: no Languages: ---------- Fortran: no C++: no Features: --------- Parallel HDF5: yes High Level library: yes Threadsafety: no Default API Mapping: v18 With Deprecated Public Symbols: yes I/O filters (external): deflate(zlib) MPE: Direct VFD: no dmalloc: no Clear file buffers before write: yes Using memory checker: no Function Stack Tracing: no Strict File Format Checks: no Optimization Instrumentation: no Bye... [boogaloo:04465] *** Process received signal *** [boogaloo:04465] Signal: Aborted (6) [boogaloo:04465] Signal code: (-6) [boogaloo:04465] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x7f35a1a35390] [boogaloo:04465] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x38)[0x7f35a168f428] [boogaloo:04465] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x16a)[0x7f35a169102a] [boogaloo:04465] [ 3] /opt/hdf5-1.8.17/hdf5/lib/libhdf5.so.10(H5check_version+0x280)[0x7f359c97b180] [boogaloo:04465] [ 4] /home/mmstastn/software/firedrake/src/h5py/h5py/h5f.cpython-35m-x86_64-linux-gnu.so(+0x84a5)[0x7f358dc6b4a5] [boogaloo:04465] [ 5] /home/mmstastn/software/firedrake/bin/python3(PyModule_ExecDef+0x85)[0x62a305] [boogaloo:04465] [ 6] /home/mmstastn/software/firedrake/bin/python3[0x523d91] [boogaloo:04465] [ 7] /home/mmstastn/software/firedrake/bin/python3(PyCFunction_Call+0xa4)[0x4e9bd4] [boogaloo:04465] [ 8] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalFrameEx+0x6edb)[0x53dbbb] [boogaloo:04465] [ 9] /home/mmstastn/software/firedrake/bin/python3[0x540199] [boogaloo:04465] [10] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalFrameEx+0x54f0)[0x53c1d0] [boogaloo:04465] [11] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalFrameEx+0x4b04)[0x53b7e4] [boogaloo:04465] [12] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalFrameEx+0x4b04)[0x53b7e4] [boogaloo:04465] [13] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalFrameEx+0x4b04)[0x53b7e4] [boogaloo:04465] [14] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalCodeEx+0x13b)[0x540f9b] [boogaloo:04465] [15] /home/mmstastn/software/firedrake/bin/python3[0x4ebd23] [boogaloo:04465] [16] /home/mmstastn/software/firedrake/bin/python3(PyObject_Call+0x47)[0x5c1797] [boogaloo:04465] [17] /home/mmstastn/software/firedrake/bin/python3(_PyObject_CallMethodIdObjArgs+0x17a)[0x5c257a] [boogaloo:04465] [18] /home/mmstastn/software/firedrake/bin/python3(PyImport_ImportModuleLevelObject+0x778)[0x5260c8] [boogaloo:04465] [19] /home/mmstastn/software/firedrake/bin/python3[0x549e78] [boogaloo:04465] [20] /home/mmstastn/software/firedrake/bin/python3(PyCFunction_Call+0x77)[0x4e9ba7] [boogaloo:04465] [21] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalFrameEx+0x6edb)[0x53dbbb] [boogaloo:04465] [22] /home/mmstastn/software/firedrake/bin/python3[0x540199] [boogaloo:04465] [23] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalFrameEx+0x54f0)[0x53c1d0] [boogaloo:04465] [24] /home/mmstastn/software/firedrake/bin/python3(PyEval_EvalCodeEx+0x13b)[0x540f9b] [boogaloo:04465] [25] /home/mmstastn/software/firedrake/bin/python3[0x4ebd23] [boogaloo:04465] [26] /home/mmstastn/software/firedrake/bin/python3(PyObject_Call+0x47)[0x5c1797] [boogaloo:04465] [27] /home/mmstastn/software/firedrake/bin/python3(_PyObject_CallMethodIdObjArgs+0x17a)[0x5c257a] [boogaloo:04465] [28] /home/mmstastn/software/firedrake/bin/python3(PyImport_ImportModuleLevelObject+0x746)[0x526096] [boogaloo:04465] [29] /home/mmstastn/software/firedrake/bin/python3[0x549e78] [boogaloo:04465] *** End of error message *** Aborted (core dumped) ------------------ Francis Poulin Professor Department of Applied Mathematics University of Waterloo email: fpoulin(a)uwaterloo.ca Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637 [X]

