May 2016 - firedrake - imperial.ac.uk

mpirun acting up
by Francis Poulin 19 May '16

19 May '16

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(a)uwaterloo.ca Web: https://uwaterloo.ca/poulin-research-group/ Telephone: +1 519 888 4567 x32637

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Re: [firedrake] Expression on extruded mesh
by David Ham 19 May '16

19 May '16

Hi TJ, Can you use the direct UFL interpolation feature instead? It's documented in the manual. Cheers, David On Wed, 18 May 2016 at 20:48 Sun, Tianjiao <tianjiao.sun14(a)imperial.ac.uk> wrote: > Hi team, > > I run into a "NotImplemented" exception when trying to assign values to > an function on extruded mesh of 1 layer. I'm wondering is it really not > implemented or (more likely) just my bad usage? The situation is that I > have this function on DG(0) x CG(1), and I just need to assign values to > the top and bottom surfaces. > > Many thanks! > -TJ > > code: > --------------------------------------------------------------------------- > m = RectangleMesh(5,5,5,5,quadrilateral=True) > mesh = ExtrudedMesh(m, layers=1) > W_h = FiniteElement("DG", "quadrilateral", 0) > W_v = FiniteElement("CG", "interval", 1) > W_elt = TensorProductElement(W_h, W_v) > W = FunctionSpace(mesh, W_elt) > > # This Expression reads values from an array > class Ex_intensity(Expression): > def eval(self, value, X): > # this is not quite completed, there will be more logic here > x0 = int(X[0]) > x1 = int(X[1]) > value[:] = p0[x1,x0] > > I = Function(W) > I.interpolate(Ex_intensity()) > I.at(2.5,2.5,0) > > Error message: > --------------------------------------------------------------------------- > NotImplementedError Traceback (most recent call last) > <ipython-input-12-055ffdeb8731> in <module>() > ----> 1 I.at(2.5,2.5,0) > > > /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/firedrake/function.pyc > in at(self, arg, *args, **kwargs) > 492 else: > 493 p_result = np.empty(value_shape, dtype=float) > --> 494 single_eval(points[i:i+1], p_result) > 495 l_result.append((i, p_result)) > 496 except PointNotInDomainError: > > > /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/firedrake/function.pyc > in single_eval(x, buf) > 470 def single_eval(x, buf): > 471 """Helper function to evaluate at a single point.""" > --> 472 err = self._c_evaluate(self._ctypes, > 473 x.ctypes.data_as(POINTER(c_double)), > 474 buf.ctypes.data_as(POINTER(c_double))) > > > /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/pyop2/utils.pyc > in __get__(self, obj, cls) > 62 if obj is None: > 63 return self > ---> 64 obj.__dict__[self.__name__] = result = self.fget(obj) > 65 return result > 66 > > > /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/firedrake/function.pyc > in _ctypes(self) > 406 else: > 407 c_function.n_layers = 1 > --> 408 c_function.coords = > coordinates.dat.data.ctypes.data_as(POINTER(c_double)) > 409 c_function.coords_map = > coordinates_space.cell_node_list.ctypes.data_as(POINTER(c_int)) > 410 c_function.f = > self.dat.data.ctypes.data_as(POINTER(c_double)) > > <decorator-gen-136> in data(self) > > > /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/pyop2/versioning.pyc > in modifies(method, self, *args, **kwargs) > 113 _force_copies(self) > 114 > --> 115 retval = method(self, *args, **kwargs) > 116 > 117 self._version_bump() > > > /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/pyop2/base.pyc > in data(self) > 1759 > 1760 """ > -> 1761 _trace.evaluate(set([self]), set([self])) > 1762 if self.dataset.total_size > 0 and self._data.size == 0 > and self.cdim > 0: > 1763 raise RuntimeError("Illegal access: no data > associated with this Dat!") > > > /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/pyop2/base.pyc > in evaluate(self, reads, writes) > 169 to_run = fuse('from_trace', to_run, 0) > 170 for comp in to_run: > --> 171 comp._run() > 172 > 173 > > > /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/pyop2/base.pyc > in _run(self) > 4073 > 4074 def _run(self): > -> 4075 return self.compute() > 4076 > 4077 def prepare_arglist(self, iterset, *args): > > > /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/pyop2/base.pyc > in compute(self) > 4115 arglist = self.prepare_arglist(iterset, *self.args) > 4116 fun = self._jitmodule > -> 4117 self._compute(iterset.core_part, fun, *arglist) > 4118 self.halo_exchange_end() > 4119 self._compute(iterset.owned_part, fun, *arglist) > > > /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/pyop2/pyparloop.pyc > in _compute(self, part, *arglist) > 106 def _compute(self, part, *arglist): > 107 if part.set._extruded: > --> 108 raise NotImplementedError > 109 subset = isinstance(self._it_space._iterset, base.Subset) > 110 > > NotImplementedError: > > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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Expression on extruded mesh
by Tianjiao Sun 18 May '16

