<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear PETSc users,<div class=""><br class=""></div><div class="">I would like to use petsc4py to create (say) PETSc vectors and</div><div class="">then pass them to a routine from a module written in Cython,</div><div class="">which in turn passes them to a routine written in C:</div><div class=""><br class=""></div><div class="">main.py ========================================================</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="color: #0433ff" class="">from</span> petsc4py <span style="color: #0433ff" class="">import</span> PETSc</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="color: #0433ff" class="">import</span> m3d4py</div><div style="margin: 0px; line-height: normal; background-color: rgb(255, 255, 255); min-height: 14px;" class=""><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="color: #0433ff" class="">if</span> __name__ == <span style="color: #b4261a" class="">"__main__"</span>:</div><div style="margin: 0px; line-height: normal; background-color: rgb(255, 255, 255); min-height: 14px;" class=""><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> v = PETSc.Vec()</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> v.create()</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> v.setType(<span style="color: #b4261a" class="">"standard"</span>)</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> v.setSizes(3)</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> v.set(0.3)</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> v.assemble()</div><div style="margin: 0px; line-height: normal; background-color: rgb(255, 255, 255); min-height: 14px;" class=""><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> m3d4py.sub_pyx(v)</div></div><div class=""><br class=""></div><div class="">m3d4py.pyx ========================================================</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">cimport petsc4py.PETSc as PETSc</div><div style="margin: 0px; line-height: normal; background-color: rgb(255, 255, 255); min-height: 14px;" class=""><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">cdef extern from "sub.c":</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> int sub_c(Vec)</div><div style="margin: 0px; line-height: normal; background-color: rgb(255, 255, 255); min-height: 14px;" class=""><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">def sub_pyx(PETSc.Vec vec):</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> vec.view()</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> sub_c(vec.vec)</div></div><div class=""><br class=""></div><div class=""><div class="">sub.c ========================================================</div></div><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(4, 51, 255); background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; color: rgb(4, 51, 255); background-color: rgb(255, 255, 255);" class="">#include <span style="color: #b4261a" class="">"petsc.h"</span></div><div style="margin: 0px; line-height: normal; background-color: rgb(255, 255, 255); min-height: 14px;" class=""><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="color: #0433ff" class="">extern</span> PetscErrorCode sub_c(Vec);</div><div style="margin: 0px; line-height: normal; background-color: rgb(255, 255, 255); min-height: 14px;" class=""><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">PetscErrorCode sub_c(Vec vec) {</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> PetscFunctionBegin;</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> VecView(vec, PETSC_VIEWER_STDOUT_WORLD);</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> PetscFunctionReturn(0);</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">}</div><div style="margin: 0px; line-height: normal; background-color: rgb(255, 255, 255); min-height: 14px;" class=""><br class=""></div></div><div class="">========================================================</div><div class=""><br class=""></div><div class="">I used (ana/mini)conda to install petsc4py and cython. When I try to</div><div class="">compile the cython file I get the following error:</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">$> cython -f m3d4py.pyx -I /Users/jpicau/miniconda3/lib/python3.6/site-packages/petsc4py/include/</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255); min-height: 13px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Error compiling Cython file:</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">------------------------------------------------------------</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">...</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">cdef extern from "sub.c":</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> int sub_c(Vec)</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255); min-height: 13px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">def sub_pyx(PETSc.Vec vec):</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> vec.view()</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> sub_c(vec.vec)</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> ^</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">------------------------------------------------------------</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255); min-height: 13px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">m3d4py.pyx:8:13: Cannot convert 'PetscVec' to Python object</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">make: *** [all] Error 1</span></div></div><div class=""><span style="font-variant-ligatures: no-common-ligatures" class=""><br class=""></span></div><div class="">========================================================</div><div class=""><br class=""></div><div class="">I somehow realize that this is not correct. But comparing this to the petsc4py implementation ...</div><div class=""><br class=""></div><div class="">petscvec.pxi:</div><div class=""><span style="background-color: rgb(255, 255, 255);" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>int VecView(PetscVec,PetscViewer)</span></div><div class=""><br class=""></div><div class="">Vec.pyx:</div><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> def view(self, Viewer viewer=None):</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> cdef PetscViewer vwr = NULL</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> if viewer is not None: vwr = viewer.vwr</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> CHKERR( VecView(self.vec, vwr) )</div></div><div class=""><br class=""></div><div class="">… I do not understand why.</div><div class=""><br class=""></div><div class="">Can some explain this to me or just give me a hint where I can dig further, please?</div><div class=""><br class=""></div><div class="">And just out of pure curiosity, why isn’t the return value of VecView() in petscvec.pxi defined as <span style="font-family: Menlo; font-size: 11px; background-color: rgb(255, 255, 255);" class="">PetscErrorCode?</span></div><div class=""><span style="font-family: Menlo; font-size: 11px; background-color: rgb(255, 255, 255);" class="">The type seems to be defined:</span></div><div class=""><span style="font-family: Menlo; font-size: 11px; background-color: rgb(255, 255, 255);" class=""><br class=""></span></div><div class="">libpetsc4py.pyx:</div><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class=""> ctypedef int PetscErrorCode</div></div><div class=""><br class=""></div><div class="">Thanks in advance,</div><div class="">Jaroslaw</div><div class=""><br class=""></div><div class=""><div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">—</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><br class=""></div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">Dr. Jaroslaw Piwonski<br class=""><br class="">Christian-Albrechts-Universität zu Kiel<br class="">Institut für Informatik<br class="">Algorithmische Optimale Steuerung — CO2-Aufnahme des Meeres<br class="">Christian-Albrechts-Platz 4<br class="">24118 Kiel<br class=""><br class="">Telefon: +49 431 880-7452<br class="">Telefax: +49 431 880-7618</div></div>
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