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Re: [firedrake] help with installation
by Lawrence Mitchell 04 Jul '19

04 Jul '19

Dear Max, (re-adding firedrake(a)imperial.ac.uk, please don't just email me when responding, you will likely get better/more timely advice if you keep the mailing list in the CC list, moreover, that way, the final solution is visible to everyone. Thanks!) > On 1 Jul 2019, at 07:29, Heldman, Max <heldmanm(a)bu.edu> wrote: > > Hi, > > I was able to fix the problem with the eigen download by reinstalling openssl. I am having a different issue now though during the PETSc build. The install log is attached. The relevant part of the install log is: configure: WARNING: To override this behavior, please use --enable-unsupported configure option. dyld: Library not loaded: /usr/local/opt/readline/lib/libreadline.7.dylib Referenced from: /usr/local/bin/awk Reason: image not found dyld: Library not loaded: /usr/local/opt/readline/lib/libreadline.7.dylib Referenced from: /usr/local/bin/awk Reason: image not found dyld: Library not loaded: /usr/local/opt/readline/lib/libreadline.7.dylib Referenced from: /usr/local/bin/gawk Reason: image not found sed: stdout: Broken pipe ./config.status: line 1590: 81450 Done(1) eval sed \"\$ac_sed_extra\" "$ac_file_inputs" It looks like you have a package-manager installed awk version in /usr/local/bin which is non-functional (macOS ships with awk in /usr/bin/awk). Can you run /usr/local/bin/awk on its own? Can you also post the output of "brew doctor" to see if homebrew spots any issues. Thanks, Lawrence

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Parallel
by Luca Mechelli 03 Jul '19

03 Jul '19

Dear all, I am working with a simple Poisson equation to understand better the parallel computing. So far, according to the plot in paraview, I am able to get the same correct solution using a different number of processes. For later use, I want to access the solution data as a unique local sequential numpy array that has as components the value of the solution for each node of the mesh. I thought that u.vector().gather() is the option I need, but when I print it I get different values for each processor. Here is an example for print(uu.vector().gather()) for different N processors : N= 1 [2. 2. 2.01686578 2.02107396 2.01943246 2.02655103 2. 1.98313432 2.01309658 2.02310037 1.98056756 2. 1.97892594 1.98690342 1.97344897 1.97689964] N=2 [2. 2. 2.01686578 2.02107396 2.01943246 2.02655103 2. 1.98313432 2.01309658 2.02310037 1.98056756 2. 1.97892594 1.98690342 1.97344897 1.97689964] [2. 2. 2.01788253 2.01556306 2.02651517 2. 2.01725592 1.98544718 2.02588859 2. 2.01137299 1.98085025 1.98009714 1.9850916 1.97727273 1.98118216] N=4 [1.97689956 1.98690345 2.01309647 2.02655104 2.02310037 2. 2. 2. 1.98313422 2. 1.97892604 2.01686572 2.02107399 2.01943249 1.98056736 1.97344906] [1.97689956 1.98690345 2.01309647 2.02655104 2.02310037 2. 2. 2. 1.98313422 2. 1.97892604 2.01686572 2.02107399 2.01943249 1.98056736 1.97344906] [2. 2. 2.01788253 2. 2.01556304 2.02651515 2.01137299 1.98085017 1.98509166 1.97727273 1.98118219 1.98009727 2.01725589 2.02588851 1.98544706 2. ] [2. 2. 2.01788253 2. 2.01556304 2.02651515 2.01137299 1.98085017 1.98509166 1.97727273 1.98118219 1.98009727 2.01725589 2.02588851 1.98544706 2. ] What I would like to have is that for each processor the output coincide with the sequential solution for N=1, i.e. [2. 2. 2.01686578 2.02107396 2.01943246 2.02655103 2. 1.98313432 2.01309658 2.02310037 1.98056756 2. 1.97892594 1.98690342 1.97344897 1.97689964] Could someone please suggest how to do it? Thank you in advance, best regards, Luca Mechelli -- Luca Mechelli Wissenschaftlicher Mitarbeiter Arbeitsgruppe Numerik Fachbereich Mathematik und Statistik Universität Konstanz Fach D 198 D-78457 Konstanz Telefon: +49-(0) 7531-88-4637

