- firedrake - imperial.ac.uk

Installation fail inquiry
by Qiwei Zhan, Ph.D. 07 Oct '19

07 Oct '19

Hi colleagues, I have spent several weeks to install firedrake, but still failed. I have totally uninstall anaconda to make sure "conda deactivate", but my installation still fails, even earlier in the initial steps, mainly related to "pip is configured with locations that require TLS/SSL, however the ssl module in Python is not available." My installation command is "python3 firedrake-install" , I am using LinuxMint17. The log file is attached as "firedrake-install.log" On the opposite side, if I use Anaconda ("conda activate"), I can go to the very last steps, but fails with " firedrake/supermeshimpl.c:1606:3: error: unknown type name ‘MPI_Message’ MPI_Message ob_mpi" The log file is attached as the second file "firedrake-install-Anaconda.log". I would appreicate it, if anyone could help me with this, thank you! Thank you! Qiwei *Qiwei Zhan，Ph.D.* Peter O’Donnell, Jr. Postdoctoral Fellow Oden Institute for Computational Engineering and Sciences University of Texas at Austin Email: qiwei.zhan(a)utexas.edu; qiwei.zhan(a)alumni.duke.edu <qiwei.zhan(a)duke.edu>

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Re: [firedrake] Gathering D.O.F.s onto one process
by Matthew Knepley 03 Oct '19

03 Oct '19

On Mon, Sep 30, 2019 at 10:46 PM Sentz, Peter <sentz2(a)illinois.edu> wrote: > So is there a way to return how the global degrees of freedom are > distributed across processors? > I would recommend changing your workflow so that you do not need this, since it complicates everything. However, if you still really want to do this, you can 1) Tell the DM to constructs mappings back to the original ordering https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/DM/DMSetUseNatu… 2) After distribution, map a vector back to that ordering https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/DMPLEX/DMPlexGl… 3) Output that vector using view() Note that DMDA outputs in the natural ordering by default since it is not expensive in the structured case. Thanks, Matt > -Peter > ------------------------------ > *From:* Matthew Knepley <knepley(a)gmail.com> > *Sent:* Monday, September 30, 2019 6:33 PM > *To:* Sentz, Peter <sentz2(a)illinois.edu> > *Cc:* Firedrake Project <firedrake(a)imperial.ac.uk> > *Subject:* Re: [firedrake] Gathering D.O.F.s onto one process > > On Mon, Sep 30, 2019 at 3:45 PM Sentz, Peter <sentz2(a)illinois.edu> wrote: > > Hi, > > u.vector().view() does not work because a Firedrake.vector.Vector has no > such method. > > However, I did try the following: > > > Q = PETSc.Viewer().createBinary('name.dat','w') > > with u.dat.vec_ro as vu: > vu.view(Q) > > Then in separate .py file loaded this .dat file and looked at the > resulting vector. Unfortunately it does not maintain the serial ordering. > This is perplexing because according to > https://www.firedrakeproject.org/demos/parprint.py.html, shouldn't the > .view() maintain serial ordering? > > > I think we may have a misunderstanding about what maintaining an ordering > means. If you