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Happy Thanksgiving! :-)
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<div>On Nov 26, 2014, at 3:53 PM, Berk Geveci <<a href="mailto:berk.geveci@kitware.com">berk.geveci@kitware.com</a>> wrote:</div>
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<div dir="ltr">Thanks Rich. The molecule data gets into the range that requires parallel visualization extremely rarely. However, this may affect others, such as those loading large vtu files. We'll make sure that this is fixed very soon.
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<div>-berk</div>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Nov 25, 2014 at 5:15 PM, Cook, Rich <span dir="ltr">
<<a href="mailto:cook47@llnl.gov" target="_blank">cook47@llnl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">I do not have an urgent need to view this data. However, be advised that I got it from what appears to be the PDB canonical source, so I assumed our molecular people would appreciate being able to visualize their stuff. This
kind of model doesn’t usually get that big, though, probably.
<div><br>
<div><a href="http://www.rcsb.org/pdb/explore.do?structureId=1lmb" target="_blank">http://www.rcsb.org/pdb/explore.do?structureId=1lmb</a></div>
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<div>Thank you kindly. No workaround is needed. <br>
<div>— Rich </div>
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<div><span class="">
<div>On Nov 25, 2014, at 12:55 PM, Berk Geveci <<a href="mailto:berk.geveci@kitware.com" target="_blank">berk.geveci@kitware.com</a>> wrote:</div>
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<div dir="ltr">Marcus will investigate the errors.
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<div>They are not related to why the dataset is no longer distributed. There was code in 4.1 that automatically redistributed data from serial readers using a very naive approach. That code is no longer there. We are investigating various options of improving
on the 4.1 functionality. I would normally say that you can use the D3 filter to distribute the data but I was cautious and tried it first. It crashes :-( This dataset has string arrays in it, which it seems D3 does not handle.</div>
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<div>Do you have a particular use case driving parallel PDB capability? If you do, I can find some workarounds of these issues. If not, D3 should nicely work on most polydata and unstructured grid sources. We are working on better ways of redistributing the
other data types.</div>
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<div>Best,</div>
<div>-berk</div>
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<div class="gmail_extra"><br>
<div class="gmail_quote"><span class="">On Tue, Nov 25, 2014 at 9:44 AM, Marcus D. Hanwell
<span dir="ltr"><<a href="mailto:marcus.hanwell@kitware.com" target="_blank">marcus.hanwell@kitware.com</a>></span> wrote:<br>
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<div>Hi,<br>
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</div>
I think I know the cause, the PDB reader was modified to produce a vtkMolecule in addition to the vtkPolyData I think it has always produced. It looks like there is a packaging issue, and the XML file cannot be found. We should probably just statically compile
the file in, or convert it to a header as the data is pretty static - atomic radii, colors, etc.<span><font color="#888888"><br>
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</font></span></div>
<span><font color="#888888">Marcus</font></span> </span>
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<div class="gmail_quote"><span class="">On Tue, Nov 25, 2014 at 9:06 AM, Berk Geveci
<span dir="ltr"><<a href="mailto:berk.geveci@kitware.com" target="_blank">berk.geveci@kitware.com</a>></span> wrote:<br>
</span>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<span class="">
<div dir="ltr">Hey Rich,
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<div>Can you send me the dataset?</div>
<div><br>
</div>
<div>Best,</div>
<div>-berk</div>
</div>
</span>
<div class="gmail_extra"><br>
<div class="gmail_quote"><span class="">
<div>On Mon, Nov 24, 2014 at 7:25 PM, Cook, Rich <span dir="ltr"><<a href="mailto:cook47@llnl.gov" target="_blank">cook47@llnl.gov</a>></span> wrote:<br>
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<div style="word-wrap:break-word"><span class="">Hi,
<div>I have recently compiled paraview 4.2.0 on our clusters in the same way I compile with 4.1.0 and am getting some errors. </div>
<div>I run pvserver in parallel, and it does not give any weird outputs. </div>
<div>I connect with it from my desktop (Mac OS X). I can see in the desktop GUI that four remote servers are connected. </div>
<div>I open up a PDB dataset and it is different. I see two “Output” objects in the pipeline browser. This is different than the behavior in 4.1.0. </div>
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<div><span><Voila_Capture 2014-11-24_04-23-27_PM.png></span></div>
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<div>I click Apply and get smacked in the face with an error dialog. </div>
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<div style="margin:0px"><span style="font-family:'Courier';font-size:13pt;color:#800000">ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release-Python27/paraview/src/paraview/VTK/Domains/Chemistry/vtkBlueObeliskDataParser.cxx,
line 68</span></div>
<div style="margin:0px"><span style="font-family:'Courier';font-size:13pt;color:#800000">vtkBlueObeliskDataParser (0x7fea5e2a9980): Cannot find elements.xml. Checked /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release-Python27/paraview/src/paraview-build/CMakeFiles/__macos_install/share/paraview-4.2/vtkDomainsChemistry
and /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release-Python27/paraview/src/paraview/VTK/Domains/Chemistry</span></div>
<div style="margin:0px;font-family:Courier;font-size:13pt;color:rgb(128,0,0)"><br>
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<div style="margin:0px;font-family:Courier;font-size:13pt;color:rgb(128,0,0)"><br>