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Re: [firedrake] Solve no longer applies BC's to pre-assembled matrices
by Ham, David A 02 Jul '19

02 Jul '19

Hi Peter, It appears our documentation is lagging development here. The ability to add boundary conditions after assembling a matrix was removed recently, basically because it causes a lot of complication under the hood and doesn’t really add any functionality. If you want to pre-assemble systems for some reason (and there is usually no reason to do this), then you should apply the boundary conditions at assembly time. Regards, David From: <firedrake-bounces(a)imperial.ac.uk> on behalf of "Sentz, Peter" <psentz(a)sandia.gov> Date: Monday, 1 July 2019 at 23:44 To: firedrake <firedrake(a)imperial.ac.uk> Subject: [firedrake] Solve no longer applies BC's to pre-assembled matrices It appears to me that passing in boundary conditions in the solve command when using pre-assembled matrices is not working correctly. Consider the following problem: ************************************************** mesh = UnitSquareMesh(10,10) V = FunctionSpace(mesh,'CG',1) x,y = SpatialCoordinate(mesh) f_ex = 10.*exp(-(x-0.5)**2/0.02 - (y-0.5)**2/0.02) f = interpolate(f_ex,V) g_ex = sin(5*x) g = interpolate(g_ex,V) u, v = TrialFunction(V), TestFunction(V) bc = DirichletBC(V,0.0,(1,2)) A = assemble(inner(grad(u),grad(v))*dx,bcs=bc) b = assemble(f*v*dx + g*v*ds((3,4)),bcs=bc) U_1 = Function(V) solve(A,U_1,b) A = assemble(inner(grad(u),grad(v))*dx) b = assemble(f*v*dx + g*v*ds((3,4))) U_2 = Function(V) solve(A,U_2,b,bcs=bc) A = inner(grad(u),grad(v))*dx b = f*v*dx + g*v*ds((3,4)) U_3 = Function(V) solve(A==b,U_3,bcs=bc) **************************************************** The solve commands for U_1 and U_3 both converge, and the solutions agree to within machine precision. However, Firedrake fails to solve for U_2, with the error message: ConvergenceError: ('LinearSolver failed to converge after %d iterations with reason: %s', 1320, 'DIVERGED_DTOL' I suspect that boundary conditions are not being applied in the second solve command to the pre-assembled system. But according to the documentation on firedrakeproject.org, this should work as coded above. Am I doing something incorrectly? I'm also wondering how this would affect LinearVariationalSolver if there is indeed a problem with the boundary conditions. Thanks, Peter Sentz

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Solve no longer applies BC's to pre-assembled matrices
by Sentz, Peter 01 Jul '19

01 Jul '19

It appears to me that passing in boundary conditions in the solve command when using pre-assembled matrices is not working correctly. Consider the following problem: ************************************************** mesh = UnitSquareMesh(10,10) V = FunctionSpace(mesh,'CG',1) x,y = SpatialCoordinate(mesh) f_ex = 10.*exp(-(x-0.5)**2/0.02 - (y-0.5)**2/0.02) f = interpolate(f_ex,V) g_ex = sin(5*x) g = interpolate(g_ex,V) u, v = TrialFunction(V), TestFunction(V) bc = DirichletBC(V,0.0,(1,2)) A = assemble(inner(grad(u),grad(v))*dx,bcs=bc) b = assemble(f*v*dx + g*v*ds((3,4)),bcs=bc) U_1 = Function(V) solve(A,U_1,b) A = assemble(inner(grad(u),grad(v))*dx) b = assemble(f*v*dx + g*v*ds((3,4))) U_2 = Function(V) solve(A,U_2,b,bcs=bc) A = inner(grad(u),grad(v))*dx b = f*v*dx + g*v*ds((3,4)) U_3 = Function(V) solve(A==b,U_3,bcs=bc) **************************************************** The solve commands for U_1 and U_3 both converge, and the solutions agree to within machine precision. However, Firedrake fails to solve for U_2, with the error message: ConvergenceError: ('LinearSolver failed to converge after %d iterations with reason: %s', 1320, 'DIVERGED_DTOL' I suspect that boundary conditions are not being applied in the second solve command to the pre-assembled system. But according to the documentation on firedrakeproject.org, this should work as coded above. Am I doing something incorrectly? I'm also wondering how this would affect LinearVariationalSolver if there is indeed a problem with the boundary conditions. Thanks, Peter Sentz

