Re: [firedrake] Firedrake Installation
Hi all, Suet [cc'd], one of Colin's project students, is encoutering the following error when using the PyOP2 'quick install' script. Can anyone help? IIRC, this is running in a (32-bit?) Ubuntu 14.04 virtual machine. (Last night, she was getting an mpi4py error, but I believe this <https://github.com/OP2/PyOP2/commit/e15b3ee8d72369f10c9a84d944a3ecbf06f7e927> fixed that). Cheers, Andrew On 16 November 2014 13:28, Lee, Suet <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 (github.com)... 192.30.252.131 Connecting to github.com (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 (raw.githubusercontent.com)... 185.31.18.133 Connecting to raw.githubusercontent.com (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
This looks like you might have mpich2 installed in addition to openmpi. Can you please check and verify? If so, please remove mpich2. Florian On 16/11/14 13:39, Andrew McRae wrote:
Hi all,
Suet [cc'd], one of Colin's project students, is encoutering the following error when using the PyOP2 'quick install' script.
Can anyone help? IIRC, this is running in a (32-bit?) Ubuntu 14.04 virtual machine.
(Last night, she was getting an mpi4py error, but I believe this <https://github.com/OP2/PyOP2/commit/e15b3ee8d72369f10c9a84d944a3ecbf06f7e927> fixed that).
Cheers,
Andrew
On 16 November 2014 13:28, Lee, Suet <suet.lee11@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
Dear all, I am trying to install Firedrake on a Mac OS X (version 10.9.5). I am following the installation instructions but I get an error during the PETSc installation step. I would really appreciate it if someone can help. Thank you very much! Best, Anna. ******************************************************************************* UNABLE to EXECUTE BINARIES for ./configure ------------------------------------------------------------------------------- Cannot run executables created with FC. If this machine uses a batch system to submit jobs you will need to configure using ./configure with the additional option --with-batch. Otherwise there is problem with the compilers. Can you compile and run code with your compiler '/usr/local/bin/mpif90'? ******************************************************************************* ---------------------------------------- Cleaning up... Command /usr/local/opt/python/bin/python2.7 -c "import setuptools, tokenize;__file__='/tmp/pip-NOkbbE-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-eEaDI5-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /tmp/pip-NOkbbE-build
On 16 Nov 2014, at 14:16, Anna Kalogirou <A.Kalogirou@leeds.ac.uk> wrote:
Dear all,
I am trying to install Firedrake on a Mac OS X (version 10.9.5). I am following the installation instructions but I get an error during the PETSc installation step. I would really appreciate it if someone can help. Thank you very much!
Best,
Anna.
*******************************************************************************
UNABLE to EXECUTE BINARIES for ./configure
-------------------------------------------------------------------------------
Cannot run executables created with FC. If this machine uses a batch system
to submit jobs you will need to configure using ./configure with the additional option --with-batch.
Otherwise there is problem with the compilers. Can you compile and run code with your compiler '/usr/local/bin/mpif90'?
*******************************************************************************
Does /usr/local/bin/mpif90 exist and is it able to compile a simple fortran file? Furthermore, is the resulting binary runnable? That appears to be the problem petsc is complaining about it. Lawrence
Thanks. I have now reached the point where I need test the PyOP2 installation, but when I write make test I get an error which I believe is related to open-mpi. It looks like libpetsc references the path /private/tmp/pip-hBwvhb-build/macosx-10.9-x86_64-python/lib/libhwloc.5.dylib which seems strange to me. The error log is: cd test; py.test unit --backend=sequential Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/_pytest/config.py", line 543, in importconftest mod = conftestpath.pyimport() File "/usr/local/lib/python2.7/site-packages/py/_path/local.py", line 641, in pyimport __import__(modname) File "/Users/matak/PyOP2/test/conftest.py", line 40, in <module> from pyop2 import op2 File "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_124_ge15b3ee-py2.7-macosx-10.9-x86_64.egg/pyop2/__init__.py", line 9, in <module> from op2 import * File "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_124_ge15b3ee-py2.7-macosx-10.9-x86_64.egg/pyop2/op2.py", line 39, in <module> import base File "/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_124_ge15b3ee-py2.7-macosx-10.9-x86_64.egg/pyop2/base.py", line 54, in <module> from sparsity import build_sparsity ImportError: dlopen(/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyOP2-0.11.0_124_ge15b3ee-py2.7-macosx-10.9-x86_64.egg/pyop2/sparsity.so, 2): Library not loaded: /private/tmp/pip-hBwvhb-build/macosx-10.9-x86_64-python/lib/libhwloc.5.dylib