undefined symbol: kspfgmresmodifypcksp_
Dear Firedrake Developers, I tried to start the helmholtz.py example, but I get the following error: File "helmholtz.py", line 47, in <module> from firedrake import * File "/home/user/.local/lib/python2.7/site-packages/firedrake/__init__.py", line 8, in <module> import firedrake.petsc as petsc File "/home/user/.local/lib/python2.7/site-packages/firedrake/petsc.py", line 5, in <module> petsc4py.init(sys.argv) File "/home/user/.local/lib/python2.7/site-packages/petsc4py/__init__.py", line 42, in init PETSc = petsc4py.lib.ImportPETSc(arch) File "/home/user/.local/lib/python2.7/site-packages/petsc4py/lib/__init__.py", line 29, in ImportPETSc return Import('petsc4py', 'PETSc', path, arch) File "/home/user/.local/lib/python2.7/site-packages/petsc4py/lib/__init__.py", line 64, in Import module = imp.load_module(fullname, fo, fn, stuff) ImportError: /home/user/.local/lib/python2.7/site-packages/petsc/lib/libpetsc.so.3.06: undefined symbol: kspfgmresmodifypcksp_ Is there anything I can do about it? Thank you! Henrik -- Dipl.-Math. Henrik Büsing Applied Geophysics and Geothermal Energy E.ON Energy Research Center RWTH Aachen University ----------------------------------------------- Mathieustr. 10 | Tel +49 (0)241 80 49907 52074 Aachen, Germany | Fax +49 (0)241 80 49889 ----------------------------------------------- http://www.eonerc.rwth-aachen.de/GGE hbuesing@eonerc.rwth-aachen.de -----------------------------------------------
I tried to rebuild everything from scratch, but the error persists. It already occurs in the tests for pyop2 (see attachement). Henrik Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake-bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik Gesendet: 16 September 2015 23:19 An: firedrake@imperial.ac.uk Betreff: [firedrake] undefined symbol: kspfgmresmodifypcksp_ Dear Firedrake Developers, I tried to start the helmholtz.py example, but I get the following error: File "helmholtz.py", line 47, in <module> from firedrake import * File "/home/user/.local/lib/python2.7/site-packages/firedrake/__init__.py", line 8, in <module> import firedrake.petsc as petsc File "/home/user/.local/lib/python2.7/site-packages/firedrake/petsc.py", line 5, in <module> petsc4py.init(sys.argv) File "/home/user/.local/lib/python2.7/site-packages/petsc4py/__init__.py", line 42, in init PETSc = petsc4py.lib.ImportPETSc(arch) File "/home/user/.local/lib/python2.7/site-packages/petsc4py/lib/__init__.py", line 29, in ImportPETSc return Import('petsc4py', 'PETSc', path, arch) File "/home/user/.local/lib/python2.7/site-packages/petsc4py/lib/__init__.py", line 64, in Import module = imp.load_module(fullname, fo, fn, stuff) ImportError: /home/user/.local/lib/python2.7/site-packages/petsc/lib/libpetsc.so.3.06: undefined symbol: kspfgmresmodifypcksp_ Is there anything I can do about it? Thank you! Henrik -- Dipl.-Math. Henrik Büsing Applied Geophysics and Geothermal Energy E.ON Energy Research Center RWTH Aachen University ----------------------------------------------- Mathieustr. 10 | Tel +49 (0)241 80 49907 52074 Aachen, Germany | Fax +49 (0)241 80 49889 ----------------------------------------------- http://www.eonerc.rwth-aachen.de/GGE hbuesing@eonerc.rwth-aachen.de<mailto:hbuesing@eonerc.rwth-aachen.de> -----------------------------------------------
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Henrik, On 17/09/15 09:07, Buesing, Henrik wrote:
I tried to rebuild everything from scratch, but the error persists. It already occurs in the tests for pyop2 (see attachement).