output > using the PETSc parallel viewer, then it will definitely output in the > same order in which the vector > is distributed in parallel, meaning the dofs from proc0, then proc1, etc. > However, it now sounds like > this order does not match the order you have in serial, which is > completely understandable. When > you distribute meshes, it is normal to partition them to reduce > communication, which necessitates > reordering. > > Thanks, > > Matt > > > Peter > ------------------------------ > *From:* Matthew Knepley <knepley(a)gmail.com> > *Sent:* Saturday, September 28, 2019 12:14 AM > *To:* Sentz, Peter <sentz2(a)illinois.edu> > *Cc:* firedrake(a)imperial.ac.uk <firedrake(a)imperial.ac.uk> > *Subject:* Re: [firedrake] Gathering D.O.F.s onto one process > > On Thu, Sep 26, 2019 at 8:15 PM Sentz, Peter <sentz2(a)illinois.edu> wrote: > > Hello, > > I am working on a project where I need to save the Numpy arrays of degrees > of freedom of FE functions and use them in another script. I am wondering > how to get consistent results when using MPI. > > Here's a minimal example of what I would like to do: > > ---------------------------------------- > from firedrake import * > import numpy as np > > mesh = UnitSquareMesh(3, 3) > > V = FunctionSpace(mesh, "CG", 1) > u = TrialFunction(V) > v = TestFunction(V) > f = Function(V) > x, y = SpatialCoordinate(mesh) > f.interpolate((1+8*pi*pi)*cos(x*pi*2)*cos(y*pi*2)) > a = (dot(grad(v), grad(u)) + v * u) * dx > L = f * v * dx > > u = Function(V) > solve(a == L, u, solver_parameters={'ksp_type': 'cg'}) > > U = u.vector().gather() > > > Here I think you can just use > > u.vector().view(viewer) > > with a petsc4py Viewer of the appropriate type (maybe binary?). > > Thanks, > > Matt > > > if u.comm.rank == 0: > print(U) > name = 'U_global_' + str(u.comm.size) + '.npy' > np.save(name,U) > --------------------------------------------------------------------- > > If I run this in serial, and then with two processes in MPI, I get two > files 'U_global_1.npy' and 'U_global_2.npy' but they do not agree. The > first (in serial) has values: > > [-0.29551776 -0.67467152 -0.67467152 -0.15155862 0.06606523 0.06606523 > 0.36508954 0.36508954 1.33298501 1.33298501 0.06606523 -0.15155862 > 0.06606522 -0.67467153 -0.67467153 -0.29551776] > > > while the second has values: > > [-0.67467152 -0.67467152 -0.29551776 0.06606523 -0.15155862 0.06606523 > 0.06606523 -0.67467152 -0.15155862 -0.29551776 -0.67467152 0.06606523 > 1.33298501 0.36508954 0.36508954 1.33298502] > > > How do I get the parallel implementation to match the ordering of the > d.o.f.s in the serial case? And avoiding this .gather() approach would be > good, because I really only need the array gathered on a single process. > > Thanks, > > Peter > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > <http://www.cse.buffalo.edu/~knepley/> > > > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > <http://www.cse.buffalo.edu/~knepley/> > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [firedrake] Gathering D.O.F.s onto one process
by Matthew Knepley 01 Oct '19

