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Ryo et al., <div>The seg fault happens when you try to display the 3-dimensional variable tr with the Z dimension set to something other than 1. That is a bug in the sdfopen code in GrADS 1.9. That code is no longer in version 2.0, and I am unlikely to spend any time debugging it since the problem is readily fixed if you use a 'dtype netcdf' descriptor file:</div><div><br class="webkit-block-placeholder"></div><div><div>DSET ^mom_clim46.nc</div><div>dtype netcdf</div><div>options zrev</div><div>TITLE Ocean Only Model to Case 45</div><div>UNDEF -2.56E33 missing_value</div><div>XDEF 362 LINEAR 115.0 0.5 </div><div>YDEF 142 LINEAR -35.0 0.5 </div><div>ZDEF 30 LEVELS</div><div> 5.0000 15.0000 25.0000 35.0000 45.0000 55.0000 65.0000 75.0000 85.0000 95.0000</div><div> 105.0000 115.9789 129.7985 148.0428 171.8625 201.8625 238.0428 279.7985 325.9789 375.0000</div><div> 425.0000 491.1513 604.1757 790.2066 1068.2310 1448.2310 1930.2066 2504.1757 3151.1513 3845.0000</div><div>TDEF 12 LINEAR 1JAN1998 1mo</div><div>VARS 5 </div><div>u 30 t,z,y,x U velocity</div><div>v 30 t,z,y,x V velocity</div><div>temp 30 t,z,y,x Temperature</div><div>s 30 t,z,y,x Salinity(PSU)</div><div>tr 0 t,y,x Transport(Sv)</div><div>ENDVARS </div><div><br class="webkit-block-placeholder"></div><div>With this descriptor, the variable tr displays correctly no matter what the Z dimension is set to. If you continue to have problems, please let me know. </div><div><br class="webkit-block-placeholder"></div><div>Debugging this problem also revealed a little bug in the netcdf handling code in version 2.0 for Z-reversed data, so thanks for helping me uncover that. </div><div><br></div><div>More inline below on the Z index: </div><div><br class="webkit-block-placeholder"></div><div><div>On Feb 21, 2008, at 4:50 AM, Ryo Furue wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi Jennifer,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| You will have to provide all the ncdump -c</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| output from your file -- maybe this will help me to reproduce the</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| error.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I've created a more complete "kit" to reproduce the error:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span><a href="http://iprc.soest.hawaii.edu/~furue/tmp/grads-segfault.tar.gz">http://iprc.soest.hawaii.edu/~furue/tmp/grads-segfault.tar.gz</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Download this archive, expand it, descend into the directory,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">and run the GrADS script "segfault.gs" contained in it.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">The archive is about 370MB.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| As for the positive:down attribute, GrADS was designed with the</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| atmosphere in mind, so z=1 is the bottom (close to the surface) and</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| z=zmax is at the top.<span class="Apple-converted-space"> </span>When your z axis is depth, this orientation</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| is maintained, so that the bottom (deepest) level is z=1 and the top</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| (shallowest) layer is z=30. That is somewhat opposite to the way</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| oceanographers think of the Z (depth) axis, where z=1 is usually at</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| or just below the surface.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Does that mean "z" is NOT an index into the underlying array?</div></blockquote>No it does not mean that. Z is the grid index for the vertical dimension in GrADS. <br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">After opening my netCDF file (such as the ones contained</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">in the kit above), this command</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>ga-> set lev 5</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>ga-> d temp</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><span class="Apple-style-span" style="-webkit-text-stroke-width: -1; ">correctly plots sea surface temperature, and</span></div></blockquote><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><span class="Apple-style-span" style="-webkit-text-stroke-width: -1; "> ga-> set lev 3845</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>ga-> d temp</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><span class="Apple-style-span" style="-webkit-text-stroke-width: -1; ">correctly plots bottom temperature.</span></div></blockquote>these commands work because you're using world coordinates (set lev) and not grid indices (set z). </div><div><br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><span class="Apple-style-span" style="-webkit-text-stroke-width: -1; ">So, unless GrADS bothers to transpose the temperature array</span></div></blockquote>GrADS bothers to do this when you have 'options zrev' in your descriptor file or 'positive down' as a netcdf attribute.</div><div><br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">on memory, index 1 of the array's 3rd dimension must be</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">correctly pointing to lev=5, and index 30 must be pointing</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">to lev=3845, because that's how my array is stored in</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">my netCDF file.<span class="Apple-converted-space"> </span>Therefore, "z" is not an index. . . .</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Is there a variable which is a true index into the</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">underlying array? such as i, j, and k?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Ryo</div> </blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div>--</div><div>Jennifer M. Adams</div><div>IGES/COLA</div><div>4041 Powder Mill Road, Suite 302</div><div>Calverton, MD 20705</div><div><a href="mailto:jma@cola.iges.org">jma@cola.iges.org</a></div><div><br class="khtml-block-placeholder"></div><br class="Apple-interchange-newline"></span></span></span> </div><br></div></body></html>