[petsc-users] Quick Question on /src/ksp/ksp/example/ex29.c
On Tue, Sep 13, 2011 at 05:59, Alan Wei zhenglun.wei at gmail.com wrote: I'm still working on this poisson solver, and find a small problem. I found from the original code that DMMGGetx(dmmg) can get the solution vector after calculation. However, I want to have them as a format of 2-dimensional array (since I solve for a 2D Poisson Equation), like coors[j][i]. How can I do that? http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/DM/DMDAVecGetArray.html See also the section of the users manual regarding structured grids. If you upgrade to petsc-3.2, you can also do multigrid without DMMG. See src/ksp/ksp/examples/tutorials/ex45.c for an example. This is now the preferred interface: we would like to eventually remove DMMG because is more complicated to use and does not compose well with other solvers, e.g. TS. -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20110913/a9c3e26c/attachment.htm
[petsc-users] [petsc-maint #86567] Question on KSPs
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[petsc-users] Neumann BC for interface elliptic problem
Hi to everybody, I'm trying to solve this equation nabla(k*nabla(u))=f, with neumann homogeneous boundary conditions, where k is piecewise constant and f is a zero mean source (compatibility is respected). To do this I solve an extended by transmission conditions linear system, obtained with FD second order scheme. Everything works fine with dirichlet bc and with neumann bc too, if the interface, where k jumps, cut the computational domain. But if the interface is in the middle of the computational domain, something wrong happens where the processes overlap, with an overall loss of symmetry: the source, the interface and the bc are symmetric. I use gmres with asm. These are the lines to create the nullspace has_cnst=PETSC_TRUE call MatNullSpaceCreate(MPI_CART_COMM,has_cnst,0,PETSC_NULL_OBJECT,nsppoi,ierr) call KSPSetNullSpace(ksppoi,nsppoi,ierr) Ask me everything you need to better understand the problem. Could you help me? Thanks. Marco -- Marco Cisternino PhD Student Politecnico di Torino Email:marco.cisternino at polito.it
[petsc-users] [petsc-maint #86567] Question on KSPs
On Tue, Sep 13, 2011 at 3:03 AM, Michele De Stefano mstefano at milan.westerngeco.slb.com wrote: ** Jed and others, we would like to explore more in detail the possibility to have a completely matrix-free preconditioner. May you explain which are the few methods that we should implement and that you was talking of ? Second question: are there algorithms for creating matrix-free preconditioners ? If yes, may you suggest at least one, please ? There is really no conceptual difference between Krylov methods and preconditioners in that they are both approximate linear solvers. The distinction was made mostly because Krylov solvers only need the action of the matrix (or its transpose) and thus are matrix-free. Therefore, matrix-free preconditioner basically means Krylov method (where I include Chebychev, which is a KSP in PETSc). So what many scalable solvers do is combine KSPs in a nice way, like a multigrid iteration. There may be things you can do for your particular equations, like analytic simplifications, but these would not be in PETSc since they are not generic. Thanks, Matt Thank you in advance. Best regards, Michele Jed Brown wrote: On Mon, Sep 12, 2011 at 16:28, Michele De Stefano mstefano at milan.westerngeco.slb.com wrote: KSPSetOperators is able to accept a shell matrix for the Amat and the manual says that the Pmat is usually the same as the Amat. Does this really work also when Amat is a shell matrix ? I mean, in the multi-process case, the default preconditioning method is block Jacobi ... but does this work also when Pmat is a shell matrix ? Only if a few methods are implemented for the shell matrix. This is usually not practical. It would be more common to assemble some approximation Pmat (e.g. in AIJ format) and use that for preconditioning. To do everything matrix-free, you would normally have to put some effort into writing your own custom preconditioner. -- Michele De Stefano Senior Geophysicist - REMS Integrated EM Center of Excellence WesternGeco GeoSolutions, Via Clericetti 42/A, 20133, Milan - Italy +39 02 266279232 (direct) +39 02 266279279 (fax) mstefano at slb.com Schlumberger Private -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20110913/199805b2/attachment.htm
