<html><head></head><body><div style="color:#000; background-color:#fff; font-family:Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10px"><div id="yui_3_16_0_ym19_1_1507139245921_4000">When I link the petsc library, the application side code is not properly compiled and the solver is not available for selection<br></div><div id="yui_3_16_0_ym19_1_1507139245921_3962"><br></div><div id="yui_3_16_0_ym19_1_1507139245921_3963" dir="ltr">--> FOAM FATAL IO ERROR:<br id="yui_3_16_0_ym19_1_1507139245921_3988">Unknown asymmetric matrix solver petGMRES<br id="yui_3_16_0_ym19_1_1507139245921_3989"><br id="yui_3_16_0_ym19_1_1507139245921_3990">Valid asymmetric matrix solvers are :<br id="yui_3_16_0_ym19_1_1507139245921_3991"><br id="yui_3_16_0_ym19_1_1507139245921_3992">4<br id="yui_3_16_0_ym19_1_1507139245921_3993">(<br id="yui_3_16_0_ym19_1_1507139245921_3994">GAMG<br id="yui_3_16_0_ym19_1_1507139245921_3995">PBiCG<br id="yui_3_16_0_ym19_1_1507139245921_3996">PBiCGStab<br id="yui_3_16_0_ym19_1_1507139245921_3997">smoothSolver<br id="yui_3_16_0_ym19_1_1507139245921_3998">)</div><div dir="ltr" id="yui_3_16_0_ym19_1_1507139245921_4582"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1507139245921_4673">I added the following to my makefile to link the petsc library<br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1507139245921_4699"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1507139245921_4700"> -L$(PETSC_DIR)/arch-linux2-c-debug/lib</div><div dir="ltr" id="yui_3_16_0_ym19_1_1507139245921_4831"> -lpetsc<br></div><div id="yui_3_16_0_ym19_1_1507139245921_3906"><span></span></div> <div class="qtdSeparateBR"><br><br></div><div class="yahoo_quoted" style="display: block;"> <div style="font-family: Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 10px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"><font size="2" face="Arial"> Jed Brown <jed@jedbrown.org> schrieb am 18:45 Mittwoch, 4.Oktober 2017:<br></font></div> <br><br> <div class="y_msg_container"><div dir="ltr">Klaus Burkart <<a shape="rect" ymailto="mailto:k_burkart@yahoo.com" href="mailto:k_burkart@yahoo.com">k_burkart@yahoo.com</a>> writes:<br clear="none"><br clear="none">> My setup:<br clear="none">><br clear="none">> .bashrc<br clear="none">> export PETSC_DIR=/home/klaus/OpenFOAM/klaus-5.0/petsc-3.7.6<br clear="none">> export PETSC_ARCH=arch-linux2-c-debug<br clear="none">> export PETSC_CONFIGDIR=${PETSC_DIR}/lib/petsc<br clear="none">><br clear="none">><br clear="none">> make options<br clear="none">> -I$(PETSC_CONFIGDIR)/conf \<br clear="none"><br clear="none">The above should not be needed.<br clear="none"><br clear="none">> -I$(PETSC_DIR)/include \<br clear="none">> -I$(PETSC_DIR)/arch-linux2-c-debug/include<br clear="none">><br clear="none">> Installation and tests worked fine.<br clear="none">><br clear="none">> The output using: PetscInitialize(0,0,NULL,NULL); at the beginning and PetscFinalize(); at the end of the code section including PETSc (solver section) is:<br clear="none">><br clear="none">> simpleFoam: symbol lookup error: /home/klaus/OpenFOAM/klaus-5.0/platforms/linux64GccDPInt32Opt/lib/libpetFoam.so: undefined symbol: PetscInitialize<br clear="none"><br clear="none">How have you linked libpetFoam.so to libpetsc.so and did you use RPATH?<br clear="none">That seems to be the problem.<br clear="none"><br clear="none">> No simulation is triggered<br clear="none">><br clear="none">><br clear="none">> When I just declare Mat M; and call a function with M as a parameter which outputs "Petsc - Hello" and sets the matrix M to symmetric (using: MatSetOption(A, MAT_SYMMETRIC, PETSC_TRUE);), the execution of a simulation is triggered but MatSetOption is causing a problem, I assume because PetscInitialize is missing<br clear="none">><br clear="none">> Petsc - Hello nonepetGMRES: Solving for Ux, Initial residual = 1, Final residual = 1, No Iterations 0<br clear="none">> Petsc - Hello nonepetGMRES: Solving for Uz, Initial residual = 1, Final residual = 1, No Iterations 0<br clear="none">> simpleFoam: symbol lookup error: /home/klaus/OpenFOAM/klaus-5.0/platforms/linux64GccDPInt32Opt/lib/libpetFoam.so: undefined symbol: MatSetOption<br clear="none">><br clear="none">> Maybe important to know, there's no way to enter commmand line input in the terminal while a simulation is running because the application displays continuously the intermediate simulation results. That's why I use PetscInitialize(0,0,NULL,NULL); There's now way to provide command line input.<br clear="none"><br clear="none">That's fine. You can use the PETSC_OPTIONS environment variable or a<br clear="none">configuration file to get run-time options to PETSc.<div class="yqt9297394078" id="yqtfd87183"><br clear="none"><br clear="none">> I came back to this simple test after writing "the complete code" which showed these problems and stripped it down, step-by-step, to figure out what causes the problem i.e. everything but a declaration. <br clear="none">><br clear="none">> <br clear="none">><br clear="none">> Jed Brown <<a shape="rect" ymailto="mailto:jed@jedbrown.org" href="mailto:jed@jedbrown.org">jed@jedbrown.org</a>> schrieb am 17:17 Mittwoch, 4.Oktober 2017:<br clear="none">> <br clear="none">><br clear="none">> Klaus Burkart <<a shape="rect" ymailto="mailto:k_burkart@yahoo.com" href="mailto:k_burkart@yahoo.com">k_burkart@yahoo.com</a>> writes:<br clear="none">><br clear="none">>> What's the concept to interface with PETSc from another application to solve a linear system with PETSc?<br clear="none">>><br clear="none">>> The standard procedure of the job:<br clear="none">>><br clear="none">>> 1: The application provides a matrix which needs to be converted and be loaded into PETSc<br clear="none">>><br clear="none">>> 2: The application provides the rhs vector (containing pointers!) which needs to be loaded into PETSc <br clear="none">>><br clear="none">>> 3: The linear system is to be solved using PETSc<br clear="none">>><br clear="none">>> 4: The application provides the result vector x, the PETSc result needs to be copied back to the application into vector x (also expecting pointers)<br clear="none">>><br clear="none">>><br clear="none">>> The problem - maybe a completely wrong approach when it comes to using PETSc: <br clear="none">>><br clear="none">>> With other linear algebra libraries, I included the library functionality in the code of a new solver accessing the functionality usually via header files and created a plugin which can be called from the application when running a simulation. <br clear="none">>><br clear="none">>> Even so the mixed code including PETSc code can be compiled, the bit of the plugin, interfacing with the application is broken as soon as I include more than a PETSc declaration in the mixed code.<br clear="none">><br clear="none">> Sounds like maybe you haven't correctly linked to the PETSc library.<br clear="none">> Sending us the commands run and output/errors would be helpful to debug.<br clear="none">><br clear="none">>> How to interface with PETSc from a software application? (I am using c++ and Ubuntu)<br clear="none">>><br clear="none">>> Klaus<br clear="none">><br clear="none">> </div></div><br><br></div> </div> </div> </div></div></body></html>