- firedrake - imperial.ac.uk

Obtaining the solution for a subset of nodes in Parallel
by Venketeswaran, Abhishek (FN) 12 Feb '22

12 Feb '22

Hi, I am running a simulation on a mesh with large number of nodes. I need to capture the results at a subset of the nodes. I am running into trouble when I execute the job in parallel. Kindly take a look at the lines in red to understand the problem. While I am not getting an error, I am also not able to get the correct results here. I would appreciate your assistance in this regard. Thanks Abhishek ########################################### # Obtaining the solution for a subset of mesh nodes ########################################## x,y,z = SpatialCoordinate(W.mesh()) phi=ufl.mathfunctions.Atan2(y,x) Nsteps=int(T/deltat) time=np.linspace(0,T,Nsteps+1) resnodesx,rescoords=axialslice(mesh,Ro,np.pi/2) # axialslice returns a set of nodes and their coordinates corresponding to a particular criterion resnodes=resnodesx.astype(np.int32) #PETSc gives an error if the indices are not int32 # Trying to save the solution components at all time instants for a particular subset uradial=np.zeros((len(resnodes),len(time)+3)) utang=np.zeros((len(resnodes),len(time)+3)) uaxial=np.zeros((len(resnodes),len(time)+3)) uradial[:,:3]=rescoords utang[:,:3]=rescoords uaxial[:,:3]=rescoords for i in range(len(time)): t = time[i] collar_disp.assign([0.0,0.0,collar_load(t,T_pulse,f_c,amp=dispamp)]) solver1.solve() # Update old fields with new quantities u_nm1.assign(u_n) u_n.assign(u_np1) u_r.assign(interpolate(u_n[0]*cos(phi)+u_n[1]*sin(phi),W)) u_t.assign(interpolate(-u_n[0]*sin(phi)+u_n[1]*cos(phi),W)) u_z.assign(interpolate(u_n[2],W)) with u_r.dat.vec_ro as vur: #Obtained this idea from Printing in Parallel page of Firedrake Docs urad=vur.getValues(resnodes) print(len(urad)) # length of urad seems to differ for each process uradial[:,i+3]=urad with u_t.dat.vec_ro as vut: utan=vut.getValues(resnodes) utang[:,i+3]=utan with u_z.dat.vec_ro as vuz: uax=vuz.getValues(resnodes) uaxial[:,i+3]=uax if i%20 ==0: outfile.write(u_n,u_r,u_t,u_z, time=t) gc.collect() #Consequently the CSV's contain only a subset of the nodal results np.savetxt(csvradfilename,uradial,fmt='%1.6e',delimiter=',') np.savetxt(csvtangfilename,utang,fmt='%1.6e',delimiter=',') np.savetxt(csvaxialfilename,uaxial,fmt='%1.6e',delimiter=',') -- Abhishek Venketeswaran NETL Research Associate - ORISE National Energy Technology Laboratory Department of Energy abhishek.venketeswaran(a)netl.doe.gov Work: 412-386-4833 Mobile: 716-507-7890 www.netl.doe.gov<http://www.netl.doe.gov> [cid:fc8c5c43-be1a-42c1-880c-cb38951ae7af]

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Firedrake support on GitHub Discussions
by Ham, David A 02 Feb '22

02 Feb '22

Dear Firedrakers, I’m writing to update you on a change to the preferred support routes for Firedrake. The preferred way to ask for Firedrake help is now on GitHub Discussions. This will enable the Firedrake community to build up a persistent and searchable collection of answers to Firedrake questions, and means that users only need a GitHub account to post questions. Please post your requests here: https://github.com/firedrakeproject/firedrake/discussions/categories/firedr… Please also always feel welcome to discuss your issues with us on the Firedrake Slack channel. We always enjoy interacting with and helping our users. Yours, David -- Reader in Computational Mathematics Department of Mathematics Imperial College London [Graphical user interface, text Description automatically generated]<https://www.amazon.co.uk/dp/B09NR9R9P3>

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Help with implementing steps in simulation
by Venketeswaran, Abhishek (FN) 01 Feb '22

