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Ok -- yes -- I got a clean build by removing the<font
face="monospace"> --with-mpi</font> flag.<br>
<br>
What about this <font face="monospace">--enable-large-single-req</font>
flag, though?<br>
Does it require that I build OpenMPI specially, or use a specific
kind of switch or FileSystem?<br>
I only use 64-but systems these days...<br>
<br>
Thanks,<br>
<br>
Carl<br>
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<th valign="BASELINE" nowrap="nowrap" align="RIGHT">Subject:
</th>
<td>Re: Path oddity in PNetCDF build/configure</td>
</tr>
<tr>
<th valign="BASELINE" nowrap="nowrap" align="RIGHT">Date: </th>
<td>Sun, 24 Oct 2021 21:27:44 +0000</td>
</tr>
<tr>
<th valign="BASELINE" nowrap="nowrap" align="RIGHT">From: </th>
<td>Wei-Keng Liao <a class="moz-txt-link-rfc2396E" href="mailto:wkliao@northwestern.edu"><wkliao@northwestern.edu></a></td>
</tr>
<tr>
<th valign="BASELINE" nowrap="nowrap" align="RIGHT">To: </th>
<td>Carl Ponder <a class="moz-txt-link-rfc2396E" href="mailto:cponder@nvidia.com"><cponder@nvidia.com></a></td>
</tr>
<tr>
<th valign="BASELINE" nowrap="nowrap" align="RIGHT">CC: </th>
<td>Bruno Pagani <a class="moz-txt-link-rfc2396E" href="mailto:bruno.pagani@astrophysics.eu"><bruno.pagani@astrophysics.eu></a>,
<a class="moz-txt-link-abbreviated" href="mailto:parallel-netcdf@lists.mcs.anl.gov">parallel-netcdf@lists.mcs.anl.gov</a>
<a class="moz-txt-link-rfc2396E" href="mailto:parallel-netcdf@lists.mcs.anl.gov"><parallel-netcdf@lists.mcs.anl.gov></a></td>
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<td><font size="1" face="verdana" color="black"><b>External
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<br>
<div>I checked the configure command line used.
<div class="">While debugging this issue, I suggest you to
remove</div>
<div class="">"--with-mpi --enable-large-single-req" from the
configure command.</div>
<div class=""><br class="">
</div>
<div class="">Option --with-mpi was designed to let users to
provide the</div>
<div class="">path of MPI installation, e.g.
--with-mpi=/usr/local</div>
<div class=""><br class="">
</div>
<div class="">Use option --enable-large-single-req is when the
underlying</div>
<div class="">MPI-IO supports reading and writing more than 2GiB
in a</div>
<div class="">single call (i.e. MPI_File_read and MPI_File_write
call.)</div>
<div class=""><br class="">
<div class="">Wei-keng </div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Oct 24, 2021, at 4:07 PM, Carl Ponder
<<a href="mailto:cponder@nvidia.com" class=""
moz-do-not-send="true">cponder@nvidia.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><br style="caret-color: rgb(0, 0, 0);
font-family: Monaco; font-size: 14px; font-style:
normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Monaco; font-size: 14px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none; float: none; display:
inline !important;" class="">I attached the<span
class="Apple-converted-space"> </span></span><font
style="caret-color: rgb(0, 0, 0); font-size: 14px;
font-style: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal;
text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; text-decoration:
none;" class="" face="monospace">config.log</font><span
style="caret-color: rgb(0, 0, 0); font-family: Monaco;
font-size: 14px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none; float: none; display:
inline !important;" class=""><span
class="Apple-converted-space"> </span>here, but it
doesn't show the steps used in the<span
class="Apple-converted-space"> </span></span><font
style="caret-color: rgb(0, 0, 0); font-size: 14px;
font-style: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal;
text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; text-decoration:
none;" class="" face="monospace">mpicc</font><span
style="caret-color: rgb(0, 0, 0); font-family: Monaco;
font-size: 14px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none; float: none; display:
inline !important;" class="">checking:</span><br
style="caret-color: rgb(0, 0, 0); font-family: Monaco;
font-size: 14px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none;" class="">
<blockquote style="caret-color: rgb(0, 0, 0);
font-family: Monaco; font-size: 14px; font-style:
normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none;" class="">
<font class="" face="monospace">configure:4284:
