November 2014 - firedrake - imperial.ac.uk

Re: [firedrake] parallel weirdness
by Hiroe Yamazaki 19 Nov '14

19 Nov '14

Hi Lawrence, you can reproduce the problem by runing test_linear.py at bitbucket.org/colinjcotter/slicemodels/branch/periodic_parallel. With 1 and 2 cores, it gives different results. The code Colin is describing with line numbers is an old-version of slicemodels.py, which is found here: https://gist.github.com/anonymous/c308131558ff54fec9c4 In this version I added this term - (-dt*div(w)*pbar)*dx in line 270, which was previously added to the RHS in line 139. With this change, the parallelization problem seemed to be fixed and I got the same results with 1 and 2 cores, but but it makes no sense to us. All the best, Hiroe 2014-11-18 20:46 GMT+00:00 Mitchell, Lawrence <lawrence.mitchell(a)imperial.ac.uk>: > Hello, > > On 18 Nov 2014, at 18:57, Colin Cotter <colin.cotter(a)imperial.ac.uk> wrote: > >> Dear all, >> We have a rather weird parallel bug, and Hiroe and I would appreciate some suggestions. The relevant code is in bitbucket.org/colinjcotter/slicemodels/branch/periodic_parallel revision 622fb24. >> We were observing different results on 1 and 2 cores, which Hiroe fixed by moving some code, but it makes no sense to us! >> In line 270, you can see an extra term, >> - (-dt*div(w)*pbar)*dx, >> which was previously added to the RHS in line 139 >> so, this changes implementation but not the algorithm >> either, this extra term is solved into a contribution of self.ures in L142, in which case it pops up as part of self.ures in l270, or we write it explicitly in the form there in general, we don't wish to write it explicitly in the form though, and I want to understand what is going on! >> >> Some further investigation showed that the problem seems to occur in the pressure solve on line 393, resulting in a nonsense value of self.Deltap occurring. This is just inverting a DG mass system so it ought to be straightforward, and the inputs are (approximately) the same. >> >> Do let me know if you have any ideas, > > > Can you describe what I need to do to reproduce the problem? I have looked at the repository, but don't know where to begin. > > Lawrence

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parallel weirdness
by Colin Cotter 18 Nov '14

18 Nov '14

Dear all, We have a rather weird parallel bug, and Hiroe and I would appreciate some suggestions. The relevant code is in bitbucket.org/colinjcotter/slicemodels/branch/periodic_parallel revision 622fb24. We were observing different results on 1 and 2 cores, which Hiroe fixed by moving some code, but it makes no sense to us! In line 270, you can see an extra term, - (-dt*div(w)*pbar)*dx, which was previously added to the RHS in line 139 so, this changes implementation but not the algorithm either, this extra term is solved into a contribution of self.ures in L142, in which case it pops up as part of self.ures in l270, or we write it explicitly in the form there in general, we don't wish to write it explicitly in the form though, and I want to understand what is going on! Some further investigation showed that the problem seems to occur in the pressure solve on line 393, resulting in a nonsense value of self.Deltap occurring. This is just inverting a DG mass system so it ought to be straightforward, and the inputs are (approximately) the same. Do let me know if you have any ideas, cheers --cjc

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Re: [firedrake] Firedrake Installation
by Florian Rathgeber 18 Nov '14

