date:20130910

[Paraview] build failure

2013-09-10 Thread Scott, W Alan

I am getting the following error with a make install.  Anyone have any ideas?

Thanks!

Alan

-- Installing: 
/projects/viz/paraview/ParaView/4.1.0-alan/Linux-eng-sci-rhel6-x86_64/bin/pvpython
-- Installing: 
/projects/viz/paraview/ParaView/4.1.0-alan/Linux-eng-sci-rhel6-x86_64/lib/paraview-4.0/paraview
CMake Error at Applications/ParaView/cmake_install.cmake:45 (FILE):
  file RPATH_CHANGE given FILE
  
"/projects/viz/paraview/ParaView/4.1.0-alan/Linux-eng-sci-rhel6-x86_64/lib/paraview-4.0/paraview"
  that does not exist.
Call Stack (most recent call first):
  Applications/cmake_install.cmake:37 (INCLUDE)
  cmake_install.cmake:99 (INCLUDE)


gmake: *** [install] Error 1


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Re: [Paraview] Building on Titan using ParaViewSuperbuild

2013-09-10 Thread Vanmoer, Mark W

Hi Hong and David,

I was able to get FortranCInterface to build in the tools directory. Even 
though we were doing module load gcc, CMake was picking up $CC and $CXX as gcc 
4.3.4, instead of gcc 4.7.2 like it should have. The fix is to do as in 
configcross.sh and export CC and CXX,

So my configtools.sh is now

# from David DeMarle
# system CMake is too old
export PATH=/ccs/home/vanmoer/builds/byhand/CMake/2.8.11.2/bin:$PATH
#switch compiler to compile for front end
module unload PrgEnv-pgi
module load gcc
export CC=/opt/gcc/4.7.2/bin/gcc
export CXX=/opt/gcc/4.7.2/bin/g++
#configure settings to build compile tools only

cmake \
-DCROSS_BUILD_STAGE:STRING=TOOLS -Dcross_target:STRING=xk7_gnu \
-DCMAKE_BUILD_TYPE:STRING=Release \
-DBUILD_TESTING:BOOL=FALSE \
-DParaView_FROM_GIT:BOOL=OFF \
-DENABLE_paraview:BOOL=TRUE \
-DENABLE_boost:BOOL=TRUE \
-DENABLE_python:BOOL=TRUE \
-DENABLE_portfwd:BOOL=FALSE \
../ParaViewSuperbuild

I just started a cross compile based on that and will report back when that 
finishes.
Mark


From: Hong Yi [mailto:hon...@renci.org]
Sent: Tuesday, September 10, 2013 4:11 PM
To: Vanmoer, Mark W; David E DeMarle
Cc: paraview@paraview.org
Subject: RE: [Paraview] Building on Titan using ParaViewSuperbuild

Thanks, Mark. It is good to know it is not only me having this problem. I found 
if I remove "-L/usr/lib64/gcc/x86_64-suse-linux/4.3  
-L/usr/x86_64-suse-linux/lib" from the build line, I can successfully build 
FortranCInterface. So the question now becomes how I can remove those two lib 
paths within CMake so that it can build FortranCInterface and set corresponding 
flags correctly. Let me know if anybody has some pointers on how to do that 
within CMake.

Thanks,
Hong

From: Vanmoer, Mark W [mailto:mvanm...@illinois.edu]
Sent: Tuesday, September 10, 2013 2:47 PM
To: Hong Yi; David E DeMarle; Vanmoer, Mark W
Cc: paraview@paraview.org
Subject: RE: [Paraview] Building on Titan using ParaViewSuperbuild

I have the same errors in my CMakeError.log, if I understand what's going on 
right, those symbols are defined in libgcc_s.so in the same directory, and so 
that lib isn't being linked?