[petsc-users] Neumann BC for interface elliptic problem
On Tue, Sep 13, 2011 at 5:56 AM, Marco Cisternino marco.cisternino at polito.it wrote: Hi to everybody, I'm trying to solve this equation nabla(k*nabla(u))=f, with neumann homogeneous boundary conditions, where k is piecewise constant and f is a zero mean source (compatibility is respected). To do this I solve an extended by transmission conditions linear system, obtained with FD second order scheme. Everything works fine with dirichlet bc and with neumann bc too, if the interface, where k jumps, cut the computational domain. But if the interface is in the middle of the computational domain, something wrong happens where the processes overlap, with an overall loss of symmetry: the source, the interface and the bc are symmetric. I use gmres with asm. These are the lines to create the nullspace has_cnst=PETSC_TRUE call MatNullSpaceCreate(MPI_CART_**COMM,has_cnst,0,PETSC_NULL_** OBJECT,nsppoi,ierr) call KSPSetNullSpace(ksppoi,nsppoi,**ierr) Ask me everything you need to better understand the problem. Could you help me? If you have matrices, or submatrices, which must be symmetric, you can check this using http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/Mat/MatIsSymmetric.html Thanks, Matt Thanks. Marco -- Marco Cisternino PhD Student Politecnico di Torino Email:marco.cisternino at polito.**it Email%3Amarco.cisternino at polito.it -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20110913/8054b03f/attachment.htm
[petsc-users] Building PETSc with cmake
What are the requirements for building PETSc with cmake? I have cmake version 2.8.1 installed, and configure finds it, but it does nothing with it. Is it because my python version is too old? This is on CentOS 5, I get these messages about cmake in the configure.log (with 3.2-p0): Checking for program /usr/local/bin/cmake...found Defined make macro CMAKE to /usr/local/bin/cmake ... Skipping cmakegen due to old python version: (2, 4, 3, 'final', 0) Skipping cmakeboot due to old python version: (2, 4, 3, 'final', 0) At the end of the configure, I'm not offered a way to build with cmake. I presume that cmake is the only way to do a parallel build? John
[petsc-users] Building PETSc with cmake
On Tue, Sep 13, 2011 at 8:55 AM, John Fettig john.fettig at gmail.com wrote: What are the requirements for building PETSc with cmake? I have cmake version 2.8.1 installed, and configure finds it, but it does nothing with it. Is it because my python version is too old? This is on CentOS 5, I get these messages about cmake in the configure.log (with 3.2-p0): Checking for program /usr/local/bin/cmake...found Defined make macro CMAKE to /usr/local/bin/cmake ... Skipping cmakegen due to old python version: (2, 4, 3, 'final', 0) Skipping cmakeboot due to old python version: (2, 4, 3, 'final', 0) At the end of the configure, I'm not offered a way to build with cmake. I presume that cmake is the only way to do a parallel build? Yes, and it is because your Python version is too old. I believe it needs 2.6. I would install 2.7 if you are upgrading. Matt John -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20110913/70137259/attachment.htm
[petsc-users] Building PETSc with cmake
On Tue, 13 Sep 2011, John Fettig wrote: What are the requirements for building PETSc with cmake? I have cmake version 2.8.1 installed, and configure finds it, but it does nothing with it. Is it because my python version is too old? This is on CentOS 5, I get these messages about cmake in the configure.log (with 3.2-p0): Checking for program /usr/local/bin/cmake...found Defined make macro CMAKE to /usr/local/bin/cmake ... Skipping cmakegen due to old python version: (2, 4, 3, 'final', 0) Skipping cmakeboot due to old python version: (2, 4, 3, 'final', 0) yes - cmake part of configure requires python-2.5. Perhaps we should look at this code and see if it can be made to work with 2.3+ [current configure requirement] If configure determines that cmake build won't work [either due to the python version issue - or some other configue issue - for eg: windows compilers - it won't offer this build option at tthe end. At the end of the configure, I'm not offered a way to build with cmake. I presume that cmake is the only way to do a parallel build? Yes - currently cmake build is the only way to do parallel builds. . Also builder.py [if it works for your config] could be faster than the 'make all-legacy' build. Satish