result: /usr/bin/sed -i''</font><br class="">
<b class=""><font class="" face="monospace">configure:4682:
checking mpicc under yes</font></b><br class="">
<font class="" face="monospace">configure:4689:
result: no</font><br class="">
<font class="" face="monospace">configure:4772: error:<span
class="Apple-converted-space"> </span></font><br
class="">
<font class="" face="monospace">
-----------------------------------------------------------------------</font><br
class="">
<font class="" face="monospace"> Specified MPI C
compiler "mpicc" cannot be found under yes</font><br
class="">
<font class="" face="monospace"> PnetCDF requires
a working MPI C compiler. Please specify the
location</font><br class="">
<font class="" face="monospace"> of an MPI C
compiler, either in the MPICC environment variable</font><br
class="">
<font class="" face="monospace"> (not CC variable)
or through --with-mpi configure flag. Abort.</font><br
class="">
<font class="" face="monospace">
-----------------------------------------------------------------------</font><br
class="">
</blockquote>
<span style="caret-color: rgb(0, 0, 0); font-family:
Monaco; font-size: 14px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none; float: none; display:
inline !important;" class="">The command-line I used
was</span><br style="caret-color: rgb(0, 0, 0);
font-family: Monaco; font-size: 14px; font-style:
normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none;" class="">
<blockquote style="caret-color: rgb(0, 0, 0);
font-family: Monaco; font-size: 14px; font-style:
normal; font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none;" class="">
<font class="" face="monospace">./configure
--prefix=/usr/local --enable-shared --with-mpi
--enable-large-single-req<span
class="Apple-converted-space"> </span></font><br
class="">
</blockquote>
<div class="moz-forward-container" style="caret-color:
rgb(0, 0, 0); font-family: Monaco; font-size: 14px;
font-style: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal;
text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; text-decoration:
none;">
<br class="">
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cellpadding="0" border="0">
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<tr class="">
<th class="" valign="BASELINE" nowrap="nowrap"
align="RIGHT">Subject:</th>
<td class="">Re: Path oddity in PNetCDF
build/configure</td>
</tr>
<tr class="">
<th class="" valign="BASELINE" nowrap="nowrap"
align="RIGHT">Date:<span
class="Apple-converted-space"> </span></th>
<td class="">Sun, 24 Oct 2021 19:22:06 +0000</td>
</tr>
<tr class="">
<th class="" valign="BASELINE" nowrap="nowrap"
align="RIGHT">From:<span
class="Apple-converted-space"> </span></th>
<td class="">Wei-Keng Liao<span
class="Apple-converted-space"> </span><a
class="moz-txt-link-rfc2396E"
href="mailto:wkliao@northwestern.edu"
moz-do-not-send="true"><wkliao@northwestern.edu></a></td>
</tr>
<tr class="">
<th class="" valign="BASELINE" nowrap="nowrap"
align="RIGHT">To:<span
class="Apple-converted-space"> </span></th>
<td class="">Carl Ponder<span
class="Apple-converted-space"> </span><a
class="moz-txt-link-rfc2396E"
href="mailto:cponder@nvidia.com"
moz-do-not-send="true"><cponder@nvidia.com></a></td>
</tr>
<tr class="">
<th class="" valign="BASELINE" nowrap="nowrap"
align="RIGHT">CC:<span
class="Apple-converted-space"> </span></th>
<td class="">Bruno Pagani<span
class="Apple-converted-space"> </span><a
class="moz-txt-link-rfc2396E"
href="mailto:bruno.pagani@astrophysics.eu"
moz-do-not-send="true"><bruno.pagani@astrophysics.eu></a>,<span
class="Apple-converted-space"> </span><a
class="moz-txt-link-abbreviated"
href="mailto:parallel-netcdf@lists.mcs.anl.gov"
moz-do-not-send="true">parallel-netcdf@lists.mcs.anl.gov</a><span
class="Apple-converted-space"> </span><a
class="moz-txt-link-rfc2396E"
href="mailto:parallel-netcdf@lists.mcs.anl.gov"
moz-do-not-send="true"><parallel-netcdf@lists.mcs.anl.gov></a></td>
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<td class=""><font class="" size="1"
face="verdana"><b class="">External email:
Use caution opening links or attachments</b><span
class="Apple-converted-space"> </span>
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class="Apple-converted-space"> </span>
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<br class="">
<div class="">Please let me know the configure command
used.
