<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi<div class="">Yes, I was missing a make variable (linking to the conf/variables directory).</div><div class="">thank you very much!</div><div class="">Diana</div><div class=""><br class=""></div><div class=""><div class="">
<div class="">_______________________<br class="">Diana Valencia<br class="">Assistant Professor, Physics & Astrophysics<br class="">Department of Physical and Environmental Sciences <br class="">University of Toronto, Scarborough<br class="">1265 Military Trail, Toronto, ON, Canada, M1C 1A4<br class="">Voice 416 208-2986</div>
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<br class=""><div><blockquote type="cite" class=""><div class="">On Sep 24, 2015, at 8:42 PM, Matthew Knepley <<a href="mailto:knepley@gmail.com" class="">knepley@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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;" class=""><div class="gmail_extra"><div class="gmail_quote">On Thu, Sep 24, 2015 at 7:39 PM, Diana Valencia<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:valencia@astro.utoronto.ca" target="_blank" class="">valencia@astro.utoronto.ca</a>></span><span class="Apple-converted-space"> </span>wrote:<br class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;"><div style="word-wrap: break-word;" class="">Thanks for the response. In compiling the subroutines, one that uses petsc is compiled successfully with:<div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class="">gfortran -fdefault-real-8 -fdefault-double-8 -w -O2 -I /Users/valencia/software/petsc/petsc-3.2-p7/arch-darwin-c-opt/include -c PETScimple_mod.f90</div></div></div></blockquote><div class=""><br class=""></div><div class="">Yes, this is _compilation_, and it was successful. However, in order for the _link_ to be successful, you</div><div class="">will need the PETSc library on the link line. I am guessing that there is a make variable you must define.</div><div class=""><br class=""></div><div class="">I am Cc'ing one of the people at ETH since I think that place is responsible for this irresponsible build system.</div><div class=""><br class=""></div><div class=""> Matt</div><div class=""> </div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;"><div style="word-wrap: break-word;" class=""><div class=""><div class=""><div class="">_______________________<br class="">Diana Valencia<br class="">Assistant Professor, Physics & Astrophysics<br class="">Department of Physical and Environmental Sciences <br class="">University of Toronto, Scarborough<br class="">1265 Military Trail, Toronto, ON, Canada, M1C 1A4<br class="">Voice<span class="Apple-converted-space"> </span><a href="tel:416%20208-2986" value="+14162082986" target="_blank" class="">416 208-2986</a></div></div><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Sep 24, 2015, at 8:34 PM, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank" class="">knepley@gmail.com</a>> wrote:</div><br class=""><div class=""><div dir="ltr" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><div class="gmail_extra"><div class="gmail_quote">On Thu, Sep 24, 2015 at 7:21 PM, Diana Valencia<span class=""> </span><span dir="ltr" class=""><<a href="mailto:valencia@astro.utoronto.ca" target="_blank" class="">valencia@astro.utoronto.ca</a>></span><span class=""> </span>wrote:<br class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;"><div style="word-wrap: break-word;" class="">Hi,<div class=""><br class=""></div><div class=""><br class=""><div class=""><div class="">I am trying to compile a third party software written in fortran90 that uses petsc. There is the option of compiling the code with or without petsc. Without it I have no problems, however when I use petsc, I encounter this:</div><div class=""><br class=""></div><div class="">After building the subroutines the error is:</div></div></div></div></blockquote><div class=""><br class=""></div><div class="">Nowhere in this link line do I see -lpetsc. Are you sure you have this build system configured correctly?</div><div class=""><br class=""></div><div class=""> Matt</div><div class=""> </div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;"><div style="word-wrap: break-word;" class=""><div class=""><div class=""><div class=""><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class="">gfortran -fdefault-real-8 -fdefault-double-8 -w -O2 -o stagyy main.o advdif.o communication.o continents.o evocore.o geometry.o init.o io.o iter.o melting.o miscellaneous.o MPDATA.o multi.o refstate.o phase_change.o poisson.o prolongate_restrict.o relax_all.o relax_cell.o relax_point.o residues.o tracers.o v_advection.o vee_cycle.o viscosity.o crw.o geoid.o implicit_diffusion.o linpack.o plot.o wrtpng.o blas123.o lapack.o nxs_dummy.o PETScimple_mod.o xdmf_hdf5_io_dummy.o bcs_mod.o composition_mod.o control_mod.o continents_mod.o vgrid_mod.o init_mod.o io_mod.o iter_mod.o melting_mod.o meltingfns_mod.o multi_mod.o phase_change_mod.o plot_mod.o precision_mod.o refstat_mod.o stencil_mod.o timestep_mod.o timing_mod.o tracers_mod.o viscosity_mod.o thermochem_mod.o platesLea_mod.o /opt/X11/lib/libpng.dylib </div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class="">Undefined symbols for architecture x86_64:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_kspcreate_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_create_everything in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_kspdestroy_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_destroy_everything in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_kspgetpc_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_solve in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_kspsetfromoptions_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_solve in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_kspsetoperators_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_solve in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_kspsettype_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_solve in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_kspsolve_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_solve in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_matassemblybegin_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_solve in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_matassemblyend_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_solve in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_matcreateseqaij_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_create_everything in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_matdestroy_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_destroy_everything in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_matsetvalues_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_insert_compactrow in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_mpi_comm_size_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_initialize in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_pcfactorsetmatsolverpackage_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_solve in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_pcsettype_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_solve in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_petscfinalize_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_finalize in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_petscinitialize_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_initialize in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_veccreateseqwitharray_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_create_everything in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_vecdestroy_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_destroy_everything in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_vecplacearray_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_solve in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>"_vecresetarray_", referenced from:</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""> <span class=""> </span>___petscimple_MOD_simplepetsc_solve in PETScimple_mod.o</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class="">ld: symbol(s) not found for architecture x86_64</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class="">collect2: error: ld returned 1 exit status</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class="">make: *** [stagyy] Error 1</div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">My machine is OS X 10.10 and I am working with 64 bytes. I configured petsc with the following flags:</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class="">./configure --with-fc=gfortran --with-fortran-datatypes --with-x=0 --download-mpich --download-parmetis --download-superlu --download-superlu_dist --download-blacs --download-scalapack --download-mumps --download-umfpack --download-ml --with-debugging=no --download-f-blas-lapack=yes</div></div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class=""><br class=""></div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class="">Any help is greatly appreciated!!</div><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class="">Thanks</div><span class=""><font color="#888888" class=""><div style="margin: 0px; font-size: 13px; font-family: Menlo;" class="">Diana</div><div class=""><br class=""></div><div class=""><br class=""></div></font></span></div></div></div></blockquote></div><br class=""><br clear="all" class=""><span class="HOEnZb"><font color="#888888" class=""><div class=""><br class=""></div>--<span class=""> </span><br class=""><div class="">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br class="">-- Norbert Wiener</div></font></span></div></div></div></blockquote></div><br class=""></div></div></blockquote></div><br class=""><br clear="all" class=""><div class=""><br class=""></div>--<span class="Apple-converted-space"> </span><br class=""><div class="gmail_signature">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br class="">-- Norbert Wiener</div></div></div></div></blockquote></div><br class=""></div></body></html>