[petsc-users] Preallocation Memory of Finite Element Method's Sparse Matrices
Your faithfully: Last e-mail has some literal error, sorry~ program src/ksp/ksp/examples/tutorials/ex3.c.html is about Bilinear elements on the unit square for Laplacian. After preallocation using ierr = MatMPIAIJSetPreallocation(A,9,NULL,5,NULL);CHKERRQ(ierr); /* More than necessary */, Results of commands of mpiexec -n 2 ./ex3 and mpiexec -n 3 ./ex3 are Norm of error 2.22327e-06 Iterations 6 and Norm of error 3.12849e-07 Iterations 8. Both results are good! However, if I use mpiexec -n 4 ./ex3 or 5,6,7...precesses, error [2]PETSC ERROR: New nonzero at (4,29) (here is for process 4, other positions for different processes) caused a malloc! appear!. For me, this error is unbelievable, because first, the preallocation is more than necessary,how can the new malloc appear? Second, the global number 4 point originally has no neighbor vertices whose global number is 29! This error has tortured me for a long time. This error seems meaningless, however, my recent 3d finite element method cannot be caculated by more processes owing to the new nonzero malloc error! And this is why I want to use 4 or much more processes to compute ex3.c. Thank you for all previous assistence and hope you have a good life! your sincerely LV CHAO 2014/3/21
Re: [petsc-users] Preallocation Memory of Finite Element Method's Sparse Matrices
Thank you for reporting this. It was our error. In fact 4 is not enough under certain circumstances; consider where each process has only a single degree of freedom (vertex) then it is coupled to 8 other vertices ALL on other processes. Thus we really need to use 8 instead of 4 as the maximum number of off process coupling. I have fixed this in master so it now runs on any number of processes. Barry On Mar 21, 2014, at 9:11 AM, 吕超 luc...@mail.iggcas.ac.cn wrote: Your faithfully: Last e-mail has some literal error, sorry~ program src/ksp/ksp/examples/tutorials/ex3.c.html is about Bilinear elements on the unit square for Laplacian. After preallocation using ierr = MatMPIAIJSetPreallocation(A,9,NULL,5,NULL);CHKERRQ(ierr); /* More than necessary */, Results of commands of mpiexec -n 2 ./ex3 and mpiexec -n 3 ./ex3 are Norm of error 2.22327e-06 Iterations 6 and Norm of error 3.12849e-07 Iterations 8. Both results are good! However, if I use mpiexec -n 4 ./ex3 or 5,6,7...precesses, error [2]PETSC ERROR: New nonzero at (4,29) (here is for process 4, other positions for different processes) caused a malloc! appear!. For me, this error is unbelievable, because first, the preallocation is more than necessary,how can the new malloc appear? Second, the global number 4 point originally has no neighbor vertices whose global number is 29! This error has tortured me for a long time. This error seems meaningless, however, my recent 3d finite element method cannot be caculated by more processes owing to the new nonzero malloc error! And this is why I want to use 4 or much more processes to compute ex3.c. Thank you for all previous assistence and hope you have a good life! your sin cerely LV CHAO 2014/3/21
Re: [petsc-users] Preallocation Memory of Finite Element Method's Sparse Matrices
Barry Smith bsm...@mcs.anl.gov writes: Thank you for reporting this. It was our error. In fact 4 is not enough under certain circumstances; consider where each process has only a single degree of freedom (vertex) then it is coupled to 8 other vertices ALL on other processes. Thus we really need to use 8 instead of 4 as the maximum number of off process coupling. Note that _your_ code should generally not have this problem because you should use a non-pathological partition. pgpWf1NEACFhu.pgp Description: PGP signature
[petsc-users] Preallocation Memory of Finite Element Method's Sparse Matrices
Your faithfully: program src/ksp/ksp/examples/tutorials/ex3.c.html is about Bilinear elements on the unit square for Laplacian. After preallocation using ierr = MatMPIAIJSetPreallocation(A,9,NULL,5,NULL);CHKERRQ(ierr); /* More than necessary */, Results of commands of mpiexec -n 2 ./ex3 and mpiexec -n 2 ./ex3 are Norm of error 2.22327e-06 Iterations 6 and Norm of error 3.12849e-07 Iterations 8. Both results is good! However, if I use mpiexec -n 4 ./ex3 or 5,6,7...precesses, error [2]PETSC ERROR: New nonzero at (4,29) (here is for process 4, other positions for different processes) caused a malloc! appear!. For me, this error is unbelievable, because first, the preallocation is more than necessary,how can the new malloc appear? Second, the global number 4 point originally have no neighbor vertices whose global number is 29! This error have tortured me for long times. This error seems meaningless, however, my recent 3d finite element method cannot be caculated by more processesowing to the new nonzero malloc!And this is why I want to use 4 or much more processes to compute ex3.c. Thank you for all previous assistence and hope you have a good life! your sincerely LV CHAO 2014/3/21