Mark

From: Hong Yi [mailto:hon...@renci.org]
Sent: Tuesday, September 10, 2013 1:21 PM
To: David E DeMarle; Vanmoer, Mark W
Cc: paraview@paraview.org
Subject: RE: [Paraview] Building on Titan using ParaViewSuperbuild

Hi David,

I found FortranCInterface was not built even in the first TOOLS pass. Here are 
the errors I am getting from CMakeError.log:

-
/opt/gcc/4.7.2/bin/gfortran  CMakeFiles/FortranCInterface.dir/main.F.o 
CMakeFiles/FortranCInterface.dir/call_sub.f.o 
CMakeFiles/FortranCInterface.dir/call_mod.f90.o  -o FortranCInterface  
-L/usr/lib64/gcc/x86_64-suse-linux/4.3  -L/usr/x86_64-suse-linux/lib -rdynamic 
libsymbols.a libmyfort.a
/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64/libgfortran.so:
 undefined reference to `__gttf2@GCC_4.3.0'
/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64/libgfortran.so:
 undefined reference to `__netf2@GCC_4.3.0'
/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64/libgfortran.so:
 undefined reference to `__lttf2@GCC_4.3.0'
/usr/bin/ld: link errors found, deleting executable `FortranCInterface'
-

Could you confirm whether you are getting this error also for your superbuild 
on Titan? If you are not seeing these errors, could you confirm whether you are 
using the default gcc version 4.7.2 or some newer version?

Superbuild is able to build other libraries successfully for me on Titan except 
for this FortranCInterface problems, so I am hoping to confirm with you to see 
whether this is a specific problem on my part.

Thanks for all your help!

Hong

From: paraview-boun...@paraview.org 
[paraview-boun...@paraview.org] on behalf of David E DeMarle 
[dave.dema...@kitware.com]
Sent: Thursday, August 29, 2013 1:21 PM
To: Vanmoer, Mark W
Cc: paraview@paraview.org
Subject: Re: [Paraview] Building on Titan using ParaViewSuperbuild
Your tools build is pointing to the compiler wrapper that you normally would 
use to make code for the back end.
The tools build should just use plain old local gcc since we only build things 
at that point that run on the login node.

Try these setup scripts:
I source configtools.sh to set up my environment before I build the compile 
tools, and configcross.sh before before I cross compile ParaView.

configtools.sh
#use my own cmake, system one is too old
setenv PATH /autofs/na4_proj/csc035/demarle/pvdev/titan/cmake-build/bin:${PATH}
#switch compiler to compile code for front end
module unload PrgEnv-pgi
module load gcc
#configure settings for to build compile tools only
cmake \
  -DCROSS_BUILD_STAGE:STRING=TOOLS -Dcross_target:STRING=xk7_gnu \
  -DCMAKE_BUILD_TYPE:STRING=Release \
  -D

Re: [Paraview] Building on Titan using ParaViewSuperbuild

2013-09-10 Thread Vanmoer, Mark W

Hong, those libs appear to get added by CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES. 
There's a discussion on the CMake mailing list where someone asks about not 
linking to the C++ standard library:
http://www.cmake.org/pipermail/cmake/2012-October/052304.html

Where it seems one suggestion is to set this to blank and another is to remove 
the particular library from the list. I'm not sure where one would put this, 
though, in the top ParaViewDefaults.cmake? I'll try and report back.

Mark


From: Hong Yi [mailto:hon...@renci.org]
Sent: Tuesday, September 10, 2013 4:11 PM
To: Vanmoer, Mark W; David E DeMarle
Cc: paraview@paraview.org
Subject: RE: [Paraview] Building on Titan using ParaViewSuperbuild

Thanks, Mark. It is good to know it is not only me having this problem. I found 
if I remove "-L/usr/lib64/gcc/x86_64-suse-linux/4.3  
-L/usr/x86_64-suse-linux/lib" from the build line, I can successfully build 
FortranCInterface. So the question now becomes how I can remove those two lib 
paths within CMake so that it can build FortranCInterface and set corresponding 
flags correctly. Let me know if anybody has some pointers on how to do that 
within CMake.

Thanks,
Hong

From: Vanmoer, Mark W [mailto:mvanm...@illinois.edu]
Sent: Tuesday, September 10, 2013 2:47 PM
To: Hong Yi; David E DeMarle; Vanmoer, Mark W
Cc: paraview@paraview.org
Subject: RE: [Paraview] Building on Titan using ParaViewSuperbuild

I have the same errors in my CMakeError.log, if I understand what's going on 
right, those symbols are defined in libgcc_s.so in the same directory, and so 
that lib isn't being linked?