18 Nov '14

[Please keep list in CC] On 16/11/14 14:12, Lee, Suet wrote: > Not sure if I'm doing it correctly but I tried this: > > mosh@ubuntu:~$ dpkg -s mpich2 > dpkg-query: package 'mpich2' is not installed and no information is > available > Use dpkg --info (= dpkg-deb --info) to examine archive files, > and dpkg --contents (= dpkg-deb --contents) to list their contents. > > So the problem isn't down to mpich2? Sorry, the package you want to look for is libmpich-dev Is there any reason to use a 32bit system? We explicitly do *not* support 32bit systems and there isn't really a reason not to use 64bit. Florian > Suet > > > ------------------------------------------------------------------------ > *From:* Andrew McRae <a.mcrae12(a)imperial.ac.uk> > *Sent:* 16 November 2014 13:41 > *To:* Lee, Suet > *Subject:* Re: Firedrake Installation > > I have no idea, but I've forwarded your problem to the Firedrake mailing > list; some people on there know a lot more than me about MPI. > > On 16 November 2014 13:28, Lee, Suet <suet.lee11(a)imperial.ac.uk > <mailto:suet.lee11@imperial.ac.uk>> wrote: > > I ran the install mpi4py commange but I have a new error now: > > > mosh@ubuntu:~$ wget -O - > https://github.com/OP2/PyOP2/raw/master/install.sh | sudo bash > --2014-11-16 13:20:14-- > https://github.com/OP2/PyOP2/raw/master/install.sh > Resolving github.com <http://github.com> (github.com > <http://github.com>)... 192.30.252.131 > Connecting to github.com <http://github.com> (github.com > <http://github.com>)|192.30.252.131|:443... connected. > HTTP request sent, awaiting response... 302 Found > Location: > https://raw.githubusercontent.com/OP2/PyOP2/master/install.sh > [following] > --2014-11-16 13:20:16-- > https://raw.githubusercontent.com/OP2/PyOP2/master/install.sh > Resolving raw.githubusercontent.com > <http://raw.githubusercontent.com> (raw.githubusercontent.com > <http://raw.githubusercontent.com>)... 185.31.18.133 > Connecting to raw.githubusercontent.com > <http://raw.githubusercontent.com> (raw.githubusercontent.com > <http://raw.githubusercontent.com>)|185.31.18.133|:443... connected. > HTTP request sent, awaiting response... 200 OK > Length: 3667 (3.6K) [text/plain] > Saving to: ‘STDOUT’ > > 100%[======================================>] 3,667 --.-K/s > in 0s > > 2014-11-16 13:20:16 (40.6 MB/s) - written to stdout [3667/3667] > > PyOP2 installation started at Sun Nov 16 13:20:16 GMT 2014 > on Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 > 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux > > *** Privileged installation *** > Running unprivileged commands as mosh > > *** Preparing system *** > > *** Installing dependencies *** > > *** Installing PETSc *** > > *** Installing PyOP2 *** > > [ubuntu:31603] *** Process received signal *** > [ubuntu:31603] Signal: Floating point exception (8) > [ubuntu:31603] Signal code: Integer divide-by-zero (1) > [ubuntu:31603] Failing at address: 0xb74d6da0 > [ubuntu:31603] [ 0] [0xb779a40c] > [ubuntu:31603] [ 1] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2cda0) > [0xb74d6da0] > [ubuntu:31603] [ 2] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2e71c) > [0xb74d871c] > [ubuntu:31603] [ 3] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2ea8b) > [0xb74d8a8b] > [ubuntu:31603] [ 4] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x98f6) > [0xb74b38f6] > [ubuntu:31603] [ 5] > /usr/lib/i386-linux-gnu/libhwloc.so.5(hwloc_topology_load+0x1c6) > [0xb74b48ec] > [ubuntu:31603] [ 6] > /usr/lib/libopen-rte.so.4(orte_odls_base_open+0x7b1) [0xb76fa881] > [ubuntu:31603] [ 7] > /usr/lib/openmpi/lib/openmpi/mca_ess_hnp.so(+0x2445) [0xb7488445] > [ubuntu:31603] [ 8] /usr/lib/libopen-rte.so.4(orte_init+0x1cf) > [0xb76cfb3f] > [ubuntu:31603] [ 9] /usr/lib/libopen-rte.so.4(orte_daemon+0x256) > [0xb76ec1c6] > [ubuntu:31603] [10] orted() [0x80485b3] > [ubuntu:31603] [11] > /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0xb7504a83] > [ubuntu:31603] [12] orted() [0x80485f8] > [ubuntu:31603] *** End of error message *** > [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a > daemon on the local node in file ess_singleton_module.c at line 343 > [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a > daemon on the local node in file ess_singleton_module.c at line 140 > [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a > daemon on the local node in file runtime/orte_init.c at line 128 > -------------------------------------------------------------------------- > It looks like orte_init failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during orte_init; some of which are due to configuration or > environment problems. This failure appears to be an internal failure; > here's some additional information (which may only be relevant to an > Open MPI developer): > > orte_ess_set_name failed > --> Returned value Unable to start a daemon on the local node > (-128) instead of ORTE_SUCCESS > -------------------------------------------------------------------------- > -------------------------------------------------------------------------- > It looks like MPI_INIT failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during MPI_INIT; some of which are due to configuration or > environment > problems. This failure appears to be an internal failure; here's some > additional information (which may only be relevant to an Open MPI > developer): > > ompi_mpi_init: orte_init failed > --> Returned "Unable to start a daemon on the local node" (-128) > instead of "Success" (0) > -------------------------------------------------------------------------- > [ubuntu:31601] *** An error occurred in MPI_Init_thread > [ubuntu:31601] *** on a NULL communicator > [ubuntu:31601] *** Unknown error > [ubuntu:31601] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort > -------------------------------------------------------------------------- > An MPI process is aborting at a time when it cannot guarantee that all > of its peer processes in the job will be killed properly. You should > double check that everything has shut down cleanly. > > Reason: Before MPI_INIT completed > Local host: ubuntu > PID: 31601 > -------------------------------------------------------------------------- > PyOP2 installation failed > See /home/mosh/PyOP2/pyop2_install.log for details > > Any idea what's going on? > > Suet > > > ------------------------------------------------------------------------ > *From:* Andrew McRae <a.mcrae12(a)imperial.ac.uk > <mailto:a.mcrae12@imperial.ac.uk>> > *Sent:* 15 November 2014 23:13 > *To:* Lee, Suet > *Subject:* Re: Firedrake Installation > > Or, if you want to be a guinea pig, don't run the 'sudo pip install > mpi4py' command and just run the install script again :) > > (I updated > <https://github.com/OP2/PyOP2/commit/e15b3ee8d72369f10c9a84d944a3ecbf06f7e927> > the script just now -- thanks for alerting us to that bug) > > On 15 November 2014 23:09, Andrew McRae <a.mcrae12(a)imperial.ac.uk > <mailto:a.mcrae12@imperial.ac.uk>> wrote: > > Hi Suet, > > Sorry about that. This should fix the mpi4py problem: sudo pip > install mpi4py > > Then try the quick install script again. > > Yes, PyOP2, FFC, FIAT and UFL need to be installed before > firerake. However, installing FFC/FIAT/UFL is easy -- you just > run the 'sudo pip install \ six \ sympy \ ...' command, as > described on http://www.firedrakeproject.org/download.html. > > Let me know if there's any other problems. > > Best, > > Andrew > > > On 15 November 2014 23:00, Lee, Suet <suet.lee11(a)imperial.ac.uk > <mailto:suet.lee11@imperial.ac.uk>> wrote: > > Hi Andrew, > > > So I finally got round to the Firedrake installation! > > > I'm trying to install PyOP2. The only problem is that I'm > running up against the following error: > > > PyOP2 installation started at Sat Nov 15 22:38:45 GMT 2014 > on Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr > 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux > > *** Privileged installation *** > Running unprivileged commands as mosh > > *** Preparing system *** > > *** Installing dependencies *** > > *** Installing PETSc *** > > *** Installing PyOP2 *** > > Traceback (most recent call last): > File "<string>", line 1, in <module> > File "pyop2/__init__.py", line 9, in <module> > from op2 import * > File "pyop2/op2.py", line 38, in <module> > import backends > File "pyop2/backends.py", line 41, in <module> > from logger import warning > File "pyop2/logger.py", line 38, in <module> > from mpi import MPI > File "pyop2/mpi.py", line 37, in <module> > from mpi4py import MPI as _MPI > ImportError: No module named mpi4py > PyOP2 installation failed > See /home/mosh/pyop2_install.log for details > > > I must be missing the file mpi4py? Do I have to install > > PyOP2 <http://op2.github.io/PyOP2>, FFC > <https://bitbucket.org/mapdes/ffc>, FIAT > <https://bitbucket.org/mapdes/fiat>, and UFL > <https://bitbucket.org/mapdes/ufl>, before Firedrake? I > attempted the quick installation for PyOP2 but do I need to > install other packages before that? > > Best, > > Suet

