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Hi,
<div class=""><br class="">
</div>
<div class="">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 class="">I am able to read / write exodus files. I am attaching my configure command lines:</div>
<div class=""><br class="">
</div>
<div class="">with intel 17.0:</div>
<div class="">
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">./configure ./configure \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --download-chaco=1 \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --download-exodusii=1 \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --download-hdf5=1 \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --download-hypre=1 \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --download-metis=1 \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --download-ml=1 \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --download-netcdf=1 \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --download-parmetis=1 \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --download-triangle=1 \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --with-blas-lapack-dir=$MKLROOT \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --with-debugging=1 \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --with-mpi-dir=$MPI_HOME \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --with-pic \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --with-shared-libraries=1 \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --with-vendor-compilers=intel \</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> --with-x11=1</span></div>
</div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""><br class="">
</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">with gcc:</span></div>
<div style="margin: 0px; line-height: normal; font-family: 'Source Code Pro'; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">./configure \</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> --download-exodusii=1 \</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> --download-chaco=1 \</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> --download-ctetgen=1 \</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> --download-hdf5=1 \</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> --download-hypre=1 \</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> --download-metis=1 \</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> --download-ml=1 \</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> --download-netcdf=1 \</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> --download-parmetis=1 \</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> --download-triangle=1 \</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> --download-yaml=1 \</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> --with-debugging=1 \</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> --with-shared-libraries=1 \</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> --with-x11=1</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures" class=""><br class="">
</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Blaise</span></div>
</span></div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Jan 23, 2017, at 7:55 AM, Mark Adams <<a href="mailto:mfadams@lbl.gov" class="">mfadams@lbl.gov</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">And I trust you updated all system software (like gcc, NetCDF and ExodusII). OSX upgrades are hell.</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Mon, Jan 23, 2017 at 12:36 AM, Matthew Knepley <span dir="ltr" class="">
<<a href="mailto:knepley@gmail.com" target="_blank" class="">knepley@gmail.com</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" class="">
<div class="gmail_extra">
<div class="gmail_quote"><span class="">On Sun, Jan 22, 2017 at 11:18 PM, Fande Kong
<span dir="ltr" class=""><<a href="mailto:fdkong.jd@gmail.com" target="_blank" class="">fdkong.jd@gmail.com</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" class="">Thanks, Matt,
<div class=""><br class="">
</div>
<div class="">Clang does not have this issue. The code runs fine with clang. </div>
</div>
</blockquote>
<div class=""><br class="">
</div>
</span>
<div class="">Okay, it sounds like a gcc bug on Mac 10.6, or at least in the version you have.</div>
<div class=""><br class="">
</div>
<div class=""> Matt</div>
<div class="">
<div class="h5">
<div class=""> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" class="">
<div class="">Fande,</div>
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Sun, Jan 22, 2017 at 8:03 PM, Matthew Knepley <span dir="ltr" class="">
<<a href="mailto:knepley@gmail.com" target="_blank" class="">knepley@gmail.com</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" class="">
<div class="gmail_extra">