01 Feb '22

Hi, I would like to prescribe a boundary condition for an initial time duration and then remove it for the remaining time duration. Commercial finite element solvers allow you to do this by specifying steps. I tried to implement it using the code below. This is giving nonsensical results at and after the time at which the BCs change. Can you please assist me in how I may implement this properly. I can share the full code if needed. m = rho*inner((u - 2.0 * u_n + u_nm1),v) / Constant(dt * dt) * dxlump k= inner(sigma(u_n),epsilon(v))*dx def collar_load(t,T,freq,amp=1.0): return amp*hanning(t,T)*stepfn(t,T)*np.sin(freq*t) # Define the loading as an expression depending on t t=0 collar_disp= Constant([0.0, 0.0, 0.0]) F = m+k a, r = lhs(F), rhs(F) zero = Constant((0.0, 0.0, 0.0)) # Dirichlet BC that is valid for the entire time duration bc1 = DirichletBC(V, zero, 11) # Collar BC that remains on till T_pulse bc2= DirichletBC(V, collar_disp, 21) # My attempt of defining two problems to mimic two simulation steps problem1 = LinearVariationalProblem(a, r, u_np1, bcs=[bc1,bc2], constant_jacobian=True) solver1 = LinearVariationalSolver(problem1, solver_parameters=params) problem2 = LinearVariationalProblem(a, r, u_np1, bcs=[bc1], constant_jacobian=True) solver2 = LinearVariationalSolver(problem2, solver_parameters=params) for i in range(len(time)): t = time[i] if (t<=T_pulse): solver1.solve() else: solver2.solve() u_nm1.assign(u_n) u_n.assign(u_np1) -- Abhishek Venketeswaran NETL Research Associate - ORISE National Energy Technology Laboratory Department of Energy abhishek.venketeswaran(a)netl.doe.gov Work: 412-386-4833 Mobile: 716-507-7890 www.netl.doe.gov<http://www.netl.doe.gov> [cid:97ebd409-8c9c-4361-9753-e4c626433151]

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Erroneous results for ultrasonic guided wave simulation with KMV elements
by Venketeswaran, Abhishek (FN) 28 Jan '22

28 Jan '22

Hi, The KMV discretized elastic wave solver seems to be doing something weird. I am essentially prescribing a sinusoidal impulse as displacement at a circumferential section for a short duration (150 microseconds). I have attached snapshots at 200 microseconds and 600 microseconds. Instead to the pulse traveling at group velocity, some random error is increasing near the loading section. I am not able to figure out what could be the problem. I have tried out different preconditioners while maintaining a direct "preonly" KSP iterations. Do you have any idea where I could be going wrong? -- Abhishek Venketeswaran NETL Research Associate - ORISE National Energy Technology Laboratory Department of Energy abhishek.venketeswaran(a)netl.doe.gov Work: 412-386-4833 Mobile: 716-507-7890 www.netl.doe.gov<http://www.netl.doe.gov> [cid:5c03a053-94d0-49c7-84af-375ffa90acbb]

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Elastic Wave Propagation in Pipe Simulation Failing
by Venketeswaran, Abhishek (FN) 21 Jan '22

21 Jan '22

Hi, I have spent considerable time trying to debug my code and am not able to find the bug in the code. I am essentially trying to simulate 3D elastic wave propagation in a pipe fixed on both ends and having an ultrasonic collar triggering ultrasonic impulse on a portion of the outer pipe segment. I would ideally like to use the KMV elements (similar to the spyro package). I generated a tetrahedral mesh of the pipe using GMsh and labeled the ends of the pipe using tag "1" and the collar segment as "2". Next I wrote the UFL expressions for 2nd order central difference for acceleration term and the elasticity as well as traction terms. The code runs but the displacement at certain nodes diverges to infinity and results in nonsensical results. I have tried multiple things including 1. specifying the collar load as displacement as well as traction 2. trying out KMV and CG element 3. trying out different KSP methods and preconditioners 4. Formulating the problem using semi-implicit HHT as well as second order explicit difference method 5. Ensuring the Gamma value of the tetrahedral mesh is atleast 0.2 I would really appreciate it if someone could help me out with this. -- Abhishek Venketeswaran NETL Research Associate - ORISE National Energy Technology Laboratory Department of Energy abhishek.venketeswaran(a)netl.doe.gov Work: 412-386-4833 Mobile: 716-507-7890 www.netl.doe.gov<http://www.netl.doe.gov> [cid:abfe3d17-ce71-45f1-8175-8e0cd802eaee]

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Apple silicon installation
by MUFANG YING 17 Jan '22

17 Jan '22

Hi, When I wanted to install the package on my M1 chip macbook, I found out that the installation is not that smooth since the home brew has some updates on the prefix. I was wondering if you could give me some advice on how to successfully install firedrake on M1 macbook. I would really appreciate any feedback. Thank you. Best, Mufang Ying