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Error to run a script converted from FEniCS
by Simone Puel 26 Jun '19

26 Jun '19

Hi all, My name is Simone Puel, a graduate student at the University of Texas at Austin. I think I have installed Firedrake correctly since I can run the example in the online tutorial. Thank you so much. I am trying to convert a script I made in FEniCS in Firedrake. I modified some syntax, but I have the following error: Traceback (most recent call last): File "/home/simone/firedrake/src/PyOP2/pyop2/caching.py", line 197, in __new__ return cls._cache_lookup(key) File "/home/simone/firedrake/src/firedrake/firedrake/tsfc_interface.py", line 53, in _cache_lookup return cls._cache.get(key) or cls._read_from_disk(key, comm) File "/home/simone/firedrake/src/firedrake/firedrake/tsfc_interface.py", line 74, in _read_from_disk raise KeyError("Object with key %s not found" % key) KeyError: 'Object with key aec71f5f7a30a3d0b4db90beac07de85 not found' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "Elasticity2D_Firedrake.py", line 161, in <module> solve(lhs_varf == rhs_varf, sol, bcs=[bc1,bc2]) File "/home/simone/firedrake/src/firedrake/firedrake/solving.py", line 125, in solve _solve_varproblem(*args, **kwargs) File "/home/simone/firedrake/src/firedrake/firedrake/solving.py", line 152, in _solve_varproblem appctx=appctx) File "/home/simone/firedrake/src/firedrake/firedrake/variational_solver.py", line 335, in __init__ super(LinearVariationalSolver, self).__init__(*args, **kwargs) File "/home/simone/firedrake/src/firedrake/firedrake/variational_solver.py", line 182, in __init__ options_prefix=self.options_prefix) File "/home/simone/firedrake/src/firedrake/firedrake/solving_utils.py", line 131, in __init__ form_compiler_parameters=self.fcp) File "/home/simone/firedrake/src/firedrake/firedrake/assemble.py", line 158, in create_assembly_callable loops = tuple(loops) File "/home/simone/firedrake/src/firedrake/firedrake/assemble.py", line 228, in _assemble kernels = tsfc_interface.compile_form(f, "form", parameters=form_compiler_parameters, inverse=inverse) File "/home/simone/firedrake/src/firedrake/firedrake/tsfc_interface.py", line 212, in compile_form number_map, interface, coffee).kernels File "/home/simone/firedrake/src/PyOP2/pyop2/caching.py", line 199, in __new__ obj = make_obj() File "/home/simone/firedrake/src/PyOP2/pyop2/caching.py", line 189, in make_obj obj.__init__(*args, **kwargs) File "/home/simone/firedrake/src/firedrake/firedrake/tsfc_interface.py", line 121, in __init__ tree = tsfc_compile_form(form, prefix=name, parameters=parameters, interface=interface, coffee=coffee) File "/home/simone/firedrake/src/tsfc/tsfc/driver.py", line 57, in compile_form fd = ufl_utils.compute_form_data(form, complex_mode=complex_mode) File "/home/simone/firedrake/src/tsfc/tsfc/ufl_utils.py", line 59, in compute_form_data complex_mode=complex_mode File "/home/simone/firedrake/src/ufl/ufl/algorithms/compute_form_data.py", line 298, in compute_form_data form = apply_function_pullbacks(form) File "/home/simone/firedrake/src/ufl/ufl/algorithms/apply_function_pullbacks.py", line 267, in apply_function_pullbacks return map_integrand_dags(FunctionPullbackApplier(), expr) File "/home/simone/firedrake/src/ufl/ufl/algorithms/map_integrands.py", line 58, in map_integrand_dags form, only_integral_type) File "/home/simone/firedrake/src/ufl/ufl/algorithms/map_integrands.py", line 39, in map_integrands for itg in form.integrals()] File "/home/simone/firedrake/src/ufl/ufl/algorithms/map_integrands.py", line 39, in <listcomp> for itg in form.integrals()] File "/home/simone/firedrake/src/ufl/ufl/algorithms/map_integrands.py", line 46, in map_integrands return itg.reconstruct(function(itg.integrand())) File "/home/simone/firedrake/src/ufl/ufl/algorithms/map_integrands.py", line 57, in <lambda> return map_integrands(lambda expr: map_expr_dag(function, expr, compress), File "/home/simone/firedrake/src/ufl/ufl/corealg/map_dag.py", line 37, in map_expr_dag result, = map_expr_dags(function, [expression], compress=compress) File "/home/simone/firedrake/src/ufl/ufl/corealg/map_dag.py", line 84, in map_expr_dags r = handlers[v._ufl_typecode_](v) File "/home/simone/firedrake/src/ufl/ufl/corealg/multifunction.py", line 42, in _memoized_handler r = handler(self, o) File "/home/simone/firedrake/src/ufl/ufl/algorithms/apply_function_pullbacks.py", line 256, in form_argument return apply_single_function_pullbacks(o) File "/home/simone/firedrake/src/ufl/ufl/algorithms/apply_function_pullbacks.py", line 151, in apply_single_function_pullbacks assert len(gsh) == 1 AssertionError I made a very simple mesh in Gmsh (attached) and the script is the linear elasticity using a mixed formulation (Arnold et al., 2007). The problem is a 2D rectangle with a vertical fault where I prescribe 1 m of slip. I attached the mesh (.msh file) and the script. If anyone is able to help, I would appreciate it. Thank you so much in advance. Have a wonderful day! Best regards, Simone -- *Simone Puel* Ph.D. student in Geological Sciences at the University of Texas at Austin Jackson School of Geosciences & Institute for Geophysics (UTIG) JGB 5.332 & ROC 2.116L spuel(a)utexas.edu +1 (737)-230-6811

