<div dir="ltr"><div class="gmail_default" style="font-family:"comic sans ms",sans-serif;color:rgb(56,118,29)">It turns out that openmpi puts it's mpi.mod in the lib instead of include directory and the pnetcdf configure wasn't finding it.</div><div class="gmail_default" style="font-family:"comic sans ms",sans-serif;color:rgb(56,118,29)">Once I fixed this and use mpi.mod instead of mpif.h that solved the problem, however then I run into another problem at the</div><div class="gmail_default" style="font-family:"comic sans ms",sans-serif;color:rgb(56,118,29)">link step: </div><div class="gmail_default" style="font-family:"comic sans ms",sans-serif;color:rgb(56,118,29)"><br></div><div class="gmail_default" style="font-family:"comic sans ms",sans-serif;color:rgb(56,118,29)">
<p class="gmail-p1"><span class="gmail-s1"><span class="gmail-Apple-converted-space"> </span>CCLD <span class="gmail-Apple-converted-space"> </span>ncmpivalid</span></p>
<p class="gmail-p1"><span class="gmail-s1">ld: cannot find -lpbs</span></p><p class="gmail-p1"><span class="gmail-s1">I haven't figured out where the requirement on a library pbs comes from or how to get rid of it?</span></p></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Nov 6, 2017 at 9:36 AM, Jim Edwards <span dir="ltr"><<a href="mailto:jedwards@ucar.edu" target="_blank">jedwards@ucar.edu</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"><br><div class="gmail_quote"><span class="">On Mon, Nov 6, 2017 at 9:16 AM, Jim Edwards <span dir="ltr"><<a href="mailto:jedwards@ucar.edu" target="_blank">jedwards@ucar.edu</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 style="font-family:"comic sans ms",sans-serif;color:rgb(56,118,29)">I am trying to build with openmpi/3.0.0 and intel17 and hanging in the build</div><div style="font-family:"comic sans ms",sans-serif;color:rgb(56,118,29)">of pnetcdf.f90. </div><div style="font-family:"comic sans ms",sans-serif;color:rgb(56,118,29)"><br></div><div style="font-family:"comic sans ms",sans-serif;color:rgb(56,118,29)">The make output at the time is:</div><div style="font-family:"comic sans ms",sans-serif;color:rgb(56,118,29)">
<p class="m_3223796142421346821m_-8828403455049859842gmail-p1"><span class="m_3223796142421346821m_-8828403455049859842gmail-s1">make[4]: Entering directory '/glade/u/home/jedwards/src/pa<wbr>rallel-netcdf/src/binding/f90'</span></p>
<p class="m_3223796142421346821m_-8828403455049859842gmail-p1"><span class="m_3223796142421346821m_-8828403455049859842gmail-s1"><span class="m_3223796142421346821m_-8828403455049859842gmail-Apple-converted-space"> </span>FC <span class="m_3223796142421346821m_-8828403455049859842gmail-Apple-converted-space"> </span>pnetcdf.lo</span></p><p class="m_3223796142421346821m_-8828403455049859842gmail-p1"><span class="m_3223796142421346821m_-8828403455049859842gmail-s1">examining the process I see:</span></p><p class="m_3223796142421346821m_-8828403455049859842gmail-p1"><span class="m_3223796142421346821m_-8828403455049859842gmail-s1">
</span></p><p class="m_3223796142421346821m_-8828403455049859842gmail-p1"><span class="m_3223796142421346821m_-8828403455049859842gmail-s1">/glade/u/apps/opt/intel/2017u1<wbr>/compilers_and_libraries/<wbr>linux/bin/intel64/ifort -I. -I. -debug minimal -g -O0 -c pnetcdf.f90 -o pnetcdf.o -I/glade/u/apps/ch/os/usr/incl<wbr>ude -L/glade/u/apps/opt/intel/2017<wbr>u1/compilers_and_libraries/<wbr>linux/lib/intel64_lin -L/glade/u/apps/ch/os/usr/lib6<wbr>4 -L/glade/u/apps/ch/os/lib64 -L/glade/u/apps/ch/os/usr/lib -L/glade/u/apps/ch/os/lib -L/glade/u/apps/ch/opt/openmpi<wbr>/3.0.0/intel/17.0.1/lib -Wl,--disable-new-dtags -Wl,-rpath,/glade/u/apps/opt/i<wbr>ntel/2017u1/compilers_and_libr<wbr>aries/linux/lib/intel64_lin -Wl,-rpath,/glade/u/apps/ch/os<wbr>/usr/lib64 -Wl,-rpath,/glade/u/apps/ch/os<wbr>/lib64 -Wl,-rpath,/glade/u/apps/ch/os<wbr>/usr/lib -Wl,-rpath,/glade/u/apps/ch/os<wbr>/lib -Wl,-rpath,/glade/u/apps/ch/op<wbr>t/openmpi/3.0.0/intel/17.0.1/<wbr>lib -lrt -ldl</span></p><p class="m_3223796142421346821m_-8828403455049859842gmail-p1"><span class="m_3223796142421346821m_-8828403455049859842gmail-s1"><br></span></p></div></div></blockquote></span><div><div class="gmail_default" style="font-family:"comic sans ms",sans-serif;color:rgb(56,118,29)">Please ignore the following incorrect statement, I did this in another window where I still had the default mpt loaded instead of openmpi, if I do this with openmpi, it still hangs. </div><br></div><span class=""><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div style="font-family:"comic sans ms",sans-serif;color:rgb(56,118,29)"><p class="m_3223796142421346821m_-8828403455049859842gmail-p1"><span class="m_3223796142421346821m_-8828403455049859842gmail-s1"></span></p><p class="m_3223796142421346821m_-8828403455049859842gmail-p1"><span class="m_3223796142421346821m_-8828403455049859842gmail-s1">If I remove all of the -L and -rpath flags and just do:</span></p>
<p class="m_3223796142421346821m_-8828403455049859842gmail-p1"><span class="m_3223796142421346821m_-8828403455049859842gmail-s1"><span class="m_3223796142421346821m_-8828403455049859842gmail-Apple-converted-space" style="font-variant-ligatures:no-common-ligatures;background-color:rgb(235,235,235);color:rgb(0,0,0);font-family:"Lucida Console""> </span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(235,235,235);color:rgb(0,0,0);font-family:"Lucida Console"">/glade/u/apps/opt/intel/2017u<wbr>1/compilers_and_libraries/<wbr>linux/bin/intel64/ifort -I. -I. -debug minimal -g -O0 -c pnetcdf.f90 -o pnetcdf.o</span> </span></p></div><div style="font-family:"comic sans ms",sans-serif;color:rgb(56,118,29)">That completes right away, so the problem seems to have to do with libtool. Also building with mpt instead of openmpi on the same system works. </div><div style="font-family:"comic sans ms",sans-serif;color:rgb(56,118,29)"><br></div><div style="font-family:"comic sans ms",sans-serif;color:rgb(56,118,29)">Any ideas?</div><span class="m_3223796142421346821HOEnZb"><font color="#888888"><div><br></div>-- <br><div class="m_3223796142421346821m_-8828403455049859842gmail_signature"><div dir="ltr"><div><div><div>Jim Edwards<br><br></div><font size="1">CESM Software Engineer<br></font></div><font size="1">National Center for Atmospheric Research<br></font></div><font size="1">Boulder, CO</font> <br></div></div>
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</blockquote></span></div><span class=""><br><br clear="all"><div><br></div>-- <br><div class="m_3223796142421346821gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div><div>Jim Edwards<br><br></div><font size="1">CESM Software Engineer<br></font></div><font size="1">National Center for Atmospheric Research<br></font></div><font size="1">Boulder, CO</font> <br></div></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div><div>Jim Edwards<br><br></div><font size="1">CESM Software Engineer<br></font></div><font size="1">National Center for Atmospheric Research<br></font></div><font size="1">Boulder, CO</font> <br></div></div>
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