Just for sanity checking, I presume you used the provided "firedrake-install" script to install firedrake? I think the problem has already started when installing PETSc (and/or petsc4py). Let's try and figure out what's gone wrong. Can you first try building and running the attached PETSc C program. You'll need to do: PETSC_DIR=/home/user/.local/lib/python2.7/site-packages/petsc/ make testksp Having saved the provided testksp.c and Makefile. Then, if that builds, try running. I get something like: $ ./testksp KSP Object: 1 MPI processes type: fgmres GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement GMRES: happy breakdown tolerance 1e-30 maximum iterations=10000, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000 right preconditioning using UNPRECONDITIONED norm type for convergence test PC Object: 1 MPI processes type: ilu ILU: out-of-place factorization 0 levels of fill tolerance for zero pivot 2.22045e-14 matrix ordering: natural factor fill ratio given 1, needed 1 Factored matrix follows: Mat Object: 1 MPI processes type: seqaij rows=1, cols=1 package used to perform factorization: petsc total: nonzeros=1, allocated nonzeros=1 total number of mallocs used during MatSetValues calls =0 not using I-node routines linear system matrix = precond matrix: Mat Object: 1 MPI processes type: seqaij rows=1, cols=1 total: nonzeros=1, allocated nonzeros=5 total number of mallocs used during MatSetValues calls =0 not using I-node routines If that doesn't work, we know the problem has already appeared and need to figure out what went wrong when installing PETSc. If it does work let's then see if petsc4py works: $ python -c "from petsc4py import PETSc; print PETSc.__file__" I suspect you'll already run into trouble at one of those two points. Cheers, Lawrence -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBAgAGBQJV+nw/AAoJECOc1kQ8PEYvqRUH/1YLbWyPnwwDx5kOGQwKCQUz x2OzQ+uXEScIR8IUeZ2MGwvQ4/uHpLFxXeT+ZPqZR1wYON1F/oGNkPx9rJm3dDsn 5mmESToh+dznE8S/bmRDlI/4j3QURS9+52rStl8GMG2S/Vb7figFiBA6/EuL5sBg kf4Crbj6+JpQW8UNo9Z3xHVD3SAMyhssdtYHXmR5baRgY/b5vkxdbttT65BkGt5c Ll7y2Gkauu9EpfWFob6mjZFJFcbeKGmRGgrwJ5Wdt6PLVs3VF1zPzOpoxYWWj+k1 xh8YG7yu8qcAW5z1fRbe+dd5bKFkC//Zycn2+kcqWtg9ysn57JjSN9f+2/M56u4= =xjd7 -----END PGP SIGNATURE-----
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 17/09/15 09:39, Lawrence Mitchell wrote:
Dear Henrik,
On 17/09/15 09:07, Buesing, Henrik wrote:
I tried to rebuild everything from scratch, but the error persists. It already occurs in the tests for pyop2 (see attachement).
Just for sanity checking, I presume you used the provided "firedrake-install" script to install firedrake?
I think the problem has already started when installing PETSc (and/or petsc4py). Let's try and figure out what's gone wrong. Can you first try building and running the attached PETSc C program. You'll need to do:
PETSC_DIR=/home/user/.local/lib/python2.7/site-packages/petsc/ ^^^^^^^^^^ Replace this bit by the path to your actual home directory!
Lawrence -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBAgAGBQJV+n03AAoJECOc1kQ8PEYviYIH/Au6dW3KGkNJsTIkihOxUS2G PFh+RvTyJoZl2nq9PxDkppdcADqCaRQzrDeX3wJb1CdMSY7m9n+t+mOBC3Xi76++ 46zFHv9dHFi2KN0dQpZKa0mAo6NtgtD/pVmfjsHf88n2hYwjsvVsKaOc7j8f0C/D ut/UqVj6/DOH/fDNO1gcelljjQkmkC0cMt5VMu5Fa+FPfmLaxQ6TdSKih6l/BG0j sro6OhNOJnDikKRjjfQeCgIT5o4zphaCQzsVsGirTKC0PePdWeVPIiww1cM+Dnza wmDABrBI6di/7kg/BDirq+G1swrXjTy2K7HGtq4HpTXhRcQ8BXdfn47+jSnH6X8= =umSc -----END PGP SIGNATURE-----
@Lawrence: I will go through your tests. At the moment I try to use my own petsc version (and not the pip installed one) for petsc4py. This crashed because I did not have "--download-ctetgen --download-triangle --download-chaco". I'm doing a petsc ./configure atm. I will see how that goes. I will then kill this version install petsc with pip again and do your tests. Will take a while due to all the PETSc configuring. Thank you! Henrik
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake- bounces@imperial.ac.uk] Im Auftrag von Lawrence Mitchell Gesendet: 17 September 2015 10:40 An: firedrake@imperial.ac.uk Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
Dear Henrik,
On 17/09/15 09:07, Buesing, Henrik wrote:
I tried to rebuild everything from scratch, but the error persists. It already occurs in the tests for pyop2 (see attachement).
Just for sanity checking, I presume you used the provided "firedrake- install" script to install firedrake?
I think the problem has already started when installing PETSc (and/or petsc4py). Let's try and figure out what's gone wrong. Can you first try building and running the attached PETSc C program. You'll need to do:
PETSC_DIR=/home/user/.local/lib/python2.7/site-packages/petsc/ make testksp
Having saved the provided testksp.c and Makefile.