[petsc-users] Building PETSc with cmake
On Tue, Sep 13, 2011 at 9:59 AM, Matthew Knepley knepley at gmail.com wrote: On Tue, Sep 13, 2011 at 8:55 AM, John Fettig john.fettig at gmail.com wrote: What are the requirements for building PETSc with cmake? ?I have cmake version 2.8.1 installed, and configure finds it, but it does nothing with it. ?Is it because my python version is too old? ?This is on CentOS 5, I get these messages about cmake in the configure.log (with 3.2-p0): Checking for program /usr/local/bin/cmake...found ? ? ? ? ? ?Defined make macro CMAKE to /usr/local/bin/cmake ... ? ? ?Skipping cmakegen due to old python version: (2, 4, 3, 'final', 0) ? ? ?Skipping cmakeboot due to old python version: (2, 4, 3, 'final', 0) At the end of the configure, I'm not offered a way to build with cmake. ?I presume that cmake is the only way to do a parallel build? Yes, and it is because your Python version is too old. I believe it needs 2.6. I would install 2.7 if you are upgrading. Is there any way to tell configure which python to use? I have python 2.6 installed, it's just not what runs when you type `python`. I don't think I can change the default python in CentOS 5 without breaking a lot of other things. John
[petsc-users] Building PETSc with cmake
On Tue, 13 Sep 2011, John Fettig wrote: On Tue, Sep 13, 2011 at 9:59 AM, Matthew Knepley knepley at gmail.com wrote: On Tue, Sep 13, 2011 at 8:55 AM, John Fettig john.fettig at gmail.com wrote: What are the requirements for building PETSc with cmake? ?I have cmake version 2.8.1 installed, and configure finds it, but it does nothing with it. ?Is it because my python version is too old? ?This is on CentOS 5, I get these messages about cmake in the configure.log (with 3.2-p0): Checking for program /usr/local/bin/cmake...found ? ? ? ? ? ?Defined make macro CMAKE to /usr/local/bin/cmake ... ? ? ?Skipping cmakegen due to old python version: (2, 4, 3, 'final', 0) ? ? ?Skipping cmakeboot due to old python version: (2, 4, 3, 'final', 0) At the end of the configure, I'm not offered a way to build with cmake. ?I presume that cmake is the only way to do a parallel build? Yes, and it is because your Python version is too old. I believe it needs 2.6. I would install 2.7 if you are upgrading. Is there any way to tell configure which python to use? I have python 2.6 installed, it's just not what runs when you type `python`. I don't think I can change the default python in CentOS 5 without breaking a lot of other things. /path/to/python2.6 configure [configure_options] Satish
[petsc-users] Quick Question on /src/ksp/ksp/example/ex29.c
Thanks, Jed. Let me finish this part first and I will upgrade to version 3.2 to try new things. best, Alan On Tue, Sep 13, 2011 at 1:10 AM, Jed Brown jedbrown at mcs.anl.gov wrote: On Tue, Sep 13, 2011 at 05:59, Alan Wei zhenglun.wei at gmail.com wrote: I'm still working on this poisson solver, and find a small problem. I found from the original code that DMMGGetx(dmmg) can get the solution vector after calculation. However, I want to have them as a format of 2-dimensional array (since I solve for a 2D Poisson Equation), like coors[j][i]. How can I do that? http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/DM/DMDAVecGetArray.html See also the section of the users manual regarding structured grids. If you upgrade to petsc-3.2, you can also do multigrid without DMMG. See src/ksp/ksp/examples/tutorials/ex45.c for an example. This is now the preferred interface: we would like to eventually remove DMMG because is more complicated to use and does not compose well with other solvers, e.g. TS. -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20110913/9aef0129/attachment.htm
[petsc-users] Building PETSc with cmake
