scirun-users - Re: [SCIRUN-USERS] InterfaceWithMatlab: Could not read output matrix

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Re: [SCIRUN-USERS] InterfaceWithMatlab: Could not read output matrix

From: Jeroen Stinstra <jeroen@cvrti.utah.edu>
To: Michael Callahan <callahan@sci.utah.edu>
Cc: Farid Harhad <fharhad@cct.lsu.edu>, Lydia Dux-Santoy Hurtado <lyduxhur@teleco.upv.es>, scirun-users@sci.utah.edu
Subject: Re: [SCIRUN-USERS] InterfaceWithMatlab: Could not read output matrix
Date: Tue, 2 Oct 2007 04:52:54 -0600

Hi

It looks like SCIRun cannot find the /tmp directory which it needs for communicating with matlab. It was originally designed to only work on OSX and Linux.

Try to change the SCIRUN_SERV_TMP_DIR in the .scirunrc file. That variable should control where the files are written.

best,

Jeroen

On Oct 1, 2007, at 9:08 PM, Michael Callahan wrote:

It's in the nets directory specific to the matlab package.

src/Packages/MatlabInterface/nets/Optional/matlab-cage-tank- example.srn

  Michael

On Mon, 2007-10-01 at 09:29 -0500, Farid Harhad wrote:

Hi Lydia,

I'm new to scirun+matlab as well. I wanted to try what you did, but I
was unable to find the following network:

"matlab-cage-tank-example.srn"

in the "nets" folder.

Where did you get it from?  Is this is some network you created?  If
it's a scirun example, where can I get it from?

Thank you,

--Farid

On 10/1/07, Lydia Dux-Santoy Hurtado <lyduxhur@teleco.upv.es> wrote:

        Hi all,

        I'm a new user. I have installed SCIRun/BioPSE using CMake
        2.4.7 and MS Visual
        Studio .NET 2003.