Then, if that builds, try running. I get something like:
$ ./testksp KSP Object: 1 MPI processes type: fgmres GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement GMRES: happy breakdown tolerance 1e-30 maximum iterations=10000, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000 right preconditioning using UNPRECONDITIONED norm type for convergence test PC Object: 1 MPI processes type: ilu ILU: out-of-place factorization 0 levels of fill tolerance for zero pivot 2.22045e-14 matrix ordering: natural factor fill ratio given 1, needed 1 Factored matrix follows: Mat Object: 1 MPI processes type: seqaij rows=1, cols=1 package used to perform factorization: petsc total: nonzeros=1, allocated nonzeros=1 total number of mallocs used during MatSetValues calls =0 not using I-node routines linear system matrix = precond matrix: Mat Object: 1 MPI processes type: seqaij rows=1, cols=1 total: nonzeros=1, allocated nonzeros=5 total number of mallocs used during MatSetValues calls =0 not using I-node routines
If that doesn't work, we know the problem has already appeared and need to figure out what went wrong when installing PETSc.
If it does work let's then see if petsc4py works:
$ python -c "from petsc4py import PETSc; print PETSc.__file__"
I suspect you'll already run into trouble at one of those two points.
Cheers,
Lawrence
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-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake- bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik Gesendet: 17 September 2015 10:53 An: firedrake@imperial.ac.uk Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
@Lawrence: I will go through your tests. At the moment I try to use my own petsc version (and not the pip installed one) for petsc4py. This crashed because I did not have "--download-ctetgen --download-triangle - -download-chaco". I'm doing a petsc ./configure atm. I will see how that goes.
[Buesing, Henrik] This gave at least different errors (see the attached pyop2 test). I get "Import errors" No module named sparsity cannot import name plan No module named computeind
I will then kill this version install petsc with pip again and do your tests. Will take a while due to all the PETSc configuring.
[Buesing, Henrik] For the tests see below.
Just for sanity checking, I presume you used the provided "firedrake- install" script to install firedrake?
[Buesing, Henrik] No, I'm using the step-by-step instructions.
I think the problem has already started when installing PETSc (and/or petsc4py). Let's try and figure out what's gone wrong. Can you first try building and running the attached PETSc C program. You'll need to do:
PETSC_DIR=/home/user/.local/lib/python2.7/site-packages/petsc/ make testksp
[Buesing, Henrik] This already fails with /home/hb111949/.local/lib/python2.7/site-packages/petsc/lib/libpetsc.so: undefined reference to `kspfgmresmodifypcnochange_' /home/hb111949/.local/lib/python2.7/site-packages/petsc/lib/libpetsc.so: undefined reference to `tsmonitordefault_' /home/hb111949/.local/lib/python2.7/site-packages/petsc/lib/libpetsc.so: undefined reference to `kspfgmresmodifypcksp_'
If that doesn't work, we know the problem has already appeared and need to figure out what went wrong when installing PETSc.
If it does work let's then see if petsc4py works:
[Buesing, Henrik] It's only working with my own petsc version.
$ python -c "from petsc4py import PETSc; print PETSc.__file__"
[Buesing, Henrik] ...yields for pip petsc ImportError: /home/hb111949/.local/lib/python2.7/site-packages/petsc/lib/libpetsc.so.3.06: undefined symbol: kspfgmresmodifypcksp_ for own petsc /home/hb111949/.local/lib/python2.7/site-packages/petsc4py/lib/arch-linux2-c-opt/PETSc.so
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake- bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik Gesendet: 17 September 2015 11:43 An: firedrake@imperial.ac.uk Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake- bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik Gesendet: 17 September 2015 10:53 An: firedrake@imperial.ac.uk Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
@Lawrence: I will go through your tests. At the moment I try to use my own petsc version (and not the pip installed one) for petsc4py. This crashed because I did not have "--download-ctetgen --download-triangle - -download-chaco". I'm doing a petsc ./configure atm. I will see how that goes.
[Buesing, Henrik] This gave at least different errors (see the attached pyop2 test). I get "Import errors" No module named sparsity cannot import name plan No module named computeind
[Buesing, Henrik] There are shared object files computeind.so plan.so sparsity.so in the pyop2 directory build/lib.linux-x86_64-2.7/pyop2 Maybe he does not find these files somehow? Henrik
I will then kill this version install petsc with pip again and do your tests. Will take a while due to all the PETSc configuring.
[Buesing, Henrik] For the tests see below.
Just for sanity checking, I presume you used the provided "firedrake- install" script to install firedrake?