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Re: [firedrake] help with installation
by Lawrence Mitchell 25 Jun '19

25 Jun '19

(readding firedrake(a)imperial.ac.uk to CC) > On 25 Jun 2019, at 15:10, Heldman, Max <heldmanm(a)bu.edu> wrote: > > Hmm, I ran 'pip3 install certifi’ which installed the module but I am still getting the same error message. Can you then try with "python3" rather than just "python"? Thanks, Lawrence

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help with installation
by Heldman, Max 25 Jun '19

25 Jun '19

Hi, I’m trying to install firedrake but I’m getting the following error message: … Failed to clone loopy using ssh, falling back to https. Successfully cloned repository loopy. Checking out branch firedrake Successfully checked out branch firedrake Installing petsc/ Downloading Eigen from 'https://bitbucket.org/eigen/eigen/get/3.3.3.tar.gz' to 'eigen-3.3.3.tgz<https://bitbucket.org/eigen/eigen/get/3.3.3.tar.gz'%20to%20'eigen-3.3.3.tgz>' Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 1317, in do_open encode_chunked=req.has_header('Transfer-encoding')) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1229, in request self._send_request(method, url, body, headers, encode_chunked) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1275, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1224, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1016, in _send_output self.send(msg) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 956, in send self.connect() File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1392, in connect server_hostname=server_hostname) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py", line 412, in wrap_socket session=session File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py", line 853, in _create self.do_handshake() File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py", line 1117, in do_handshake self._sslobj.do_handshake() ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1056) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "firedrake-install", line 1196, in <module> install("petsc/") File "firedrake-install", line 670, in install build_and_install_petsc() File "firedrake-install", line 756, in build_and_install_petsc urllib.request.urlretrieve(url, filename=tarball) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 247, in urlretrieve with contextlib.closing(urlopen(url, data)) as fp: File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 222, in urlopen return opener.open(url, data, timeout) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 525, in open response = self._open(req, data) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 543, in _open '_open', req) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 503, in _call_chain result = func(*args) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 1360, in https_open context=self._context, check_hostname=self._check_hostname) File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 1319, in do_open raise URLError(err) urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1056)> I’d appreciate any insight you might have. Sincerely, Max Heldman

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Problem to install Firedrake on Ubuntu 18.04.2 LTS
by Simone Puel 21 Jun '19