        I'd like to use MATLAB with SCIRun. I've tried to execute the
        example
        "matlab-cage-tank-example.srn ", but the module
        "InterfaceWithMatlab" doesn't
        work properly and the Output Matrix cannot be readen. The log
        for
        InterfaceWithMatlab says:
--------------------------------------------------------------------- -----------
        REMARK: Dynamically compiling some code.
        DynamicLoader - Successfully created
C:/scirun/SCIRun/bin/on-the-fly-libs/ FldTMtlbAlgT.GFldTrSrfMhTrLnrLgnPtNDtBssdblvctrdbl.cc
        DynamicLoader - Executing:
        C:\\scirun\\SCIRun\\bin\\on-the-fly-libs\\win32make.bat
        FldTMtlbAlgT.GFldTrSrfMhTrLnrLgnPtNDtBssdblvctrdbl. release
        FldTMtlbAlgT.GFldTrSrfMhTrLnrLgnPtNDtBssdblvctrdbl.cc
        C:/scirun\\SCIRun\\src\\Core\\Datatypes\\TetVolMesh.h(720) :
        warning C4996:
'std::hash_map<SCIRun::TetVolMesh<_Kty>::PFace,SCIRun::TetVolMesh<_Kt y>::Face::index_type,SCIRun::TetVolMesh<_Kty>::FaceHash>':
        el s?mbolo se ha declarado como deprecated
                C:/scirun\\SCIRun\\src\\Core\\Datatypes\
        \TetVolMesh.h(841) : vea la
        referencia a la creaci?n de instancias de plantilla de clase
        'SCIRun::TetVolMesh<Basis>' que se est? compilando
        C:/scirun\\SCIRun\\src\\Core\\Datatypes\\TetVolMesh.h(721) :
        warning C4996:
'std::hash_map<SCIRun::TetVolMesh<_Kty>::PEdge,SCIRun::TetVolMesh<_Kt y>::Edge::index_type,SCIRun::TetVolMesh<_Kty>::EdgeHash>':
        el s?mbolo se ha declarado como deprecated
C:/scirun\\SCIRun\\src\\Core\\Datatypes\\PrismVolMesh.h (248) :
        warning C4996:
'std::hash_multiset<SCIRun::PrismVolMesh<_Kty>::Edge::index_type,SCIR un::PrismVolMesh<_Kty>::Edge::CellEdgeHasher>':
        el s?mbolo se ha declarado como deprecated
                C:/scirun\\SCIRun\\src\\Core\\Datatypes\
        \PrismVolMesh.h(127) : vea la
        referencia a la creaci?n de instancias de plantilla de clase
        'SCIRun::PrismVolMesh<Basis>::Edge' que se est? compilando
                C:/scirun\\SCIRun\\src\\Core\\Datatypes\
        \PrismVolMesh.h(1059) : vea la
        referencia a la creaci?n de instancias de plantilla de clase
        'SCIRun::PrismVolMesh<Basis>' que se est? compilando
C:/scirun\\SCIRun\\src\\Core\\Datatypes\\PrismVolMesh.h (249) :
        warning C4996:
'std::hash_set<SCIRun::PrismVolMesh<_Kty>::Edge::index_type,SCIRun::P rismVolMesh<_Kty>::Edge::CellEdgeHasher>':
        el s?mbolo se ha declarado como deprecated
C:/scirun\\SCIRun\\src\\Core\\Datatypes\\PrismVolMesh.h (471) :
        warning C4996:
'std::hash_multiset<SCIRun::PrismVolMesh<_Kty>::Face::index_type,SCIR un::PrismVolMesh<_Kty>::Face::CellFaceHasher>':
        el s?mbolo se ha declarado como deprecated
                C:/scirun\\SCIRun\\src\\Core\\Datatypes\
        \PrismVolMesh.h(274) : vea la
        referencia a la creaci?n de instancias de plantilla de clase
        'SCIRun::PrismVolMesh<Basis>::Face' que se est? compilando
C:/scirun\\SCIRun\\src\\Core\\Datatypes\\PrismVolMesh.h (472) :
        warning C4996:
'std::hash_set<SCIRun::PrismVolMesh<_Kty>::Face::index_type,SCIRun::P rismVolMesh<_Kty>::Face::CellFaceHasher>':
        el s?mbolo se ha declarado como deprecated
        C:/scirun\\SCIRun\\src\\Core\\Datatypes\\HexVolMesh.h(811) :
        warning C4996:
'std::hash_map<SCIRun::HexVolMesh<_Kty>::PFace,SCIRun::HexVolMesh<_Kt y>::Face::index_type,SCIRun::HexVolMesh<_Kty>::FaceHash>':
        el s?mbolo se ha declarado como deprecated
                C:/scirun\\SCIRun\\src\\Core\\Datatypes\
        \HexVolMesh.h(869) : vea la
        referencia a la creaci?n de instancias de plantilla de clase
        'SCIRun::HexVolMesh<Basis>' que se est? compilando
        C:/scirun\\SCIRun\\src\\Core\\Datatypes\\HexVolMesh.h(812) :
        warning C4996:
'std::hash_map<SCIRun::HexVolMesh<_Kty>::PEdge,SCIRun::HexVolMesh<_Kt y>::Edge::index_type,SCIRun::HexVolMesh<_Kty>::EdgeHash>':
        el s?mbolo se ha declarado como deprecated
        Microsoft (R) Incremental Linker Version 7.10.3077
        Copyright (C) Microsoft Corporation.  All rights reserved.