<div class=""><br class="">
<div class="">Wei-keng<span
class="Apple-converted-space"> </span></div>
<div class="">
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cellspacing="0" cellpadding="0" border="0">
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<tr class="">
<th class="" valign="BASELINE"
nowrap="nowrap" align="RIGHT">Subject:</th>
<td class="">Re: Path oddity in PNetCDF
build/configure</td>
</tr>
<tr class="">
<th class="" valign="BASELINE"
nowrap="nowrap" align="RIGHT">Date:</th>
<td class="">Sun, 24 Oct 2021 17:06:01
+0000</td>
</tr>
<tr class="">
<th class="" valign="BASELINE"
nowrap="nowrap" align="RIGHT">From:</th>
<td class="">Wei-Keng Liao<span
class="Apple-converted-space"> </span><a
class="moz-txt-link-rfc2396E"
href="mailto:wkliao@northwestern.edu"
moz-do-not-send="true"><wkliao@northwestern.edu></a></td>
</tr>
<tr class="">
<th class="" valign="BASELINE"
nowrap="nowrap" align="RIGHT">To:</th>
<td class="">Carl Ponder<span
class="Apple-converted-space"> </span><a
class="moz-txt-link-rfc2396E"
href="mailto:cponder@nvidia.com"
moz-do-not-send="true"><cponder@nvidia.com></a></td>
</tr>
<tr class="">
<th class="" valign="BASELINE"
nowrap="nowrap" align="RIGHT">CC:</th>
<td class=""><a
class="moz-txt-link-abbreviated"
href="mailto:parallel-netcdf@lists.mcs.anl.gov"
moz-do-not-send="true">parallel-netcdf@lists.mcs.anl.gov</a><span
class="Apple-converted-space"> </span><a
class="moz-txt-link-rfc2396E"
href="mailto:parallel-netcdf@lists.mcs.anl.gov"
moz-do-not-send="true"><parallel-netcdf@lists.mcs.anl.gov></a></td>
</tr>
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<br class="">
<br class="">
<table class="" border="1" bgcolor="#FFEB9C">
<tbody class="">
<tr class="">
<td class=""><font class="" size="1"
face="verdana"><b class="">External
email: Use caution opening links or
attachments</b><span
class="Apple-converted-space"> </span>
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class="Apple-converted-space"> </span>
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class="Apple-converted-space"> </span>
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<br class="">
<div class="">Hi, Carl
<div class=""><br class="">
</div>
<div class="">Please send me the file
config.log.</div>
<div class=""><br class="">
<div class="">Wei-keng<span
class="Apple-converted-space"> </span></div>
<div class=""><br class="">
</div>
</div>
</div>
<hr class="" width="100%" size="2">
<blockquote type="cite" class="">
<div class="">On Oct 24, 2021, at 1:29 PM,
Carl Ponder <<a
href="mailto:cponder@nvidia.com" class=""
moz-do-not-send="true">cponder@nvidia.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class=""><br class="">
<div class="moz-forward-container">This is
in a Dockerfile rather than my usual
bash scripting.<br class="">
Here's the<span
class="Apple-converted-space"> </span><font
class="" face="monospace">PATH</font><span
class="Apple-converted-space"> </span>being
printed during the build<br class="">
<blockquote class=""><font class=""
face="monospace">Step 95/156 : RUN
echo ${PATH}</font><br class="">
<font class="" face="monospace"> --->
Running in 8586a4aef68a</font><br
class="">
<font class="" face="monospace">/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/bin:/usr/local/cuda/bin:/usr/local/pgi/Linux_x86_64/21.9/com</font><font
class="" face="monospace">pilers/bin</font><br
class="">
</blockquote>
And the<span
class="Apple-converted-space"> </span><font
class="" face="monospace">mpicc</font><span
class="Apple-converted-space"> </span>location
tests correctly:<br class="">
<blockquote class=""><font class=""
face="monospace">Step 95/155 : RUN
which mpicc</font><br class="">
<font class="" face="monospace"> --->
Running in e2161d554278</font><br
class="">
<b class=""><font class=""
face="monospace">/usr/local/bin/mpicc</font></b><br
class="">
</blockquote>
<hr class="" width="100%" size="2">
<table class="moz-email-headers-table"
cellspacing="0" cellpadding="0"
border="0">
<tbody class="">
<tr class="">
<th class="" valign="BASELINE"
nowrap="nowrap" align="RIGHT">Subject:<span
class="Apple-converted-space"> </span></th>
<td class="">Re: Path oddity in
PNetCDF build/configure</td>
</tr>
<tr class="">
<th class="" valign="BASELINE"
nowrap="nowrap" align="RIGHT">Date:<span
class="Apple-converted-space"> </span></th>
<td class="">Sun, 24 Oct 2021
16:32:42 +0400</td>
</tr>
<tr class="">
<th class="" valign="BASELINE"
nowrap="nowrap" align="RIGHT">From:<span
class="Apple-converted-space"> </span></th>
<td class="">Bruno Pagani<span
class="Apple-converted-space"> </span><a
class="moz-txt-link-rfc2396E"
href="mailto:bruno.pagani@astrophysics.eu" moz-do-not-send="true"><bruno.pagani@astrophysics.eu></a></td>
</tr>
<tr class="">
<th class="" valign="BASELINE"
nowrap="nowrap" align="RIGHT">To:<span
class="Apple-converted-space"> </span></th>
<td class="">Carl Ponder<span
class="Apple-converted-space"> </span><a
class="moz-txt-link-rfc2396E"
href="mailto:cponder@nvidia.com" moz-do-not-send="true"><cponder@nvidia.com></a>,
