NAMIC Wiki - User contributions [en]

SCRun on SPL Machines

2009-04-06T03:53:52Z

Mjolley: /* Building SCIRun on an SPL Machine */

== Building SCIRun on an SPL Machine ==

----

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines.

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk/SCIRun

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation cd to SCIRun/bin directory:

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''unsetenv LD_LIBRARY_PATH'''

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory.

You may run into this problem repeatedly and should check prior to running SCIRun. To check it, as per discussion above, you can do the following:

For example SCIRun gets pointed at the correct drivers as shown here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)'''

In contrast SCIRun gets pointed to the wrong, non-hardware accelleration drivers here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003f84800000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)'''

Usually if the above script has been run you can get back to the correct drivers by:

'''unsetenv LD_LIBRARY_PATH'''

and then rechecking whether the correct drivers are being utilized. It is a good idea to check this before starting SCIRun.

Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

NA-MIC Childrens Collaboration

2008-12-11T04:22:12Z

Mjolley:

Back to [[NA-MIC_External_Collaborations]]

{|
|[[Image:smallkidcxr.png| 200px]] [[Image:27y-leftabdcan-T6SQ-voltage-withheart4.png | 200px]]
|-
|[[Image:27y-leftabdcan-T6SQ-current4.png| 200px]] [[Image:27y-leftabdcan-T6SQ-heart-cut3.png| 200px]]
|}

= Introduction =

Placement of Implantable Cardiac Defibrillators(ICDs)is a unique and challenging problem for children due to the variety of shapes and sizes, ranging from neonate to adolescent. As a result, a variety of novel implant techniques have been employed. Although these have generally been successful inasmuch as they result in a clinically acceptable defibrillation threshold, nothing is known about the mechanisms by which this threshold is attained, the optimal geometries for defibrillation, and whether unsafe electric field strengths are a result of novel implant approaches. Finite element modeling has been shown in adult torso models to correlate well with clinical results. Our goal is to model defibrillation in child torso models to gain insight into this important problem. We are also interested in developing new orientations in adults with the goal of lowering DFTs and providing options in patients with contraindications to standard techniques.

= Participants =
===Stanford===
Matthew Jolley, Anne Dubin, Paul Wang
===Children's Hospital Boston===
John Triedman, Frank Cecchin
===Scientific Computing Institute, Utah===
Jeroen Stinstra, Rob Macleod
===SPL===
Steve Pieper, Kilian Pohl
===NorthEastern University===
Dana Brooks

= Goals of Project =

==Segmentation==

Segmentation is currently done using tools within the open source tools 3D Slicer and Seg3D. We are actively working with members of SCI and SPL on developing automated segmentation techniques for torso and cardiac modeling. In the future we would like to integrate DT-MRI fiber structure into our cardiac models.

==Modeling==

We have worked with members of the SCI Institute in Utah to develop a modeling framework within their SCIRun package which allows rapid placement of realistic electrodes within finite element models of adult and child torsos. All tools to do so are available open source to download from the SCI website. We continue to improve this platform, integrating new technology and insight as we progress.

==Understanding Defibrillation==
Ultimately this project is part of a larger goal of understanding defibrillation as a therapy. Members of the group are also working with members of John Hopkins to further this goal.

= Building and Running SCIRun on SPL Machines =
[[SCRun on SPL Machines]]

=== Citations ===

1. Jolley M, Stinstra J, Weinstein D, et al. Open-Source Environment for Interactive Finite Element Modeling of Optimal ICD Electrode Placement Functional Imaging and Modeling of the Heart, Lecture Notes in Computer Science. Berlin/Heidelberg: Springer, 2007:373-382.

2. Jolley M, Stinstra J, Weinsten D, et al. Finite Element Modeling of Novel Defibrillation Approaches in Children and Adult Heart Rhythm Society. Denver, Colorado, 2007.

3. Jolley M, Triedman J, Westin CF, et al. Image based modeling of defibrillation in children. Conf Proc IEEE Eng Med Biol Soc 2006;1:2564-7.

4. Stinstra JG, Jolley M, Callahan M, et al. Evaluation of different meshing algorithms in the computation of defibrillator thresholds in children. Conf Proc IEEE Eng Med Biol Soc 2007;1:1422-5.

5. Matthew Jolley, Jeroen Stinstra, Steve Pieper, Rob MacLeod, Dana H. Brooks, Frank Cecchin, John K. Triedman A Computer Modeling Tool for Comparing Novel ICD Electrode Orientations in Children and Adults. Heart Rhythm. 2008 Apr;5(4):565-572.

SCRun on SPL Machines

2008-01-28T19:31:47Z

Mjolley: /* Building SCIRun on an SPL Machine */

== Building SCIRun on an SPL Machine ==

----

[[Problems and Solutions on SPL Machine Blog]]

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines.

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk/SCIRun

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation cd to SCIRun/bin directory:

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''unsetenv LD_LIBRARY_PATH'''

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory.

You may run into this problem repeatedly and should check prior to running SCIRun. To check it, as per discussion above, you can do the following:

For example SCIRun gets pointed at the correct drivers as shown here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)'''

In contrast SCIRun gets pointed to the wrong, non-hardware accelleration drivers here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003f84800000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)'''

Usually if the above script has been run you can get back to the correct drivers by:

'''unsetenv LD_LIBRARY_PATH'''

and then rechecking whether the correct drivers are being utilized. It is a good idea to check this before starting SCIRun.

Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

SCRun on SPL Machines

2008-01-28T19:30:31Z

Mjolley: /* Building SCIRun on an SPL Machine */

== Building SCIRun on an SPL Machine ==

----

[[Problems and Solutions on SPL Machine Blog]]

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines.

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk/SCIRun

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation:

'''cd to SCIRun/bin:'''

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''unsetenv LD_LIBRARY_PATH'''

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory.

You may run into this problem repeatedly and should check prior to running SCIRun. To check it, as per discussion above, you can do the following:

For example SCIRun gets pointed at the correct drivers as shown here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)'''

In contrast SCIRun gets pointed to the wrong, non-hardware accelleration drivers here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003f84800000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)'''

Usually if the above script has been run you can get back to the correct drivers by:

'''unsetenv LD_LIBRARY_PATH'''

and then rechecking whether the correct drivers are being utilized. It is a good idea to check this before starting SCIRun.

Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

SCRun on SPL Machines

2008-01-28T19:29:05Z

Mjolley: /* Building SCIRun on an SPL Machine */

== Building SCIRun on an SPL Machine ==

----

[[Problems and Solutions on SPL Machine Blog]]

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines.

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk/SCIRun

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation cd to SCIRun/bin:

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''unsetenv LD_LIBRARY_PATH'''

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory.

You may run into this problem repeatedly and should check prior to running SCIRun. To check it, as per discussion above, you can do the following:

For example SCIRun gets pointed at the correct drivers as shown here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)'''

In contrast SCIRun gets pointed to the wrong, non-hardware accelleration drivers here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003f84800000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)'''

Usually if the above script has been run you can get back to the correct drivers by:

'''unsetenv LD_LIBRARY_PATH'''

and then rechecking whether the correct drivers are being utilized. It is a good idea to check this before starting SCIRun.

Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

SCRun on SPL Machines

2008-01-28T19:26:35Z

Mjolley: /* Building SCIRun on an SPL Machine */

== Building SCIRun on an SPL Machine ==

----

[[Problems and Solutions on SPL Machine Blog]]

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines.

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk/SCIRun

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''unsetenv LD_LIBRARY_PATH'''

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory.

You may run into this problem repeatedly and should check prior to running SCIRun. To check it, as per discussion above, you can do the following:

For example SCIRun gets pointed at the correct drivers as shown here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)'''

In contrast SCIRun gets pointed to the wrong, non-hardware accelleration drivers here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003f84800000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)'''

Usually if the above script has been run you can get back to the correct drivers by:

'''unsetenv LD_LIBRARY_PATH'''

and then rechecking whether the correct drivers are being utilized. It is a good idea to check this before starting SCIRun.

Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

SCRun on SPL Machines

2008-01-28T19:21:40Z

Mjolley: /* Building SCIRun on an SPL Machine */

== Building SCIRun on an SPL Machine ==

----

[[Problems and Solutions on SPL Machine Blog]]

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines.

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''unsetenv LD_LIBRARY_PATH'''

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory.

You may run into this problem repeatedly and should check prior to running SCIRun. To check it, as per discussion above, you can do the following:

For example SCIRun gets pointed at the correct drivers as shown here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)'''

In contrast SCIRun gets pointed to the wrong, non-hardware accelleration drivers here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003f84800000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)'''

Usually if the above script has been run you can get back to the correct drivers by:

'''unsetenv LD_LIBRARY_PATH'''

and then rechecking whether the correct drivers are being utilized. It is a good idea to check this before starting SCIRun.

Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

SCRun on SPL Machines

2008-01-28T19:20:29Z

Mjolley: /* Building SCIRun on an SPL Machine */

== Building SCIRun on an SPL Machine ==

----

[[Problems and Solutions on SPL Machine Blog]]

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines.

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''unsetenv LD_LIBRARY_PATH'''

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory.

You may run into this problem repeatedly and should check prior to running SCIRun. To check it, as per discussion above, you can do the following:

For example SCIRun gets pointed at the correct drivers as shown here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)'''

In contrast SCIRun gets pointed to the correct drivers here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003f84800000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)'''

Usually if the above script has been run you can get back to the correct drivers by:

'''unsetenv LD_LIBRARY_PATH'''

and then rechecking whether the correct drivers are being utilized. It is a good idea to check this before starting SCIRun.

Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

SCRun on SPL Machines

2008-01-28T19:20:09Z

Mjolley: /* Building SCIRun on an SPL Machine */

== Building SCIRun on an SPL Machine ==

----

[[Problems and Solutions on SPL Machine Blog:Current Threadsafety Issue]]

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines.

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''unsetenv LD_LIBRARY_PATH'''

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory.

You may run into this problem repeatedly and should check prior to running SCIRun. To check it, as per discussion above, you can do the following:

For example SCIRun gets pointed at the correct drivers as shown here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)'''

In contrast SCIRun gets pointed to the correct drivers here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003f84800000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)'''

Usually if the above script has been run you can get back to the correct drivers by:

'''unsetenv LD_LIBRARY_PATH'''

and then rechecking whether the correct drivers are being utilized. It is a good idea to check this before starting SCIRun.

Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

SCRun on SPL Machines

2008-01-28T19:19:46Z

Mjolley: /* Building SCIRun on an SPL Machine */

== Building SCIRun on an SPL Machine ==

----

[[Problems and Solutions on SPL Machine Blog]]

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines.

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''unsetenv LD_LIBRARY_PATH'''

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory.

You may run into this problem repeatedly and should check prior to running SCIRun. To check it, as per discussion above, you can do the following:

For example SCIRun gets pointed at the correct drivers as shown here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)'''

In contrast SCIRun gets pointed to the correct drivers here:

'''spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003f84800000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)'''

Usually if the above script has been run you can get back to the correct drivers by:

'''unsetenv LD_LIBRARY_PATH'''

and then rechecking whether the correct drivers are being utilized. It is a good idea to check this before starting SCIRun.

Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

Problems and Solutions on SPL Machine Blog

2008-01-28T19:14:08Z

Mjolley: /* Current Problems on Debugging for SCIRun on SPL Machines */

== Current Problems on Debugging for SCIRun on SPL Machines ==

----

Jan 08: There are currently no SPL specific problems with SCIRun on SPL machines. There is a more general bug in SCIRun related to questionably threadsafe code, specifically DLOpen calls which are primarily in the dynamic compilation portion of SCIRun. These show up often on the fat nodes. Jeroen is working to eliminate dynamic compilation, and eliminate these bugs which manifest more frequently and randomly with large networks and multicore machines which "stress" the thread safety of code. If you are using SCIRun and running into these bugs please let him know.

NA-MIC Childrens Collaboration

2008-01-23T09:21:11Z

Mjolley: /* Citations */

Back to [[NA-MIC_External_Collaborations]]

{|
|[[Image:smallkidcxr.png| 200px]] [[Image:27y-leftabdcan-T6SQ-voltage-withheart4.png | 200px]]
|-
|[[Image:27y-leftabdcan-T6SQ-current4.png| 200px]] [[Image:27y-leftabdcan-T6SQ-heart-cut3.png| 200px]]
|}

=== Introduction ===

Placement of Implantable Cardiac Defibrillators(ICDs)is a unique and challenging problem for children due to the variety of shapes and sizes, ranging from neonate to adolescent. As a result, a variety of novel implant techniques have been employed. Although these have generally been successful inasmuch as they result in a clinically acceptable defibrillation threshold, nothing is known about the mechanisms by which this threshold is attained, the optimal geometries for defibrillation, and whether unsafe electric field strengths are a result of novel implant approaches. Finite element modeling has been shown in adult torso models to correlate well with clinical results. Our goal is to model defibrillation in child torso models to gain insight into this important problem. We are also interested in developing new orientations in adults with the goal of lowering DFTs and providing options in patients with contraindications to standard techniques.