<div class="gmail_quote"><span class="">On Sun, Jan 22, 2017 at 8:40 PM, Fande Kong
<span dir="ltr" class=""><<a href="mailto:fdkong.jd@gmail.com" target="_blank" class="">fdkong.jd@gmail.com</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" class="">
<div class="">Thanks, Matt.</div>
<div class=""><br class="">
</div>
<div class="">It is a weird bug. </div>
<div class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
</span>
<div class="">Well, ExodusII is only a think layer on NetCDF, just like other wrappers are thin layers on HDF5. It is</div>
<div class="">really NetCDF that is failing. Can you switch compilers and see if that helps?</div>
<div class=""><br class="">
</div>
<div class=""> Matt</div>
<div class="">
<div class="m_7372593255479590743m_4419773826590688416h5">
<div class=""> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" class="">
<div class="">Fande Kong, </div>
<div class=""><br class="">
</div>
<br class="">
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Sun, Jan 22, 2017 at 6:50 PM, Matthew Knepley <span dir="ltr" class="">
<<a href="mailto:knepley@gmail.com" target="_blank" class="">knepley@gmail.com</a>></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 dir="ltr" class="">
<div class="gmail_extra">
<div class="gmail_quote">
<div class="">
<div class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-h5">
On Sun, Jan 22, 2017 at 5:28 PM, Fande Kong <span dir="ltr" class=""><<a href="mailto:fdkong.jd@gmail.com" target="_blank" class="">fdkong.jd@gmail.com</a>></span> wrote:<br class="">
<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" class="">
<div class="gmail_extra">
<div class="gmail_quote">On Sun, Jan 22, 2017 at 12:35 PM, Matthew Knepley <span dir="ltr" class="">
<<a href="mailto:knepley@gmail.com" target="_blank" class="">knepley@gmail.com</a>></span> wrote:<br class="">
<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" class="">
<div class="gmail_extra">
<div class="gmail_quote">
<div class="">
<div class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-h5">
On Sun, Jan 22, 2017 at 12:41 PM, Fande Kong <span dir="ltr" class=""><<a href="mailto:fdkong.jd@gmail.com" target="_blank" class="">fdkong.jd@gmail.com</a>></span> wrote:<br class="">
<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" class="">
<div class="gmail_extra">
<div class="gmail_quote">On Sat, Jan 21, 2017 at 10:47 PM, Matthew Knepley <span dir="ltr" class="">
<<a href="mailto:knepley@gmail.com" target="_blank" class="">knepley@gmail.com</a>></span> wrote:<br class="">
<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" class="">
<div class="gmail_extra">
<div class="gmail_quote"><span class="m_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" class=""><<a href="mailto:fdkong.jd@gmail.com" target="_blank" class="">fdkong.jd@gmail.com</a>></span> wrote:<br class="">
<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" class="">Hi All,
<div class=""><br class="">
</div>
<div class="">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 class=""><b class="">exodus</b></i>, and PETSc might not pick up the right enveriment variables for the
<i class=""><b class="">exodus.</b></i></div>
<div class=""><br class="">
</div>
<div class="">This issue can be reproduced using the following simple code:</div>
</div>
</blockquote>
<div class=""><br class="">
</div>
</span>
<div class="">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 class=""><br class="">
</div>
<div class="">2) If so, can you get a stack trace with gdb or lldb?</div>
</div>
</div>
</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">
<div class="">0 libsystem_kernel.dylib <span class="m_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 class="">1 libsystem_pthread.dylib <span class="m_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 class="">2 libsystem_c.dylib <span class="m_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 class="">3 libpetsc.3.7.dylib <span class="m_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 class="">4 libpetsc.3.7.dylib <span class="m_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 class="">5 libpetsc.3.7.dylib <span class="m_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 class="">6 libpetsc.3.7.dylib <span class="m_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 class="">) + 630 (signal.c:49)</div>