        /out:FldTMtlbAlgT.GFldTrSrfMhTrLnrLgnPtNDtBssdblvctrdbl.exe
        /out:FldTMtlbAlgT.GFldTrSrfMhTrLnrLgnPtNDtBssdblvctrdbl.dll
        -dll
C:/scirun/SCIRun/bin/lib/Release/ Core_Algorithms_ArrayMath.lib
C:/scirun/SCIRun/bin/lib/Release/ Core_Algorithms_Converter.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Algorithms_DataIO.lib
C:/scirun/SCIRun/bin/lib/Release/ Core_Algorithms_DataStreaming.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Algorithms_Fields.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Algorithms_Geometry.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Algorithms_Math.lib
C:/scirun/SCIRun/bin/lib/Release/ Core_Algorithms_Regression.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Algorithms_Util.lib
C:/scirun/SCIRun/bin/lib/Release/ Core_Algorithms_Visualization.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Basis.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Bundle.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Comm.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Containers.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Datatypes.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Events.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Exceptions.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Geom.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Geometry.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_GeomInterface.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_ICom.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_ImportExport.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Init.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Malloc.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Math.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Matlab.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_OS.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Persistent.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Services.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Skinner.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_SystemCall.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Thread.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Util.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_Volume.lib
        C:/scirun/SCIRun/bin/lib/Release/Core_XMLUtil.lib
        C:/scirun/SCIRun/bin/lib/Release/Dataflow_Comm.lib
        C:/scirun/SCIRun/bin/lib/Release/Dataflow_Constraints.lib
        C:/scirun/SCIRun/bin/lib/Release/Dataflow_GuiInterface.lib
        C:/scirun/SCIRun/bin/lib/Release/Dataflow_Modules_Bundle.lib
C:/scirun/SCIRun/bin/lib/Release/ Dataflow_Modules_Converters.lib
C:/scirun/SCIRun/bin/lib/Release/ Dataflow_Modules_DataArrayMath.lib
        C:/scirun/SCIRun/bin/lib/Release/Dataflow_Modules_DataIO.lib
C:/scirun/SCIRun/bin/lib/Release/ Dataflow_Modules_Examples.lib
        C:/scirun/SCIRun/bin/lib/Release/Dataflow_Modules_Fields.lib
        C:/scirun/SCIRun/bin/lib/Release/Dataflow_Modules_Math.lib
        C:/scirun/SCIRun/bin/lib/Release/Dataflow_Modules_Render.lib
        C:/scirun/SCIRun/bin/lib/Release/Dataflow_Modules_String.lib
        C:/scirun/SCIRun/bin/lib/Release/Dataflow_Modules_Time.lib
C:/scirun/SCIRun/bin/lib/Release/ Dataflow_Modules_Visualization.lib
        C:/scirun/SCIRun/bin/lib/Release/Dataflow_Network.lib
        C:/scirun/SCIRun/bin/lib/Release/Dataflow_TCLThread.lib
        C:/scirun/SCIRun/bin/lib/Release/Dataflow_TkExtensions.lib
        C:/scirun/SCIRun/bin/lib/Release/Dataflow_Widgets.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_BioPSE_Core_Algorithms_Forward.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_BioPSE_Core_Algorithms_NumApproximation.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_BioPSE_Core_Datatypes.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_BioPSE_Dataflow_Modules_DataIO.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_BioPSE_Dataflow_Modules_Forward.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_BioPSE_Dataflow_Modules_Inverse.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_BioPSE_Dataflow_Modules_LeadField.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_BioPSE_Dataflow_Modules_Modeling.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_BioPSE_Dataflow_Modules_NeuroFEM.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_BioPSE_Dataflow_Modules_Visualization.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_MatlabInterface_Dataflow_Modules_DataIO.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_MatlabInterface_Dataflow_Modules_Interface.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_MatlabInterface_Services.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_Teem_Dataflow_Modules_Converters.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_Teem_Dataflow_Modules_DataIO.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_Teem_Dataflow_Modules_Misc.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_Teem_Dataflow_Modules_Tend.lib
C:/scirun/SCIRun/bin/lib/Release/ Packages_Teem_Dataflow_Modules_Unu.lib
        C:/scirun/thirdparty/lib/blt.lib
        C:/scirun/thirdparty/lib/freetype.lib
        C:/scirun/thirdparty/lib/itcl.lib
        C:/scirun/thirdparty/lib/itclstubs32.lib
        C:/scirun/thirdparty/lib/itk.lib
        C:/scirun/thirdparty/lib/png.lib
        C:/scirun/thirdparty/lib/tcl.lib
        C:/scirun/thirdparty/lib/tclstub84.lib
        C:/scirun/thirdparty/lib/teem.lib
        C:/scirun/thirdparty/lib/tk.lib
        C:/scirun/thirdparty/lib/tkstub84.lib
        C:/scirun/thirdparty/lib/xml2.lib
        C:/scirun/thirdparty/lib/z.lib
        FldTMtlbAlgT.GFldTrSrfMhTrLnrLgnPtNDtBssdblvctrdbl.obj
           Creando biblioteca
        FldTMtlbAlgT.GFldTrSrfMhTrLnrLgnPtNDtBssdblvctrdbl.lib y
        objeto FldTMtlbAlgT.GFldTrSrfMhTrLnrLgnPtNDtBssdblvctrdbl.exp
        DynamicLoader - Successfully compiled
        FldTMtlbAlgT.GFldTrSrfMhTrLnrLgnPtNDtBssdblvctrdbl.dll
        REMARK: Dynamic compilation completed.
        ERROR: InterfaceWithMatlab: Could not read output matrix
--------------------------------------------------------------------- ----------