=== Goals of Project ===

1. Create 3D models of children based on CT and MRI datasets for modeling internal and external defibrillation in the SCIRun environment. The processes required address the larger question of how to take any CT or MRI DICOM dataset, segment it into various label maps, combine those label maps in a hierarchical manner, then import and utilize them in the SCIRun/BioPSE environment. This represents part of an expanding collaboration between [http://www.sci.utah.edu/ SCI] and [http://splweb.bwh.harvard.edu:8000/ SPL] to integrate open source tools to allow creation, visualization, and computational modeling of image based 3D models.

2. Create modules which allow insertion of electrode shapes into finite element models in in the SCIRun environment.

3. Utilize the above innovations to model the placement of internal defibrillator electrodes to maximize efficacy, minimize potential cardiac damage, and gain further insight into optimizing defibrillation in children of various sizes as shown above.

=== Slicer and SPL Tools in the Project ===

[[Outline of Torso Segmentation Problem]]

[[Segmentation Tools Currently Utilized]]

[[Tools In Development and Wishlist]]

=== Building and Running SCIRun on SPL Machines ===
[[SCRun on SPL Machines]]

=== Citations ===

1. Jolley M, Stinstra J, Weinstein D, et al. Open-Source Environment for Interactive Finite Element Modeling of Optimal ICD Electrode Placement Functional Imaging and Modeling of the Heart, Lecture Notes in Computer Science. Berlin/Heidelberg: Springer, 2007:373-382.

2. Jolley M, Stinstra J, Weinsten D, et al. Finite Element Modeling of Novel Defibrillation Approaches in Children and Adult Heart Rhythm Society. Denver, Colorado, 2007.

3. Jolley M, Triedman J, Westin CF, et al. Image based modeling of defibrillation in children. Conf Proc IEEE Eng Med Biol Soc 2006;1:2564-7.

4. Stinstra JG, Jolley M, Callahan M, et al. Evaluation of different meshing algorithms in the computation of defibrillation thresholds in children. Conf Proc IEEE Eng Med Biol Soc 2007;1:1422-5.

5. A Computer Modeling Tool for Comparing Novel ICD Electrode Orientations in Children and Adults. In Press Accepted Manuscript for Heart Rhythm, Available online 18 January 2008, http://www.heartrhythmjournal.com/inpress

NA-MIC Childrens Collaboration

2008-01-23T09:20:06Z

Mjolley: /* Building and Running SCIRun on SPL Machines */

Back to [[NA-MIC_External_Collaborations]]

{|
|[[Image:smallkidcxr.png| 200px]] [[Image:27y-leftabdcan-T6SQ-voltage-withheart4.png | 200px]]
|-
|[[Image:27y-leftabdcan-T6SQ-current4.png| 200px]] [[Image:27y-leftabdcan-T6SQ-heart-cut3.png| 200px]]
|}

=== Introduction ===

Placement of Implantable Cardiac Defibrillators(ICDs)is a unique and challenging problem for children due to the variety of shapes and sizes, ranging from neonate to adolescent. As a result, a variety of novel implant techniques have been employed. Although these have generally been successful inasmuch as they result in a clinically acceptable defibrillation threshold, nothing is known about the mechanisms by which this threshold is attained, the optimal geometries for defibrillation, and whether unsafe electric field strengths are a result of novel implant approaches. Finite element modeling has been shown in adult torso models to correlate well with clinical results. Our goal is to model defibrillation in child torso models to gain insight into this important problem. We are also interested in developing new orientations in adults with the goal of lowering DFTs and providing options in patients with contraindications to standard techniques.

=== Goals of Project ===

1. Create 3D models of children based on CT and MRI datasets for modeling internal and external defibrillation in the SCIRun environment. The processes required address the larger question of how to take any CT or MRI DICOM dataset, segment it into various label maps, combine those label maps in a hierarchical manner, then import and utilize them in the SCIRun/BioPSE environment. This represents part of an expanding collaboration between [http://www.sci.utah.edu/ SCI] and [http://splweb.bwh.harvard.edu:8000/ SPL] to integrate open source tools to allow creation, visualization, and computational modeling of image based 3D models.

2. Create modules which allow insertion of electrode shapes into finite element models in in the SCIRun environment.

3. Utilize the above innovations to model the placement of internal defibrillator electrodes to maximize efficacy, minimize potential cardiac damage, and gain further insight into optimizing defibrillation in children of various sizes as shown above.

=== Slicer and SPL Tools in the Project ===

[[Outline of Torso Segmentation Problem]]

[[Segmentation Tools Currently Utilized]]

[[Tools In Development and Wishlist]]

=== Building and Running SCIRun on SPL Machines ===
[[SCRun on SPL Machines]]

=== Citations ===

1. Jolley M, Stinstra J, Weinstein D, et al. Open-Source Environment for Interactive Finite Element Modeling of Optimal ICD Electrode Placement Functional Imaging and Modeling of the Heart, Lecture Notes in Computer Science. Berlin/Heidelberg: Springer, 2007:373-382. (Paper)
2. Jolley M, Stinstra J, Weinsten D, et al. Finite Element Modeling of Novel Defibrillation Approaches in Children and Adult Heart Rhythm Society. Denver, Colorado, 2007. (Abstract Oral Presentation)
3. Jolley M, Triedman J, Westin CF, et al. Image based modeling of defibrillation in children. Conf Proc IEEE Eng Med Biol Soc 2006;1:2564-7. (Paper and Presentation)
4. Stinstra JG, Jolley M, Callahan M, et al. Evaluation of different meshing algorithms in the computation of defibrillation thresholds in children. Conf Proc IEEE Eng Med Biol Soc 2007;1:1422-5. (Paper and Presentation)
5. A Computer Modeling Tool for Comparing Novel ICD Electrode Orientations in Children and Adults. In Press Accepted Manuscript for Heart Rhythm, Available online 18 January 2008,

SCRun on SPL Machines

2007-09-17T21:47:36Z

Mjolley: /* Building SCIRun on an SPL Machine */

== Building SCIRun on an SPL Machine ==

----

[[Problems and Solutions on SPL Machine Blog]]

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines.

