<div dir="ltr">Thanks!<div><br></div><div> Matt</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jan 24, 2017 at 8:57 AM, Blaise A Bourdin <span dir="ltr"><<a href="mailto:bourdin@lsu.edu" target="_blank">bourdin@lsu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
Hi,
<div><br>
</div>
<div>I was able to build petsc master with home-brew gcc 6.3 and intel 17.0 under macOS sierra. As Mark said, it is important to reinstall the entire home-brew compiler + libs after upgrading macOS (and often Xcode).</div>
<div>I am able to read / write exodus files. I am attaching my configure command lines:</div>
<div><br>
</div>
<div>with intel 17.0:</div>
<div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">./configure ./configure \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --download-chaco=1 \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --download-exodusii=1 \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --download-hdf5=1 \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --download-hypre=1 \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --download-metis=1 \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --download-ml=1 \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --download-netcdf=1 \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --download-parmetis=1 \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --download-triangle=1 \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --with-blas-lapack-dir=$<wbr>MKLROOT \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --with-debugging=1 \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --with-mpi-dir=$MPI_HOME \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --with-pic \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --with-shared-libraries=1 \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --with-vendor-compilers=intel \</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"> --with-x11=1</span></div>
</div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures"><br>
</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">with gcc:</span></div>
<div style="margin:0px;line-height:normal;font-family:'Source Code Pro';background-color:rgb(255,255,255)">
<span style="font-variant-ligatures:no-common-ligatures">
<div style="margin:0px;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures">./configure \</span></div>
<div style="margin:0px;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"> --download-exodusii=1 \</span></div>
<div style="margin:0px;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"> --download-chaco=1 \</span></div>
<div style="margin:0px;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"> --download-ctetgen=1 \</span></div>
<div style="margin:0px;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"> --download-hdf5=1 \</span></div>
<div style="margin:0px;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"> --download-hypre=1 \</span></div>
<div style="margin:0px;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"> --download-metis=1 \</span></div>
<div style="margin:0px;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"> --download-ml=1 \</span></div>
<div style="margin:0px;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"> --download-netcdf=1 \</span></div>
<div style="margin:0px;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"> --download-parmetis=1 \</span></div>
<div style="margin:0px;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"> --download-triangle=1 \</span></div>
<div style="margin:0px;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"> --download-yaml=1 \</span></div>
<div style="margin:0px;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"> --with-debugging=1 \</span></div>
<div style="margin:0px;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"> --with-shared-libraries=1 \</span></div>
<div style="margin:0px;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures"> --with-x11=1</span></div>
<div><span style="font-variant-ligatures:no-common-ligatures"><br>
</span></div>
<div><span style="font-variant-ligatures:no-common-ligatures">Blaise</span></div>
</span></div>
<div><br>
<div>
<blockquote type="cite">
<div>On Jan 23, 2017, at 7:55 AM, Mark Adams <<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>> wrote:</div>
<br class="m_4568811219969245007Apple-interchange-newline">
<div>
<div dir="ltr">And I trust you updated all system software (like gcc, NetCDF and ExodusII). OSX upgrades are hell.</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Jan 23, 2017 at 12:36 AM, Matthew Knepley <span dir="ltr">
<<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote"><span>On Sun, Jan 22, 2017 at 11:18 PM, Fande Kong
<span dir="ltr"><<a href="mailto:fdkong.jd@gmail.com" target="_blank">fdkong.jd@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Thanks, Matt,