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Re: [firedrake] Firedrake Installation
by Andrew McRae 16 Nov '14

16 Nov '14

On 16 November 2014 14:22, Rathgeber, Florian < florian.rathgeber(a)imperial.ac.uk> wrote: > [Please keep list in CC] > > On 16/11/14 14:12, Lee, Suet wrote: > > Not sure if I'm doing it correctly but I tried this: > > > > mosh@ubuntu:~$ dpkg -s mpich2 > > dpkg-query: package 'mpich2' is not installed and no information is > > available > > Use dpkg --info (= dpkg-deb --info) to examine archive files, > > and dpkg --contents (= dpkg-deb --contents) to list their contents. > > > > So the problem isn't down to mpich2? > > Sorry, the package you want to look for is libmpich-dev > > Is there any reason to use a 32bit system? We explicitly do *not* > support 32bit systems and there isn't really a reason not to use 64bit. > Ah, I wasn't aware of this. Context: Suet got the following error when she tried powering up a 64bit VM, a couple of months ago: "This virtual machine is configured for 64-bit guest operating systems. However, 64-bit operation is not possible. This host does not support Intel VT-x. For more detailed information, see http://vmware.com/info?id=152." [The graphics problem was something different] I guessed that pointing her at the 32bit Ubuntu iso would be easier than making BIOS changes (assuming her processor does support VT-x, but that it's disabled in BIOS). Florian: do you think the problem is related to 32bit-ness? If so, Suet can bring her laptop to Huxley or WPL some time this week and we'll go the 64bit route. Andrew Florian > > > Suet > > > > > > ------------------------------------------------------------------------ > > *From:* Andrew McRae <a.mcrae12(a)imperial.ac.uk> > > *Sent:* 16 November 2014 13:41 > > *To:* Lee, Suet > > *Subject:* Re: Firedrake Installation > > > > I have no idea, but I've forwarded your problem to the Firedrake mailing > > list; some people on there know a lot more than me about MPI. > > > > On 16 November 2014 13:28, Lee, Suet <suet.lee11(a)imperial.ac.uk > > <mailto:suet.lee11@imperial.ac.uk>> wrote: > > > > I ran the install mpi4py commange but I have a new error now: > > > > > > mosh@ubuntu:~$ wget -O - > > https://github.com/OP2/PyOP2/raw/master/install.sh | sudo bash > > --2014-11-16 13:20:14-- > > https://github.com/OP2/PyOP2/raw/master/install.sh > > Resolving github.com <http://github.com> (github.com > > <http://github.com>)... 192.30.252.131 > > Connecting to github.com <http://github.com> (github.com > > <http://github.com>)|192.30.252.131|:443... connected. > > HTTP request sent, awaiting response... 302 Found > > Location: > > https://raw.githubusercontent.com/OP2/PyOP2/master/install.sh > > [following] > > --2014-11-16 13:20:16-- > > https://raw.githubusercontent.com/OP2/PyOP2/master/install.sh > > Resolving raw.githubusercontent.com > > <http://raw.githubusercontent.com> (raw.githubusercontent.com > > <http://raw.githubusercontent.com>)... 185.31.18.133 > > Connecting to raw.githubusercontent.com > > <http://raw.githubusercontent.com> (raw.githubusercontent.com > > <http://raw.githubusercontent.com>)|185.31.18.133|:443... connected. > > HTTP request sent, awaiting response... 200 OK > > Length: 3667 (3.6K) [text/plain] > > Saving to: ‘STDOUT’ > > > > 100%[======================================>] 3,667 --.