        What can I do?
        Thanks,
             Lydia
===================================================================== ======
        == The SCIRun Users mailing list: send email to
        majordomo@sci.utah.edu   ==
        == for more details.
        ==
        == Please acknowledge use of SCIRun in your papers and
        reports:          ==
        ==   see
        http://software.sci.utah.edu/scirun-biopse_citation.bib
        ==
===================================================================== ======

====================================================================== =====
== The SCIRun Users mailing list: send email to majordomo@sci.utah.edu ==
== for more details. ==
== Please acknowledge use of SCIRun in your papers and reports: ==
== see http://software.sci.utah.edu/scirun- biopse_citation.bib ==
====================================================================== =====

====================================================================== =====
== The SCIRun Users mailing list: send email to majordomo@sci.utah.edu ==
== for more details. ==
== Please acknowledge use of SCIRun in your papers and reports: ==
== see http://software.sci.utah.edu/scirun- biopse_citation.bib ==
====================================================================== =====

===========================================================================
== The SCIRun Users mailing list: send email to majordomo@sci.utah.edu   ==
== for more details.                                                     ==
== Please acknowledge use of SCIRun in your papers and reports:          ==
==   see http://software.sci.utah.edu/scirun-biopse_citation.bib         ==
===========================================================================

===========================================================================
== The SCIRun Users mailing list: send email to majordomo@sci.utah.edu   ==
== for more details.                                                     ==
== Please acknowledge use of SCIRun in your papers and reports:          ==
==   see http://software.sci.utah.edu/scirun-biopse_citation.bib         ==
===========================================================================

[SCIRUN-USERS] InterfaceWithMatlab: Could not read output matrix, Lydia Dux-Santoy Hurtado, 10/01/2007
- Re: [SCIRUN-USERS] InterfaceWithMatlab: Could not read output matrix, Farid Harhad, 10/01/2007
  - Re: [SCIRUN-USERS] InterfaceWithMatlab: Could not read output matrix, Michael Callahan, 10/01/2007
    - Re: [SCIRUN-USERS] InterfaceWithMatlab: Could not read output matrix, Farid Harhad, 10/02/2007
    - Re: [SCIRUN-USERS] InterfaceWithMatlab: Could not read output matrix, Farid Harhad, 10/02/2007
  - Re: [SCIRUN-USERS] InterfaceWithMatlab: Could not read output matrix, Michael Callahan, 10/02/2007
    - Re: [SCIRUN-USERS] InterfaceWithMatlab: Could not read output matrix, Jeroen Stinstra, 10/02/2007
      - Re: [SCIRUN-USERS] InterfaceWithMatlab: Could not read output matrix, Farid Harhad, 10/02/2007
      - Re: [SCIRUN-USERS] InterfaceWithMatlab: Could not read output matrix, Farid Harhad, 10/02/2007
    - Re: [SCIRUN-USERS] InterfaceWithMatlab: Could not read output matrix, Jeroen Stinstra, 10/02/2007
- Re: [SCIRUN-USERS] InterfaceWithMatlab: Could not read output matrix, Farid Harhad, 10/01/2007
- <Possible follow-up(s)>
- [SCIRUN-USERS] InterfaceWithMatlab: Could not read output matrix, Lydia Dux-Santoy Hurtado, 10/01/2007

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