21 Jun '19

Hi, My name is Simone Puel, a graduate student at the University of Texas at Austin. I would like to use Firedrake for my research, but once installed I run the test suggested to check that the Firedrake installation is fully functional, but I got the following error. I am using Ubuntu-Mate distribution with ubuntu bionic 18.04.2 LTS with Python 3.6.8 in Anaconda environment. Could you help me in the installation, please? Thank you so much in advance. Have a wonderful day. Best regards, Simone ERROR: simone@simone:~$ source firedrake/bin/activate (firedrake) simone@simone:~$ cd firedrake/src/firedrake/ (firedrake) simone@simone:~/firedrake/src/firedrake$ make alltest Building extension modules Linting firedrake codebase Linting firedrake test suite Linting firedrake scripts Running all regression tests ============================================================ test session starts ============================================================= platform linux -- Python 3.6.6, pytest-4.4.0, py-1.8.0, pluggy-0.9.0 rootdir: /home/simone/firedrake/src/firedrake, inifile: setup.cfg plugins: xdist-1.27.0, forked-1.0.2 collected 0 items / 1 errors =================================================================== ERRORS =================================================================== _______________________________________________________ ERROR collecting test session ________________________________________________________ ../../lib/python3.6/site-packages/_pytest/config/__init__.py:435: in _importconftest return self._conftestpath2mod[conftestpath] E KeyError: local('/home/simone/firedrake/src/firedrake/tests/extrusion/conftest.py') During handling of the above exception, another exception occurred: ../h5py/h5py/__init__.py:26: in <module> from . import _errors E ImportError: libhdf5.so.101: cannot open shared object file: No such file or directory During handling of the above exception, another exception occurred: ../../lib/python3.6/site-packages/_pytest/config/__init__.py:441: in _importconftest mod = conftestpath.pyimport() ../../lib/python3.6/site-packages/py/_path/local.py:701: in pyimport __import__(modname) ../../lib/python3.6/site-packages/_pytest/assertion/rewrite.py:299: in load_module six.exec_(co, mod.__dict__) tests/extrusion/conftest.py:2: in <module> from firedrake import ExtrudedMesh, UnitSquareMesh, UnitIntervalMesh firedrake/__init__.py:48: in <module> from firedrake.checkpointing import * firedrake/checkpointing.py:3: in <module> from firedrake import hdf5interface as h5i firedrake/hdf5interface.pyx:1: in init firedrake.hdf5interface import h5py ../h5py/h5py/__init__.py:30: in <module> raise ImportError("You cannot import h5py from inside the install directory.\nChange to another directory first.") E ImportError: You cannot import h5py from inside the install directory. E Change to another directory first. During handling of the above exception, another exception occurred: ../../lib/python3.6/site-packages/py/_path/common.py:377: in visit for x in Visitor(fil, rec, ignore, bf, sort).gen(self): ../../lib/python3.6/site-packages/py/_path/common.py:418: in gen dirs = self.optsort([p for p in entries ../../lib/python3.6/site-packages/py/_path/common.py:419: in <listcomp> if p.check(dir=1) and (rec is None or rec(p))]) ../../lib/python3.6/site-packages/_pytest/main.py:660: in _recurse ihook = self.gethookproxy(dirpath) ../../lib/python3.6/site-packages/_pytest/main.py:481: in gethookproxy my_conftestmodules = pm._getconftestmodules(fspath) ../../lib/python3.6/site-packages/_pytest/config/__init__.py:419: in _getconftestmodules mod = self._importconftest(conftestpath.realpath()) ../../lib/python3.6/site-packages/_pytest/config/__init__.py:458: in _importconftest raise ConftestImportFailure(conftestpath, sys.exc_info()) E _pytest.config.ConftestImportFailure: (local('/home/simone/firedrake/src/firedrake/tests/extrusion/conftest.py'), (<class 'ImportError'>, ImportError('You cannot import h5py from inside the install directory.\nChange to another directory first.',), <traceback object at 0x7fe2527a1848>)) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ========================================================== 1 error in 4.85 seconds =========================================================== Makefile:64: recipe for target 'test' failed make: *** [test] Error 2 -- *Simone Puel* Ph.D. student in Geological Sciences at the University of Texas at Austin Jackson School of Geosciences & Institute for Geophysics (UTIG) JGB 5.332 & ROC 2.116L spuel(a)utexas.edu +1 (737)-230-6811

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