scirun-users - Re: [SCIRUN-USERS] problems with running SCIRun on Fedora

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Re: [SCIRUN-USERS] problems with running SCIRun on Fedora

From: David Weinstein <dmw@sci.utah.edu>
To: Linxin Guo <lguo@postoffice.utas.edu.au>
Cc: scirun-users@sci.utah.edu
Subject: Re: [SCIRUN-USERS] problems with running SCIRun on Fedora
Date: Mon, 3 May 2004 00:09:28 -0600

Hi,

[Lin forwarded me the error message in a separate email, which I've attached below.]

From the error message, it appears that your /tmp/ directory is full -- try making some space in there and then re-running. (At run-time, SCIRun attempts to dynamically compile algorithms as they are needed -- however the compilation is failing because /tmp/ is full.)

Cheers,
Dave

On May 2, 2004, at 10:00 PM, Linxin Guo wrote:

Dear SCIRun users,

I have installed SCIRun/BioPSE 1.20.3 on our group server, which is
running Linux--Fedora release 1. When I tested the sample data, I have
got the attached error message. Does anyone have experience in running
SCIRun on Linux machine? Any response would be very much appreciated.

Regards

Lin

======================================================================= ====
== 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::TetVolMesh::Cell]':
/usr/local/SCIRun/src/Core/Datatypes/GenericField.h:46:   instantiated from
here
/usr/local/SCIRun/src/Core/Datatypes/FieldInterfaceAux.h:584: error: no
   matching function for call to `SCIRun::TetVolField<int>::value(
   SCIRun::Tensor&, SCIRun::CellIndex<int>&)'
/usr/local/SCIRun/src/Core/Datatypes/GenericField.h:278: error: candidates
are:
   bool SCIRun::GenericField<Mesh, FData>::value(typename FData::value_type&,
   typename Mesh::Node::index_type) const [with Mesh = SCIRun::TetVolMesh,
   FData = std::vector<int, std::allocator<int> >]
/usr/local/SCIRun/src/Core/Datatypes/GenericField.h:285: error:

   bool SCIRun::GenericField<Mesh, FData>::value(typename FData::value_type&,
   typename Mesh::Edge::index_type) const [with Mesh = SCIRun::TetVolMesh,
   FData = std::vector<int, std::allocator<int> >]
/usr/local/SCIRun/src/Core/Datatypes/GenericField.h:292: error:

   bool SCIRun::GenericField<Mesh, FData>::value(typename FData::value_type&,
   typename Mesh::Face::index_type) const [with Mesh = SCIRun::TetVolMesh,
   FData = std::vector<int, std::allocator<int> >]
/usr/local/SCIRun/src/Core/Datatypes/GenericField.h:299: error:

   bool SCIRun::GenericField<Mesh, FData>::value(typename FData::value_type&,
   typename Mesh::Cell::index_type) const [with Mesh = SCIRun::TetVolMesh,
   FData = std::vector<int, std::allocator<int> >]
/usr/local/SCIRun/src/Core/Datatypes/GenericField.h:332: error:

   typename FData::value_type SCIRun::GenericField<Mesh,
FData>::value(typename
   Mesh::Node::index_type) const [with Mesh = SCIRun::TetVolMesh, FData =
   std::vector<int, std::allocator<int> >]
/usr/local/SCIRun/src/Core/Datatypes/GenericField.h:338: error:

   typename FData::value_type SCIRun::GenericField<Mesh,
FData>::value(typename
   Mesh::Edge::index_type) const [with Mesh = SCIRun::TetVolMesh, FData =
   std::vector<int, std::allocator<int> >]
/usr/local/SCIRun/src/Core/Datatypes/GenericField.h:344: error:

   typename FData::value_type SCIRun::GenericField<Mesh,
FData>::value(typename
   Mesh::Face::index_type) const [with Mesh = SCIRun::TetVolMesh, FData =
   std::vector<int, std::allocator<int> >]
/usr/local/SCIRun/src/Core/Datatypes/GenericField.h:350: error:

   typename FData::value_type SCIRun::GenericField<Mesh,
FData>::value(typename
   Mesh::Cell::index_type) const [with Mesh = SCIRun::TetVolMesh, FData =
   std::vector<int, std::allocator<int> >]
cc1plus: No space left on device: error writing to /tmp/ccQar1nK.s
gmake: *** [TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.o] Error 1
DynamicLoader - Successfully created
/home/lguo/on-the-fly-libs//TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.cc
DynamicLoader - Executing: cd /home/lguo/on-the-fly-libs/; /usr/bin/gmake
TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.so
DynamicLoader::compile_so() syscal error 512: command was 'cd
/home/lguo/on-the-fly-libs/; /usr/bin/gmake
TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.so >
TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.log 2>&1'
set -e; g++ -M -Wall -O2    -I/usr/X11R6/include
-I/usr/local/SCIRun/Thirdparty/1.20/Linux/gcc-3.3.2-32bit/include
-I/usr/local/SCIRun/Thirdparty/1.20/Linux/gcc-3.3.2-32bit/src/tcl8.3.2/generic