18 May '16

Hi team, I run into a "NotImplemented" exception when trying to assign values to an function on extruded mesh of 1 layer. I'm wondering is it really not implemented or (more likely) just my bad usage? The situation is that I have this function on DG(0) x CG(1), and I just need to assign values to the top and bottom surfaces. Many thanks! -TJ code: --------------------------------------------------------------------------- m = RectangleMesh(5,5,5,5,quadrilateral=True) mesh = ExtrudedMesh(m, layers=1) W_h = FiniteElement("DG", "quadrilateral", 0) W_v = FiniteElement("CG", "interval", 1) W_elt = TensorProductElement(W_h, W_v) W = FunctionSpace(mesh, W_elt) # This Expression reads values from an array class Ex_intensity(Expression): def eval(self, value, X): # this is not quite completed, there will be more logic here x0 = int(X[0]) x1 = int(X[1]) value[:] = p0[x1,x0] I = Function(W) I.interpolate(Ex_intensity()) I.at(2.5,2.5,0) Error message: --------------------------------------------------------------------------- NotImplementedError Traceback (most recent call last) <ipython-input-12-055ffdeb8731> in <module>() ----> 1 I.at(2.5,2.5,0) /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/firedrake/function.pyc in at(self, arg, *args, **kwargs) 492 else: 493 p_result = np.empty(value_shape, dtype=float) --> 494 single_eval(points[i:i+1], p_result) 495 l_result.append((i, p_result)) 496 except PointNotInDomainError: /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/firedrake/function.pyc in single_eval(x, buf) 470 def single_eval(x, buf): 471 """Helper function to evaluate at a single point.""" --> 472 err = self._c_evaluate(self._ctypes, 473 x.ctypes.data_as(POINTER(c_double)), 474 buf.ctypes.data_as(POINTER(c_double))) /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/pyop2/utils.pyc in __get__(self, obj, cls) 62 if obj is None: 63 return self ---> 64 obj.__dict__[self.__name__] = result = self.fget(obj) 65 return result 66 /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/firedrake/function.pyc in _ctypes(self) 406 else: 407 c_function.n_layers = 1 --> 408 c_function.coords = coordinates.dat.data.ctypes.data_as(POINTER(c_double)) 409 c_function.coords_map = coordinates_space.cell_node_list.ctypes.data_as(POINTER(c_int)) 410 c_function.f = self.dat.data.ctypes.data_as(POINTER(c_double)) <decorator-gen-136> in data(self) /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/pyop2/versioning.pyc in modifies(method, self, *args, **kwargs) 113 _force_copies(self) 114 --> 115 retval = method(self, *args, **kwargs) 116 117 self._version_bump() /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/pyop2/base.pyc in data(self) 1759 1760 """ -> 1761 _trace.evaluate(set([self]), set([self])) 1762 if self.dataset.total_size > 0 and self._data.size == 0 and self.cdim > 0: 1763 raise RuntimeError("Illegal access: no data associated with this Dat!") /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/pyop2/base.pyc in evaluate(self, reads, writes) 169 to_run = fuse('from_trace', to_run, 0) 170 for comp in to_run: --> 171 comp._run() 172 173 /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/pyop2/base.pyc in _run(self) 4073 4074 def _run(self): -> 4075 return self.compute() 4076 4077 def prepare_arglist(self, iterset, *args): /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/pyop2/base.pyc in compute(self) 4115 arglist = self.prepare_arglist(iterset, *self.args) 4116 fun = self._jitmodule -> 4117 self._compute(iterset.core_part, fun, *arglist) 4118 self.halo_exchange_end() 4119 self._compute(iterset.owned_part, fun, *arglist) /home/ts2914/projects/firedrake/local/lib/python2.7/site-packages/pyop2/pyparloop.pyc in _compute(self, part, *arglist) 106 def _compute(self, part, *arglist): 107 if part.set._extruded: --> 108 raise NotImplementedError 109 subset = isinstance(self._it_space._iterset, base.Subset) 110 NotImplementedError:

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New Firedrake dependencies
by Homolya, Miklós 17 May '16

17 May '16

Dear Firedrakers, Firedrake now depends on autotools, which consists the following packages: - autoconf - automake - libtool The install/update script will take care of installing these packages with apt or homebrew. If you use --no-package-manager, you will have to install these packages yourself. Regards, Miklós