<div><br>
</div>
<div>Clang does not have this issue. The code runs fine with clang. </div>
</div>
</blockquote>
<div><br>
</div>
</span>
<div>Okay, it sounds like a gcc bug on Mac 10.6, or at least in the version you have.</div>
<div><br>
</div>
<div> Matt</div>
<div>
<div class="m_4568811219969245007h5">
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>Fande,</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sun, Jan 22, 2017 at 8:03 PM, Matthew Knepley <span dir="ltr">
<<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote"><span>On Sun, Jan 22, 2017 at 8:40 PM, Fande Kong
<span dir="ltr"><<a href="mailto:fdkong.jd@gmail.com" target="_blank">fdkong.jd@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>Thanks, Matt.</div>
<div><br>
</div>
<div>It is a weird bug. </div>
<div><br>
</div>
<div>Do we have an alternative solution to this? I was wondering whether it is possible to read the ".exo" files without using the ExodusII. For example, can we read the ".exo" files using the netcdf only?</div>
</div>
</blockquote>
<div><br>
</div>
</span>
<div>Well, ExodusII is only a think layer on NetCDF, just like other wrappers are thin layers on HDF5. It is</div>
<div>really NetCDF that is failing. Can you switch compilers and see if that helps?</div>
<div><br>
</div>
<div> Matt</div>
<div>
<div class="m_4568811219969245007m_7372593255479590743m_4419773826590688416h5">
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>Fande Kong, </div>
<div><br>
</div>
<br>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sun, Jan 22, 2017 at 6:50 PM, Matthew Knepley <span dir="ltr">
<<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<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 dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">
<div>
<div class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-h5">
On Sun, Jan 22, 2017 at 5:28 PM, Fande Kong <span dir="ltr"><<a href="mailto:fdkong.jd@gmail.com" target="_blank">fdkong.jd@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Sun, Jan 22, 2017 at 12:35 PM, Matthew Knepley <span dir="ltr">
<<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">
<div>
<div class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-h5">
On Sun, Jan 22, 2017 at 12:41 PM, Fande Kong <span dir="ltr"><<a href="mailto:fdkong.jd@gmail.com" target="_blank">fdkong.jd@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Sat, Jan 21, 2017 at 10:47 PM, Matthew Knepley <span dir="ltr">
<<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote"><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-">On Sat, Jan 21,
2017 at 10:38 PM, Fande Kong <span dir="ltr"><<a href="mailto:fdkong.jd@gmail.com" target="_blank">fdkong.jd@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Hi All,
<div><br>
</div>
<div>I upgraded the OS system to macOS Sierra, and observed that PETSc can not read the exodus file any more. The same code runs fine on macOS Capitan. I also tested the function DMPlexCreateExodusFromFile() against different versions of the GCC compiler
such as GCC-5.4 and GCC-6, and neither of them work. I guess this issue is related to the external package
<i><b>exodus</b></i>, and PETSc might not pick up the right enveriment variables for the
<i><b>exodus.</b></i></div>
<div><br>
</div>
<div>This issue can be reproduced using the following simple code:</div>
</div>
</blockquote>
<div><br>
</div>
</span>
<div>1) This is just a standard check. Have you reconfigured so that you know ExodusII was built with the same compilers and system libraries?</div>
<div><br>
</div>
<div>2) If so, can you get a stack trace with gdb or lldb?</div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>
<div>0 libsystem_kernel.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x00007fffad8b8dda __pthread_kill + 10</div>
<div>1 libsystem_pthread.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x00007fffad9a4787 pthread_kill + 90</div>
<div>2 libsystem_c.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x00007fffad81e420 abort + 129</div>
<div>3 libpetsc.3.7.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x00000001100eb9ee PetscAbortErrorHandler + 506 (errstop.c:40)</div>
<div>4 libpetsc.3.7.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x00000001100e631d PetscError + 916 (err.c:379)</div>
<div>5 libpetsc.3.7.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x00000001100ed830 PetscSignalHandlerDefault + 1927 (signal.c:160)</div>
<div>6 libpetsc.3.7.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x00000001100ed088 PetscSignalHandler_Private(int<wbr>) + 630 (signal.c:49)</div>
<div>7 libsystem_platform.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x00007fffad997bba _sigtramp + 26</div>