-I/usr/local/SCIRun/Thirdparty/1.20/Linux/gcc-3.3.2-32bit/src/tk8.3.2/generic
-I/usr/local/SCIRun/computing -I/usr/local/SCIRun/src
-I/usr/local/SCIRun/src/Packages -I/usr/local/SCIRun/src/include
TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.cc \
          | sed 's/\(TFInterfaceMaker.TetVolFieldint.TetVolMeshCell\)\.o[
:]*/\1.o TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.d : /g' >
TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.d; \
          [ -s TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.d ] || rm -f
TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.d
rm -f TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.o
TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.so
TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.dylib
g++ -c -Wall -O2    -I/usr/X11R6/include
-I/usr/local/SCIRun/Thirdparty/1.20/Linux/gcc-3.3.2-32bit/include
-I/usr/local/SCIRun/Thirdparty/1.20/Linux/gcc-3.3.2-32bit/src/tcl8.3.2/generic

-I/usr/local/SCIRun/Thirdparty/1.20/Linux/gcc-3.3.2-32bit/src/tk8.3.2/generic
-I/usr/local/SCIRun/computing -I/usr/local/SCIRun/src
-I/usr/local/SCIRun/src/Packages -I/usr/local/SCIRun/src/include
TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.cc -o
TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.o

cc1plus
:

No

space

left

on

device
:

error

closing

/tmp/ccLvivCI.s
gmake: *** [TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.o] Error 1
DYNAMIC COMPILATION ERROR:
/home/lguo/on-the-fly-libs//TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.so
does not compile!!
/home/lguo/on-the-fly-libs//TFInterfaceMaker.TetVolFieldint.TetVolMeshCell.so:
cannot open shared object file: No such file or directory
REMARK: Dynamic compilation completed.
ERROR: Could not compile algorithm for 'TFInterfaceMaker<TetVolField<int> ,
TetVolMesh::Cell>'.
REMARK: Dynamically compiling some code.
DynamicLoader - Successfully created
/home/lguo/on-the-fly-libs//RenderField.TetVolFieldint.TetVolMeshCell.cc
DynamicLoader - Executing: cd /home/lguo/on-the-fly-libs/; /usr/bin/gmake
RenderField.TetVolFieldint.TetVolMeshCell.so
DynamicLoader::compile_so() syscal error 512: command was 'cd
/home/lguo/on-the-fly-libs/; /usr/bin/gmake
RenderField.TetVolFieldint.TetVolMeshCell.so >
RenderField.TetVolFieldint.TetVolMeshCell.log 2>&1'
set -e; g++ -M -Wall -O2    -I/usr/X11R6/include
-I/usr/local/SCIRun/Thirdparty/1.20/Linux/gcc-3.3.2-32bit/include
-I/usr/local/SCIRun/Thirdparty/1.20/Linux/gcc-3.3.2-32bit/src/tcl8.3.2/generic

-I/usr/local/SCIRun/Thirdparty/1.20/Linux/gcc-3.3.2-32bit/src/tk8.3.2/generic
-I/usr/local/SCIRun/computing -I/usr/local/SCIRun/src
-I/usr/local/SCIRun/src/Packages -I/usr/local/SCIRun/src/include
RenderField.TetVolFieldint.TetVolMeshCell.cc \
          | sed 's/\(RenderField.TetVolFieldint.TetVolMeshCell\)\.o[ :]*/\1.o
RenderField.TetVolFieldint.TetVolMeshCell.d : /g' >
RenderField.TetVolFieldint.TetVolMeshCell.d; \
          [ -s RenderField.TetVolFieldint.TetVolMeshCell.d ] || rm -f
RenderField.TetVolFieldint.TetVolMeshCell.d
rm -f RenderField.TetVolFieldint.TetVolMeshCell.o
RenderField.TetVolFieldint.TetVolMeshCell.so
RenderField.TetVolFieldint.TetVolMeshCell.dylib
g++ -c -Wall -O2    -I/usr/X11R6/include
-I/usr/local/SCIRun/Thirdparty/1.20/Linux/gcc-3.3.2-32bit/include
-I/usr/local/SCIRun/Thirdparty/1.20/Linux/gcc-3.3.2-32bit/src/tcl8.3.2/generic

-I/usr/local/SCIRun/Thirdparty/1.20/Linux/gcc-3.3.2-32bit/src/tk8.3.2/generic
-I/usr/local/SCIRun/computing -I/usr/local/SCIRun/src
-I/usr/local/SCIRun/src/Packages -I/usr/local/SCIRun/src/include
RenderField.TetVolFieldint.TetVolMeshCell.cc -o
RenderField.TetVolFieldint.TetVolMeshCell.o

cc1plus
:

No

space

left

on

device
:

error

writing

to

/tmp/ccGWTTCp.s
gmake: *** [RenderField.TetVolFieldint.TetVolMeshCell.o] Error 1
DYNAMIC COMPILATION ERROR:
/home/lguo/on-the-fly-libs//RenderField.TetVolFieldint.TetVolMeshCell.so does
not compile!!
REMARK: Dynamic compilation completed.
ERROR: Could not compile algorithm for 'RenderField<TetVolField<int> ,
TetVolMesh::Cell>'.

[SCIRUN-USERS] problems with running SCIRun on Fedora, Linxin Guo, 05/02/2004
- Re: [SCIRUN-USERS] problems with running SCIRun on Fedora, David Weinstein, 05/03/2004

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