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Re: [firedrake] installation Linux
by David Ham 17 May '16

17 May '16

Hi Floriane, The error message says that you don't have MPI installed. A quick google suggests that the package you need for scientific Linux might be openmpi-devel. Regards, David On Tue, 17 May 2016 at 13:38 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> wrote: > Dear David, > > > Indeed, pip was not installed correctly. This is now fixed but another > error occurs during the installation of Firedrake: > > > > > > ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log > for details): > > ------------------------------------------------------------------------------- > Did not find package MPI needed by hdf5. > Enable the package using --with-mpi > > ******************************************************************************* > > > Traceback (most recent call last): > File "<string>", line 1, in <module> > File "/tmp/pip-nn0xv2-build/setup.py", line 302, in <module> > **metadata) > File "/usr/lib64/python2.7/distutils/core.py", line 152, in setup > dist.run_commands() > File "/usr/lib64/python2.7/distutils/dist.py", line 953, in > run_commands > self.run_command(cmd) > File "/usr/lib64/python2.7/distutils/dist.py", line 972, in > run_command > cmd_obj.run() > File "/tmp/pip-nn0xv2-build/setup.py", line 218, in run > config(prefix, self.dry_run) > File "/tmp/pip-nn0xv2-build/setup.py", line 148, in config > if status != 0: raise RuntimeError(status) > RuntimeError: 256 > > ---------------------------------------- > Command "/home/fgidel/firedrake/bin/python -u -c "import setuptools, > tokenize;__file__='/tmp/pip-nn0xv2-build/setup.py';exec(compile(getattr(tokenize, > 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" > install --record /tmp/pip-_EAAFI-record/install-record.txt > --single-version-externally-managed --compile --install-headers > /home/fgidel/firedrake/include/site/python2.7/petsc" failed with error code > 1 in /tmp/pip-nn0xv2-build/ > > Traceback (most recent call last): > File "firedrake-install", line 876, in <module> > install("petsc/") > File "firedrake-install", line 491, in install > run_pip_install(["--ignore-installed", package]) > File "firedrake-install", line 354, in run_pip_install > check_call(pipinstall + pipargs) > > File "firedrake-install", line 205, in check_call > subprocess.check_call(arguments, env=env) > File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call > raise CalledProcessError(retcode, cmd) > subprocess.CalledProcessError: Command '['/home/fgidel/firedrake/bin/pip', > 'install', '--no-deps', '--ignore-installed', 'petsc/']' returned non-zero > exit status 1 > > > > > Do you know what's missing? > > > Best wishes, > > > Floriane > > > ------------------------------ > *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> > de la part de David Ham <David.Ham(a)imperial.ac.uk> > *Envoyé :* mercredi 11 mai 2016 11:05:33 > *À :* firedrake > > *Objet :* Re: [firedrake] installation Linux > Hi Floriane, > > That error strongly suggests that pip is not installed. Can you please > tell us what the result of: > > pip install --user virtualenv > > is? > > In addition, I notice that you are installing Firedrake as root. We > recommend in the strongest possible terms that you do not do this. You > should install Firedrake yourself as your normal user. > > Regards, > > David > > On Wed, 11 May 2016 at 10:58 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> > wrote: > >> Dear all, >> >> The IT team is still struggling to install Firedrake on the linux >> machine. This is the error that they get: >> >> root@lin0320 ~ # firedrake-install --no-package-manager >> -bash: firedrake-install: command not found >> root@lin0320 ~ # python firedrake-install --no-package-manager apt-get >> not found or disabled. Proceeding on the rash assumption that your compiled >> dependencies are in place. >> If this is not the case, please install the following and try again: >> * A C and C++ compiler (for example gcc/g++ or clang), GNU make >> * A Fortran compiler (for PETSc) >> * MPI >> * Blas and Lapack >> * Git, Mercurial >> * Python version 2.7 >> * pip and the Python headers >> * CMake >> * libspatialindex and headers >> * zlib >> Installing virtualenv. >> Traceback (most recent call last): >> File "firedrake-install", line 813, in <module> >> check_call(["pip", "install", "--user", "virtualenv"]) >> File "firedrake-install", line 205, in check_call >> subprocess.check_call(arguments, env=env) >> File "/usr/lib64/python2.7/subprocess.py", line 537, in check_call >> retcode = call(*popenargs, **kwargs) >> File "/usr/lib64/python2.7/subprocess.py", line 524, in call >> return Popen(*popenargs, **kwargs).wait() >> File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__ >> errread, errwrite) >> File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child >> raise child_exception >> OSError: [Errno 2] No such file or directory >> >> >> Do you have any suggestion? >> Thanks, >> Floriane >> ________________________________________ >> De : firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >> de la part de Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >> Envoyé : mardi 10 mai 2016 09:46:54 >> À : firedrake(a)imperial.ac.uk >> Objet : Re: [firedrake] installation Linux >> >> Ok, thanks! >> >> Floriane >> >> ________________________________________ >> De : firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >> de la part de Lawrence Mitchell <lawrence.mitchell(a)imperial.ac.uk> >> Envoyé : mardi 10 mai 2016 09:42:37 >> À : firedrake(a)imperial.ac.uk >> Objet : Re: [firedrake] installation Linux >> >> On 10/05/16 09:34, Floriane Gidel [RPG] wrote: >> > Hi David, >> > >> > >> > Thanks for your reply. I am now based at MARIN where I work on a >> > machine with Scientific Linux release 7.2 (Nitrogen). Which packages >> > do I need in that case? >> >> The same as on CentOS (SL is basically the same, just with a different >> badge). I'm not sure what those are called. They probably have very >> similar names to the packages on ubuntu. >> >> Lawrence >> >> >> _______________________________________________ >> firedrake mailing list >> firedrake(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >> >> _______________________________________________ >> firedrake mailing list >> firedrake(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >> >

