<div dir="ltr">Let me get back to you. Thanks a lot. </div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Mar 25, 2017 at 11:15 PM, Barry Smith <span dir="ltr"><<a href="mailto:bsmith@mcs.anl.gov" target="_blank">bsmith@mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
First set a new PETSC_ARCH say arch-opt and ./configure with the additional argument --with-debugging=0 then recompile PETSc with the new PETSC_ARCH and recompile your code then send the new -log_view output.<br>
<br>
Barry<br>
<br>
<br>
##############################<wbr>############################<br>
# #<br>
# WARNING!!! #<br>
# #<br>
# This code was compiled with a debugging option, #<br>
# To get timing results run ./configure #<br>
# using --with-debugging=no, the performance will #<br>
# be generally two or three times faster. #<br>
# #<br>
##############################<wbr>############################<br>
<div><div class="h5"><br>
<br>
> On Mar 25, 2017, at 11:08 PM, Bodhisatta Pramanik <<a href="mailto:bodhi91@iastate.edu">bodhi91@iastate.edu</a>> wrote:<br>
><br>
><br>
> Send all the output in the error message:<br>
><br>
> [0]PETSC ERROR: --------------------- Error Message ------------------------------<wbr>------------------------------<wbr>--<br>
> [0]PETSC ERROR: Object is in wrong state<br>
> [0]PETSC ERROR: Must call EPSSolve() first: Parameter #1<br>
> [0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/<wbr>documentation/faq.html</a> for trouble shooting.<br>
> [0]PETSC ERROR: Petsc Release Version 3.7.5, Jan, 01, 2017<br>
> [0]PETSC ERROR: ./RunPart on a arch-linux2-c-debug named <a href="http://research-5.ece.iastate.edu" rel="noreferrer" target="_blank">research-5.ece.iastate.edu</a> by bodhi91 Sat Mar 25 22:33:56 2017<br>
> [0]PETSC ERROR: Configure options --with-cc=gcc --with-css=g++ -with-fc=gfortran --download-fblaslapack --download-mpich<br>
> [0]PETSC ERROR: #10468 EPSComputeError() line 643 in /tmp/Bodhi/slepc-3.7.3/src/<wbr>eps/interface/epssolve.c<br>
> 0.000000 2.0795e-317<br>
><br>
><br>
> Send the output from -log_view:<br>
> I have attached the .txt file: "Log Summary".txt<br>
><br>
><br>
> Ok. Since it only stores half the matrix it requires less memory and because of the way it does the MatMult and MatSolve it can be a tiny bit faster.<br>
> I do get a little improvement in speed, but nothing significant.<br>
><br>
> Thanks,<br>
> Bodhi<br>
><br>
><br>
> On Sat, Mar 25, 2017 at 10:56 PM, Barry Smith <<a href="mailto:bsmith@mcs.anl.gov">bsmith@mcs.anl.gov</a>> wrote:<br>
><br>
> > On Mar 25, 2017, at 10:48 PM, Bodhisatta Pramanik <<a href="mailto:bodhi91@iastate.edu">bodhi91@iastate.edu</a>> wrote:<br>
> ><br>
> > Try -st_pc_type gamg:<br>
> ><br>
> > Doing this with the existing eigensolver,linear solver : ./RunPart -eps_type jd -eps_nev 3 -st_ksp_type cg -st_ksp_rtol 0.001 -eps_tol 0.001 -st_pc_type gamg -eps_smallest_real results in the following issues:-<br>
> > PETSC ERROR: Object is in wrong state<br>
> > PETSC ERROR: Must call EPSSolve() first: Parameter #1<br>
><br>
> I cannot explain this. A different preconditioner with nothing else changed shouldn't cause any problem like this. Send all the output in the error message.<br>
> ><br>
> > Try -st_pc_type sor<br>
> ><br>
> > Doing this again with the existing eigensolver,linear solver returns me the eigenvalues but it takes more time. (106 seconds) for a Laplacian matrix of 200K size. The bjacobi was giving me the same eigenvalues but in 60 seconds.<br>
><br>
> Ok, this is reasonable.<br>
><br>
> ><br>
> ><br>
> > Run with -log_view to see where the computation is taking the most time:<br>
><br>
> Send the output from -log_view<br>
> ><br>
> > EPSSolve and KSPSolve take the most time to finish computation.<br>
> ><br>
> > Since the matrix is symmetric are you using the sbaij format instead of AIJ?<br>
> ><br>
> > I am using the sbaij format but with block size 1. I guess that is equivalent to the AIJ format itself.<br>
><br>
> Ok. Since it only stores half the matrix it requires less memory and because of the way it does the MatMult and MatSolve it can be a tiny bit faster.<br>