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''unsetenv LD_LIBRARY_PATH'''

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory.

Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

Problems and Solutions on SPL Machine Blog

2007-08-22T00:32:04Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-21T19:14:05Z

Mjolley: /* Current Problems on Debugging for SCIRun on SPL Machines */

== Current Problems on Debugging for SCIRun on SPL Machines ==

----

With the install of Fedora 7 we have been having some problems, namely with the OpenGL driver recognition by SCIRun.

For example when we utilize the tools on the previous page SCIRun gets pointed at the correct drivers as shown here:

spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)

When these drivers are recognized SCIRun runs as expected. However, each time SCIRun is run it reverts back to the wrong drivers as evidenced here.

spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003f84800000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)

After this, any OpenGL dependent modules crash upon opening. If you repeat the steps "unsetenv" and run Dav's script again you get back to:

spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)

To summarize:

unset LD_LIBRARY_PATH

ldd scirun | grep GL

<correct GL is reported>

run script

ldd scirun | grep GL

<wrong GL is reported>

So I put:

unset LD_LIBRARY_PATH into the first line of the script(run in bash) and into my .bashrc and I still have the same behavior where it switches back from the good OpenGL setup to the mesa drivers after initially being pointed to the correct ones.

This still didn't seem to do it so we put in the following line in the script:

create_scirun_script() {
echo "scirun -E ${NETWORK} --logfile ALL.log" >/tmp/script-fe.sh
chmod 0770 /tmp/script-fe.sh
}

to

create_scirun_script() {
echo "unset LD_LIBRARY_PATH" > /tmp/script-fe.sh
echo "scirun -E ${NETWORK} --logfile ALL.log" >> /tmp/script-fe.sh
chmod 0770 /tmp/script-fe.sh
}

And the above behavior with it switching back to the MESA drivers appears to have stopped, but the script still always hangs at JoinField within the first three bundles run in the net by the script. I went back and confirmed this set of .bdl files run without errors on my ubuntu machine and in the manual nets on the SPL machine. So it must be an environmental variable. It typically hangs in the first, second, or third run in Scripts on the SPL machines always at the same position. I am not sure what is up as there is not a good error message:

[[Image:VNCscreenshot.png]]

This is the output in the command line script window:

spl_tm64_1:/workspace/mjolley% bash
bash-3.2$ export PATH=$PATH:/workspace/mjolley/Modeling/trunk/SCIRun/bin
bash-3.2$ ./SCIRun_Scripts/run_all.sh /projects/cardio/Clinical-HClean/ /projects/cardio/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn Results/Clinical
ls: cannot access /projects/cardio/Clinical-HClean//Electrodes_Plus_Torso/2ybdls//Four/*.bdl: No such file or directory
cat: /tmp/idx1: No such file or directory
cat: /tmp/idx2: No such file or directory
cat: /tmp/idx3: No such file or directory
cat: /tmp/idx4: No such file or directory
ls: cannot access /projects/cardio/Clinical-HClean//Electrodes_Plus_Torso/10ybdls//Four/*.bdl: No such file or directory
ldd: ./scirun: No such file or directory
Parsed .scirunrc... /home/mjolley/.scirunrc
Loading Tcl,Tk,tk, Itcl,Itk,Blt,Widgets
loading scirun network file: /projects/cardio/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
scirun> loading file: SCIRun_Scripts/Permutations/P1-500-0.mat
loading file: /projects/cardio/Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+10cm-right-parasternal-T4-top.bdl
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: Compiling: ArrayObjectFieldDataScalarAlgoTMergeFieldsAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell<>
GenericField<TetVolMesh<TetLinearLgn<Point> > ,NoDataBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ALGOArrayEngine_1586526061_LCELID_FS<double>
Compiling: ALGOArrayEngine_1586525968_LCELID_FS<double>
Compiling: ALGOArrayEngine_1586526092_LCELID_FS<double>
Compiling: ALGOArrayEngine_1586525999_LCELID_FS<double>

Then SCIRun hangs...

In comparison on my ubuntu machine it is not nearly as verbose regarding compilation etc running the same script...

mj@mj-quad-desktop:~$ SCIRun_Scripts/run_all.sh Clinical-HClean/ Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn Results/Clinical
ls: Clinical-HClean//Electrodes_Plus_Torso/2ybdls//Four/*.bdl: No such file or directory
cat: /tmp/idx1: No such file or directory
cat: /tmp/idx2: No such file or directory
cat: /tmp/idx3: No such file or directory
cat: /tmp/idx4: No such file or directory
ls: Clinical-HClean//Electrodes_Plus_Torso/10ybdls//Four/*.bdl: No such file or directory
Parsed .scirunrc... .scirunrc
Loading Tcl,Tk,tk, Itcl,Itk,Blt,Widgets
loading scirun network file: Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = /home/mj/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
scirun> loading file: SCIRun_Scripts/Permutations/P1-500-0.mat
loading file: Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+10cm-right-parasternal-T4-top.bdl
Creating /home/mj/Results/Clinical/mj-21-Aug/
Creating /home/mj/Results/Clinical/mj-21-Aug/
Creating /home/mj/Results/Clinical/mj-21-Aug/
saving file: /home/mj/Results/Clinical/mj-21-Aug/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix-10y-Left-abd-can+10cm-right-parasternal-T4-top-P1-500-0.txt
Parsed .scirunrc... .scirunrc
Loading Tcl,Tk,tk, Itcl,Itk,Blt,Widgets
loading scirun network file: Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = /home/mj/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
scirun> loading file: Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+10cm-right-parasternal-T6-top.bdl
loading file: SCIRun_Scripts/Permutations/P1-500-0.mat
saving file: /home/mj/Results/Clinical/mj-21-Aug/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix-10y-Left-abd-can+10cm-right-parasternal-T6-top-P1-500-0.txt
saving file: /home/mj/Results/Clinical/mj-21-Aug/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix-10y-Left-abd-can+10cm-right-parasternal-T6-top-P1-500-0.db.txt
saving file: /home/mj/Results/Clinical/mj-21-Aug/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix-10y-Left-abd-can+10cm-right-parasternal-T6-top-P1-500-0.bdl
Parsed .scirunrc... .scirunrc
Loading Tcl,Tk,tk, Itcl,Itk,Blt,Widgets
loading scirun network file: Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = /home/mj/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
scirun> loading file: SCIRun_Scripts/Permutations/P1-500-0.mat
loading file: Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl

And everything runs fine...

