Re: [firedrake] mpirun acting up
You mistyped. dof_dset not dot_dset David On Thu, 19 May 2016 at 15:17 Francis Poulin <fpoulin@uwaterloo.ca> wrote:
Hello David and Lawrence,
I specified Uj it like a I would a regular python variable, maybe a bad idea.
You can see the code below.
https://github.com/francispoulin/firedrakeQG/blob/master/qg3d_jet.py
I tried to take David's advance and modified the following
q0 = Function(Vdg, name='pv').interpolate(Expression("-2.*Uj/Lj*tanh((x[1]-yc)/Lj)/pow(cosh((x[1]-yc)/Lj),2)",Uj=Uj, Lj=Lj, yc=yc)) V = q0.function_space() q0.dat.data[:] += 0.01*Uj*np.random.randn(V.dot_dset.size, *V.shape)
but that didn't seem to work. Now I get the following error,
Traceback (most recent call last): File "qg3d_jet.py", line 39, in <module> q0.dat.data[:] += 0.01*Uj*np.random.randn(V.dot_dset.size, *V.shape) File "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/functionspaceimpl.py", line 202, in __getattr__ return getattr(self.topological, name) AttributeError: 'FunctionSpace' object has no attribute 'dot_dset'
Sorry if I misunderstood the advice.
Francis
Francis Poulin Associate Professor Department of Applied Mathematics University of Waterloo
email: fpoulin@uwaterloo.ca Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637
------------------------------ *From:* firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk] on behalf of David Ham [David.Ham@imperial.ac.uk] *Sent:* Thursday, May 19, 2016 9:03 AM *To:* firedrake *Subject:* Re: [firedrake] mpirun acting up
How is Uj set? It looks like Uj has halos attached, while the others do not.
Regards,
David
On Thu, 19 May 2016 at 14:55 Francis Poulin <fpoulin@uwaterloo.ca> wrote:
Hello,
I am trying to run something with mpiand for some reason I am getting an error. This is both on my mac and ubuntu machines. Any ideas what might be the problem? I was able to do this before the upgrade and thought it should work in the same way but maybe something has change? Or maybe I'm doing something very silly.
Cheers, Francis
fpoulin@fpoulin-Gazelle:~/Research/Firedrake/QG/firedrakeQG$ mpirun -np 2 ~/software/firedrake/bin/python qg3d_jet.py Discontinuous Lagrange element requested on quadrilateral, creating DQ element. Discontinuous Lagrange element requested on quadrilateral, creating DQ element. Discontinuous Lagrange element requested on quadrilateral, creating DQ element. Discontinuous Lagrange element requested on quadrilateral, creating DQ element. COFFEE finished in 0.00156093 seconds (flops: 0 -> 0) Discontinuous Lagrange element requested on None, creating DQ element. COFFEE finished in 0.00156093 seconds (flops: 0 -> 0) Discontinuous Lagrange element requested on None, creating DQ element. Discontinuous Lagrange element requested on None, creating DQ element. Discontinuous Lagrange element requested on None, creating DQ element. COFFEE finished in 0.00232983 seconds (flops: 0 -> 0) Traceback (most recent call last): File "qg3d_jet.py", line 38, in <module> q0.dat.data[:] += 0.01*Uj*np.random.randn(*q0.dat.shape) ValueError: operands could not be broadcast together with shapes (500000,) (520000,) (500000,) Traceback (most recent call last): File "qg3d_jet.py", line 38, in <module> q0.dat.data[:] += 0.01*Uj*np.random.randn(*q0.dat.shape) ValueError: operands could not be broadcast together with shapes (500000,) (520000,) (500000,) COFFEE finished in 0.00234294 seconds (flops: 0 -> 0) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.
