July 2019 - firedrake - imperial.ac.uk

Installation problem on macOS Mojave (libspatialindex)
by Stern, Ari 01 Aug '19

01 Aug '19

Hi all, I've been attempting to install Firedrake using the standard install script, but the installation throws an error when attempting to compile/link libspatialindex. The firedrake-install.log is attached. A couple pieces of pertinent info: 1. I'm running macOS Mojave 10.14.5 with Homebrew Python 3. 2. Although I have a miniconda installation on my system, I did a "conda deactivate" before running the install script, so nothing from miniconda (except the conda binary itself) is in my path. Cheers, Ari

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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 03 Jul '19

03 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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