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Re: [SCIRUN-USERS] Error Messages and Help

Chronological Thread 
  • From: Moritz Dannhauer <>
  • To: Palig Mouradian <>
  • Cc: Dan White <>, Petar Petrov <>,, mathew yarossi <>
  • Subject: Re: [SCIRUN-USERS] Error Messages and Help
  • Date: Wed, 10 Jan 2018 13:32:22 -0500

Hi Palig, your build log indicates that the external libs for SCIRun are not built, and that the problem is related to lzma.h (where the error occurred).

You could try to install lzma using macport or homebrew:
1) port install lzma liblzma
2)  brew install xz

Those header files are usually in *dev packages, so if it does not work installing those packages look for a *lzma*lib*dev* package in either macport or homebrew.

And make sure your PATH includes the directory:
locate lzma.h
I hope that is the only library (lzma) that is missing, if not, you may be able to track it down any additional libs with the same approach.
Good luck!

On Jan 10, 2018, at 12:26 PM, Palig Mouradian wrote:

Hi Dan,

I have attached the entire build log that results from running 'make' in the /bin folder.

I will work on the bug fixes, thank you!!

Thanks again for all the help,


On Tue, Jan 9, 2018 at 2:15 PM, Dan White <> wrote:

I second these tips. For the build log, I meant the complete version of what you showed in the terminal screenshot--most of it was cut off (not the CMake output you sent). For ViewScene not showing a working ShowField output, that is a known bug, which has the workaround below. If ShowField itself is producing an error (turning red), then it's a problem upstream, perhaps the output of GetFieldBoundary is null.


On 1/9/2018 1:45 AM, Petar Petrov wrote:
Hi guys,

my quick tips:

1) on a first build, try without multithreading : make only not make -j2 ( it happens that superbuild externals not get build corrrectly )
2) I do experience something similar, no error printed but also my geom is not visible in the scene view rendered objects :( destroying and recreating ShowFields works, till next time you open the project :(

On Mon, Jan 8, 2018 at 11:54 PM, Palig Mouradian <> wrote:
Hi Dan,

Thank you for your quick response!

I have attached the build logs for #1. --Was there a different one I may have missed?

2. The first time the error appeared was with Show Filed module. Since then, I am not getting an error message but also no output.

Thank you so much.


On Jan 8, 2018, at 5:05 PM, Dan White <> wrote:

More detail is needed for both problems:
1. Can you send your entire build log? Most likely an external is not building, since the SCIRun-proper part of the build is not even starting.
2. Which module is producing the error? That will narrow down the problem to input, processing, or visualization.

On Mon, Jan 8, 2018 at 2:01 PM, Palig Mouradian <> wrote:
Hi SCIRun HelpDesk,

I am a grad student at Northeastern working on a project with Moritz Danhauer, Dana Brooks as well as Mathew Yarossi (all cc-ed here). They suggested that I redirect my questions to the helpdesk.

I have 2 error messages that I am trying to work through.

1. The first is occurring on our desktop Mac Computer in the lab.
I downloaded the command line tools, homebrew, macports and qt4 as well as the source file for SCIRun 5.
I also then ran cmake ../Superbuild in the bin path followed by make -j2
I keep getting this error message at 94% completion
Once I got it, I peeked inside the MakeFile and I tried to run the following manually but still got error messages, even after changing the permissions of the files inside the SCIRun external path.
 Build rule for target.
SCIRun_external: cmake_check_build_system
$(MAKE) -f CMakeFiles/Makefile2 SCIRun_external


<Screen Shot 2018-01-08 at 3.43.22 PM.png>

2. The second is occurring on my personal laptop. I reconstructed a network from Moritz on SCIRUN 5 (pictured below).

<Screen Shot 2018-01-08 at 3.57.23 PM.png>

The input to this network is a model out of seg3d  in .nrrd format [data on elements]
Updated the clip field by function module to Data1 !=0; and element and clipping at element center.

In the Show Field module -- data on edges was unchecked  and unde the faces tab, invert normals was selected.

At times I was getting an error that read "Input Data Req. on Port Field" and even when i am not, I am unable to visualize anything with View Scene.

I followed the exact steps as Moritz but I don't know what could be going wrong.

Thank you for any guidance.


Palig Mouradian

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All the best,
Petar Petrov

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