<div class="">7 libsystem_platform.dylib <span class="m_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 class="">8 ??? <span class="m_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 class="">9 libnetcdf.7.dylib <span class="m_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 class="">10 libnetcdf.7.dylib <span class="m_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 class="">11 libnetcdf.7.dylib <span class="m_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 class="">12 libnetcdf.7.dylib <span class="m_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 class="">13 libnetcdf.7.dylib <span class="m_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 class="">14 libnetcdf.7.dylib <span class="m_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 class="">15 libpetsc.3.7.dylib <span class="m_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 class="">16 libpetsc.3.7.dylib <span class="m_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 class="">17 DMPlexCreateExodusFromFile <span class="m_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 class="">p:24)</div>
<div class="">18 libdyld.dylib <span class="m_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 class=""><br class="">
</div>
</div>
</div>
<div class="">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 class="">you bomb. Can you do a completely new build, meaning either reclone PETSc somewhere else, or delete the whole</div>
<div class="">$PETSC_DIR/$PETSC_ARCH/externa<wbr class="">lpackage directory and reconfigure/build?</div>
<div class=""><br class="">
</div>
<div class=""> Thanks,</div>
<div class=""><br class="">
</div>
<div class=""> Matt</div>
<div class="">
<div class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-h5">
<div class=""> </div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">Hi Matt,</div>
<div class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
</div>
</div>
<div class="">You can see that this crash happens on the call to</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""> int CPU_word_size = 0, IO_word_size = 0, exoid = -1;<br class="">
</div>
<div class=""> float version;</div>
<div class=""><br class="">
</div>
<div class=""> exoid = ex_open(filename, EX_READ, &CPU_word_size, &IO_word_size, &version);<br class="">
</div>
</div>
<div class=""><br class="">
</div>
<div class="">which means the fault is not in PETSc, but rather in ExodusII for your machine. We could definitely</div>
<div class="">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 class="">I am not sure what to do, since I am not in control of anything about ExodusII. Can you report this to</div>
<div class="">their dev team? It is strange since Blaise has not reported this, and I know he uses it all the time.</div>
<div class=""><br class="">
</div>
<div class=""> Thanks,</div>
<div class=""><br class="">
</div>
<div class=""> Matt</div>
<div class="">
<div class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-h5">
<div class=""> </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" class="">
<div class="gmail_extra">
<div class="gmail_quote">
<div class="">
<div class=""><i class="">LiviadeMacBook-Pro:partition livia$ otool -L DMPlexCreateExodusFromFile</i></div>
<div class=""><i class="">DMPlexCreateExodusFromFile:</i></div>
<div class=""><i class=""><span class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/petsc/arch-d<wbr class="">arwin-cxx-debug/lib/libpetsc.3<wbr class="">.7.dylib
(compatibility version 3.7.0, current version 3.7.5)</i></div>
<div class=""><i class=""><span class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/petsc/arch-d<wbr class="">arwin-cxx-debug/lib/libsuperlu<wbr class="">_dist.5.dylib
(compatibility version 5.0.0, current version 5.1.3)</i></div>
<div class=""><i class=""><span class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/petsc/arch-d<wbr class="">arwin-cxx-debug/lib/libparmeti<wbr class="">s.dylib
(compatibility version 0.0.0, current version 0.0.0)</i></div>
<div class=""><i class=""><span class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/petsc/arch-d<wbr class="">arwin-cxx-debug/lib/libmetis.d<wbr class="">ylib
(compatibility version 0.0.0, current version 0.0.0)</i></div>
<div class=""><i class=""><span class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/petsc/arch-d<wbr class="">arwin-cxx-debug/lib/libnetcdf.<wbr class="">7.dylib
(compatibility version 10.0.0, current version 10.0.0)</i></div>
<div class=""><i class=""><span class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/petsc/arch-d<wbr class="">arwin-cxx-debug/lib/libhdf5_hl<wbr class="">.8.dylib
(compatibility version 9.0.0, current version 9.1.0)</i></div>
<div class=""><i class=""><span class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-Apple-tab-span" style="white-space:pre-wrap"></span>/Users/livia/math/petsc/arch-d<wbr class="">arwin-cxx-debug/lib/libhdf5.8.<wbr class="">dylib
(compatibility version 9.0.0, current version 9.1.0)</i></div>
<div class=""><i class=""><span class="m_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 class=""><i class=""><span class="m_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 class="">stall/lib/libmpifort.12.dylib
(compatibility version 14.0.0, current version 14.0.0)</i></div>
<div class=""><i class=""><span class="m_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 class="">/libgfortran.3.dylib