On Tue, Sep 13, 2011 at 10:09 AM, Satish Balay balay at mcs.anl.gov wrote: On Tue, 13 Sep 2011, John Fettig wrote: Is there any way to tell configure which python to use? ?I have python 2.6 installed, it's just not what runs when you type `python`. ?I don't think I can change the default python in CentOS 5 without breaking a lot of other things. /path/to/python2.6 configure ?[configure_options] This gets configure to try cmake, but it still doesn't use it. It doesn't set PETSC_BUILD_USING_CMAKE to 1 as I see the nightly builds doing, and again doesn't offer for me to use cmake at the end of configure. Is this only available in petsc-dev? Thanks, John Invoking: ['/usr/local/bin/cmake', '/home/jfe/local/centos/petsc-3.2-p0', '-DCMAKE_C_COMPILER:FILEPATH=icc', '-DCMAKE_C_FLAGS:STRING= -fPIC -wd1572 -Qoption,cpp,--extended_float_type -g -debug inline_debug_info', '-DCMAKE_Fortran_COMPILER:FILEPATH=ifort', '-DCMAKE_Fortran_FLAGS:STRING= -fPIC -g -debug inline_debug_info'] sh: ['/usr/local/bin/cmake', '/home/jfe/local/centos/petsc-3.2-p0', '-DCMAKE_C_COMPILER:FILEPATH=icc', '-DCMAKE_C_FLAGS:STRING= -fPIC -wd1572 -Qoption,cpp,--extended_float_type -g -debug inline_debug_info', '-DCMAKE_Fortran_COMPILER:FILEPATH=ifort', '-DCMAKE_Fortran_FLAGS:STRING= -fPIC -g -debug inline_debug_info'] Executing: ['/usr/local/bin/cmake', '/home/jfe/local/centos/petsc-3.2-p0', '-DCMAKE_C_COMPILER:FILEPATH=icc', '-DCMAKE_C_FLAGS:STRING= -fPIC -wd1572 -Qoption,cpp,--extended_float_type -g -debug inline_debug_info', '-DCMAKE_Fortran_COMPILER:FILEPATH=ifort', '-DCMAKE_Fortran_FLAGS:STRING= -fPIC -g -debug inline_debug_info'] sh: -- The C compiler identification is Intel -- Check for working C compiler: /opt/intel/Compiler/11.1/072/bin/intel64/icc -- Check for working C compiler: /opt/intel/Compiler/11.1/072/bin/intel64/icc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- The Fortran compiler identification is Intel -- Check for working Fortran compiler: /opt/intel/Compiler/11.1/072/bin/intel64/ifort -- Check for working Fortran compiler: /opt/intel/Compiler/11.1/072/bin/intel64/ifort -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /opt/intel/Compiler/11.1/072/bin/intel64/ifort supports Fortran 90 -- Checking whether /opt/intel/Compiler/11.1/072/bin/intel64/ifort supports Fortran 90 -- yes -- Configuring done -- Generating done -- Build files have been written to: /home/jfe/local/centos/petsc-3.2-p0/intel-debug
[petsc-users] Building PETSc with cmake
It should work in petsc-32. Can you send configure.log to petsc-maint? Satish On Tue, 13 Sep 2011, John Fettig wrote: On Tue, Sep 13, 2011 at 10:09 AM, Satish Balay balay at mcs.anl.gov wrote: On Tue, 13 Sep 2011, John Fettig wrote: Is there any way to tell configure which python to use? ?I have python 2.6 installed, it's just not what runs when you type `python`. ?I don't think I can change the default python in CentOS 5 without breaking a lot of other things. /path/to/python2.6 configure ?[configure_options] This gets configure to try cmake, but it still doesn't use it. It doesn't set PETSC_BUILD_USING_CMAKE to 1 as I see the nightly builds doing, and again doesn't offer for me to use cmake at the end of configure. Is this only available in petsc-dev? Thanks, John Invoking: ['/usr/local/bin/cmake', '/home/jfe/local/centos/petsc-3.2-p0', '-DCMAKE_C_COMPILER:FILEPATH=icc', '-DCMAKE_C_FLAGS:STRING= -fPIC -wd1572 -Qoption,cpp,--extended_float_type -g -debug inline_debug_info', '-DCMAKE_Fortran_COMPILER:FILEPATH=ifort', '-DCMAKE_Fortran_FLAGS:STRING= -fPIC -g -debug inline_debug_info'] sh: ['/usr/local/bin/cmake', '/home/jfe/local/centos/petsc-3.2-p0', '-DCMAKE_C_COMPILER:FILEPATH=icc', '-DCMAKE_C_FLAGS:STRING= -fPIC -wd1572 -Qoption,cpp,--extended_float_type -g -debug inline_debug_info', '-DCMAKE_Fortran_COMPILER:FILEPATH=ifort', '-DCMAKE_Fortran_FLAGS:STRING= -fPIC -g -debug inline_debug_info'] Executing: ['/usr/local/bin/cmake', '/home/jfe/local/centos/petsc-3.2-p0', '-DCMAKE_C_COMPILER:FILEPATH=icc', '-DCMAKE_C_FLAGS:STRING= -fPIC -wd1572 -Qoption,cpp,--extended_float_type -g -debug inline_debug_info', '-DCMAKE_Fortran_COMPILER:FILEPATH=ifort', '-DCMAKE_Fortran_FLAGS:STRING= -fPIC -g -debug inline_debug_info'] sh: -- The C compiler identification is Intel -- Check for working C compiler: /opt/intel/Compiler/11.1/072/bin/intel64/icc -- Check for working C compiler: /opt/intel/Compiler/11.1/072/bin/intel64/icc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- The Fortran compiler identification is Intel -- Check for working Fortran compiler: /opt/intel/Compiler/11.1/072/bin/intel64/ifort -- Check for working Fortran compiler: /opt/intel/Compiler/11.1/072/bin/intel64/ifort -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /opt/intel/Compiler/11.1/072/bin/intel64/ifort supports Fortran 90 -- Checking whether /opt/intel/Compiler/11.1/072/bin/intel64/ifort supports Fortran 90 -- yes -- Configuring done -- Generating done -- Build files have been written to: /home/jfe/local/centos/petsc-3.2-p0/intel-debug