<div>8 ??? <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x000000011ea09370 initialPoolContent + 19008</div>
<div>9 libnetcdf.7.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x000000011228fc62 utf8proc_map + 210 (dutf8proc.c:543)</div>
<div>10 libnetcdf.7.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x000000011228fd0f utf8proc_NFC + 38 (dutf8proc.c:568)</div>
<div>11 libnetcdf.7.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x00000001122a7928 NC_findattr + 110 (attr.c:341)</div>
<div>12 libnetcdf.7.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x00000001122a7a4e NC_lookupattr + 119 (attr.c:384)</div>
<div>13 libnetcdf.7.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x00000001122a93ef NC3_get_att + 47 (attr.c:1138)</div>
<div>14 libnetcdf.7.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x0000000112286126 nc_get_att_float + 90 (dattget.c:192)</div>
<div>15 libpetsc.3.7.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x00000001117f3a5b ex_open_int + 171 (ex_open.c:259)</div>
<div>16 libpetsc.3.7.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x0000000110c36609 DMPlexCreateExodusFromFile + 781 (plexexodusii.c:43)</div>
<div>17 DMPlexCreateExodusFromFile <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x000000010fed4cfc main + 397 (DMPlexCreateExodusFromFile.cp<wbr>p:24)</div>
<div>18 libdyld.dylib <span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-Apple-tab-span" style="white-space:pre-wrap">
</span>0x00007fffad78a255 start + 1</div>
</div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
</div>
</div>
<div>This is a NetCDF error on ex_open_int(). My guess is that your NetCDF build is old and when it calls the system DLL</div>
<div>you bomb. Can you do a completely new build, meaning either reclone PETSc somewhere else, or delete the whole</div>
<div>$PETSC_DIR/$PETSC_ARCH/externa<wbr>lpackage directory and reconfigure/build?</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div>
<div class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-h5">
<div> </div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>Hi Matt,</div>
<div><br>
</div>
<div>Thanks for reply. I recloned PETSc (the old petsc folder is deleted completely) and reconfigure. And still has the same issue. I also checked if the binary is complied against any other netcdf. The binary is actually complied against the right
netcdf installed through PETSc.</div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
</div>
</div>
<div>You can see that this crash happens on the call to</div>
<div><br>
</div>
<div>
<div> int CPU_word_size = 0, IO_word_size = 0, exoid = -1;<br>
</div>
<div> float version;</div>
<div><br>
</div>
<div> exoid = ex_open(filename, EX_READ, &CPU_word_size, &IO_word_size, &version);<br>
</div>
</div>
<div><br>
</div>
<div>which means the fault is not in PETSc, but rather in ExodusII for your machine. We could definitely</div>
<div>confirm this if you made a 5 line program that only called this, but I don't see why it should be different.</div>
<div>I am not sure what to do, since I am not in control of anything about ExodusII. Can you report this to</div>
<div>their dev team? It is strange since Blaise has not reported this, and I know he uses it all the time.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div>
<div class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-h5">
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">
<div>
<div><i>LiviadeMacBook-Pro:partition livia$ otool -L DMPlexCreateExodusFromFile</i></div>
<div><i>DMPlexCreateExodusFromFile:</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/petsc/arch-d<wbr>arwin-cxx-debug/lib/libpetsc.3<wbr>.7.dylib
(compatibility version 3.7.0, current version 3.7.5)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/petsc/arch-d<wbr>arwin-cxx-debug/lib/libsuperlu<wbr>_dist.5.dylib
(compatibility version 5.0.0, current version 5.1.3)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/petsc/arch-d<wbr>arwin-cxx-debug/lib/libparmeti<wbr>s.dylib
(compatibility version 0.0.0, current version 0.0.0)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/petsc/arch-d<wbr>arwin-cxx-debug/lib/libmetis.d<wbr>ylib
(compatibility version 0.0.0, current version 0.0.0)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/petsc/arch-d<wbr>arwin-cxx-debug/lib/libnetcdf.<wbr>7.dylib
(compatibility version 10.0.0, current version 10.0.0)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/petsc/arch-d<wbr>arwin-cxx-debug/lib/libhdf5_hl<wbr>.8.dylib
(compatibility version 9.0.0, current version 9.1.0)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/petsc/arch-d<wbr>arwin-cxx-debug/lib/libhdf5.8.<wbr>dylib
(compatibility version 9.0.0, current version 9.1.0)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/opt/X11/lib/libX11.6.dylib