I checked and all the bundles in GetFieldsFromBundle are Defined, it just won't run the JoinField. Is there some environmental variable that is not set and does not allow this to run?

[[Image:VNC2.png]]

--[[User:Mjolley|Mjolley]] 11:51, 21 August 2007 (EDT)

File:VNC2.png

2007-08-21T19:13:17Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-21T19:12:20Z

Mjolley:

== Current Problems on Debugging for SCIRun on SPL Machines ==

----

With the install of Fedora 7 we have been having some problems, namely with the OpenGL driver recognition by SCIRun.

For example when we utilize the tools on the previous page SCIRun gets pointed at the correct drivers as shown here:

spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)

When these drivers are recognized SCIRun runs as expected. However, each time SCIRun is run it reverts back to the wrong drivers as evidenced here.

spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003f84800000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)

After this, any OpenGL dependent modules crash upon opening. If you repeat the steps "unsetenv" and run Dav's script again you get back to:

spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)

To summarize:

unset LD_LIBRARY_PATH

ldd scirun | grep GL

<correct GL is reported>

run script

ldd scirun | grep GL

<wrong GL is reported>

So I put:

unset LD_LIBRARY_PATH into the first line of the script(run in bash) and into my .bashrc and I still have the same behavior where it switches back from the good OpenGL setup to the mesa drivers after initially being pointed to the correct ones.

This still didn't seem to do it so we put in the following line in the script:

create_scirun_script() {
echo "scirun -E ${NETWORK} --logfile ALL.log" >/tmp/script-fe.sh
chmod 0770 /tmp/script-fe.sh
}

to

create_scirun_script() {
echo "unset LD_LIBRARY_PATH" > /tmp/script-fe.sh
echo "scirun -E ${NETWORK} --logfile ALL.log" >> /tmp/script-fe.sh
chmod 0770 /tmp/script-fe.sh
}

And the above behavior with it switching back to the MESA drivers appears to have stopped, but the script still always hangs at JoinField within the first three bundles run in the net by the script. I went back and confirmed this set of .bdl files run without errors on my ubuntu machine and in the manual nets on the SPL machine. So it must be an environmental variable. It typically hangs in the first, second, or third run in Scripts on the SPL machines always at the same position. I am not sure what is up as there is not a good error message:

[[Image:VNCscreenshot.png]]

This is the output in the command line script window:

spl_tm64_1:/workspace/mjolley% bash
bash-3.2$ export PATH=$PATH:/workspace/mjolley/Modeling/trunk/SCIRun/bin
bash-3.2$ ./SCIRun_Scripts/run_all.sh /projects/cardio/Clinical-HClean/ /projects/cardio/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn Results/Clinical
ls: cannot access /projects/cardio/Clinical-HClean//Electrodes_Plus_Torso/2ybdls//Four/*.bdl: No such file or directory
cat: /tmp/idx1: No such file or directory
cat: /tmp/idx2: No such file or directory
cat: /tmp/idx3: No such file or directory
cat: /tmp/idx4: No such file or directory
ls: cannot access /projects/cardio/Clinical-HClean//Electrodes_Plus_Torso/10ybdls//Four/*.bdl: No such file or directory
ldd: ./scirun: No such file or directory
Parsed .scirunrc... /home/mjolley/.scirunrc
Loading Tcl,Tk,tk, Itcl,Itk,Blt,Widgets
loading scirun network file: /projects/cardio/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
scirun> loading file: SCIRun_Scripts/Permutations/P1-500-0.mat
loading file: /projects/cardio/Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+10cm-right-parasternal-T4-top.bdl
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: Compiling: ArrayObjectFieldDataScalarAlgoTMergeFieldsAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell<>
GenericField<TetVolMesh<TetLinearLgn<Point> > ,NoDataBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ALGOArrayEngine_1586526061_LCELID_FS<double>
Compiling: ALGOArrayEngine_1586525968_LCELID_FS<double>
Compiling: ALGOArrayEngine_1586526092_LCELID_FS<double>
Compiling: ALGOArrayEngine_1586525999_LCELID_FS<double>

Then SCIRun hangs...

In comparison on my ubuntu machine it is not nearly as verbose regarding compilation etc running the same script...

mj@mj-quad-desktop:~$ SCIRun_Scripts/run_all.sh Clinical-HClean/ Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn Results/Clinical
ls: Clinical-HClean//Electrodes_Plus_Torso/2ybdls//Four/*.bdl: No such file or directory
cat: /tmp/idx1: No such file or directory
cat: /tmp/idx2: No such file or directory
cat: /tmp/idx3: No such file or directory
cat: /tmp/idx4: No such file or directory
ls: Clinical-HClean//Electrodes_Plus_Torso/10ybdls//Four/*.bdl: No such file or directory
Parsed .scirunrc... .scirunrc
Loading Tcl,Tk,tk, Itcl,Itk,Blt,Widgets
loading scirun network file: Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = /home/mj/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
scirun> loading file: SCIRun_Scripts/Permutations/P1-500-0.mat
loading file: Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+10cm-right-parasternal-T4-top.bdl
Creating /home/mj/Results/Clinical/mj-21-Aug/
Creating /home/mj/Results/Clinical/mj-21-Aug/
Creating /home/mj/Results/Clinical/mj-21-Aug/
saving file: /home/mj/Results/Clinical/mj-21-Aug/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix-10y-Left-abd-can+10cm-right-parasternal-T4-top-P1-500-0.txt
Parsed .scirunrc... .scirunrc
Loading Tcl,Tk,tk, Itcl,Itk,Blt,Widgets
loading scirun network file: Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = /home/mj/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
scirun> loading file: Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+10cm-right-parasternal-T6-top.bdl
loading file: SCIRun_Scripts/Permutations/P1-500-0.mat
saving file: /home/mj/Results/Clinical/mj-21-Aug/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix-10y-Left-abd-can+10cm-right-parasternal-T6-top-P1-500-0.txt
saving file: /home/mj/Results/Clinical/mj-21-Aug/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix-10y-Left-abd-can+10cm-right-parasternal-T6-top-P1-500-0.db.txt
saving file: /home/mj/Results/Clinical/mj-21-Aug/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix-10y-Left-abd-can+10cm-right-parasternal-T6-top-P1-500-0.bdl
Parsed .scirunrc... .scirunrc
Loading Tcl,Tk,tk, Itcl,Itk,Blt,Widgets
loading scirun network file: Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = /home/mj/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
scirun> loading file: SCIRun_Scripts/Permutations/P1-500-0.mat
loading file: Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl

And everything runs fine...