Referenced from: /usr/local/lib/python2.7/site-packages/petsc/lib/libpetsc.3.05.2.dylib Reason: image not found ERROR: could not load /Users/matak/PyOP2/test/conftest.py make: *** [unit_sequential] Error 4 Thank you. Best, Anna. On 16 Nov 2014, at 15:20, Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk<mailto:lawrence.mitchell@imperial.ac.uk>> wrote: On 16 Nov 2014, at 14:16, Anna Kalogirou <A.Kalogirou@leeds.ac.uk<mailto:A.Kalogirou@leeds.ac.uk>> wrote: Dear all, I am trying to install Firedrake on a Mac OS X (version 10.9.5). I am following the installation instructions but I get an error during the PETSc installation step. I would really appreciate it if someone can help. Thank you very much! Best, Anna. ******************************************************************************* UNABLE to EXECUTE BINARIES for ./configure ------------------------------------------------------------------------------- Cannot run executables created with FC. If this machine uses a batch system to submit jobs you will need to configure using ./configure with the additional option --with-batch. Otherwise there is problem with the compilers. Can you compile and run code with your compiler '/usr/local/bin/mpif90'? ******************************************************************************* Does /usr/local/bin/mpif90 exist and is it able to compile a simple fortran file? Furthermore, is the resulting binary runnable? That appears to be the problem petsc is complaining about it. Lawrence <signature.asc>_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Hi Anna,
On 16 Nov 2014, at 18:24, Anna Kalogirou <A.Kalogirou@leeds.ac.uk> wrote:
I have now reached the point where I need test the PyOP2 installation, but when I write
make test
I get an error which I believe is related to open-mpi. It looks like libpetsc references the path
/private/tmp/pip-hBwvhb-build/macosx-10.9-x86_64-
Ok, this appears to be an issue with the way some external packages are installed by petsc when using pip. Hwloc is non essential so can you add --download-hwloc=0 to the petsc configure options. In the mean time I will report a bug upstream. Cheers, Lawrence
Thank you Lawrence. I re-installed PETSc with the new configure option and the PyOP2 tests now run. With backend=opencl the tests were successful, but about 600 fail with backend=openmp. They all seem to have the same error, see below. Thank you for all the help. Best, Anna. ========================================================= /var/folders/cs/cbmmbcd13mv9jq1cptvdljzsl5jfkj/T/pyop2-cache-uid1717090897/22cdb1aae83a18075e91d543ddeb9fc3.c:43:15: warning: implicit declaration of function 'omp_get_thread_num' $ int tid = omp_get_thread_num(); ^ /var/folders/cs/cbmmbcd13mv9jq1cptvdljzsl5jfkj/T/pyop2-cache-uid1717090897/22cdb1aae83a18075e91d543ddeb9fc3.c:43:9: warning: unused variable 'tid' [-Wunused-variable] int tid = omp_get_thread_num(); ^ 2 warnings generated. Undefined symbols for architecture x86_64: "_omp_get_thread_num", referenced from: _wrap_copy in 22cdb1aae83a18075e91d543ddeb9fc3-48732d.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) ========================================================= On 17 Nov 2014, at 08:32, Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk<mailto:lawrence.mitchell@imperial.ac.uk>> wrote: Hi Anna, On 16 Nov 2014, at 18:24, Anna Kalogirou <A.Kalogirou@leeds.ac.uk<mailto:A.Kalogirou@leeds.ac.uk>> wrote: I have now reached the point where I need test the PyOP2 installation, but when I write make test I get an error which I believe is related to open-mpi. It looks like libpetsc references the path /private/tmp/pip-hBwvhb-build/macosx-10.9-x86_64- Ok, this appears to be an issue with the way some external packages are installed by petsc when using pip. Hwloc is non essential so can you add --download-hwloc=0 to the petsc configure options. In the mean time I will report a bug upstream. Cheers, Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Hi Anna,
On 23 Nov 2014, at 13:21, Anna Kalogirou <A.Kalogirou@leeds.ac.uk> wrote:
I re-installed PETSc with the new configure option and the PyOP2 tests now run. With backend=opencl the tests were successful, but about 600 fail with backend=openmp. They all seem to have the same error, see below.
Openmp failures are expected on Mac OS, since the compiler has no openmp support. I will update the make file and docs appropriately. Lawrence
Dear all, How would I solve multiple nonlinear variational problems simultaneously? For example, say that I have three residuals F(u1,u2,u3;v) = 0 G(u1,u2,u3;v) = 0 H(u1,u2,u3;v) = 0, where v is the test function. I need to solve all three of them together. Any suggestions? Thank you. Best, Anna.
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 26/11/14 10:19, Anna Kalogirou wrote:
Dear all,
How would I solve multiple nonlinear variational problems simultaneously? For example, say that I have three residuals
F(u1,u2,u3;v) = 0 G(u1,u2,u3;v) = 0 H(u1,u2,u3;v) = 0,
where v is the test function. I need to solve all three of them together. Any suggestions?
