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[SCIRUN-USERS] Re: Announcing SCIRun 4.7 with BioMesh3D

Chronological Thread 
  • From: Ayla Khan <>
  • To: Petar Petrov <>
  • Cc: " List" <>
  • Subject: [SCIRUN-USERS] Re: Announcing SCIRun 4.7 with BioMesh3D
  • Date: Fri, 15 Nov 2013 17:23:09 -0700

Hi Peter,

Rendering over a forwarded X11 connection is tricky at the best of times - this link has a good overview of the problem.  Basically, some of our OpenGL rendering code depends on OpenGL code that won't necessarily work with indirect rendering. Sometimes, the client machine will support it, but there are no guarantees.


On Nov 15, 2013, at 6:30 AM, Petar Petrov wrote:

Hi Ayla,
good to hear. I've already deployed 4.7 on debian with mesaGL.
Since, I'm back using SCIRun, this time for my PhD. Expect more bug
reports soon :)

Already, I have some issues. Not sure if directly SCIRun related.
I'm using a server rag with 16CPUs , handy for BioMesh3D, but has an
arcane video card, ala ATI Rage !!!
What we try is to remotely ssh to the machine and have the X session
on a local linux PC , hopefully utilizing the rendering capabilities
of the local GPU.
The thing is, it works fine when ssh from yet another remote machine
(CentOS) to it, but not in the case of local Debian machine with ssh -
The result is quite unexpected, at least to me, scirun runs, I load a
net, I run it, no error in ReadField module, but when I open the 3D
Window, all I see is the origin and no data (field or any other mesh I
tried) simply doesn't show :(

I will appreciate if anyone has a slight idea what might cause such
behavior and all thogether give me some tips of what's best in my

Cheers and greets to the community,

On Thu, Nov 14, 2013 at 8:27 PM, Ayla Khan <> wrote:
Dear SCIRun users,

We are pleased to announce the release of SCIRun 4.7 with meshing tools.
SCIRun 4.7 is available as a binary download for Windows and OS X, and as a
source download for Linux.

The new binaries and source tar archives can be downloaded from:

Click on the Download button and then select the distribution for your

Release notes are available from:

SCIRun 4.7 is primarily a bug-fix release with one new module,
BuildTDCSMatrix, added to the SCIRun package.
SCIRun 4.7 also contains the new ECGToolkit, which is a collection of
software tools and example SCIRun networks for solving forward and inverse
problems in electrocardiography. Special documentation is available to
describe these tools and their use. The tools feature BEM and FEM solvers
for most of the important cases of activation-based and potential-based
source models and a number of inverse solution methods. Some of the code is
written in Matlab and connects with SCIRun through our interface module, and
some functionality depends on ECGSim, a free package distributed separately,
and which is available from

SCIRun 4.7 and BioMesh3D  ON OSX:

For OS X, there is a binary distribution for intel-based Macs. The binary
download provides both the SCIRun application as well as the BioMesh3D
application, which is a drag and drop application for building meshes.
Documentation on running the OS X application is provided inside the SCIRun
4.7 disk image.

SCIRun 4.7 and BioMesh3D ON WINDOWS:

For Windows there are binaries available as well. Currently BioMesh3D is
installed together with SCIRun in the SCIRun 4.7 directory. Currently Python
(either version 2 or 3) needs to be installed separately on Windows in order
to run BioMesh3D, and BioMesh3D needs to be run from the command prompt.
More details can be found in the BioMesh3D documentation.

SCIRun 4.7 and BioMesh3D ON LINUX:

Please download the SCIRun 4.7 source tar archive. After unpacking the
application, run the build script called, which should build both
SCIRun 4.7 and BioMesh3D. On Linux, BioMesh3D is a series of python scripts
that run various SCIRun applications to build a tetrahedral mesh.
Documentation is provided inside the tar archive which explains how to build
meshes with BioMesh3D.

As we want to keep improving our software, suggestions and bug reports are
always welcome.  Please contact us at with general
SCIRun questions or with any specific problems
you encounter.

All the best,
Petar Petrov

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