I checked and all the bundles in GetFieldsFromBundle are Defined, it just won't run the JoinField. Is there some environmental variable that is not set and does not allow this to run?
[[Image:VNC2]]

--[[User:Mjolley|Mjolley]] 11:51, 21 August 2007 (EDT)

Problems and Solutions on SPL Machine Blog

2007-08-21T19:00:16Z

Mjolley: /* Current Problems on Debugging for SCIRun on SPL Machines */

== Current Problems on Debugging for SCIRun on SPL Machines ==

----

With the install of Fedora 7 we have been having some problems, namely with the OpenGL driver recognition by SCIRun.

For example when we utilize the tools on the previous page SCIRun gets pointed at the correct drivers as shown here:

spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)

When these drivers are recognized SCIRun runs as expected. However, each time SCIRun is run it reverts back to the wrong drivers as evidenced here.

spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003f84800000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)

After this, any OpenGL dependent modules crash upon opening. If you repeat the steps "unsetenv" and run Dav's script again you get back to:

spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)

To summarize:

unset LD_LIBRARY_PATH

ldd scirun | grep GL

<correct GL is reported>

run script

ldd scirun | grep GL

<wrong GL is reported>

So I put:

unset LD_LIBRARY_PATH into the first line of the script(run in bash) and into my .bashrc and I still have the same behavior where it switches back from the good OpenGL setup to the mesa drivers after initially being pointed to the correct ones.

This still didn't seem to do it so we put in the following line in the script:

create_scirun_script() {
echo "scirun -E ${NETWORK} --logfile ALL.log" >/tmp/script-fe.sh
chmod 0770 /tmp/script-fe.sh
}

to

create_scirun_script() {
echo "unset LD_LIBRARY_PATH" > /tmp/script-fe.sh
echo "scirun -E ${NETWORK} --logfile ALL.log" >> /tmp/script-fe.sh
chmod 0770 /tmp/script-fe.sh
}

And the above behavior with it switching back to the MESA drivers appears to have stopped, but the script still always hangs at JoinField within the first three bundles run in the net by the script. I went back and confirmed this set of .bdl files run without errors on my ubuntu machine and in the manual nets on the SPL machine. So it must be an environmental variable. It typically hangs in the first, second, or third run in Scripts on the SPL machines always at the same position. I am not sure what is up as there is not a good error message:

[[Image:VNCscreenshot.png]]

This is the output in the command line script window:

spl_tm64_1:/workspace/mjolley% bash
bash-3.2$ export PATH=$PATH:/workspace/mjolley/Modeling/trunk/SCIRun/bin
bash-3.2$ ./SCIRun_Scripts/run_all.sh /projects/cardio/Clinical-HClean/ /projects/cardio/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn Results/Clinical
ls: cannot access /projects/cardio/Clinical-HClean//Electrodes_Plus_Torso/2ybdls//Four/*.bdl: No such file or directory
cat: /tmp/idx1: No such file or directory
cat: /tmp/idx2: No such file or directory
cat: /tmp/idx3: No such file or directory
cat: /tmp/idx4: No such file or directory
ls: cannot access /projects/cardio/Clinical-HClean//Electrodes_Plus_Torso/10ybdls//Four/*.bdl: No such file or directory
ldd: ./scirun: No such file or directory
Parsed .scirunrc... /home/mjolley/.scirunrc
Loading Tcl,Tk,tk, Itcl,Itk,Blt,Widgets
loading scirun network file: /projects/cardio/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
scirun> loading file: SCIRun_Scripts/Permutations/P1-500-0.mat
loading file: /projects/cardio/Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+10cm-right-parasternal-T4-top.bdl
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: Compiling: ArrayObjectFieldDataScalarAlgoTMergeFieldsAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell<>
GenericField<TetVolMesh<TetLinearLgn<Point> > ,NoDataBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ALGOArrayEngine_1586526061_LCELID_FS<double>
Compiling: ALGOArrayEngine_1586525968_LCELID_FS<double>
Compiling: ALGOArrayEngine_1586526092_LCELID_FS<double>
Compiling: ALGOArrayEngine_1586525999_LCELID_FS<double>

Then SCIRun hangs...

In comparison on my ubuntu machine it is not nearly as verbose regarding compilation etc running the same script...

mj@mj-quad-desktop:~$ SCIRun_Scripts/run_all.sh Clinical-HClean/ Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn Results/Clinical
ls: Clinical-HClean//Electrodes_Plus_Torso/2ybdls//Four/*.bdl: No such file or directory
cat: /tmp/idx1: No such file or directory
cat: /tmp/idx2: No such file or directory
cat: /tmp/idx3: No such file or directory
cat: /tmp/idx4: No such file or directory
ls: Clinical-HClean//Electrodes_Plus_Torso/10ybdls//Four/*.bdl: No such file or directory
Parsed .scirunrc... .scirunrc
Loading Tcl,Tk,tk, Itcl,Itk,Blt,Widgets
loading scirun network file: Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = /home/mj/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
scirun> loading file: SCIRun_Scripts/Permutations/P1-500-0.mat
loading file: Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+10cm-right-parasternal-T4-top.bdl
Creating /home/mj/Results/Clinical/mj-21-Aug/
Creating /home/mj/Results/Clinical/mj-21-Aug/
Creating /home/mj/Results/Clinical/mj-21-Aug/
saving file: /home/mj/Results/Clinical/mj-21-Aug/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix-10y-Left-abd-can+10cm-right-parasternal-T4-top-P1-500-0.txt
Parsed .scirunrc... .scirunrc
Loading Tcl,Tk,tk, Itcl,Itk,Blt,Widgets
loading scirun network file: Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = /home/mj/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
scirun> loading file: Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+10cm-right-parasternal-T6-top.bdl
loading file: SCIRun_Scripts/Permutations/P1-500-0.mat
saving file: /home/mj/Results/Clinical/mj-21-Aug/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix-10y-Left-abd-can+10cm-right-parasternal-T6-top-P1-500-0.txt
saving file: /home/mj/Results/Clinical/mj-21-Aug/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix-10y-Left-abd-can+10cm-right-parasternal-T6-top-P1-500-0.db.txt
saving file: /home/mj/Results/Clinical/mj-21-Aug/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix-10y-Left-abd-can+10cm-right-parasternal-T6-top-P1-500-0.bdl
Parsed .scirunrc... .scirunrc
Loading Tcl,Tk,tk, Itcl,Itk,Blt,Widgets
loading scirun network file: Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = /home/mj/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
scirun> loading file: SCIRun_Scripts/Permutations/P1-500-0.mat
loading file: Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl

And everything runs fine...