[Buesing, Henrik] No, I'm using the step-by-step instructions.
I think the problem has already started when installing PETSc (and/or petsc4py). Let's try and figure out what's gone wrong. Can you first try building and running the attached PETSc C program. You'll need to do:
PETSC_DIR=/home/user/.local/lib/python2.7/site-packages/petsc/ make testksp
[Buesing, Henrik] This already fails with /home/hb111949/.local/lib/python2.7/site-packages/petsc/lib/libpetsc.so: undefined reference to `kspfgmresmodifypcnochange_' /home/hb111949/.local/lib/python2.7/site-packages/petsc/lib/libpetsc.so: undefined reference to `tsmonitordefault_' /home/hb111949/.local/lib/python2.7/site-packages/petsc/lib/libpetsc.so: undefined reference to `kspfgmresmodifypcksp_'
If that doesn't work, we know the problem has already appeared and need to figure out what went wrong when installing PETSc.
If it does work let's then see if petsc4py works:
[Buesing, Henrik] It's only working with my own petsc version.
$ python -c "from petsc4py import PETSc; print PETSc.__file__"
[Buesing, Henrik] ...yields
for pip petsc ImportError: /home/hb111949/.local/lib/python2.7/site- packages/petsc/lib/libpetsc.so.3.06: undefined symbol: kspfgmresmodifypcksp_
for own petsc /home/hb111949/.local/lib/python2.7/site-packages/petsc4py/lib/arch- linux2-c-opt/PETSc.so
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake- bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik Gesendet: 17 September 2015 12:29 An: firedrake@imperial.ac.uk Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake- bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik Gesendet: 17 September 2015 11:43 An: firedrake@imperial.ac.uk Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake- bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik Gesendet: 17 September 2015 10:53 An: firedrake@imperial.ac.uk Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
@Lawrence: I will go through your tests. At the moment I try to use my own petsc version (and not the pip installed one) for petsc4py. This crashed because I did not have "--download-ctetgen --download-triangle - -download-chaco". I'm doing a petsc ./configure atm. I will see how that goes.
[Buesing, Henrik] This gave at least different errors (see the attached pyop2 test). I get "Import errors" No module named sparsity cannot import name plan No module named computeind
[Buesing, Henrik] There are shared object files
computeind.so plan.so sparsity.so
in the pyop2 directory
build/lib.linux-x86_64-2.7/pyop2
Maybe he does not find these files somehow?
[Buesing, Henrik] I have added the above directory to the PYTHONPATH. He now does not complain about sparsity anymore. I get a Intel MKL FATAL ERROR: Cannot load libmkl_mc3.so or libmkl_def.so. Well, I guess that has to do with Petsc and its blas-lapack-dir. I will try to reconfigure with --download-fblaslapack and not set the directory.
I will then kill this version install petsc with pip again and do your tests. Will take a while due to all the PETSc configuring.
[Buesing, Henrik] For the tests see below.
Just for sanity checking, I presume you used the provided "firedrake- install" script to install firedrake?
[Buesing, Henrik] No, I'm using the step-by-step instructions.
I think the problem has already started when installing PETSc (and/or petsc4py). Let's try and figure out what's gone wrong. Can you first try building and running the attached PETSc C
program.
You'll need to do:
PETSC_DIR=/home/user/.local/lib/python2.7/site-packages/petsc/ make testksp
[Buesing, Henrik] This already fails with /home/hb111949/.local/lib/python2.7/site- packages/petsc/lib/libpetsc.so: undefined reference to `kspfgmresmodifypcnochange_' /home/hb111949/.local/lib/python2.7/site- packages/petsc/lib/libpetsc.so: undefined reference to `tsmonitordefault_' /home/hb111949/.local/lib/python2.7/site- packages/petsc/lib/libpetsc.so: undefined reference to `kspfgmresmodifypcksp_'
If that doesn't work, we know the problem has already appeared and need to figure out what went wrong when installing PETSc.
If it does work let's then see if petsc4py works:
[Buesing, Henrik] It's only working with my own petsc version.
$ python -c "from petsc4py import PETSc; print PETSc.__file__"
[Buesing, Henrik] ...yields
for pip petsc ImportError: /home/hb111949/.local/lib/python2.7/site- packages/petsc/lib/libpetsc.so.3.06: undefined symbol: kspfgmresmodifypcksp_
for own petsc /home/hb111949/.local/lib/python2.7/site-packages/petsc4py/lib/arch- linux2-c-opt/PETSc.so
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 17/09/15 11:57, Buesing, Henrik wrote:
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake- bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik Gesendet: 17 September 2015 12:29 An: firedrake@imperial.ac.uk Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake- bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik Gesendet: 17 September 2015 11:43 An: firedrake@imperial.ac.uk Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake- bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik Gesendet: 17 September 2015 10:53 An: firedrake@imperial.ac.uk Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
@Lawrence: I will go through your tests. At the moment I try to use my own petsc version (and not the pip installed one) for petsc4py. This crashed because I did not have "--download-ctetgen --download-triangle - -download-chaco". I'm doing a petsc ./configure atm. I will see how that goes.