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another job
by Cotter, Colin J 13 Jan '22

13 Jan '22

Dear Firedrake friends, I've got another job advert out, this time for a 26 month postdoctoral contract. Please let me know offlist if you have any questions. https://www.imperial.ac.uk/jobs/description/NAT01069/research-associate-com… all the best ---cjc Professor Colin Cotter (he/him) Department of Mathematics 755, Huxley Building Imperial College London South Kensington Campus United Kingdom of Great Britain and Northern Ireland +44 2075943468

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Postdoc
by Cotter, Colin J 09 Dec '21

09 Dec '21

Dear all, Here is a one year position that I am currently advertising. Please drop me a line off-list if you have questions about it. https://www.imperial.ac.uk/jobs/description/NAT01051/research-associate-com… all the best --cjc Professor Colin Cotter (he/him) Department of Mathematics 755, Huxley Building Imperial College London South Kensington Campus United Kingdom of Great Britain and Northern Ireland +44 2075943468

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Find out more about our updated Terms of Service
by Google 08 Dec '21

08 Dec '21

firedrake(a)imperial.ac.uk On 5 January 2022, we’re making some changes to our Terms of Service. These changes won’t affect the way that you use Google services, but they’ll make it easier for you to understand what to expect from Google – and what we expect from you – as you use our services. You can review the new terms here <https://accounts.google.com/AccountChooser?Email=firedrake%40imperial.ac.uk…>. At a glance, here’s what this update means for you: - *More clarity on what you can expect from Google and what we expect from you*: We’re providing more examples to describe the mutually respectful conduct that we expect from all of our users. - *Improved readability*: While our terms remain a legal document, we’ve done our best to make them easier to understand, including reorganising some topics so that they’re easier to find. If you use Family Link to manage a Google Account for someone else, please take some time to talk to them about these changes. Thank you for using Google! Google LLC, 1600 Amphitheatre Parkway, Mountain View, CA, 94043, USA You have received this email to update you about important changes to Google’s Terms of Service.

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firedrake install failed when downloading Eigen
by Yamazaki, Hiroe 06 Dec '21

06 Dec '21

Hi firedrake team, I am installing firedrake on my Ubuntu 14.04 and failed when downloading Eigen due to ssl.SSLCertVerificationError. Some of the error messages are as below, and I’ve attached firedrake-install.log. Any help to fix this would be appreciated. All the best, Hiroe *** Downloading Eigen from 'https://github.com/eigenteam/eigen-git-mirror/archive/3.3.3.tar.gz' to 'eigen-3.3.3.tgz' Traceback (most recent call last): File "/usr/local/lib/python3.7/urllib/request.py", line 1317, in do_open encode_chunked=req.has_header('Transfer-encoding')) File "/usr/local/lib/python3.7/http/client.py", line 1229, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/local/lib/python3.7/http/client.py", line 1275, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/local/lib/python3.7/http/client.py", line 1224, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/local/lib/python3.7/http/client.py", line 1016, in _send_output self.send(msg) File "/usr/local/lib/python3.7/http/client.py", line 956, in send self.connect() File "/usr/local/lib/python3.7/http/client.py", line 1392, in connect server_hostname=server_hostname) File "/usr/local/lib/python3.7/ssl.py", line 412, in wrap_socket session=session File "/usr/local/lib/python3.7/ssl.py", line 850, in _create self.do_handshake() File "/usr/local/lib/python3.7/ssl.py", line 1108, in do_handshake self._sslobj.do_handshake() ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1045) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "firedrake-install", line 1649, in <module> install("petsc/") File "firedrake-install", line 882, in install build_and_install_petsc() File "firedrake-install", line 995, in build_and_install_petsc urllib.request.urlretrieve(url, filename=tarball) File "/usr/local/lib/python3.7/urllib/request.py", line 247, in urlretrieve with contextlib.closing(urlopen(url, data)) as fp: File "/usr/local/lib/python3.7/urllib/request.py", line 222, in urlopen return opener.open(url, data, timeout) File "/usr/local/lib/python3.7/urllib/request.py", line 525, in open response = self._open(req, data) File "/usr/local/lib/python3.7/urllib/request.py", line 543, in _open '_open', req) File "/usr/local/lib/python3.7/urllib/request.py", line 503, in _call_chain result = func(*args) File "/usr/local/lib/python3.7/urllib/request.py", line 1360, in https_open context=self._context, check_hostname=self._check_hostname) File "/usr/local/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:1045)> ***

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