<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">I wonder if this could be related to this (fixed) bug:<div class=""><br class=""></div><div class=""><a href="https://bugtracking.unidata.ucar.edu/browse/NCF-234" class="">https://bugtracking.unidata.ucar.edu/browse/NCF-234</a></div><div class=""><br class=""></div><div class="">As with that one, it's possible that the problem is actually in netCDF and not in pnetcdf. Does anyone have an idea for how to determine if this is a pnetcdf problem or a netcdf problem? Or should I go ahead and post this to the netcdf bug list as well?</div><div class=""><br class=""></div><div class="">Charlie: I'm feeling more and more that NCO is probably off the hook here: sorry for dragging you into this initially :-)</div><div class=""><br class=""></div><div class="">Bill</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 27, 2015, at 9:21 AM, Bill Sacks <<a href="mailto:wsacks@gmail.com" class="">wsacks@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=us-ascii" class=""><meta http-equiv="Content-Type" content="text/html charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi,<div class=""><br class=""></div><div class="">I have run into what appears to be a bug in pnetcdf: I have a file written by pnetcdf (via CESM). When I try to append a variable onto it using ncks -A, the new variable gets written properly, but a different variable on the file gets garbage values put into it. If the original file is written with standard netcdf rather than pnetcdf, the problem does not occur.</div><div class=""><br class=""></div><div class="">I am attaching a tar file that contains files needed to see the problem. It contains two restart files written by CESM (file names beginning check_ncks...): one written with pnetcdf and one with standard netcdf (the latter has "netcdf" in its name). It also contains a third file from which I was trying to copy variables onto this file.</div><div class=""><br class=""></div><div class="">To reproduce:</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 12px; font-family: Monaco;" class="">cp check_ncks_problem_noInterp_1027.clm2.r.0001-01-01-01800.nc test.nc</div></div><div style="margin: 0px; font-size: 12px; font-family: Monaco;" class=""><div style="margin: 0px;" class="">ncks -A -v COL_Z_p,LEVGRND_CLASS_p finidat_interp_dest.nc test.nc </div></div><div style="margin: 0px;" class=""><div style="font-family: Monaco; font-size: 12px; margin: 0px;" class="">ncdump -v plant_nalloc check_ncks_problem_noInterp_1027.clm2.r.0001-01-01-01800.nc > dump1</div><div style="margin: 0px;" class=""><div style="font-family: Monaco; font-size: 12px; margin: 0px;" class="">ncdump -v plant_nalloc test.nc > dump2</div><div style="margin: 0px;" class=""><div style="font-family: Monaco; font-size: 12px; margin: 0px;" class="">diff dump1 dump2 | less</div><div style="font-family: Monaco; font-size: 12px; margin: 0px;" class=""><br class=""></div><div style="margin: 0px;" class="">Notice that many points that were FillValue have been replaced by garbage. </div><div style="margin: 0px;" class=""><br class=""></div><div style="margin: 0px;" class="">If you do the same thing, but using check_ncks_problem_noInterp_netcdf_1027.clm2.r.0001-01-01-01800.nc, then the dumps are identical.</div><div style="margin: 0px;" class=""><br class=""></div><div style="margin: 0px;" class="">I originally filed a bug report with NCO <<a href="https://sourceforge.net/p/nco/bugs/84/" class="">https://sourceforge.net/p/nco/bugs/84/</a>>, but Charlie Zender and Jim Edwards both feel that this is most likely a problem in the writing of the original file, which points to a possible pnetcdf problem.</div><div style="margin: 0px;" class=""><br class=""></div><div style="margin: 0px;" class="">CESM was built with</div><div style="margin: 0px;" class=""><br class=""></div><div style="margin: 0px;" class=""> module load netcdf-mpi/4.3.3.1<br class=""> module load pnetcdf/1.6.0<br class=""><br class=""></div><div style="margin: 0px;" class="">(on NCAR's yellowstone machine).</div><div style="margin: 0px;" class=""><br class=""></div><div style="margin: 0px;" class="">Thank you,</div><div style="margin: 0px;" class="">Bill</div><div style="margin: 0px;" class=""><br class=""></div></div></div></div><div apple-content-edited="true" class="">
<div class="">--</div><div class="">Bill Sacks</div><div class="">CESM Software Engineering Group</div><div class="">National Center for Atmospheric Research</div><div class="">(303) 497-1762</div><div class=""><br class=""></div><object type="application/x-apple-msg-attachment" data="cid:B18C15E3-3958-49B9-8104-565EC7BC1DFD@cgd.ucar.edu" apple-inline="no" id="C280E65C-7A80-46EC-85C6-C42ACA8B4D02" height="86" width="128" apple-width="yes" apple-height="yes" class=""></object>
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