--[[User:Mjolley|Mjolley]] 11:51, 21 August 2007 (EDT)

Problems and Solutions on SPL Machine Blog

2007-08-21T18:53:23Z

Mjolley: /* Current Problems on Debugging for SCIRun on SPL Machines */

== Current Problems on Debugging for SCIRun on SPL Machines ==

----

With the install of Fedora 7 we have been having some problems, namely with the OpenGL driver recognition by SCIRun.

For example when we utilize the tools on the previous page SCIRun gets pointed at the correct drivers as shown here:

spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)

When these drivers are recognized SCIRun runs as expected. However, each time SCIRun is run it reverts back to the wrong drivers as evidenced here.

spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003f84800000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)

After this, any OpenGL dependent modules crash upon opening. If you repeat the steps "unsetenv" and run Dav's script again you get back to:

spl_tm64_1:/workspace/mjolley/Modeling/trunk/SCIRun/bin% ldd scirun | grep GL
libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003f8e200000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x000000360c200000)
libGLcore.so.1 => /usr/lib64/nvidia/libGLcore.so.1 (0x0000003f80e00000)

To summarize:

unset LD_LIBRARY_PATH

ldd scirun | grep GL

<correct GL is reported>

run script

ldd scirun | grep GL

<wrong GL is reported>

So I put:

unset LD_LIBRARY_PATH into the first line of the script(run in bash) and into my .bashrc and I still have the same behavior where it switches back from the good OpenGL setup to the mesa drivers after initially being pointed to the correct ones.

This still didn't seem to do it so we put in the following line in the script:

create_scirun_script() {
echo "scirun -E ${NETWORK} --logfile ALL.log" >/tmp/script-fe.sh
chmod 0770 /tmp/script-fe.sh
}

to

create_scirun_script() {
echo "unset LD_LIBRARY_PATH" > /tmp/script-fe.sh
echo "scirun -E ${NETWORK} --logfile ALL.log" >> /tmp/script-fe.sh
chmod 0770 /tmp/script-fe.sh
}

And the above behavior with it switching back to the MESA drivers appears to have stopped, but the script still always hangs at JoinField within the first three bundles run in the net by the script. I went back and confirmed this set of .bdl files run without errors on my ubuntu machine and in the manual nets on the SPL machine. So it must be an environmental variable. It typically hangs in the first, second, or third run in Scripts on the SPL machines always at the same position. I am not sure what is up as there is not a good error message:

[[Image:VNCscreenshot.png]]

This is the output in the command line script window:

spl_tm64_1:/workspace/mjolley% bash
bash-3.2$ export PATH=$PATH:/workspace/mjolley/Modeling/trunk/SCIRun/bin
bash-3.2$ ./SCIRun_Scripts/run_all.sh /projects/cardio/Clinical-HClean/ /projects/cardio/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn Results/Clinical
ls: cannot access /projects/cardio/Clinical-HClean//Electrodes_Plus_Torso/2ybdls//Four/*.bdl: No such file or directory
cat: /tmp/idx1: No such file or directory
cat: /tmp/idx2: No such file or directory
cat: /tmp/idx3: No such file or directory
cat: /tmp/idx4: No such file or directory
ls: cannot access /projects/cardio/Clinical-HClean//Electrodes_Plus_Torso/10ybdls//Four/*.bdl: No such file or directory
ldd: ./scirun: No such file or directory
Parsed .scirunrc... /home/mjolley/.scirunrc
Loading Tcl,Tk,tk, Itcl,Itk,Blt,Widgets
loading scirun network file: /projects/cardio/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
scirun> loading file: SCIRun_Scripts/Permutations/P1-500-0.mat
loading file: /projects/cardio/Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+10cm-right-parasternal-T4-top.bdl
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldCreateAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double >,vector<double > > >
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: Compiling: ArrayObjectFieldDataScalarAlgoTMergeFieldsAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell<>
GenericField<TetVolMesh<TetLinearLgn<Point> > ,NoDataBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldDataScalarAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldLocationElemAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > >
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ArrayObjectFieldElemVolumeAlgoT<GenericField<TetVolMesh<TetLinearLgn<Point> > ,ConstantBasis<double> ,vector<double> > ,TetVolMesh<TetLinearLgn<Point> > ::Cell>
Compiling: ALGOArrayEngine_1586526061_LCELID_FS<double>
Compiling: ALGOArrayEngine_1586525968_LCELID_FS<double>
Compiling: ALGOArrayEngine_1586526092_LCELID_FS<double>
Compiling: ALGOArrayEngine_1586525999_LCELID_FS<double>

Then SCIRun hangs...

In comparison on my ubuntu machine it is not nearly as verbose regarding compilation etc running the same script...

mj@mj-quad-desktop:~$ SCIRun_Scripts/run_all.sh Clinical-HClean/ Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn Results/Clinical
ls: Clinical-HClean//Electrodes_Plus_Torso/2ybdls//Four/*.bdl: No such file or directory
cat: /tmp/idx1: No such file or directory
cat: /tmp/idx2: No such file or directory
cat: /tmp/idx3: No such file or directory
cat: /tmp/idx4: No such file or directory
ls: Clinical-HClean//Electrodes_Plus_Torso/10ybdls//Four/*.bdl: No such file or directory
Parsed .scirunrc... .scirunrc
Loading Tcl,Tk,tk, Itcl,Itk,Blt,Widgets
loading scirun network file: Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
NETFILE = /home/mj/Clinical-HClean/SCIRun_Nets/Script2_FEM/Script2-FE-refine-elec-dilate-5-100x100x150-all-cases-permut-matrix.srn
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+25cm-sc-left-T10back.bdl
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
filename=SCIRun_Scripts/Permutations/P1-500-0.mat
scirun> loading file: SCIRun_Scripts/Permutations/P1-500-0.mat
loading file: Clinical-HClean//Electrodes_Plus_Torso/10ybdls//One/10y-Left-abd-can+10cm-right-parasternal-T4-top.bdl

And everything runs fine...