01 Oct '19

On Mon, Sep 30, 2019 at 3:45 PM Sentz, Peter <sentz2(a)illinois.edu> wrote: > Hi, > > u.vector().view() does not work because a Firedrake.vector.Vector has no > such method. > > However, I did try the following: > > > Q = PETSc.Viewer().createBinary('name.dat','w') > > with u.dat.vec_ro as vu: > vu.view(Q) > > Then in separate .py file loaded this .dat file and looked at the > resulting vector. Unfortunately it does not maintain the serial ordering. > This is perplexing because according to > https://www.firedrakeproject.org/demos/parprint.py.html, shouldn't the > .view() maintain serial ordering? > I think we may have a misunderstanding about what maintaining an ordering means. If you output using the PETSc parallel viewer, then it will definitely output in the same order in which the vector is distributed in parallel, meaning the dofs from proc0, then proc1, etc. However, it now sounds like this order does not match the order you have in serial, which is completely understandable. When you distribute meshes, it is normal to partition them to reduce communication, which necessitates reordering. Thanks, Matt > Peter > ------------------------------ > *From:* Matthew Knepley <knepley(a)gmail.com> > *Sent:* Saturday, September 28, 2019 12:14 AM > *To:* Sentz, Peter <sentz2(a)illinois.edu> > *Cc:* firedrake(a)imperial.ac.uk <firedrake(a)imperial.ac.uk> > *Subject:* Re: [firedrake] Gathering D.O.F.s onto one process > > On Thu, Sep 26, 2019 at 8:15 PM Sentz, Peter <sentz2(a)illinois.edu> wrote: > > Hello, > > I am working on a project where I need to save the Numpy arrays of degrees > of freedom of FE functions and use them in another script. I am wondering > how to get consistent results when using MPI. > > Here's a minimal example of what I would like to do: > > ---------------------------------------- > from firedrake import * > import numpy as np > > mesh = UnitSquareMesh(3, 3) > > V = FunctionSpace(mesh, "CG", 1) > u = TrialFunction(V) > v = TestFunction(V) > f = Function(V) > x, y = SpatialCoordinate(mesh) > f.interpolate((1+8*pi*pi)*cos(x*pi*2)*cos(y*pi*2)) > a = (dot(grad(v), grad(u)) + v * u) * dx > L = f * v * dx > > u = Function(V) > solve(a == L, u, solver_parameters={'ksp_type': 'cg'}) > > U = u.vector().gather() > > > Here I think you can just use > > u.vector().view(viewer) > > with a petsc4py Viewer of the appropriate type (maybe binary?). > > Thanks, > > Matt > > > if u.comm.rank == 0: > print(U) > name = 'U_global_' + str(u.comm.size) + '.npy' > np.save(name,U) > --------------------------------------------------------------------- > > If I run this in serial, and then with two processes in MPI, I get two > files 'U_global_1.npy' and 'U_global_2.npy' but they do not agree. The > first (in serial) has values: > > [-0.29551776 -0.67467152 -0.67467152 -0.15155862 0.06606523 0.06606523 > 0.36508954 0.36508954 1.33298501 1.33298501 0.06606523 -0.15155862 > 0.06606522 -0.67467153 -0.67467153 -0.29551776] > > > while the second has values: > > [-0.67467152 -0.67467152 -0.29551776 0.06606523 -0.15155862 0.06606523 > 0.06606523 -0.67467152 -0.15155862 -0.29551776 -0.67467152 0.06606523 > 1.33298501 0.36508954 0.36508954 1.33298502] > > > How do I get the parallel implementation to match the ordering of the > d.o.f.s in the serial case? And avoiding this .gather() approach would be > good, because I really only need the array gathered on a single process. > > Thanks, > > Peter > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > <http://www.cse.buffalo.edu/~knepley/> > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Gathering D.O.F.s onto one process
by Sentz, Peter 28 Sep '19

28 Sep '19

Hello, I am working on a project where I need to save the Numpy arrays of degrees of freedom of FE functions and use them in another script. I am wondering how to get consistent results when using MPI. Here's a minimal example of what I would like to do: ---------------------------------------- from firedrake import * import numpy as np mesh = UnitSquareMesh(3, 3) V = FunctionSpace(mesh, "CG", 1) u = TrialFunction(V) v = TestFunction(V) f = Function(V) x, y = SpatialCoordinate(mesh) f.interpolate((1+8*pi*pi)*cos(x*pi*2)*cos(y*pi*2)) a = (dot(grad(v), grad(u)) + v * u) * dx L = f * v * dx u = Function(V) solve(a == L, u, solver_parameters={'ksp_type': 'cg'}) U = u.vector().gather() if u.comm.rank == 0: print(U) name = 'U_global_' + str(u.comm.size) + '.npy' np.save(name,U) --------------------------------------------------------------------- If I run this in serial, and then with two processes in MPI, I get two files 'U_global_1.npy' and 'U_global_2.npy' but they do not agree. The first (in serial) has values: [-0.29551776 -0.67467152 -0.67467152 -0.15155862 0.06606523 0.06606523 0.36508954 0.36508954 1.33298501 1.33298501 0.06606523 -0.15155862 0.06606522 -0.67467153 -0.67467153 -0.29551776] while the second has values: [-0.67467152 -0.67467152 -0.29551776 0.06606523 -0.15155862 0.06606523 0.06606523 -0.67467152 -0.15155862 -0.29551776 -0.67467152 0.06606523 1.33298501 0.36508954 0.36508954 1.33298502] How do I get the parallel implementation to match the ordering of the d.o.f.s in the serial case? And avoiding this .gather() approach would be good, because I really only need the array gathered on a single process. Thanks, Peter