[petsc-users] Neumann BC for interface elliptic problem
Thanks, Matthew, for the quick reply. My matrices are not symmetric. The differential problem is symmetric, but matrices are not. And not only for the presence of transmission conditions at the interface but also because I explicitly put the discretization of the forward or backward second order Neumann boundary conditions as rows in my matrix. Then even if I try to solve a problem without interfaces my matrix is not symmetric. And even in this case I got problems along the processes boundaries and about the loss of symmetry of the solution. But the matrix structure is exactly the same when I solve the problem with the interface cutting the domain (always with the same implementation of Neumann boundaries conditions) with no problem. I can eliminate the bc rows nesting them in the discretization of the laplacian, but the interface will always give me an asymmetric matrix. But most of all I can't understand why for one kind of interface everything works and for the other not. Thanks again. Marco
[petsc-users] Neumann BC for interface elliptic problem
On Sep 13, 2011, at 10:58 AM, Marco Cisternino wrote: Thanks, Matthew, for the quick reply. My matrices are not symmetric. The differential problem is symmetric, but matrices are not. And not only for the presence of transmission conditions at the interface but also because I explicitly put the discretization of the forward or backward second order Neumann boundary conditions as rows in my matrix. Then even if I try to solve a problem without interfaces my matrix is not symmetric. And even in this case I got problems along the processes boundaries and about the loss of symmetry of the solution. But the matrix structure is exactly the same when I solve the problem with the interface cutting the domain (always with the same implementation of Neumann boundaries conditions) with no problem. I can eliminate the bc rows nesting them in the discretization of the laplacian, but the interface will always give me an asymmetric matrix. But most of all I can't understand why for one kind of interface everything works What is everything that works? Do you mean the iterative solver converges in one case but not the other? Do you mean it always converges but the answer is wrong in one case but not the other? Barry and for the other not. Thanks again. Marco
[petsc-users] Non-official C++ binding for PETSc
Hi Caner, Is the templating more than aesthetic? It would seem to me from, for instance, https://github.com/canercandan/petsc-cxx/blob/master/src/petsc_cxx/Vector.h that only a single datatype is supported for your Vec and Matrix wrappers (PetscScalar). So, for example, in this test https://github.com/canercandan/petsc-cxx/blob/master/test/t-create_vector_cxx.cpp could the Vector's x and y instead be built on top of int rather than Scalar? If not, why bother with the template parameter? It would seem that the main advantage of these wrappers is the syntactic sugar for printing. Jack On Tue, Sep 13, 2011 at 5:58 AM, Caner Candan caner at candan.fr wrote: Hi PETSc users, Let's introduce a non-official C++ version of PETSc developed during my MSc's degree, this work does not include all the components of the library, however you can already find some operators like KSPSolver, MultiplyMatVec and Dot. The framework uses a functors-based design requiring all components to define an operator function. There are also a Matrix and Vector data structure classes. The sources are available as free software under the terms of the GNU GPL license at https://github.com/canercandan/petsc-cxx Have a look also into the test folder in order to see how it works. (https://github.com/canercandan/petsc-cxx/tree/master/test) To build the project, kindly read the README file at https://github.com/canercandan/petsc-cxx/blob/master/README BR, Caner Candan -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20110913/346af772/attachment.htm