Wei-keng Liao<span
class="Apple-converted-space"> </span><a
class="moz-txt-link-rfc2396E"
href="mailto:wkliao@eecs.northwestern.edu" moz-do-not-send="true"><wkliao@eecs.northwestern.edu></a></td>
</tr>
<tr class="">
<th class="" valign="BASELINE"
nowrap="nowrap" align="RIGHT">CC:<span
class="Apple-converted-space"> </span></th>
<td class=""><a
class="moz-txt-link-abbreviated"
href="mailto:parallel-netcdf@lists.mcs.anl.gov" moz-do-not-send="true">parallel-netcdf@lists.mcs.anl.gov</a></td>
</tr>
</tbody>
</table>
<br class="">
<br class="">
<table class="" border="1"
bgcolor="#FFEB9C">
<tbody class="">
<tr class="">
<td class=""><font class=""
size="1" face="verdana"><b
class="">External email: Use
caution opening links or
attachments</b><span
class="Apple-converted-space"> </span>
<span
class="Apple-converted-space"> </span>
<span
class="Apple-converted-space">
</span><span
class="Apple-converted-space"> </span>
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class="Apple-converted-space">
</span><span
class="Apple-converted-space"> </span>
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class="Apple-converted-space">
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class="Apple-converted-space"> </span>
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class="Apple-converted-space">
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class="Apple-converted-space"> </span>
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<br class="">
<div class="">How do you set PATH? Did
you quote it? Seems somehow your path
end up being yes, likely due to
expansion of its previous value.<br
class="">
<br class="">
<br class="">
<hr class="" width="100%" size="2">
<div class="gmail_quote">Le 24 octobre
2021 16:30:03 GMT+04:00, Carl Ponder<span
class="Apple-converted-space"> </span><a
class="moz-txt-link-rfc2396E"
href="mailto:cponder@nvidia.com"
moz-do-not-send="true"><cponder@nvidia.com></a><span
class="Apple-converted-space"> </span>a
écrit :
<blockquote class="gmail_quote"
style="margin: 0pt 0pt 0pt 0.8ex;
border-left-width: 1px;
border-left-style: solid;
border-left-color: rgb(204, 204,
204); padding-left: 1ex;">
When I build PNetCDF with<span
class="Apple-converted-space"> </span><font
class="" face="monospace">MPICC=mpicc</font><span
class="Apple-converted-space"> </span>and<span
class="Apple-converted-space"> </span><font
class="" face="monospace">mpicc</font><span
class="Apple-converted-space"> </span>on
my<font class="" face="monospace"><span
class="Apple-converted-space"> </span>$PATH</font>,
I see this during the<span
class="Apple-converted-space"> </span><font
class="" face="monospace">configure</font><span
class="Apple-converted-space"> </span>phase:<font
class="" face="monospace"><br
class="">
</font>
<blockquote class=""><font
class="" face="monospace">ENV
PATH=${PATH}:/usr/local/bin<br
class="">
ENV MPICC mpicc<br class="">
...<br class="">
checking for sed handling
option -i ... /usr/bin/sed
-i''<br class="">
<b class="">checking mpicc
under yes... no</b></font><br
class="">
<font class="" face="monospace">configure:
error:<span
class="Apple-converted-space"> </span></font><br
class="">
<font class="" face="monospace">
-----------------------------------------------------------------------</font><br
class="">
<font class="" face="monospace">
Specified MPI C compiler
"mpicc" cannot be found under
yes</font><br class="">
<font class="" face="monospace">
PnetCDF requires a working MPI
C compiler. Please specify the
location</font><br class="">
<font class="" face="monospace">
of an MPI C compiler, either
in the MPICC environment
variable</font><br class="">
<font class="" face="monospace">
(not CC variable) or through
--with-mpi configure flag.
Abort.</font><br class="">
<font class="" face="monospace">
-----------------------------------------------------------------------</font><br
class="">
</blockquote>
I can work around it by making the
path absolute<br class="">
<blockquote class=""><font
class="" face="monospace">ENV
MPICC /usr/local/bin/mpicc<br
class="">
...</font><font class=""
face="monospace"><br class="">
</font><font class=""
face="monospace">checking for
sed handling option -i ...
/usr/bin/sed -i''<br class="">
<b class="">checking whether
/usr/local/bin/mpicc exists
and is executable... yes</b><br
class="">
</font></blockquote>
But, based on the first message,
I'm thinking there's an incorrect
path-search during the<span
class="Apple-converted-space"> </span><font
class="" face="monospace">configure</font><span
class="Apple-converted-space"> </span>phase.<br
class="">
This is with PNetCDF 1.12.2.<br
class="">
</blockquote>
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</blockquote>
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<br class="">
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<span id="cid:277B3596-96B4-43CC-80BD-7B0E5F30D58C"><config.log></span></div>
</blockquote>
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