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25 Sep '19

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Congratulations Thomas Gibson
by Ham, David A 05 Sep '19

05 Sep '19

Dear Firedrakers, Please join me in congratulating Thomas Gibson on passing his viva today! For those at Imperial, there will be drinks in the Queen’s Arms from 1700 Regards, David -- Dr David Ham Department of Mathematics Imperial College London https://www.imperial.ac.uk/people/david.ham https://www.firedrakeproject.org

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Guest posting opportunities
by Kaley Spenser 02 Sep '19

02 Sep '19

Hi firedrakeproject.org team, My name is Kaley, and I'm a content manager at Moltensoft Studio. I’ve seen you shared some engaging content on your site. I’m reaching out because I found cool posts on your site and I had some ideas. I think firedrakeproject.org audience would positively love, and I was wondering if you’d be open to a guest blog post. Our content is always unique, relevant, informative, and interesting. To give you an idea of writing style, here are two examples of our posts: 1. https://geekygadgets.in/gadgets-that-will-make-smartphone-even-smarter/ 2. https://technicalustad.com/vcruntime140-dll-is-missing/ I can deliver the post for your website in around five days, or quicker, if necessary. Looking forward to hearing from you. With Best regards Kaley Spencer

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Re: [firedrake] Installing firedrake on a HPC system without package manager
by Lawrence Mitchell 30 Aug '19

30 Aug '19

Hi Niall, (adding in firedrake cc again) > On 1 Aug 2019, at 15:43, Madden, Niall <niall.madden(a)nuigalway.ie> wrote: > > Hi Lawrence, > Thanks for the swift reply. I don't want to reply to the whole list with too much specific information on the system Please do reply with the list. That way others who might be able to help will see things. >> Can you give us some details on this system? Is it a cray, for example? > The system is ICHEC's "kay" - Ireland's national supercomputer for academic purposes: > https://www.ichec.ie/about/infrastructure/kay > >> Normally we find when building on supercomputers (contrary to the one-shot "firedrake-install" unfortunately), >> that it is best to build PETSc by hand. One then sets the appropriate environment variables and runs >> firedrake-install --honour-petsc-dir. This might be the best step forward. > > Thanks for the tip. I tried compiling PETSc myself: > > git clone https://github.com/firedrakeproject/petsc.git (but should I be cloning fromhttps://bitbucket.org/petsc/petsc ?) No, cloning from the firedrakeproject "fork" is correct. We keep a (reasonably up to date) version of petsc that is known good with all Firedrake components there: it isn't otherwise special. > ./configure --with-c2html=0 --download-chaco --download-metis --download-parmetis --download-scalapack --download-hypre --download-mumps --download-netcdf --download-hdf5 --download-pnetcdf --download-exodusii --download-mpich --download-suitesparse=1 --download-petsc4py=1 --download-mpi4py=1 --download-fblaslapack --download-zlib > > Then I set PETSC_DIR and PETSC_ARCH, and PYTHONPATH > > Then I try to install Firedrake with > python3 firedrake-install --no-package-manager -v --disable-ssh --honour-petsc-dir --honour-pythonpath > > But it eventually fails compiling libspatialindex > for reasons that seem to be related to the mpicxx , but it is a little opaque: > undefined reference to `psm2_info_query(a)PSM2_1.0' Can you attach the contents of firedrake-install.log (maybe gzip it since it is likely to be large). Thanks, Lawrence

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Problem installing Firedrake on Ubuntu 18.04
by Karin&NiKo 29 Aug '19