Assuming you have: W = MixedFunctionSpace(...) w = Function(W) u1, u2, u3 = split(w) F = fn(u1, u2, u3; v) etc... Since you're linear in v, can you not just write: solve(F + G + H == 0, w) ? Or am I missing something? Lawrence -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with undefined - http://www.enigmail.net/ iQEcBAEBAgAGBQJUdas2AAoJECOc1kQ8PEYvGzIIAM/PQ/7o82RvhWC2StXETQtm ub5cvB+sj6ceqyE73L4bJzMjNvqdjSMy61QcCErho6nyeviqtvCDKbih98Sy7tut 7QMKLFQgwB1JdtnmdU4Rc5cm6pDDo2LPE07pbHmRSAl7XUH0GZTcqRAJoBubEzcn BxcF0vRAgr++Y+4ak+Snt2k950k2mf3jE4Q3oA/KpkL8nVfEkBWU5ACb23CbKLAD lO5ZrOFuSYHoyj+Fcn8aEsrBGHEDwv6GhNoyWqo46speLCEamJN1E5D7KxYXuTCj W5lNHMPM0VeWvEiH69j4CidRbCo5Mba7rwVYJMzDWiXa0/avuFDlq2oOzxmIIIs= =BZY9 -----END PGP SIGNATURE-----
Dear all, I was in the process of updating Firedrake when I realised that the latest versions of PETSc and PyOP2 are not compatible. PyOP2 seems to be looking for libpetsc.3.05.2.dylib, while the one installed by PETSc is libpetsc.3.05.3.dylib. Best, Anna.
Uh, have you tried rebuilding/reinstalling petsc4py too? After that, please rebuild PyOP2 as well. I hope that it helps.
On 5 Apr 2015, at 12:40, Anna Kalogirou <a.kalogirou@leeds.ac.uk> wrote:
Dear all,
I was in the process of updating Firedrake when I realised that the latest versions of PETSc and PyOP2 are not compatible.
PyOP2 seems to be looking for libpetsc.3.05.2.dylib, while the one installed by PETSc is libpetsc.3.05.3.dylib.
Best,
Anna.
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Hi Miklos, I was following all the steps, and I first updated PETSc, petsc4py, PyOP2. I got errors in the tests for PyOP2 installation. Anna. On 5 Apr 2015, at 13:43, Miklos Homolya <m.homolya14@imperial.ac.uk> wrote:
Uh, have you tried rebuilding/reinstalling petsc4py too? After that, please rebuild PyOP2 as well.
I hope that it helps.
On 5 Apr 2015, at 12:40, Anna Kalogirou <a.kalogirou@leeds.ac.uk> wrote:
Dear all,
I was in the process of updating Firedrake when I realised that the latest versions of PETSc and PyOP2 are not compatible.
PyOP2 seems to be looking for libpetsc.3.05.2.dylib, while the one installed by PETSc is libpetsc.3.05.3.dylib.
Best,
Anna.
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
I don’t really know then what is wrong. It works for me on Mac OS X.
On 6 Apr 2015, at 08:49, Anna Kalogirou <a.kalogirou@leeds.ac.uk> wrote:
Hi Miklos,
I was following all the steps, and I first updated PETSc, petsc4py, PyOP2. I got errors in the tests for PyOP2 installation.
Anna.
On 5 Apr 2015, at 13:43, Miklos Homolya <m.homolya14@imperial.ac.uk> wrote:
Uh, have you tried rebuilding/reinstalling petsc4py too? After that, please rebuild PyOP2 as well.
I hope that it helps.
On 5 Apr 2015, at 12:40, Anna Kalogirou <a.kalogirou@leeds.ac.uk> wrote:
Dear all,
I was in the process of updating Firedrake when I realised that the latest versions of PETSc and PyOP2 are not compatible.
PyOP2 seems to be looking for libpetsc.3.05.2.dylib, while the one installed by PETSc is libpetsc.3.05.3.dylib.
Best,
Anna.
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
I have libpetsc.3.05.3.dylib. Can you try git clean -f -x -d in the PyOP2 directory, then building PyOP2 again? Regards, Miklos
On 6 Apr 2015, at 13:23, Miklos Homolya <m.homolya14@imperial.ac.uk> wrote:
I don’t really know then what is wrong. It works for me on Mac OS X.
On 6 Apr 2015, at 08:49, Anna Kalogirou <a.kalogirou@leeds.ac.uk> wrote:
Hi Miklos,
I was following all the steps, and I first updated PETSc, petsc4py, PyOP2. I got errors in the tests for PyOP2 installation.
Anna.
On 5 Apr 2015, at 13:43, Miklos Homolya <m.homolya14@imperial.ac.uk> wrote:
Uh, have you tried rebuilding/reinstalling petsc4py too? After that, please rebuild PyOP2 as well.
I hope that it helps.
On 5 Apr 2015, at 12:40, Anna Kalogirou <a.kalogirou@leeds.ac.uk> wrote:
Dear all,
I was in the process of updating Firedrake when I realised that the latest versions of PETSc and PyOP2 are not compatible.
PyOP2 seems to be looking for libpetsc.3.05.2.dylib, while the one installed by PETSc is libpetsc.3.05.3.dylib.
Best,
Anna.
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
participants (6)
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Andrew McRae
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Anna Kalogirou
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Anna Kalogirou
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Florian Rathgeber
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Lawrence Mitchell
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Miklos Homolya