-K/s > > in 0s > > > > 2014-11-16 13:20:16 (40.6 MB/s) - written to stdout [3667/3667] > > > > PyOP2 installation started at Sun Nov 16 13:20:16 GMT 2014 > > on Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 > > 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux > > > > *** Privileged installation *** > > Running unprivileged commands as mosh > > > > *** Preparing system *** > > > > *** Installing dependencies *** > > > > *** Installing PETSc *** > > > > *** Installing PyOP2 *** > > > > [ubuntu:31603] *** Process received signal *** > > [ubuntu:31603] Signal: Floating point exception (8) > > [ubuntu:31603] Signal code: Integer divide-by-zero (1) > > [ubuntu:31603] Failing at address: 0xb74d6da0 > > [ubuntu:31603] [ 0] [0xb779a40c] > > [ubuntu:31603] [ 1] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2cda0) > > [0xb74d6da0] > > [ubuntu:31603] [ 2] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2e71c) > > [0xb74d871c] > > [ubuntu:31603] [ 3] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2ea8b) > > [0xb74d8a8b] > > [ubuntu:31603] [ 4] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x98f6) > > [0xb74b38f6] > > [ubuntu:31603] [ 5] > > /usr/lib/i386-linux-gnu/libhwloc.so.5(hwloc_topology_load+0x1c6) > > [0xb74b48ec] > > [ubuntu:31603] [ 6] > > /usr/lib/libopen-rte.so.4(orte_odls_base_open+0x7b1) [0xb76fa881] > > [ubuntu:31603] [ 7] > > /usr/lib/openmpi/lib/openmpi/mca_ess_hnp.so(+0x2445) [0xb7488445] > > [ubuntu:31603] [ 8] /usr/lib/libopen-rte.so.4(orte_init+0x1cf) > > [0xb76cfb3f] > > [ubuntu:31603] [ 9] /usr/lib/libopen-rte.so.4(orte_daemon+0x256) > > [0xb76ec1c6] > > [ubuntu:31603] [10] orted() [0x80485b3] > > [ubuntu:31603] [11] > > /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0xb7504a83] > > [ubuntu:31603] [12] orted() [0x80485f8] > > [ubuntu:31603] *** End of error message *** > > [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a > > daemon on the local node in file ess_singleton_module.c at line 343 > > [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a > > daemon on the local node in file ess_singleton_module.c at line 140 > > [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a > > daemon on the local node in file runtime/orte_init.c at line 128 > > > -------------------------------------------------------------------------- > > It looks like orte_init failed for some reason; your parallel > process is > > likely to abort. There are many reasons that a parallel process can > > fail during orte_init; some of which are due to configuration or > > environment problems. This failure appears to be an internal > failure; > > here's some additional information (which may only be relevant to an > > Open MPI developer): > > > > orte_ess_set_name failed > > --> Returned value Unable to start a daemon on the local node > > (-128) instead of ORTE_SUCCESS > > > -------------------------------------------------------------------------- > > > -------------------------------------------------------------------------- > > It looks like MPI_INIT failed for some reason; your parallel process > is > > likely to abort. There are many reasons that a parallel process can > > fail during MPI_INIT; some of which are due to configuration or > > environment > > problems. This failure appears to be an internal failure; here's > some > > additional information (which may only be relevant to an Open MPI > > developer): > > > > ompi_mpi_init: orte_init failed > > --> Returned "Unable to start a daemon on the local node" (-128) > > instead of "Success" (0) > > > -------------------------------------------------------------------------- > > [ubuntu:31601] *** An error occurred in MPI_Init_thread > > [ubuntu:31601] *** on a NULL communicator > > [ubuntu:31601] *** Unknown error > > [ubuntu:31601] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort > > > -------------------------------------------------------------------------- > > An MPI process is aborting at a time when it cannot guarantee that > all > > of its peer processes in the job will be killed properly. You should > > double check that everything has shut down cleanly. > > > > Reason: Before MPI_INIT completed > > Local host: ubuntu > > PID: 31601 > > > -------------------------------------------------------------------------- > > PyOP2 installation failed > > See /home/mosh/PyOP2/pyop2_install.log for details > > > > Any idea what's going on? > > > > Suet > > > > > > > ------------------------------------------------------------------------ > > *From:* Andrew McRae <a.mcrae12(a)imperial.ac.uk > > <mailto:a.mcrae12@imperial.ac.uk>> > > *Sent:* 15 November 2014 23:13 > > *To:* Lee, Suet > > *Subject:* Re: Firedrake Installation > > > > Or, if you want to be a guinea pig, don't run the 'sudo pip install > > mpi4py' command and just run the install script again :) > > > > (I updated > > < > https://github.com/OP2/PyOP2/commit/e15b3ee8d72369f10c9a84d944a3ecbf06f7e927 > > > > the script just now -- thanks for alerting us to that bug) > > > > On 15 November 2014 23:09, Andrew McRae <a.mcrae12(a)imperial.ac.uk > > <mailto:a.mcrae12@imperial.ac.uk>> wrote: > > > > Hi Suet, > > > > Sorry about that. This should fix the mpi4py problem: sudo pip > > install mpi4py > > > > Then try the quick install script again. > > > > Yes, PyOP2, FFC, FIAT and UFL need to be installed before > > firerake. However, installing FFC/FIAT/UFL is easy -- you just > > run the 'sudo pip install \ six \ sympy \ ...' command, as > > described on http://www.firedrakeproject.org/download.html. > > > > Let me know if there's any other problems. > > > > Best, > > > > Andrew > > > > > > On 15 November 2014 23:00, Lee, Suet <suet.lee11(a)imperial.ac.uk > > <mailto:suet.lee11@imperial.ac.uk>> wrote: > > > > Hi Andrew, > > > > > > So I finally got round to the Firedrake installation! > > > > > > I'm trying to install PyOP2. The only problem is that I'm > > running up against the following error: > > > > > > PyOP2 installation started at Sat Nov 15 22:38:45 GMT 2014 > > on Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr > > 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux > > > > *** Privileged installation *** > > Running unprivileged commands as mosh > > > > *** Preparing system *** > > > > *** Installing dependencies *** > > > > *** Installing PETSc *** > > > > *** Installing PyOP2 *** > > > > Traceback (most recent call last): > > File "<string>", line 1, in <module> > > File "pyop2/__init__.py", line 9, in <module> > > from op2 import * > > File "pyop2/op2.py", line 38, in <module> > > import backends > > File "pyop2/backends.py", line 41, in <module> > > from logger import warning > > File "pyop2/logger.py", line 38, in <module> > > from mpi import MPI > > File "pyop2/mpi.py", line 37, in <module> > > from mpi4py import MPI as _MPI > > ImportError: No module named mpi4py > > PyOP2 installation failed > > See /home/mosh/pyop2_install.log for details > > > > > > I must be missing the file mpi4py? Do I have to install > > > > PyOP2 <http://op2.github.io/PyOP2>, FFC > > <https://bitbucket.org/mapdes/ffc>, FIAT > > <https://bitbucket.org/mapdes/fiat>, and UFL > > <https://bitbucket.org/mapdes/ufl>, before Firedrake? I > > attempted the quick installation for PyOP2 but do I need to > > install other packages before that? > > > > Best, > > > > Suet > >