--[[User:Mjolley|Mjolley]] 11:51, 21 August 2007 (EDT)

Problems and Solutions on SPL Machine Blog

2007-08-21T15:55:05Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-21T15:51:15Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-21T07:34:01Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-21T07:32:14Z

Mjolley:

File:VNCscreenshot.png

2007-08-21T07:28:24Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-21T07:28:09Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-21T07:27:31Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-21T07:27:07Z

Mjolley:

File:Screenshot-VNC-X11.png

2007-08-21T07:25:23Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-21T07:24:43Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-21T07:18:11Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-21T07:16:20Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-21T07:14:54Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-20T19:31:28Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-20T17:38:55Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-20T16:55:55Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-20T16:53:17Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-20T16:49:16Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-20T16:49:02Z

Mjolley:

Problems and Solutions on SPL Machine Blog

2007-08-20T16:46:29Z

Mjolley:

SCRun on SPL Machines

2007-08-20T16:45:24Z

Mjolley:

== Building SCIRun on an SPL Machine ==

----

[[Problems and Solutions on SPL Machine Blog]]

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines, as of August 2007. Currently we are still having some problems with the recognition of the correct open GL drivers as discussed above.

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''unsetenv LD_LIBRARY_PATH'''

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory.

Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

SCRun on SPL Machines

2007-08-20T16:45:04Z

Mjolley:

== Building SCIRun on an SPL Machine ==

----

[[Problems and Solutions on SPL Machine Blog]]

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines, as of August 2007. Currently we are still having some problems with the recognition of the correct open GL drivers as discussed above.

Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''unsetenv LD_LIBRARY_PATH'''

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory

Problems and Solutions on SPL Machine Blog

2007-08-20T16:42:54Z

Mjolley:

SCRun on SPL Machines

2007-08-20T16:37:45Z

Mjolley:

== Building SCIRun on an SPL Machine ==

----

[[Problems and Solutions on SPL Machine Blog]]

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines, as of August 2007. Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''unsetenv LD_LIBRARY_PATH'''

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory

SCRun on SPL Machines

2007-08-18T07:22:09Z

Mjolley:

== Building SCIRun on an SPL Machine ==

----

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines, as of August 2007. Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''unsetenv LD_LIBRARY_PATH'''

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory

SCRun on SPL Machines

2007-08-18T07:21:16Z

Mjolley:

== Building SCIRun on an SPL Machine ==

----

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines, as of August 2007. Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''unsetenv LD_LIBRARY_PATH" and your systems LD_LIBRARY_PATH'''

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory

SCRun on SPL Machines

2007-08-17T06:31:35Z

Mjolley:

== Building SCIRun on an SPL Machine ==

----

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines, as of August 2007. Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory

SCRun on SPL Machines

2007-08-17T06:30:53Z

Mjolley:

== Building SCIRun on an SPL Machine ==

----

hese are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines, as of August 2007. Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is not 2.4.x then you can add --get-cmake and create a local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation

If you are using 2.4.x cmake/ccmake version on the SPL machines current you can type:

'''ccmake ../src'''

If you are using the version of ccmake created for SCIRun by build.sh with the --get-cmake option then from the /trunk/SCIRun/bin directory type the following:

'''../cmake/local/bin/ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. For this we utilize a script written in ksh so you need ksh installed on the system, which all SPL machines should have. If you are on another OS/machine SCIRun might already be setup correctly with regards to OpenGL drivers and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory

Building on Fedora Core 5-OLD

2007-08-17T06:24:22Z

Mjolley:

These are the current build instructions for the Fedora Core 5 and Fedora Core 7 SPL machines, as of August 2007. Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh --get-cmake -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is 2.4.x then you can omit --get-cmake and utilize your local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation by using the version of ccmake created for SCIRun by build.sh. From the /trunk/SCIRun/bin directory type the following if you needed to utilize the --get-cmake option:

'''../cmake/local/bin/ccmake ../src'''

If you are using a local cmake/ccmake version you can instead type:

'''ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. If you are on another OS/machine it might already be setup correctly and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory

Building on Fedora Core 5-OLD

2007-08-17T06:22:23Z

Mjolley:

These are the current build instructions for the Fedora Core 5 SPL machines, as of August 2007. Follow these links for more on the [http://www.sci.utah.edu/cibc/ CIBC] and the [http://www.sci.utah.edu/ Scientific Computing Institute in Utah].

To obtain the working branch utilized in the collaboration you need subversion. To obtain it:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/trunk

If instead you want a standard release build you can check out one of the repositories listed [https://code.sci.utah.edu/svn/SCIRun/ here] such as:

svn co https://code.sci.utah.edu/svn/SCIRun/cibc/branches/3.0.x/SCIRun

For more general information on SCIRun building visit the [http://software.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Installation SCIRun Installation Wiki]

To build cd to trunk/SCIRun and run the build script:

'''./build.sh --get-cmake -jx'''

where x is the number of cores you have. The get cmake option may be necessary to build as SCIRun currently requires cmake 2.4.x. If your cmake is 2.4.x then you can omit --get-cmake and utilize your local version.

For our current project we utilize the extra package ModelCreation. If you do not use this package you can skip this step. To enable ModelCreation by using the version of ccmake created for SCIRun by build.sh. From the /trunk/SCIRun/bin directory type the following if you needed to utilize the --get-cmake option:

'''../cmake/local/bin/ccmake ../src'''

If you are using a local cmake/ccmake version you can instead type:

'''ccmake ../src'''

Once in ccmake add ModelCreation to the list of LOAD_PACKAGE. Arrow down to LOAD_PACKAGE and hit return to allow you to edit the listed packages. Once you have done this type c to configure and g to generate.

[[Image:ccmakeforSCIRun.png]]

Once this has occured it will put you back into the shell in /trunk/SCIRun/bin, then just make:

''' make -jx'''

When this is completed you currently have to direct SCIRun to the the correct drivers on the SPL machine build of Fedora as per this [[discussion]]. If you are on another OS/machine it might already be setup correctly and you will not need this step. For the SPL Fedora machines cd to the /trunk/SCIRun/bin directory type:

'''find . -name build.make | xargs ~dav/bin/updatefile.orig ~dav/changeit'''

When this is completed you need to run make again in the /trunk/SCIRun/bin directory:

''' make -jx'''

You should now have a working version of SCIRun in your /trunk/SCIRun/bin directory