(compatibility version 10.0.0, current version 10.0.0)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/mpich-3.2_in<wbr>stall/lib/libmpifort.12.dylib
(compatibility version 14.0.0, current version 14.0.0)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/usr/local/opt/gcc@5/lib/gcc/5<wbr>/libgfortran.3.dylib
(compatibility version 4.0.0, current version 4.0.0)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/usr/local/opt/gcc@5/lib/gcc/5<wbr>/libquadmath.0.dylib
(compatibility version 1.0.0, current version 1.0.0)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/mpich-3.2_in<wbr>stall/lib/libmpicxx.12.dylib
(compatibility version 14.0.0, current version 14.0.0)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/usr/local/opt/gcc@5/lib/gcc/5<wbr>/libstdc++.6.dylib
(compatibility version 7.0.0, current version 7.21.0)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/usr/local/opt/gcc@5/lib/gcc/5<wbr>/libgcc_s.1.dylib
(compatibility version 1.0.0, current version 1.0.0)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/mpich-3.2_in<wbr>stall/lib/libmpi.12.dylib
(compatibility version 14.0.0, current version 14.0.0)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/mpich-3.2_in<wbr>stall/lib/libpmpi.12.dylib
(compatibility version 14.0.0, current version 14.0.0)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/usr/lib/libSystem.B.dylib
(compatibility version 1.0.0, current version 1238.0.0)</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/usr/local/lib/gcc/5/libgcc_s.<wbr>1.dylib
(compatibility version 1.0.0, current version 1.0.0)</i></div>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
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<div class="gmail_quote">
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<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">
<div>
<div> </div>
</div>
</div>
</div>
</div>
</blockquote>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">
<div></div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">
<div><br>
</div>
<div> Matt</div>
<div>
<div class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-h5">
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div>
<div><i>static char help[] = " create mesh from exodus.\n\n";</i></div>
<div><i><br>
</i></div>
<div><i>#include <petscdm.h></i></div>
<div><i>#include <petsc/private/dmpleximpl.h></i></div>
<div><i><br>
</i></div>
<div><i>#undef __FUNCT__</i></div>
<div><i>#define __FUNCT__ "main"</i></div>
<div><i>int main(int argc,char **argv)</i></div>
<div><i>{</i></div>
<div><i> char fineMeshFileName[2048];</i></div>
<div><i> DM dm;</i></div>
<div><i> MPI_Comm comm;</i></div>
<div><i> PetscBool flg;</i></div>
<div><i><br>
</i></div>
<div><i> PetscErrorCode ierr;</i></div>
<div><i><br>
</i></div>
<div><i> ierr = PetscInitialize(&argc,&argv,(c<wbr>har *)0,help);CHKERRQ(ierr);</i></div>
<div><i> comm = PETSC_COMM_WORLD;</i></div>
<div><i> ierr = PetscOptionsGetString(NULL,NUL<wbr>L,"-file",fineMeshFileName,siz<wbr>eof(fineMeshFileName),&flg);CH<wbr>KERRQ(ierr);</i></div>
<div><i> if(!flg){</i></div>
<div><i><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-m_1135989402941268832m_-7159560215356067798gmail-Apple-tab-span" style="white-space:pre-wrap"></span>SETERRQ(comm,PETSC_ERR_ARG_NUL<wbr>L,"please
specify a fine mesh file \n");</i></div>
<div><i> }</i></div>
<div><i> ierr = DMPlexCreateExodusFromFile( comm,fineMeshFileName, PETSC_FALSE, &dm);CHKERRQ(ierr);</i></div>
<div><i> ierr = DMDestroy(&dm);CHKERRQ(ierr);</i></div>
<div><i> ierr = PetscFinalize();CHKERRQ(ierr);</i></div>
<div><i>}</i></div>
</div>
<div><i><br>
</i></div>
<div><i><br>
</i></div>
<div>
<div><i>LiviadeMacBook-Pro:partition livia$ ./DMPlexCreateExodusFromFile -file Tri3.exo </i></div>
<div><i>[0]PETSC ERROR: ------------------------------<wbr>------------------------------<wbr>------------</i></div>
<div><i>[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</i></div>
<div><i>[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</i></div>
<div><i>[0]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" target="_blank">
http://www.mcs.anl.gov/petsc/d<wbr>ocumentation/faq.html#valgrind</a></i></div>
<div><i>[0]PETSC ERROR: or try <a href="http://valgrind.org/" target="_blank">
http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors</i></div>
<div><i>[0]PETSC ERROR: likely location of problem given in stack below</i></div>
<div><i>[0]PETSC ERROR: --------------------- Stack Frames ------------------------------<wbr>------</i></div>
<div><i>[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,</i></div>
<div><i>[0]PETSC ERROR: INSTEAD the line number of the start of the function</i></div>
<div><i>[0]PETSC ERROR: is given.</i></div>
<div><i>[0]PETSC ERROR: [0] DMPlexCreateExodusFromFile line 38 /Users/livia/math/petsc/src/dm<wbr>/impls/plex/plexexodusii.c</i></div>