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<div style="margin:0px"><span style="font-family:'Courier';font-size:13pt;color:#800000">ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release-Python27/paraview/src/paraview/VTK/IO/XMLParser/vtkXMLParser.cxx, line 382</span></div>
<div style="margin:0px"><span style="font-family:'Courier';font-size:13pt;color:#800000">vtkBlueObeliskDataParser (0x7fea5e2a9980): Parse() called with no Stream set.</span></div>
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<div style="margin:0px;font-family:Courier;font-size:13pt;color:rgb(128,0,0)"><br>
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<div style="margin:0px"><span style="font-family:'Courier';font-size:13pt;color:#800000">ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release-Python27/paraview/src/paraview/VTK/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx,
line 710</span></div>
<div style="margin:0px"><span style="font-family:'Courier';font-size:13pt;color:#800000">vtkPVDataRepresentationPipeline (0x7fea5e2a4d80): Input port 0 of algorithm vtkMoleculeRepresentation(0x7fea56c005d0) has 0 connections but is not optional.</span></div>
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<div style="margin:0px;font-family:Courier;font-size:13pt;color:rgb(128,0,0)"><span style="font-family:Monaco;font-size:18px">I’m unable to color by process scalar ID, or more precisely, the Filter seems to get applied but the color does not change. Appears
all work is done on process 0. </span></div>
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<div style="margin:0px;font-family:Courier;font-size:13pt;color:rgb(128,0,0)"><span style="font-family:Monaco;font-size:18px">Something is vewwwy scwewwy. </span></div>
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<div style="margin:0px;font-family:Courier;font-size:13pt;color:rgb(128,0,0)"><span style="font-family:Monaco;font-size:18px">Help? </span></div>
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<div><span style="border-collapse:separate;font-size:13px;border-spacing:0px"><span style="border-collapse:separate;font-family:Monaco;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="border-collapse:separate;font-family:Monaco;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="border-collapse:separate;font-family:Monaco;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="border-collapse:separate;font-family:Monaco;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="border-collapse:separate;font-family:Monaco;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="border-collapse:separate;font-family:Monaco;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="border-collapse:separate;font-family:Monaco;font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<div>-- </div>
<div>✐Richard Cook </div>
<div>✇ Lawrence Livermore National Laboratory</div>
<div>Bldg-453 Rm-4024, Mail Stop L-557 </div>
<div>7000 East Avenue, Livermore, CA, 94550, USA</div>
<div>☎ (office) <a href="tel:%28925%29%20423-9605" value="+19254239605" target="_blank">
(925) 423-9605</a> </div>
<div>☎ (fax) <a href="tel:%28925%29%20423-6961" value="+19254236961" target="_blank">(925) 423-6961</a></div>
<div>---</div>
<div>Information Management & Graphics Grp., Services & Development Div., Integrated Computing & Communications Dept.</div>
<div>(opinions expressed herein are mine and not those of LLNL)</div>
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</span></span></span></span></span></span></span><br>
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<div><span style="border-collapse:separate;font-size:13px;border-spacing:0px"><span style="border-collapse: separate; font-family: Monaco; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><span style="border-collapse: separate; font-family: Monaco; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><span style="border-collapse: separate; font-family: Monaco; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><span style="border-collapse: separate; font-family: Monaco; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><span style="border-collapse: separate; font-family: Monaco; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><span style="border-collapse: separate; font-family: Monaco; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><span style="border-collapse: separate; font-family: Monaco; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;">
<div>-- </div>
<div>✐Richard Cook </div>
<div>✇ Lawrence Livermore National Laboratory</div>
<div>Bldg-453 Rm-4024, Mail Stop L-557 </div>
<div>7000 East Avenue, Livermore, CA, 94550, USA</div>
<div>☎ (office) <a href="tel:%28925%29%20423-9605" value="+19254239605" target="_blank">
(925) 423-9605</a> </div>
<div>☎ (fax) <a href="tel:%28925%29%20423-6961" value="+19254236961" target="_blank">(925) 423-6961</a></div>
<div>---</div>
<div>Information Management & Graphics Grp., Services & Development Div., Integrated Computing & Communications Dept.</div>
<div>(opinions expressed herein are mine and not those of LLNL)</div>
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</span></span></span></span></span></span></span><br>
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<div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Monaco; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Monaco; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Monaco; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Monaco; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Monaco; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Monaco; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Monaco; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Monaco; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; ">
<div>-- </div>
<div>✐Richard Cook </div>
<div>✇ Lawrence Livermore National Laboratory</div>
<div>Bldg-453 Rm-4024, Mail Stop L-557 </div>
<div>7000 East Avenue, Livermore, CA, 94550, USA</div>
<div>☎ (office) (925) 423-9605 </div>
<div>☎ (fax) (925) 423-6961</div>
<div>---</div>
<div>Information Management & Graphics Grp., Services & Development Div., Integrated Computing & Communications Dept.</div>
<div>(opinions expressed herein are mine and not those of LLNL)</div>
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