><br>
> Barry<br>
><br>
> ><br>
> ><br>
> > Thanks,<br>
> > Bodhi<br>
> ><br>
> ><br>
> ><br>
> ><br>
> > On Sat, Mar 25, 2017 at 10:22 PM, Barry Smith <<a href="mailto:bsmith@mcs.anl.gov">bsmith@mcs.anl.gov</a>> wrote:<br>
> ><br>
> > > On Mar 25, 2017, at 8:52 PM, Bodhisatta Pramanik <<a href="mailto:bodhi91@iastate.edu">bodhi91@iastate.edu</a>> wrote:<br>
> > ><br>
> > > Hi,<br>
> > ><br>
> > > I apologize for the slepc question. I could not find any user lists so I'm hoping someone on here might be able to offer some guidance.<br>
> > ><br>
> > > Problem Definition:<br>
> > > I am working on a graph partitioning problem. I have the laplacian of a large graph(500,000 nodes) and am interested in extracting its global information in order to find good partitioning. An approach is to compute the first few(4-5) eigenvalues and use that information to formulate the partition algorithm.<br>
> > ><br>
> > > I am leveraging the EPS solvers of the Slepc library. It appears that the Jacobi-davidson eigen solver gives me the eigenvalues in the shortest period of time compared to others (Krylov-Schur, Rayleigh quotient, Lanczos, etc). I use this eigensolver with the conjugate gradient linear solver and the block-jacobi preconditioner. So this is what I am basically passing through the command line:<br>
> > ><br>
> > > ./RunPart -eps_type jd -eps_nev 4 -st_ksp_type cg -st_ksp_rtol 0.001 -eps_tol 0.001 -st_pc_type bjacobi -eps_smallest_real<br>
> ><br>
> > Try -st_pc_type gamg<br>
> ><br>
> > One one process default bjacobi results in ILU which is not a great preconditioner.<br>
> ><br>
> > Also try -st_pc_type sor<br>
> ><br>
> > ><br>
> > > Question:<br>
> > > The time it takes to compute the first 4-5 eigenvectors of a matrix of size (200k) is near about 60 seconds. CPU config: Intel Xeon 2GHz. I am using a single processor to run my code. Is there any way I can gain major speedup than what I am getting?<br>
> ><br>
> > Run with -log_view to see where the computation is taking the most time.<br>
> ><br>
> > ><br>
> > > Is it possible to obtain the eigenvalues inside 10-15 seconds of such huge matrices even if I do not use multiple processor??<br>
> > ><br>
> > > Can someone provide me with some valuable guidance??<br>
> ><br>
> > Since the matrix is symmetric are you using the sbaij format instead of AIJ?<br>
> ><br>
> > ><br>
> > > Thanks,<br>
> > > Bodhi<br>
> ><br>
> ><br>
> ><br>
> ><br>
> > --<br>
> > Bodhisatta Pramanik,<br>
> > Graduate Student,<br>
> > Department of Electrical and Computer Engineering,<br>
> > 301 Durham,<br>
> > Iowa State University,<br>
> > Ames,Iowa 50011,<br>
> > <a href="mailto:bodhi91@iastate.edu">bodhi91@iastate.edu</a><br>
> > <a href="tel:515-735-6300" value="+15157356300">515-735-6300</a><br>
><br>
><br>
><br>
><br>
> --<br>
> Bodhisatta Pramanik,<br>
> Graduate Student,<br>
> Department of Electrical and Computer Engineering,<br>
> 301 Durham,<br>
> Iowa State University,<br>
> Ames,Iowa 50011,<br>
> <a href="mailto:bodhi91@iastate.edu">bodhi91@iastate.edu</a><br>
> <a href="tel:515-735-6300" value="+15157356300">515-735-6300</a><br>
</div></div>> <Log Summary><br>
<br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><b><font size="2" face="times new roman, serif">Bodhisatta Pramanik,</font></b><div><i><font size="2" face="times new roman, serif">Graduate Student,</font></i></div><div><i><font size="2" face="times new roman, serif">Department of Electrical and Computer Engineering,</font></i></div><div><i><font size="2" face="times new roman, serif">301 Durham,</font></i></div><div><i><font size="2" face="times new roman, serif">Iowa State University,</font></i></div><div><i><font size="2" face="times new roman, serif">Ames,Iowa 50011,</font></i></div><div><font size="2" face="times new roman, serif"><a href="mailto:bodhi91@iastate.edu" target="_blank">bodhi91@iastate.edu</a></font></div><div><u><font size="2" face="times new roman, serif">515-735-6300</font></u></div></div></div></div></div></div></div></div></div>
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