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problem with scripts/firedrake-clean
by Eike Mueller 14 Nov '14

14 Nov '14

Dear firedrakers, I get a strange error message when I run ./scripts/firedrake-clean (branch multigrid-parallel, just pulled from remote): eikemueller@138-38-169-12 $ ./scripts/firedrake-clean Traceback (most recent call last): File "./scripts/firedrake-clean", line 3, in <module> from firedrake.ffc_interface import clear_cache, FFCKernel File "/Users/eikemueller/PostDocBath/EllipticSolvers/firedrake/firedrake/__init__.py", line 2, in <module> import petsc File "/Users/eikemueller/PostDocBath/EllipticSolvers/firedrake/firedrake/petsc.py", line 4, in <module> petsc4py.init(sys.argv) File "/Users/eikemueller/PostDocBath/EllipticSolvers/petsc4py/arch-darwin-c-opt/lib/python2.7/site-packages/petsc4py/__init__.py", line 42, in init PETSc = petsc4py.lib.ImportPETSc(arch) File "/Users/eikemueller/PostDocBath/EllipticSolvers/petsc4py/arch-darwin-c-opt/lib/python2.7/site-packages/petsc4py/lib/__init__.py", line 29, in ImportPETSc return Import('petsc4py', 'PETSc', path, arch) File "/Users/eikemueller/PostDocBath/EllipticSolvers/petsc4py/arch-darwin-c-opt/lib/python2.7/site-packages/petsc4py/lib/__init__.py", line 64, in Import module = imp.load_module(fullname, fo, fn, stuff) File "PETSc.pyx", line 100, in init petsc4py.PETSc (src/petsc4py.PETSc.c:221273) RuntimeError: module compiled against API version 9 but this version of numpy is 7 This is odd, because I just recompiled petsc4py (git pull; make clean; python setup.py install --prefix=`pwd`/$PETSC_ARCH). I did, however, get the following during petsc4py building: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1760:0, from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from src/include/petsc4py/numpy.h:11, from src/petsc4py.PETSc.c:347, from src/PETSc.c:3: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ Also, I can build and use firedrake without any problems. Thanks, Eike -- Dr Eike Hermann Mueller Research Associate (PostDoc) Department of Mathematical Sciences University of Bath Bath BA2 7AY, United Kingdom +44 1225 38 5803 e.mueller(a)bath.ac.uk http://people.bath.ac.uk/em459/

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Anisotropic mesh
by Anna Kalogirou 12 Nov '14

12 Nov '14

Dear all, There seems to be a problem with anisotropic meshes, namely with different number of nodes in each direction. The problem is encountered closer to the x-axis if the x-direction has less points. The situation becomes even worse if I make the domain rectangular and as its length is increased. You can see an example in the attached code which uses UnitSquareMesh(20,80) on a rectangular domain 4 times longer than wide. I am not sure why this is happening, so hopefully someone can help. Kind regards, Anna Kalogirou. P.S. Does Firedrake support the use of quadrilateral meshes? -- Dr Anna Kalogirou Research Fellow School of Mathematics University of Leeds

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Firedrake paper results
by Florian Rathgeber 11 Nov '14

11 Nov '14

Dear all, I finished a first draft of the results section for the Firedrake paper. Any feedback gratefully received! If you don't have access to the repository you can get a PDF from https://wwwhomes.doc.ic.ac.uk/~fr710/paper.pdf Cheers, Florian

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Re: [firedrake] extruded circle mesh problem
by Andrew McRae 11 Nov '14

11 Nov '14

Overwriting m.coordinates doesn't change m's "ufl_cell", which remains Cell('interval', 2). This gets used during the extrusion process, leaving you with a mesh that thinks it's in 3 dimensions. I'm also not sure why you're using Expression(("0.", "0.")) in the DirichletBC, since 0 will suffice. On 11 November 2014 17:28, Shipton, Jemma <j.shipton(a)imperial.ac.uk> wrote: > Hello, > > I'm trying to solve a problem that works on an extruded periodic interval > mesh on an extruded circle mesh. I am getting the following error: > > Traceback (most recent call last): > File "extruded_circle_helmholtz.py", line 57, in <module> > bcs = [DirichletBC(W[0], Expression(("0.", "0.")), "bottom"), > File "/home/jemma/src/firedrake/firedrake/bcs.py", line 56, in __init__ > self.function_arg = g > File "/home/jemma/src/firedrake/firedrake/bcs.py", line 95, in > function_arg > g = function.Function(self._function_space).interpolate(g) > File "/home/jemma/src/firedrake/firedrake/function.py", line 182, in > interpolate > % (sum(dims), np.prod(expression.value_shape(), dtype=int))) > RuntimeError: Expression of length 3 required, got length 2 > > The problem appears to be that the mesh coordinates have 3 components > whereas the extruded interval mesh coordinates only have 2. Any idea how to > fix? > > My code is here: > > https://gist.github.com/anonymous/dff509883518ef0f5f2d > > Thanks! > > Jemma >