[petsc-users] [petsc-maint #86567] Question on KSPs
On Tue, Sep 13, 2011 at 10:03, Michele De Stefano mstefano at milan.westerngeco.slb.com wrote: we would like to explore more in detail the possibility to have a completely matrix-free preconditioner. May you explain which are the few methods that we should implement and that you was talking of ? Matrix-free multigrid, approximate the problem with a simpler model for which a fast solver (e.g. FMM or FFT-based) is available, the nested iteration that Matt mentioned, low rank + identity approximations of the inverse (e.g. built as a byproduct of an outer iteration like BFGS). None of these are truly generic. I absolutely do not recommend trying to build matrix-free preconditioners to avoid writing code to assemble a matrix. Indeed, I think it's well worth having the code to assemble a matrix even if you usually run without it because it enables you to try many algorithms without extra effort. Having the matrix available can inform the design of matrix-free methods. The performance asymptotics of matrix-free methods are better for some problems. In many cases, it makes sense to apply the Jacobian using some matrix-free method and assemble a less expensive matrix for preconditioning. -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20110913/1627dab4/attachment.htm
[petsc-users] Problem with PETSc-3.2 configuration
mumps_static_mapping.F -o mumps_static_mapping.o make[3]: Leaving directory `/home/ronglian/soft/petsc-3.2-p1/externalpackages/MUMPS_4.10.0/src' make[2]: Leaving directory `/home/ronglian/soft/petsc-3.2-p1/externalpackages/MUMPS_4.10.0/src' make[1]: Leaving directory `/home/ronglian/soft/petsc-3.2-p1/externalpackages/MUMPS_4.10.0' mumps_io_basic.c: In function ?mumps_init_file_name?: mumps_io_basic.c:564: warning: assignment discards qualifiers from pointer target type mumps_static_mapping.F: In function ?mumps_369?: mumps_static_mapping.F:333: internal compiler error: in modified_type_die, at dwarf2out.c:8495 Please submit a full bug report, with preprocessed source if appropriate. See URL:http://bugzilla.redhat.com/bugzilla for instructions. make[3]: *** [mumps_static_mapping.o] Error 1 make[2]: *** [s] Error 2 make[1]: *** [mumps_lib] Error 2 make: *** [s] Error 2 *** -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20110913/f8f88cd9/attachment.htm
[petsc-users] Problem with PETSc-3.2 configuration
On Tue, 13 Sep 2011, Jed Brown wrote: On Tue, Sep 13, 2011 at 23:26, Rongliang Chen rongliang.chan at gmail.comwrote: mumps_static_mapping.F: In function ?mumps_369?: mumps_static_mapping.F:333: internal compiler error: in modified_type_die, at dwarf2out.c:8495 Please submit a full bug report, with preprocessed source if appropriate. See URL:http://bugzilla.redhat.com/bugzilla for instructions. Um, internal compiler error. File a bug report with your vendor and/or upgrade your compilers? What version of compilers are you using? mpicc -show mpif90 -show mpicc --version mpif90 --version Satish
[petsc-users] Problem with PETSc-3.2 configuration
Hi Jed and Satish, Thank you for your reply. Following is the information of the compilers. mpicc -show gcc -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -pthread -L/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/lib -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl mpif90 -show gfortran -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -pthread -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/lib -L/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl mpicc --version gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-50) Copyright (C) 2006 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. mpif90 --version GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-50) Copyright (C) 2007 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING Best, Rongliang -- Message: 5 Date: Tue, 13 Sep 2011 23:29:56 +0200 From: Jed Brown jedbrown at mcs.anl.gov Subject: Re: [petsc-users] Problem with PETSc-3.2 configuration To: PETSc users list petsc-users at mcs.anl.gov Message-ID: CAM9tzSmy4q3u2kqNp_gVj3BQ8S65Zc79v3M4ddFoL5f0BHwZ+g at mail.gmail.com Content-Type: text/plain; charset=utf-8 On Tue, Sep 13, 2011 at 23:26, Rongliang Chen rongliang.chan at gmail.com wrote: mumps_static_mapping.F: In function ?mumps_369?: mumps_static_mapping.F:333: internal compiler error: in modified_type_die, at dwarf2out.c:8495 Please submit a full bug report, with preprocessed source if appropriate. See URL:http://bugzilla.redhat.com/bugzilla for instructions. Um, internal compiler error. File a bug report with your vendor and/or upgrade your compilers? -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20110913/eced13ed/attachment-0001.htm -- Message: 6 Date: Tue, 13 Sep 2011 16:43:04 -0500 (CDT) From: Satish Balay balay at mcs.anl.gov Subject: Re: [petsc-users] Problem with PETSc-3.2 configuration To: PETSc users list petsc-users at mcs.anl.gov Message-ID: alpine.LFD.2.02.1109131641320.2462 at asterix Content-Type: text/plain; charset=iso-8859-7 On Tue, 13 Sep 2011, Jed Brown wrote: On Tue, Sep 13, 2011 at 23:26, Rongliang Chen rongliang.chan at gmail.com wrote: mumps_static_mapping.F: In function ?mumps_369?: mumps_static_mapping.F:333: internal compiler error: in modified_type_die, at dwarf2out.c:8495 Please submit a full bug report, with preprocessed source if appropriate. See URL:http://bugzilla.redhat.com/bugzilla for instructions. Um, internal compiler error. File a bug report with your vendor and/or upgrade your compilers? What version of compilers are you using? mpicc -show mpif90 -show mpicc --version mpif90 --version Satish -- ___ petsc-users mailing list petsc-users at mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/petsc-users End of petsc-users Digest, Vol 33, Issue 36 *** -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20110913/5b346ec3/attachment.htm
[petsc-users] Problem with PETSc-3.2 configuration
Ok - this is on a RHEL5 box. And I'm able to reproduce the internal compiler error. mumps_static_mapping.F:333: internal compiler error: in modified_type_die, at dwarf2out.c:8495 The error is in debug symbol handler in the compiler. Looks like you can workarround this by using optized build. i.e --with-debugging=0 or debug build with: [default --with-debugging=1 ] FOPTFLAGS='-g -O' Satish On Tue, 13 Sep 2011, Rongliang Chen wrote: Hi Jed and Satish, Thank you for your reply. Following is the information of the compilers. mpicc -show gcc -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -pthread -L/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/lib -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl mpif90 -show gfortran -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -pthread -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/lib -L/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl mpicc --version gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-50) Copyright (C) 2006 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. mpif90 --version GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-50) Copyright (C) 2007 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING Best, Rongliang -- Message: 5 Date: Tue, 13 Sep 2011 23:29:56 +0200 From: Jed Brown jedbrown at mcs.anl.gov Subject: Re: [petsc-users] Problem with PETSc-3.2 configuration To: PETSc users list petsc-users at mcs.anl.gov Message-ID: CAM9tzSmy4q3u2kqNp_gVj3BQ8S65Zc79v3M4ddFoL5f0BHwZ+g at mail.gmail.com Content-Type: text/plain; charset=utf-8 On Tue, Sep 13, 2011 at 23:26, Rongliang Chen rongliang.chan at gmail.com wrote: mumps_static_mapping.F: In function ?mumps_369?: mumps_static_mapping.F:333: internal compiler error: in modified_type_die, at dwarf2out.c:8495 Please submit a full bug report, with preprocessed source if appropriate. See URL:http://bugzilla.redhat.com/bugzilla for instructions. Um, internal compiler error. File a bug report with your vendor and/or upgrade your compilers? -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20110913/eced13ed/attachment-0001.htm -- Message: 6 Date: Tue, 13 Sep 2011 16:43:04 -0500 (CDT) From: Satish Balay balay at mcs.anl.gov Subject: Re: [petsc-users] Problem with PETSc-3.2 configuration To: PETSc users list petsc-users at mcs.anl.gov Message-ID: alpine.LFD.2.02.1109131641320.2462 