(compatibility version 4.0.0, current version 4.0.0)</i></div>
<div class=""><i class=""><span class="m_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 class="">/libquadmath.0.dylib
(compatibility version 1.0.0, current version 1.0.0)</i></div>
<div class=""><i class=""><span class="m_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 class="">stall/lib/libmpicxx.12.dylib
(compatibility version 14.0.0, current version 14.0.0)</i></div>
<div class=""><i class=""><span class="m_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 class="">/libstdc++.6.dylib
(compatibility version 7.0.0, current version 7.21.0)</i></div>
<div class=""><i class=""><span class="m_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 class="">/libgcc_s.1.dylib
(compatibility version 1.0.0, current version 1.0.0)</i></div>
<div class=""><i class=""><span class="m_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 class="">stall/lib/libmpi.12.dylib
(compatibility version 14.0.0, current version 14.0.0)</i></div>
<div class=""><i class=""><span class="m_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 class="">stall/lib/libpmpi.12.dylib
(compatibility version 14.0.0, current version 14.0.0)</i></div>
<div class=""><i class=""><span class="m_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 class=""><i class=""><span class="m_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 class="">1.dylib
(compatibility version 1.0.0, current version 1.0.0)</i></div>
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""> </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" class="">
<div class="gmail_extra">
<div class="gmail_quote">
<div class="">
<div class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-h5">
<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" class="">
<div class="gmail_extra">
<div class="gmail_quote">
<div class="">
<div class=""> </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" class="">
<div class="gmail_extra">
<div class="gmail_quote">
<div class=""></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" class="">
<div class="gmail_extra">
<div class="gmail_quote">
<div class=""><br class="">
</div>
<div class=""> Matt</div>
<div class="">
<div class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-h5">
<div class=""> </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" class="">
<div class="">
<div class=""><i class="">static char help[] = " create mesh from exodus.\n\n";</i></div>
<div class=""><i class=""><br class="">
</i></div>
<div class=""><i class="">#include <petscdm.h></i></div>
<div class=""><i class="">#include <petsc/private/dmpleximpl.h></i></div>
<div class=""><i class=""><br class="">
</i></div>
<div class=""><i class="">#undef __FUNCT__</i></div>
<div class=""><i class="">#define __FUNCT__ "main"</i></div>
<div class=""><i class="">int main(int argc,char **argv)</i></div>
<div class=""><i class="">{</i></div>
<div class=""><i class=""> char fineMeshFileName[2048];</i></div>
<div class=""><i class=""> DM dm;</i></div>
<div class=""><i class=""> MPI_Comm comm;</i></div>
<div class=""><i class=""> PetscBool flg;</i></div>
<div class=""><i class=""><br class="">
</i></div>
<div class=""><i class=""> PetscErrorCode ierr;</i></div>
<div class=""><i class=""><br class="">
</i></div>
<div class=""><i class=""> ierr = PetscInitialize(&argc,&argv,(c<wbr class="">har *)0,help);CHKERRQ(ierr);</i></div>
<div class=""><i class=""> comm = PETSC_COMM_WORLD;</i></div>
<div class=""><i class=""> ierr = PetscOptionsGetString(NULL,NUL<wbr class="">L,"-file",fineMeshFileName,siz<wbr class="">eof(fineMeshFileName),&flg);CH<wbr class="">KERRQ(ierr);</i></div>
<div class=""><i class=""> if(!flg){</i></div>
<div class=""><i class=""><span class="m_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 class="">L,"please
specify a fine mesh file \n");</i></div>
<div class=""><i class=""> }</i></div>
<div class=""><i class=""> ierr = DMPlexCreateExodusFromFile( comm,fineMeshFileName, PETSC_FALSE, &dm);CHKERRQ(ierr);</i></div>
<div class=""><i class=""> ierr = DMDestroy(&dm);CHKERRQ(ierr);</i></div>
<div class=""><i class=""> ierr = PetscFinalize();CHKERRQ(ierr);</i></div>
<div class=""><i class="">}</i></div>
</div>
<div class=""><i class=""><br class="">
</i></div>
<div class=""><i class=""><br class="">
</i></div>
<div class="">
<div class=""><i class="">LiviadeMacBook-Pro:partition livia$ ./DMPlexCreateExodusFromFile -file Tri3.exo </i></div>
<div class=""><i class="">[0]PETSC ERROR: ------------------------------<wbr class="">------------------------------<wbr class="">------------</i></div>
<div class=""><i class="">[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</i></div>
<div class=""><i class="">[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</i></div>
<div class=""><i class="">[0]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" target="_blank" class="">