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Re: [firedrake] installation Linux
by David Ham 17 May '16

17 May '16

Hi Floriane, That error strongly suggests that pip is not installed. Can you please tell us what the result of: pip install --user virtualenv is? In addition, I notice that you are installing Firedrake as root. We recommend in the strongest possible terms that you do not do this. You should install Firedrake yourself as your normal user. Regards, David On Wed, 11 May 2016 at 10:58 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> wrote: > Dear all, > > The IT team is still struggling to install Firedrake on the linux machine. > This is the error that they get: > > root@lin0320 ~ # firedrake-install --no-package-manager > -bash: firedrake-install: command not found > root@lin0320 ~ # python firedrake-install --no-package-manager apt-get > not found or disabled. Proceeding on the rash assumption that your compiled > dependencies are in place. > If this is not the case, please install the following and try again: > * A C and C++ compiler (for example gcc/g++ or clang), GNU make > * A Fortran compiler (for PETSc) > * MPI > * Blas and Lapack > * Git, Mercurial > * Python version 2.7 > * pip and the Python headers > * CMake > * libspatialindex and headers > * zlib > Installing virtualenv. > Traceback (most recent call last): > File "firedrake-install", line 813, in <module> > check_call(["pip", "install", "--user", "virtualenv"]) > File "firedrake-install", line 205, in check_call > subprocess.check_call(arguments, env=env) > File "/usr/lib64/python2.7/subprocess.py", line 537, in check_call > retcode = call(*popenargs, **kwargs) > File "/usr/lib64/python2.7/subprocess.py", line 524, in call > return Popen(*popenargs, **kwargs).wait() > File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__ > errread, errwrite) > File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child > raise child_exception > OSError: [Errno 2] No such file or directory > > > Do you have any suggestion? > Thanks, > Floriane > ________________________________________ > De : firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> > de la part de Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> > Envoyé : mardi 10 mai 2016 09:46:54 > À : firedrake(a)imperial.ac.uk > Objet : Re: [firedrake] installation Linux > > Ok, thanks! > > Floriane > > ________________________________________ > De : firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> > de la part de Lawrence Mitchell <lawrence.mitchell(a)imperial.ac.uk> > Envoyé : mardi 10 mai 2016 09:42:37 > À : firedrake(a)imperial.ac.uk > Objet : Re: [firedrake] installation Linux > > On 10/05/16 09:34, Floriane Gidel [RPG] wrote: > > Hi David, > > > > > > Thanks for your reply. I am now based at MARIN where I work on a > > machine with Scientific Linux release 7.2 (Nitrogen). Which packages > > do I need in that case? > > The same as on CentOS (SL is basically the same, just with a different > badge). I'm not sure what those are called. They probably have very > similar names to the packages on ubuntu. > > Lawrence > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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problem with a fresh install on ubuntu 16.04
by Francis Poulin 17 May '16

