<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div><br></div> Please email your latest configure.log (with no Conda stuff) to <a href="mailto:petsc-maint@mcs.anl.gov">petsc-maint@mcs.anl.gov</a><div><br></div><div> The configuration of HDF5 (done by HDF5) is objecting to some particular aspect of your current Fortran compiler, we need to figure out the exact objection.</div><div><br></div><div> Barry</div><div><br><div><br><blockquote type="cite"><div>On Jan 6, 2023, at 5:14 PM, Danyang Su <danyang.su@gmail.com> wrote:</div><br class="Apple-interchange-newline"><div><meta charset="UTF-8"><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">Hi Pierre,<o:p></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">I have tried to exclude Conda related environment variables but it does not work. Instead, if I include ‘--download-hdf5=yes’ but exclude ‘--with-hdf5-fortran-bindings’ in the configuration, PETSc can be configured and installed without problem, even with Conda related environment activated. However, since my code requires fortran interface to HDF5, I do need ‘--with-hdf5-fortran-bindings’, otherwise, my code cannot be compiled.<o:p></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">Any other suggestions?<o:p></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">Thanks,<o:p></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">Danyang<o:p></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0cm 0cm;"><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><b><span style="font-size: 12pt;">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;">Pierre Jolivet <<a href="mailto:pierre@joliv.et">pierre@joliv.et</a>><br><b>Date:<span class="Apple-converted-space"> </span></b>Friday, January 6, 2023 at 7:59 AM<br><b>To:<span class="Apple-converted-space"> </span></b>Danyang Su <<a href="mailto:danyang.su@gmail.com">danyang.su@gmail.com</a>><br><b>Cc:<span class="Apple-converted-space"> </span></b><<a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>><br><b>Subject:<span class="Apple-converted-space"> </span></b>Re: [petsc-users] Error running configure on HDF5 in PETSc-3.18.3<o:p></o:p></span></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><br><br><o:p></o:p></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" type="cite"><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">On 6 Jan 2023, at 4:49 PM, Danyang Su <<a href="mailto:danyang.su@gmail.com">danyang.su@gmail.com</a>> wrote:<o:p></o:p></div></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div><div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-US">Hi All,</span><span style="font-size: 12pt;"><o:p></o:p></span></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-US"> </span><span style="font-size: 12pt;"><o:p></o:p></span></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-US">I get ‘Error running configure on HDF5’ in PETSc-3.18.3 on MacOS, but no problem on Ubuntu. Attached is the configuration log file.<span class="apple-converted-space"> </span></span><span style="font-size: 12pt;"><o:p></o:p></span></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-US"> </span><span style="font-size: 12pt;"><o:p></o:p></span></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span class="s1"><span style="font-size: 8.5pt; font-family: Menlo;">./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mumps --download-scalapack --download-parmetis --download-metis --download-ptscotch --download-fblaslapack --download-mpich --download-hypre --download-superlu_dist --download-hdf5=yes --with-debugging=0 --download-cmake --with-hdf5-fortran-bindings</span></span><span style="font-size: 8.5pt; font-family: Menlo;"><o:p></o:p></span></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-US"> </span><span style="font-size: 12pt;"><o:p></o:p></span></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-US">Any idea on this?</span><span style="font-size: 12pt;"><o:p></o:p></span></div></div></div></blockquote><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">Could you try to reconfigure in a shell without conda being activated?<o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">You have PATH=/Users/danyangsu/Soft/Anaconda3/bin:/Users/danyangsu/Soft/Anaconda3/condabin:[…] which typically results in a broken configuration.<o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">Thanks,<o:p></o:p></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;">Pierre<o:p></o:p></div></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><br><br><o:p></o:p></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" type="cite"><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-US">Thanks,</span><span style="font-size: 12pt;"><o:p></o:p></span></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-US"> </span><span style="font-size: 12pt;"><o:p></o:p></span></div></div><div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-US">Danyang</span></div></div></blockquote></div></div></div></blockquote></div><br></div></body></html>