<div><i>[0]PETSC ERROR: --------------------- Error Message ------------------------------<wbr>------------------------------<wbr>--</i></div>
<div><i>[0]PETSC ERROR: Signal received</i></div>
<div><i>[0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank">
http://www.mcs.anl.gov/petsc/d<wbr>ocumentation/faq.html</a> for trouble shooting.</i></div>
<div><i>[0]PETSC ERROR: Petsc Release Version 3.7.5, unknown </i></div>
<div><i>[0]PETSC ERROR: ./DMPlexCreateExodusFromFile on a arch-darwin-cxx-debug named LiviadeMacBook-Pro.local by livia Sat Jan 21 21:04:22 2017</i></div>
<div><i>[0]PETSC ERROR: Configure options --with-clanguage=cxx --with-shared-libraries=1 --download-fblaslapack=1 --with-mpi=1 --download-parmetis=1 --download-metis=1 --download-netcdf=1 --download-exodusii=1 --download-hdf5=1 --with-debugging=yes
--with-c2html=0 --download-hypre=1 --with-64-bit-indices=1 --download-superlu_dist=1 PETSC_ARCH=arch-darwin-cxx-deb<wbr>ug</i></div>
<div><i>[0]PETSC ERROR: #1 User provided function() line 0 in unknown file</i></div>
<div><i>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0</i></div>
<div><i>[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59</i></div>
<div><i>:</i></div>
<div><i>system msg for write_line failure : Bad file descriptor</i></div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>The log files of make and configuration are also attached. If you have any idea on this issue, please let me know!</div>
<span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-m_1135989402941268832HOEnZb"><font color="#888888">
<div><br>
</div>
<div>Fande Kong,</div>
<div><br>
</div>
</font></span></div>
</blockquote>
</div>
</div>
</div>
<span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-HOEnZb"><font color="#888888"><br>
<br clear="all">
<span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-HOEnZb"><font color="#888888"><span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-HOEnZb"><font color="#888888">
<div><br>
</div>
-- <br>
<div class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-m_1135989402941268832gmail_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>
-- Norbert Wiener</div>
</font></span></font></span></font></span></div>
</div>
<span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-HOEnZb"><font color="#888888"></font></span></blockquote>
</div>
<span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-HOEnZb"><font color="#888888"><br>
</font></span></div>
</div>
<span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-HOEnZb"><font color="#888888"></font></span></blockquote>
</div>
</div>
</div>
<span class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-HOEnZb"><font color="#888888">
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-- <br>
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What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener</div>
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What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener</div>
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-- <br>
<div class="m_4568811219969245007m_7372593255479590743m_4419773826590688416m_6204887073125375060gmail_signature" data-smartmail="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>
-- Norbert Wiener</div>
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-- <br>
<div class="m_4568811219969245007m_7372593255479590743gmail_signature" data-smartmail="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>
-- Norbert Wiener</div>
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<div><span class="m_4568811219969245007Apple-style-span" style="border-collapse:separate;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-alternates:normal;font-variant-east-asian:normal;line-height:normal;border-spacing:0px"><span class="m_4568811219969245007Apple-style-span" style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
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-- </div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">
Department of Mathematics and Center for Computation & Technology</div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">
Louisiana State University, Baton Rouge, LA 70803, USA</div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">
Tel. <a href="tel:(225)%20578-1612" value="+12255781612" target="_blank">+1 (225) 578 1612</a>, Fax <a href="tel:(225)%20578-4276" value="+12255784276" target="_blank">+1 (225) 578 4276</a> <a href="http://www.math.lsu.edu/~bourdin" target="_blank">
http://www.math.lsu.edu/~<wbr>bourdin</a></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="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>-- Norbert Wiener</div>
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