17 May '16

Hello again, Yesterday I started setting up a new ubuntu laptop running 16.04. I started to install firedrake and it took a long time to do the petsc install but seemed to get past that but then something went wrong, see below. Any ideas what might be wrong? Also, if I wanted to finish the install is there a way to continue rather than starting from scratch? Cheers, Francis Cloning libspatialindex Failed to clone libspatialindex using ssh, falling back to https. Successfully cloned libspatialindex branch master. HEAD is now at 34fd22b Merge pull request #82 from miklos1/master Running aclocal ./autogen.sh: 37: ./autogen.sh: aclocal: not found Something went wrong, giving up! Traceback (most recent call last): File "firedrake-install", line 885, in <module> build_and_install_libspatialindex() File "firedrake-install", line 607, in build_and_install_libspatialindex check_call(["./autogen.sh"]) File "firedrake-install", line 205, in check_call subprocess.check_call(arguments, env=env) File "/usr/lib/python2.7/subprocess.py", line 541, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['./autogen.sh']' returned non-zero exit status 1 fpoulin@fpoulin-Gazelle:~/software$ ------------------ Francis Poulin Associate 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

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Re: [firedrake] how to change pvtu files?
by David Ham 17 May '16

17 May '16

Hi Francis, Jemma is actually claiming that Stephan fixed this and the fix was merged on 27 April. When did you last update firedrake? On Tue, 17 May 2016 at 12:07 Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Hello David, > > I'm not sure if this is a bug necessarily. Paraview views these files > without any problem so it does work. Unfortunately, VisIt can't find the > functions you want to plot when the path is there. Strange but true. > > As for Jemma's comments, thanks, and I have not moved any files around. I > am trying to view them in the directory where they were created. > > I think it would be nice to have the data files generated for both systems > to give people the choice of which software they want to use. Again, they > both work in serial, which is strange, but VisIt has a problem in > parallel. Or maybe the path is specified differently with the pvtu file? > I don't know. > > If you agree I can try and figure out how to modify the output.py script > to do that. > > > Francis > > ------------------ > Francis Poulin > Associate 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 > > ------------------------------ > *From:* firedrake-bounces(a)imperial.ac.uk [firedrake-bounces(a)imperial.ac.uk] > on behalf of David Ham [David.Ham(a)imperial.ac.uk] > *Sent:* Tuesday, May 17, 2016 6:54 AM > > *To:* firedrake > *Subject:* Re: [firedrake] how to change pvtu files? > Hi Francis, > > Do you have an idea where the bug is? If it's in Firedrake (i.e. the path > is just not supposed to be there, and fixing it won't break loading these > files in preview) then sure, go ahead and propose a pull request. I think > the code you'll want is in output.py > > On Tue, 17 May 2016 at 11:36 Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > >> Hello, >> >> Recently I've been learning to use VisIt to view firedrake data instead >> of Paraview. In part because people around me use it and also I think it >> looks good. >> >> When viewing data created in serial it works very easily but I found that >> when I was trying to view data created in parallel it was having problems >> finding the files. It turns out that one can fix this by changing one line >> in each pvtu file. >> >> There is line in the file that specifies the source and has the path then >> the name of the vtu file. If I remove the path and only have the name of >> the file then VisIt can fine the files easily. I have asked them if there >> is a work around but if not is there a way to change this when the data >> files are create in firedake? >> >> Cheers, Francis >> >> >> ------------------ >> Francis Poulin >> Associate 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 >> >>

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Re: [firedrake] how to change pvtu files?
by David Ham 17 May '16

17 May '16

Hi Francis, Do you have an idea where the bug is? If it's in Firedrake (i.e. the path is just not supposed to be there, and fixing it won't break loading these files in preview) then sure, go ahead and propose a pull request. I think the code you'll want is in output.py On Tue, 17 May 2016 at 11:36 Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Hello, > > Recently I've been learning to use VisIt to view firedrake data instead of > Paraview. In part because people around me use it and also I think it > looks good. > > When viewing data created in serial it works very easily but I found that > when I was trying to view data created in parallel it was having problems > finding the files. It turns out that one can fix this by changing one line > in each pvtu file. > > There is line in the file that specifies the source and has the path then > the name of the vtu file. If I remove the path and only have the name of > the file then VisIt can fine the files easily. I have asked them if there > is a work around but if not is there a way to change this when the data > files are create in firedake? > > Cheers, Francis > > > ------------------ > Francis Poulin > Associate 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 > >

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how to change pvtu files?
by Francis Poulin 17 May '16

17 May '16

Hello, Recently I've been learning to use VisIt to view firedrake data instead of Paraview. In part because people around me use it and also I think it looks good. When viewing data created in serial it works very easily but I found that when I was trying to view data created in parallel it was having problems finding the files. It turns out that one can fix this by changing one line in each pvtu file. There is line in the file that specifies the source and has the path then the name of the vtu file. If I remove the path and only have the name of the file then VisIt can fine the files easily. I have asked them if there is a work around but if not is there a way to change this when the data files are create in firedake? Cheers, Francis ------------------ Francis Poulin Associate 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

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