------------------ Francis Poulin Associate Professor Department of Applied Mathematics University of Waterloo
email: fpoulin@uwaterloo.ca Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637
Hello David, Thanks for the correction, and sorry for the silly mistake on my part. I should really learn what these different things are so that I'll know it's dof and not dot. Thanks to you, I am doing a 3D QG run of a barotropic jet. If the movie looks good I can send you a link when I post it on youtube. I hope it'll look impressive, but we will see. Francis ------------------ Francis Poulin Associate Professor Department of Applied Mathematics University of Waterloo email: fpoulin@uwaterloo.ca Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637 ________________________________ From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk] on behalf of David Ham [David.Ham@imperial.ac.uk] Sent: Thursday, May 19, 2016 9:19 AM To: firedrake Subject: Re: [firedrake] mpirun acting up You mistyped. dof_dset not dot_dset David On Thu, 19 May 2016 at 15:17 Francis Poulin <fpoulin@uwaterloo.ca<mailto:fpoulin@uwaterloo.ca>> wrote: Hello David and Lawrence, I specified Uj it like a I would a regular python variable, maybe a bad idea. You can see the code below. https://github.com/francispoulin/firedrakeQG/blob/master/qg3d_jet.py I tried to take David's advance and modified the following q0 = Function(Vdg, name='pv').interpolate(Expression("-2.*Uj/Lj*tanh((x[1]-yc)/Lj)/pow(cosh((x[1]-yc)/Lj),2)",Uj=Uj, Lj=Lj, yc=yc)) V = q0.function_space() q0.dat.data[:] += 0.01*Uj*np.random.randn(V.dot_dset.size, *V.shape) but that didn't seem to work. Now I get the following error, Traceback (most recent call last): File "qg3d_jet.py", line 39, in <module> q0.dat.data[:] += 0.01*Uj*np.random.randn(V.dot_dset.size, *V.shape) File "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/functionspaceimpl.py", line 202, in __getattr__ return getattr(self.topological, name) AttributeError: 'FunctionSpace' object has no attribute 'dot_dset' Sorry if I misunderstood the advice. Francis Francis Poulin Associate Professor Department of Applied Mathematics University of Waterloo email: fpoulin@uwaterloo.ca<mailto:fpoulin@uwaterloo.ca> Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637 ________________________________ From: firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> [firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk>] on behalf of David Ham [David.Ham@imperial.ac.uk<mailto:David.Ham@imperial.ac.uk>] Sent: Thursday, May 19, 2016 9:03 AM To: firedrake Subject: Re: [firedrake] mpirun acting up How is Uj set? It looks like Uj has halos attached, while the others do not. Regards, David On Thu, 19 May 2016 at 14:55 Francis Poulin <fpoulin@uwaterloo.ca<mailto:fpoulin@uwaterloo.ca>> wrote: Hello, I am trying to run something with mpiand for some reason I am getting an error. This is both on my mac and ubuntu machines. Any ideas what might be the problem? I was able to do this before the upgrade and thought it should work in the same way but maybe something has change? Or maybe I'm doing something very silly. Cheers, Francis fpoulin@fpoulin-Gazelle:~/Research/Firedrake/QG/firedrakeQG$ mpirun -np 2 ~/software/firedrake/bin/python qg3d_jet.py Discontinuous Lagrange element requested on quadrilateral, creating DQ element. Discontinuous Lagrange element requested on quadrilateral, creating DQ element. Discontinuous Lagrange element requested on quadrilateral, creating DQ element. Discontinuous Lagrange element requested on quadrilateral, creating DQ element. COFFEE finished in 0.00156093 seconds (flops: 0 -> 0) Discontinuous Lagrange element requested on None, creating DQ element. COFFEE finished in 0.00156093 seconds (flops: 0 -> 0) Discontinuous Lagrange element requested on None, creating DQ element. Discontinuous Lagrange element requested on None, creating DQ element. Discontinuous Lagrange element requested on None, creating DQ element. COFFEE finished in 0.00232983 seconds (flops: 0 -> 0) Traceback (most recent call last): File "qg3d_jet.py", line 38, in <module> q0.dat.data[:] += 0.01*Uj*np.random.randn(*q0.dat.shape) ValueError: operands could not be broadcast together with shapes (500000,) (520000,) (500000,) Traceback (most recent call last): File "qg3d_jet.py", line 38, in <module> q0.dat.data[:] += 0.01*Uj*np.random.randn(*q0.dat.shape) ValueError: operands could not be broadcast together with shapes (500000,) (520000,) (500000,) COFFEE finished in 0.00234294 seconds (flops: 0 -> 0) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. ------------------ Francis Poulin Associate Professor Department of Applied Mathematics University of Waterloo email: fpoulin@uwaterloo.ca<mailto:fpoulin@uwaterloo.ca> Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637
participants (2)
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David Ham
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Francis Poulin