http://www.mcs.anl.gov/petsc/d<wbr class="">ocumentation/faq.html#valgrind</a></i></div>
<div class=""><i class="">[0]PETSC ERROR: or try <a href="http://valgrind.org/" target="_blank" class="">
http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors</i></div>
<div class=""><i class="">[0]PETSC ERROR: likely location of problem given in stack below</i></div>
<div class=""><i class="">[0]PETSC ERROR: --------------------- Stack Frames ------------------------------<wbr class="">------</i></div>
<div class=""><i class="">[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,</i></div>
<div class=""><i class="">[0]PETSC ERROR: INSTEAD the line number of the start of the function</i></div>
<div class=""><i class="">[0]PETSC ERROR: is given.</i></div>
<div class=""><i class="">[0]PETSC ERROR: [0] DMPlexCreateExodusFromFile line 38 /Users/livia/math/petsc/src/dm<wbr class="">/impls/plex/plexexodusii.c</i></div>
<div class=""><i class="">[0]PETSC ERROR: --------------------- Error Message ------------------------------<wbr class="">------------------------------<wbr class="">--</i></div>
<div class=""><i class="">[0]PETSC ERROR: Signal received</i></div>
<div class=""><i class="">[0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank" class="">
http://www.mcs.anl.gov/petsc/d<wbr class="">ocumentation/faq.html</a> for trouble shooting.</i></div>
<div class=""><i class="">[0]PETSC ERROR: Petsc Release Version 3.7.5, unknown </i></div>
<div class=""><i class="">[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 class=""><i class="">[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 class="">ug</i></div>
<div class=""><i class="">[0]PETSC ERROR: #1 User provided function() line 0 in unknown file</i></div>
<div class=""><i class="">application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0</i></div>
<div class=""><i class="">[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59</i></div>
<div class=""><i class="">:</i></div>
<div class=""><i class="">system msg for write_line failure : Bad file descriptor</i></div>
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">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_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-m_1135989402941268832HOEnZb"><font color="#888888" class="">
<div class=""><br class="">
</div>
<div class="">Fande Kong,</div>
<div class=""><br class="">
</div>
</font></span></div>
</blockquote>
</div>
</div>
</div>
<span class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-m_-6714211138418826265gmail-HOEnZb"><font color="#888888" class=""><br class="">
<br clear="all" class="">
<span class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-HOEnZb"><font color="#888888" class=""><span class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail-HOEnZb"><font color="#888888" class="">
<div class=""><br class="">
</div>
-- <br class="">
<div class="m_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 class="">
-- Norbert Wiener</div>
</font></span></font></span></font></span></div>
</div>
<span class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-HOEnZb"><font color="#888888" class=""></font></span></blockquote>
</div>
<span class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-HOEnZb"><font color="#888888" class=""><br class="">
</font></span></div>
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-- <br class="">
<div class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail-m_-4569662235748214629gmail-m_5616057590805880423gmail_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>
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<div class="m_7372593255479590743m_4419773826590688416m_6204887073125375060m_-1295862586045425915gmail-m_-1068692707458709767gmail_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>
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-- <br class="">
<div class="m_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 class="">
-- Norbert Wiener</div>
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<div class=""><br class="">
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-- <br class="">
<div class="m_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 class="">
-- Norbert Wiener</div>
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-- </div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; " class="">
Department of Mathematics and Center for Computation & Technology</div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; " class="">
Louisiana State University, Baton Rouge, LA 70803, USA</div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; " class="">
Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 <a href="http://www.math.lsu.edu/~bourdin" class="">
http://www.math.lsu.edu/~bourdin</a></div>
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