at asterix Content-Type: text/plain; charset=iso-8859-7 On Tue, 13 Sep 2011, Jed Brown wrote: On Tue, Sep 13, 2011 at 23:26, Rongliang Chen rongliang.chan at gmail.com wrote: mumps_static_mapping.F: In function ?mumps_369?: mumps_static_mapping.F:333: internal compiler error: in modified_type_die, at dwarf2out.c:8495 Please submit a full bug report, with preprocessed source if appropriate. See URL:http://bugzilla.redhat.com/bugzilla for instructions. Um, internal compiler error. File a bug report with your vendor and/or upgrade your compilers? What version of compilers are you using? mpicc -show mpif90 -show mpicc --version mpif90 --version Satish -- ___ petsc-users mailing list petsc-users at mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/petsc-users End of petsc-users Digest, Vol 33, Issue 36 ***
[petsc-users] Problem with PETSc-3.2 configuration
Also that gfortran compiler is terribly old, you really should install the 4.6 version of the Gnu compiler suite instead of living with that old stuff. Barry On Sep 13, 2011, at 6:13 PM, Satish Balay wrote: Ok - this is on a RHEL5 box. And I'm able to reproduce the internal compiler error. mumps_static_mapping.F:333: internal compiler error: in modified_type_die, at dwarf2out.c:8495 The error is in debug symbol handler in the compiler. Looks like you can workarround this by using optized build. i.e --with-debugging=0 or debug build with: [default --with-debugging=1 ] FOPTFLAGS='-g -O' Satish On Tue, 13 Sep 2011, Rongliang Chen wrote: Hi Jed and Satish, Thank you for your reply. Following is the information of the compilers. mpicc -show gcc -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -pthread -L/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/lib -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl mpif90 -show gfortran -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -pthread -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/lib -L/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl mpicc --version gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-50) Copyright (C) 2006 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. mpif90 --version GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-50) Copyright (C) 2007 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING Best, Rongliang -- Message: 5 Date: Tue, 13 Sep 2011 23:29:56 +0200 From: Jed Brown jedbrown at mcs.anl.gov Subject: Re: [petsc-users] Problem with PETSc-3.2 configuration To: PETSc users list petsc-users at mcs.anl.gov Message-ID: CAM9tzSmy4q3u2kqNp_gVj3BQ8S65Zc79v3M4ddFoL5f0BHwZ+g at mail.gmail.com Content-Type: text/plain; charset=utf-8 On Tue, Sep 13, 2011 at 23:26, Rongliang Chen rongliang.chan at gmail.com wrote: mumps_static_mapping.F: In function ?mumps_369?: mumps_static_mapping.F:333: internal compiler error: in modified_type_die, at dwarf2out.c:8495 Please submit a full bug report, with preprocessed source if appropriate. See URL:http://bugzilla.redhat.com/bugzilla for instructions. Um, internal compiler error. File a bug report with your vendor and/or upgrade your compilers? -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20110913/eced13ed/attachment-0001.htm -- Message: 6 Date: Tue, 13 Sep 2011 16:43:04 -0500 (CDT) From: Satish Balay balay at mcs.anl.gov Subject: Re: [petsc-users] Problem with PETSc-3.2 configuration To: PETSc users list petsc-users at mcs.anl.gov Message-ID: alpine.LFD.2.02.1109131641320.2462 at asterix Content-Type: text/plain; charset=iso-8859-7 On Tue, 13 Sep 2011, Jed Brown wrote: On Tue, Sep 13, 2011 at 23:26, Rongliang Chen rongliang.chan at gmail.com wrote: mumps_static_mapping.F: In function ?mumps_369?: mumps_static_mapping.F:333: internal compiler error: in modified_type_die, at dwarf2out.c:8495 Please submit a full bug report, with preprocessed source if appropriate. See URL:http://bugzilla.redhat.com/bugzilla for instructions. Um, internal compiler error. File a bug report with your vendor and/or upgrade your compilers? What version of compilers are you using? mpicc -show mpif90 -show mpicc --version mpif90 --version Satish -- ___ petsc-users mailing list petsc-users at mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/petsc-users End of petsc-users Digest, Vol 33, Issue 36 ***