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Re: [firedrake] extruded circle mesh problem
by Andrew McRae 11 Nov '14

11 Nov '14

I didn't notice any other ill effects. m._ufl_cell = Cell('interval', 1) On 11 November 2014 18:04, Cotter, Colin J <colin.cotter(a)imperial.ac.uk> wrote: > Is it sufficient to reset ufl_cell to Cell('interval',1), or will that > break other stuff? > > cheers > --cjc > ------------------------------ > *From:* firedrake-bounces(a)imperial.ac.uk [firedrake-bounces(a)imperial.ac.uk] > on behalf of Andrew McRae [a.mcrae12(a)imperial.ac.uk] > *Sent:* 11 November 2014 17:50 > *To:* firedrake > *Subject:* Re: [firedrake] extruded circle mesh problem > > Overwriting m.coordinates doesn't change m's "ufl_cell", which remains > Cell('interval', 2). This gets used during the extrusion process, leaving > you with a mesh that thinks it's in 3 dimensions. > > I'm also not sure why you're using Expression(("0.", "0.")) in the > DirichletBC, since 0 will suffice. > > On 11 November 2014 17:28, Shipton, Jemma <j.shipton(a)imperial.ac.uk> > wrote: > >> Hello, >> >> I'm trying to solve a problem that works on an extruded periodic interval >> mesh on an extruded circle mesh. I am getting the following error: >> >> Traceback (most recent call last): >> File "extruded_circle_helmholtz.py", line 57, in <module> >> bcs = [DirichletBC(W[0], Expression(("0.", "0.")), "bottom"), >> File "/home/jemma/src/firedrake/firedrake/bcs.py", line 56, in __init__ >> self.function_arg = g >> File "/home/jemma/src/firedrake/firedrake/bcs.py", line 95, in >> function_arg >> g = function.Function(self._function_space).interpolate(g) >> File "/home/jemma/src/firedrake/firedrake/function.py", line 182, in >> interpolate >> % (sum(dims), np.prod(expression.value_shape(), dtype=int))) >> RuntimeError: Expression of length 3 required, got length 2 >> >> The problem appears to be that the mesh coordinates have 3 components >> whereas the extruded interval mesh coordinates only have 2. Any idea how to >> fix? >> >> My code is here: >> >> https://gist.github.com/anonymous/dff509883518ef0f5f2d >> >> Thanks! >> >> Jemma >> > >

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extruded circle mesh problem
by Shipton, Jemma 11 Nov '14

11 Nov '14

Hello, I'm trying to solve a problem that works on an extruded periodic interval mesh on an extruded circle mesh. I am getting the following error: Traceback (most recent call last): File "extruded_circle_helmholtz.py", line 57, in <module> bcs = [DirichletBC(W[0], Expression(("0.", "0.")), "bottom"), File "/home/jemma/src/firedrake/firedrake/bcs.py", line 56, in __init__ self.function_arg = g File "/home/jemma/src/firedrake/firedrake/bcs.py", line 95, in function_arg g = function.Function(self._function_space).interpolate(g) File "/home/jemma/src/firedrake/firedrake/function.py", line 182, in interpolate % (sum(dims), np.prod(expression.value_shape(), dtype=int))) RuntimeError: Expression of length 3 required, got length 2 The problem appears to be that the mesh coordinates have 3 components whereas the extruded interval mesh coordinates only have 2. Any idea how to fix? My code is here: https://gist.github.com/anonymous/dff509883518ef0f5f2d Thanks! Jemma

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