Hi Martin, Thanks! I tried with the updated deal.II version and it worked like a charm. Thanks for the help and the bugfix!
Best, Steve On Thursday, February 23, 2017 at 1:55:30 AM UTC-5, Martin Kronbichler wrote: > > Dear Stephen, > > The first problem you are seeing is a bug in AlignedVector::push_back. We > merged a pull request last night, > https://github.com/dealii/dealii/pull/3993, which should fix this issue. > The problem was that we incorrectly invoked placement new with default > constructor rather than the copy constructor. > > Regarding your second approach: I am not sure what prevents this from > working. I have tried a similar approach and it does work in principle, at > least with the latest developer version. Apart from the fact that you > actually access invalid memory since you only call reserve(1) and never > extend the size to one. > > Could you please try with the updated deal.II version and report back in > case you have further problems? > > Thanks! > > Best, > Martin > > On 02/20/2017 11:01 PM, Stephen DeWitt wrote: > > Dear Martin, > Thank you, that makes sense. > > If I could trouble you with one more question -- I'm having a hard time > using AlignedVector, and I can't find any examples of its use online. > > I'd like to build the AlignedVector with a series of push backs, but I get > compiler errors if I try this: > > dealii::AlignedVector<typeScalar> scalar_vars; > typeScalar var1(data, 0); > scalar_vars.push_back(var1); > > tellling me that: > /Applications/deal.II.app/Contents/Resources/include/deal.II/base/aligned_vector.h:640:21: > > error: no matching constructor for initialization of > 'dealii::FEEvaluation<2, 1, 2, 1, double>' > new (_end_data) T; > > and: > /Applications/deal.II.app/Contents/Resources/include/deal.II/base/aligned_vector.h:641:16: > > error: object of type 'dealii::FEEvaluation<2, 1, 2, 1, double>' cannot be > assigned because its copy assignment operator is implicitly deleted > *_end_data++ = in_data; > > I also tried: > > dealii::AlignedVector<typeScalar> scalar_vars; > scalar_vars1.reserve(1); > typeScalar var1(data, 0); > scalar_vars1[0] = var1; > > but still got the "error: object of type 'dealii::FEEvaluation<2, 1, 2, 1, > double>' cannot be assigned because its copy assignment operator is > implicitly deleted" error. > > How should I be making my AlignedVector? > > Thanks, > Steve > > > > On Monday, February 20, 2017 at 3:23:09 PM UTC-5, Martin Kronbichler > wrote: >> >> Dear Stephen, >> >> The problem is data alignment: You create an std::vector<FEEvaluation> >> that internally arranges its data under the assumption that the start >> address of FEEvaluation is divisible by 32 (the length of the >> vectorization). If you put an FEEvaluation object on the stack, the >> compiler will automatically do it right. However, inside an std::vector it >> would be up to the std::vector to ensure this, but on usual x86-64 machines >> it only aligns to 16 byte boundaries. This is also why SSE2 works because >> it only needs 16-byte alignment. >> >> The solution is to use AlignedVector<typeScalar> scalar_vars instead of >> std::vector. The alternative is to wait until the pull request 3980 ( >> https://github.com/dealii/dealii/pull/3980) gets merged, grab the newest >> developer version because with that we will start using an external scratch >> data array that always has the correct alignment. >> >> Best, >> Martin >> >> On 20.02.2017 20:50, Stephen DeWitt wrote: >> >> Hello, >> I recently realized that I should be using "-march=native" flag for >> optimal performance of matrix-free codes. The application that I've been >> using works fine with just SSE2, but with AVX enabled I'm getting a >> segfault. Step-48 works fine, so I don't think it is an installation issue. >> >> The function where it occurs is similar to the "local_apply" function in >> step 48: >> template <int dim> >> void getRHS(const MatrixFree<dim,double> &data, >> std::vector<dealii::parallel::distributed::Vector<double>*> &dst, >> const std::vector<dealii::parallel::distributed::Vector<double>*> >> &src, >> const std::pair<unsigned int,unsigned int> &cell_range) const{ >> >> //initialize FEEvaulation objects >> std::vector<typeScalar> scalar_vars; >> >> for (unsigned int i=0; i<num_var; i++){ >> typeScalar var(data, i); >> scalar_vars.push_back(var); >> } >> >> //loop over cells >> for (unsigned int cell=cell_range.first; cell<cell_range.second; ++cell >> ){ >> >> // Initialize, read DOFs, and set evaulation flags >> scalar_vars[varInfoListRHS[i].index].reinit(cell); >> scalar_vars[varInfoListRHS[i].index].read_dof_values_plain(*src[ >> varInfoListRHS[i].global_var_index]); >> scalar_vars[varInfoListRHS[i].index].evaluate(need_value[i], >> need_gradient[i], need_hessian[i]); // <--- segfault happens here! >> >> } >> >> unsigned int num_q_points; >> num_q_points = scalar_vars[0].n_q_points; >> >> //loop over quadrature points >> for (unsigned int q=0; q<num_q_points; ++q){ >> (etc.) >> >> >> The segfault happens during the "evaluate" call. GDB tells me that it >> happens on line 5478 of /include/deal.II/matrix_free/fe_evaluation.h, in >> EvaluatorTensorProduct::apply: >> xp[i] = in[stride*i] - in[stride*(mm-1-i)]; >> >> Using the debugger to step through EvaluatorTensorProduct::apply, nothing >> seems obviously wrong. As expected, all of the vectorized arrays are four >> doubles long. The line above evaluates to xp[0]=in[0]-in[1]. >> >> Has anyone else had this issue? Does anyone have ideas what the problem >> could be, or what I should be looking for? >> >> Thanks! >> Steve >> >> System: Cluster running CentOS 7, with Intel Xeon E5-2670 processors, >> GCC v5.4.0 >> >> >> >> >> -- >> The deal.II project is located at <http://www.dealii.org/> >> http://www.dealii.org/ >> For mailing list/forum options, see >> <https://groups.google.com/d/forum/dealii?hl=en> >> https://groups.google.com/d/forum/dealii?hl=en >> --- >> You received this message because you are subscribed to the Google Groups >> "deal.II User Group" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to dealii+un...@googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. >> >> >> -- > The deal.II project is located at http://www.dealii.org/ > For mailing list/forum options, see > https://groups.google.com/d/forum/dealii?hl=en > --- > You received this message because you are subscribed to the Google Groups > "deal.II User Group" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to dealii+un...@googlegroups.com <javascript:>. > For more options, visit https://groups.google.com/d/optout. > > > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. 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