29 Aug '19

Dear Firedrake team, I am having big troubles in installing Firedrake on Ubuntu 18.04. - First I would like to report the error that I get when running : python3 ./firedrake-install --disable-ssh. Let me point that I run it behind a proxy but setting http_proxy seems to work, at least for several steps on the installation process. You can find the log as attached file.I have tried to run this script as a simple user or as root but i get the same error message. I also attach the echo of the script from the shell because it seems to me that they give some contreversial information of the origin of the error. - Second, I would like to know if there is a way to rerun the installation script *without* erasing the directory that the previous failed execution created. Indeed the script complains that "Specified venv '/home/xxxxx/dev/Firedrake/firedrake' already exists. Can't install into existing venv '/home/xxxxxx/dev/Firedrake/firedrake'" and the only solution I found is to erase the folder and rerun the script from the begining, meaning downloading again all that I have already downloaded. I thank you in advance for your help, Nicolas

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Re: [firedrake] Error instalation
by Sagiyama, Koki 28 Aug '19

28 Aug '19

Hi Emmanuel, (Added firedrake back so that others can also help.) So this is where your installation fails: mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DH5_USE_16_API -I./h5py -I/home/hpc/petsc-3.11.3/arch-FreeFem-sources/include -I/home/hpc/firedrake/src/h5py/lzf -I/home/hpc/firedrake/lib/python3.5/site-packages/numpy/core/include -I/home/hpc/firedrake/lib/python3.5/site-packages/mpi4py/include -I/home/hpc/firedrake/include -I/usr/include/python3.5m -c /home/hpc/firedrake/src/h5py/h5py/defs.c -o build/temp.linux-x86_64-3.5/home/hpc/firedrake/src/h5py/h5py/defs.o with this error: /home/hpc/firedrake/src/h5py/h5py/api_compat.h:27:18: fatal error: hdf5.h: Arquivo ou diretório não encontrado I think `-I/home/hpc/petsc-3.11.3/arch-FreeFem-sources/include` is the correct flag to find `hdf5.h,` so I don't know why it failed. Does anyone have any idea? Thanks, Koki ________________________________ From: Emmanuel Yarleque Medina <eyarmed(a)gmail.com> Sent: Tuesday, August 27, 2019 4:36:36 PM To: Sagiyama, Koki <k.sagiyama(a)imperial.ac.uk> Subject: Re: [firedrake] Error instalation Hi Koki, the configuration of Petsc, for example I installed it with the following configuration: ./configure --with-cc=gcc --with-fc=gfortran --download-mpich --download-fblaslapack --download-mumps --download-scalapack --download-hypre --download-metis --download-parmetis --download-arpack --download-hdf5 --download-eigen --download-ptscotch --download-suitesparse --with-scalar-type=real --with-debugging=no El mar., 27 ago. 2019 a las 12:59, Sagiyama, Koki (<k.sagiyama(a)imperial.ac.uk<mailto:k.sagiyama@imperial.ac.uk>>) escribió: Dear Emmanuel, It seems that you are trying to use a pre-installed PETSc, but the installer is unable to find some file (`hdf5.h`). Could you tell us the configuration options you used to install PETSc? When we make `firedrake-install` do all the installation work, it asks PETSc to install a number of dependencies (including hdf5), so if we want to build PETSc separately, we must configure it with correct options as `firedrake-install` would. You can see those options by running: python3 firedrake-install --show-petsc-configure-options To ensure compatibility with all firedrake components, we also recommend that PETSc be downloaded from the following branch (if you have not done so), which we try to keep up-to-date with the upstream PETSc as frequently as possible: https://github.com/firedrakeproject/petsc.git [https://avatars0.githubusercontent.com/u/5558005?s=400&v=4]<https://github.com/firedrakeproject/petsc.git> firedrakeproject/petsc<https://github.com/firedrakeproject/petsc.git> github.com<http://github.com> Mirror of