On Mon, Dec 3, 2012 at 1:08 PM, Jelena Slivka <slivkaje at gmail.com> wrote: > Thank you very much! > However, I have another question. I have a cluster of 4 nodes and each node > has 6 cores. If I run my code using 6 cores on one node (using the command > "mpiexec -n 6") it is much faster than running it on just one process (which > is expected). However, if I try running the code on multiple nodes (using > "mpiexec -f machinefile -ppn 4", where machinefile is the file which > contains the node names), it runs much slower than on just one process. This > also happens with tutorial examples. I have checked the number of iteration > for KSP solver when spread on multiple processors and it doesn't seem to be > the problem. Do you have any suggestions on what am I doing wrong? Are the > commands I am using wrong?
Most operations are memory bandwidth limited, and it sounds like the memory bandwidth for your cluster is maxed out by 1-2 procs. Matt > On Sat, Dec 1, 2012 at 6:03 PM, Barry Smith <bsmith at mcs.anl.gov> wrote: >> >> >> We recommend following the directions >> http://www.mcs.anl.gov/petsc/documentation/faq.html#schurcomplement for >> computing a Schur complement; just skip the unneeded step. MUMPS supports a >> parallel Cholesky but you can also use a parallel LU with MUMPS, PaSTIX or >> SuperLU_Dist and those will work fine also. With current software Cholesky >> in parallel is not tons better than LU so generally not worth monkeying >> with. >> >> Barry >> >> >> On Dec 1, 2012, at 12:05 PM, Jelena Slivka <slivkaje at gmail.com> wrote: >> >> > Hello! >> > I am trying to solve A*X = B where A and B are matrices, and then find >> > trace of the resulting matrix X. My approach has been to partition matrix B >> > in column vectors bi and then solve each system A*xi = bi. Then, for all >> > vectors xi I would extract i-th element xi(i) and sum those elements in >> > order to get Trace(X). >> > Pseudo-code: >> > 1) load matrices A and B >> > 2) transpose matrix B (so that each right-hand side bi is in the row, as >> > operation MatGetColumnVector is slow) >> > 3) set up KSPSolve >> > 4) create vector diagonal (in which xi(i) elements will be stored) >> > 5) for each row i of matrix B owned by current process: >> > - create vector bi by extracting row i from matrix B >> > - apply KSPsolve to get xi >> > - insert value xi(i) in diagonal vector (only the process >> > which >> > holds the ith value of vector x(i) should do so) >> > 6) sum vector diagonal to get the trace. >> > However, my code (attached, along with the test case) runs fine on one >> > process, but hangs if started on multiple processes. Could you please help >> > me figure out what am I doing wrong? >> > Also, could you please tell me is it possible to use Cholesky >> > factorization when running on multiple processes (I see that I cannot use >> > it >> > when I set the format of matrix A to MPIAIJ)? >> > >> > <Experiment.c><Abin><Bbin> >> > -- 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