[Buesing, Henrik] This gave at least different errors (see the attached pyop2 test). I get "Import errors" No module named sparsity cannot import name plan No module named computeind
[Buesing, Henrik] There are shared object files
computeind.so plan.so sparsity.so
in the pyop2 directory
build/lib.linux-x86_64-2.7/pyop2
Maybe he does not find these files somehow?
[Buesing, Henrik] I have added the above directory to the PYTHONPATH. He now does not complain about sparsity anymore. I get a
Intel MKL FATAL ERROR: Cannot load libmkl_mc3.so or libmkl_def.so.
Well, I guess that has to do with Petsc and its blas-lapack-dir. I will try to reconfigure with --download-fblaslapack and not set the directory.
I would start by trying to get petsc4py working on top of the PETSc you built manually (rather than through pip), which I think seemed to be working. Then we need to build PyOP2 with the correct PETSc/petsc4py combo. The MKL error may be similar to this error mentioned in the PETSc FAQ: http://www.mcs.anl.gov/petsc/documentation/faq.html#libimf Lawrence -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBAgAGBQJV+p3UAAoJECOc1kQ8PEYvNuwH/iuTymdAT0MofwrnwRV1iRwe kNj9tC3mN3E3pXVnCml8Wc4IvdGYGM0wgdlk8glUtQSyJNu+YoNuK7KRRTUhsNUr GLwxX61SV9kuwXfk5XjXjmvLGoJlxn4275jslNlUz8vXRAgajY46pPqXlb7v4D/H Et5jkHirDVC29lM42P9KmtCmX4zxjZGUpNrUAGQxRm6nbAeA+cplifHJ6zlb1Pf0 ewU4adl2ywxagtvX8Nxy5uIQt3pJmF6QX+nJBsei1OjVsoFMGMz869nEZuG6jqN9 yxkbno5PBS8LsLTAyVYsYScRo1pxWE8uaq7T4TMWrQSE+/j/85l5ZapOKuoUvmo= =WUld -----END PGP SIGNATURE-----
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake- bounces@imperial.ac.uk] Im Auftrag von Lawrence Mitchell Gesendet: 17 September 2015 13:03 An: firedrake@imperial.ac.uk Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
On 17/09/15 11:57, Buesing, Henrik wrote:
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake- bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik Gesendet: 17 September 2015 12:29 An: firedrake@imperial.ac.uk Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake- bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik Gesendet: 17 September 2015 11:43 An: firedrake@imperial.ac.uk Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
-----Ursprüngliche Nachricht----- Von: firedrake-bounces@imperial.ac.uk [mailto:firedrake- bounces@imperial.ac.uk] Im Auftrag von Buesing, Henrik Gesendet: 17 September 2015 10:53 An: firedrake@imperial.ac.uk Betreff: Re: [firedrake] undefined symbol: kspfgmresmodifypcksp_
@Lawrence: I will go through your tests. At the moment I try to use my own petsc version (and not the pip installed one) for petsc4py. This crashed because I did not have "--download-ctetgen --download-triangle - -download-chaco". I'm doing a petsc ./configure atm. I will see how that goes.
[Buesing, Henrik] This gave at least different errors (see the attached pyop2 test). I get "Import errors" No module named sparsity cannot import name plan No module named computeind
[Buesing, Henrik] There are shared object files
computeind.so plan.so sparsity.so
in the pyop2 directory
build/lib.linux-x86_64-2.7/pyop2
Maybe he does not find these files somehow?
[Buesing, Henrik] I have added the above directory to the PYTHONPATH. He now does not complain about sparsity anymore. I get a
Intel MKL FATAL ERROR: Cannot load libmkl_mc3.so or libmkl_def.so.
Well, I guess that has to do with Petsc and its blas-lapack-dir. I will try to reconfigure with --download-fblaslapack and not set the directory.
[Buesing, Henrik] This new, own version of petsc did work and I can run helmholtz.py.
Still do not know why the pip petsc did not work... Maybe this had also sth. to do with the blas-lapack-dir I passed in the configure options... Well, it's working now! Thank you! Henrik
participants (2)
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Buesing, Henrik
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Lawrence Mitchell