https://bitbucket.org/petsc/petsc. Contribute to firedrakeproject/petsc development by creating an account on GitHub. Regards, Koki ________________________________ From: firedrake-bounces(a)imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces(a)imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk>> on behalf of Emmanuel Yarleque Medina <eyarmed(a)gmail.com<mailto:eyarmed@gmail.com>> Sent: Friday, August 23, 2019 7:35:22 PM To: firedrake <firedrake(a)imperial.ac.uk<mailto:firedrake@imperial.ac.uk>> Subject: [firedrake] Error instalation Hi users, I have the following error installing Firedrake on ubuntu 16.04 (firedrake) hpc@hpc:~/firedrake/src/firedrake$ make alltest Building extension modules Traceback (most recent call last): File "setup.py", line 8, in <module> import petsc4py ImportError: No module named 'petsc4py' Linting firedrake codebase Linting firedrake test suite Linting firedrake scripts Running all regression tests ============================================ test session starts ============================================ platform linux -- Python 3.5.2, pytest-5.1.1, py-1.8.0, pluggy-0.12.0 rootdir: /home/hpc/firedrake/src/firedrake, inifile: setup.cfg plugins: forked-1.0.2, xdist-1.29.0 collected 0 items / 1 errors ================================================== ERRORS =================================================== _______________________________________ ERROR collecting test session _______________________________________ ../../lib/python3.5/site-packages/_pytest/config/__init__.py:436: in _importconftest return self._conftestpath2mod[conftestpath] E KeyError: local('/home/hpc/firedrake/src/firedrake/tests/extrusion/conftest.py') During handling of the above exception, another exception occurred: ../../lib/python3.5/site-packages/_pytest/config/__init__.py:442: in _importconftest mod = conftestpath.pyimport() ../../lib/python3.5/site-packages/py/_path/local.py:701: in pyimport __import__(modname) <frozen importlib._bootstrap>:969: in _find_and_load ??? <frozen importlib._bootstrap>:958: in _find_and_load_unlocked ??? <frozen importlib._bootstrap>:673: in _load_unlocked ??? ../../lib/python3.5/site-packages/_pytest/assertion/rewrite.py:140: in exec_module exec(co, module.__dict__) tests/extrusion/conftest.py:2: in <module> from firedrake import ExtrudedMesh, UnitSquareMesh, UnitIntervalMesh firedrake/__init__.py:5: in <module> if "PETSC_DIR" in os.environ and not config["options"]["honour_petsc_dir"]: E TypeError: 'NoneType' object is not subscriptable During handling of the above exception, another exception occurred: ../../lib/python3.5/site-packages/py/_path/common.py:377: in visit for x in Visitor(fil, rec, ignore, bf, sort).gen(self): ../../lib/python3.5/site-packages/py/_path/common.py:418: in gen dirs = self.optsort([p for p in entries ../../lib/python3.5/site-packages/py/_path/common.py:419: in <listcomp> if p.check(dir=1) and (rec is None or rec(p))]) ../../lib/python3.5/site-packages/_pytest/main.py:606: in _recurse ihook = self.gethookproxy(dirpath) ../../lib/python3.5/site-packages/_pytest/main.py:424: in gethookproxy my_conftestmodules = pm._getconftestmodules(fspath) ../../lib/python3.5/site-packages/_pytest/config/__init__.py:420: in _getconftestmodules mod = self._importconftest(conftestpath.realpath()) ../../lib/python3.5/site-packages/_pytest/config/__init__.py:450: in _importconftest raise ConftestImportFailure(conftestpath, sys.exc_info()) E _pytest.config.ConftestImportFailure: (local('/home/hpc/firedrake/src/firedrake/tests/extrusion/conftest.py'), (<class 'TypeError'>, TypeError("'NoneType' object is not subscriptable",), <traceback object at 0x7f4728146088>)) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ============================================= 1 error in 0.29s ============================================== Makefile:64: recipe for target 'test' failed make: *** [test] Error 2

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