<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div>Dear Developers,</div><div>i ran into two problems creating a code for parallel computation with PDELab. It works, but I would like DUNE to use ParMETIS and SuperLU as it requests.</div><div><br></div><div>OS: Mac OS X 10.9.3 Mavericks</div><div>GCC: <span style="font-family: Menlo; font-size: 11px;">gcc (MacPorts gcc49 4.9-20140416_2) 4.9.0 20140416 (prerelease)</span></div><div>G++: <span style="font-family: Menlo; font-size: 11px;">g++ (MacPorts gcc49 4.9-20140416_2) 4.9.0 20140416 (prerelease)</span></div><div>clang: <span class="Apple-tab-span" style="white-space:pre"> </span><span style="font-family: Menlo; font-size: 11px;">clang version 3.5.0 (trunk 210448)</span></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"> </span>Target: x86_64-apple-darwin13.2.0</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"> </span>Thread model: posix</div><div>CC: <span class="Apple-tab-span" style="white-space:pre"> </span><span style="font-family: Menlo; font-size: 11px;">Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)</span></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"> </span>Target: x86_64-apple-darwin13.2.0</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"> </span>Thread model: posix</div><div>DUNE-modules: <span class="Apple-tab-span" style="white-space:pre"> </span><span style="font-family: Menlo; font-size: 11px;">dune-common.............: version 2.3.0</span></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"> </span>dune-geometry...........: version 2.3.0</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"> </span>dune-grid...............: version 2.3.0</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"> </span>dune-istl...............: version 2.3.0</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"> </span>dune-localfunctions.....: version 2.3.0</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"> </span>dune-pdelab.............: version 2.0-dev</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"> </span>dune-typetree...........: version 2.3-dev</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"> </span>ALBERTA.................: version 2.0</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"> </span>ALUGrid.................: version 1.52 (parallel)</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span style="font-family: Helvetica; font-size: 12px;">I attached the output of ./dunecontrol as a txt-file.</span></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span style="font-family: Helvetica; font-size: 12px;"><br></span></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><div style="font-family: Helvetica; font-size: 12px;">I run the following command inside the DUNE-directory:</div><div style="font-family: Helvetica; font-size: 12px;"><span class="Apple-tab-span" style="white-space: pre;"> </span>$ ./dune-common/bin/dunecontrol --only=<module> --opts=parallel-debug.opts all</div><div style="font-family: Helvetica; font-size: 12px;"><br></div><div style="font-family: Helvetica; font-size: 12px;">I use the parallel-debug.opts file provided by the archive of the DUNE course in March 2014:</div><div style="font-family: Helvetica; font-size: 12px;"><div><span class="Apple-tab-span" style="white-space: pre;"> </span># use these options for configure if no options a provided on the cmdline</div><div><span class="Apple-tab-span" style="white-space: pre;"> </span>CONFIGURE_FLAGS="--prefix=/Users/lriedel/opt --disable-documentation -disable-mpiruntest --enable-parallel --with-alugrid=/Users/lriedel/opt/alugrid —with alberta=/Users/lriedel/opt/alberta CXX=g++ CC=gcc CXXFLAGS=\"-O0 -g -Wall -Wno-deprecated-declarations -Wa,-q\" CFLAGS=\"-O0 -g -Wall -Wno-deprecated-declarations -Wa,-q\""</div><div><span class="Apple-tab-span" style="white-space: pre;"> </span>MAKE_FLAGS=„all"</div></div></div><div><br></div><div><br></div><div>Problems:</div><div><br></div><div>1. I installed METIS and ParMETIS and DUNE recognizes them when building a module via ./dunecontrol , but while running the program on multiple processes I still receive the following output:</div><div><br></div><div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">TIME STEP [Alexander (order 2)] 1 time (from): 0.0000e+00 dt: 1.0000e-01 time (to): 1.0000e-01</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">STAGE 1 time (to): 2.9289e-02.</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> Initial defect: 9.5196e-06</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">Successive accumulation of data on coarse levels only works with ParMETIS installed. Fell back to accumulation to one domain on coarsest level</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> Newton iteration 1. New defect: 7.2254e-06. Reduction (this): 7.5900e-01. Reduction (total): 7.5900e-01</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">Successive accumulation of data on coarse levels only works with ParMETIS installed. Fell back to accumulation to one domain on coarsest level</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> Newton iteration 2. New defect: 4.1631e-07. Reduction (this): 5.7618e-02. Reduction (total): 4.3732e-02</div></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><br></div><div style="margin: 0px;"><div style="font-family: Helvetica; font-size: 12px;">I am using the following linear solver backend (currently suppressing SuperLU): </div><div style="font-family: Helvetica; font-size: 12px;"><br></div><div style="font-family: Helvetica; font-size: 12px;"> typedef Dune::PDELab::ISTLBackend_BCGS_AMG_SSOR<IGO> LS;</div><div style="font-family: Helvetica; font-size: 12px;"> LS ls(gfs,5000,0,false,false);</div><div style="font-family: Helvetica; font-size: 12px;"><br></div><div style="font-family: Helvetica; font-size: 12px;">followed by the Newton Solver</div><div style="font-family: Helvetica; font-size: 12px;"><br></div><div><div> typedef Dune::PDELab::Newton<IGO,LS,U> PDESOLVER;</div><div> PDESOLVER pdesolver(igo,ls);</div><div> pdesolver.setReassembleThreshold(0.0);</div><div> pdesolver.setVerbosityLevel(2);</div><div> pdesolver.setReduction(1e-10);</div><div> pdesolver.setMinLinearReduction(1e-4);</div><div> pdesolver.setMaxIterations(6);</div><div> pdesolver.setLineSearchMaxIterations(10);</div></div><div style="font-family: Helvetica; font-size: 12px;"><br></div><div style="font-family: Helvetica; font-size: 12px;">and a OneStepMethod</div><div style="font-family: Helvetica; font-size: 12px;"><br></div><div style="font-family: Helvetica; font-size: 12px;"> Dune::PDELab::Alexander2Parameter<Real> alex2;</div><div style="font-family: Helvetica; font-size: 12px;"> Dune::PDELab::OneStepMethod<Real,IGO,PDESOLVER,U,U> osm(alex2,igo,pdesolver);</div><div style="font-family: Helvetica; font-size: 12px;"><br></div><div style="font-family: Helvetica; font-size: 12px;">Do I have to tell DUNE explicitly that it shall use ParMETIS?</div><div style="font-family: Helvetica; font-size: 12px;"><br></div></div><div><br></div><div>2. I do not know where to install SuperLU.</div><div><br></div><div>I installed it to Users/lriedel/opt/SuperLU_4.3/ as this is the directory mentioned as „prefix“ in the opts-file, but DUNE can obviously not find it (see output-file)</div><div>DUNE seems to look for it inside <span style="font-family: Menlo; font-size: 11px;">/usr/local/SRC </span>but it is only possible to install the newest version of SuperLU inside a folder structure as follows: <span style="font-family: Menlo; font-size: 11px;">../SuperLU_4.3/SRC/</span></div><div>Is there a way to specify where I installed SuperLU so that DUNE can find its libraries?</div><div><br></div><div><br></div><div>Thank you and best regards</div><div>Lukas Riedel</div><div><br></div><div><br></div><div></div></body></html>