Mark

From: Hong Yi [mailto:hon...@renci.org]
Sent: Tuesday, September 10, 2013 1:21 PM
To: David E DeMarle; Vanmoer, Mark W
Cc: paraview@paraview.org
Subject: RE: [Paraview] Building on Titan using ParaViewSuperbuild

Hi David,

I found FortranCInterface was not built even in the first TOOLS pass. Here are 
the errors I am getting from CMakeError.log:

-
/opt/gcc/4.7.2/bin/gfortran  CMakeFiles/FortranCInterface.dir/main.F.o 
CMakeFiles/FortranCInterface.dir/call_sub.f.o 
CMakeFiles/FortranCInterface.dir/call_mod.f90.o  -o FortranCInterface  
-L/usr/lib64/gcc/x86_64-suse-linux/4.3  -L/usr/x86_64-suse-linux/lib -rdynamic 
libsymbols.a libmyfort.a
/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64/libgfortran.so:
 undefined reference to `__gttf2@GCC_4.3.0'
/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64/libgfortran.so:
 undefined reference to `__netf2@GCC_4.3.0'
/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64/libgfortran.so:
 undefined reference to `__lttf2@GCC_4.3.0'
/usr/bin/ld: link errors found, deleting executable `FortranCInterface'
-

Could you confirm whether you are getting this error also for your superbuild 
on Titan? If you are not seeing these errors, could you confirm whether you are 
using the default gcc version 4.7.2 or some newer version?

Superbuild is able to build other libraries successfully for me on Titan except 
for this FortranCInterface problems, so I am hoping to confirm with you to see 
whether this is a specific problem on my part.

Thanks for all your help!

Hong

From: paraview-boun...@paraview.org 
[paraview-boun...@paraview.org] on behalf of David E DeMarle 
[dave.dema...@kitware.com]
Sent: Thursday, August 29, 2013 1:21 PM
To: Vanmoer, Mark W
Cc: paraview@paraview.org
Subject: Re: [Paraview] Building on Titan using ParaViewSuperbuild
Your tools build is pointing to the compiler wrapper that you normally would 
use to make code for the back end.
The tools build should just use plain old local gcc since we only build things 
at that point that run on the login node.

Try these setup scripts:
I source configtools.sh to set up my environment before I build the compile 
tools, and configcross.sh before before I cross compile ParaView.

configtools.sh
#use my own cmake, system one is too old
setenv PATH /autofs/na4_proj/csc035/demarle/pvdev/titan/cmake-build/bin:${PATH}
#switch compiler to compile code for front end
module unload PrgEnv-pgi
module load gcc
#configure settings for to build compile tools only
cmake \
  -DCROSS_BUILD_STAGE:STRING=TOOLS -Dcross_target:STRING=xk7_gnu \
  -DCMAKE_BUILD_TYPE:STRING=Release \
  -DBUILD_TESTING:BOOL=FALSE \
  -DParaView_FROM_GIT:BOOL=OFF \
  -DENABLE_paraview:BOOL=TRUE \
  -DENABLE_boost:BOOL=TRUE \
  -DENABLE_python:BOOL=TRUE \
  -DENABLE_portfwd:BOOL=FALSE \
  ../../ParaViewSuperbuild


then make

configcross.sh
#use my own cmake, system one is too old
setenv PATH /autofs/na4_proj/csc035/demarle/pvdev/titan/cmake-build/bin:${PATH}
#switch compiler to compile code for back end
module unload PrgEnv-pgi
module unload gcc
module load PrgEnv-gnu
#not sure why module load wasn't sufficient, but ended up needing to fo

[Paraview] Bug Report

2013-09-10 Thread Adam Dershowitz

I am using paraview 4.0.1 and found a bug.  I am not sure if this is the best 
location to report it, but figured I would try it here.  I hope that it can 
help someone else avoid this problem, and perhaps can get it fixed.

I am running on a Mac OS 10.8.4.  I had an existing pvsm state file.  But, 
every time I tried to open it, I would get an error about a file not found, and 
then paraview would crash.  At first I thought that this was a major bug.  I 
finally figured out that a file path to one of the input files had changed, and 
that is what was causing the problem.
But, the fact that paraview will crash in that case is still a bug.  If 
paraview can't find a file in a state file, it should just report the error 
rather then causing a fatal crash.

-- Adam

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Visit other Kitware open-source projects at 
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Please keep messages on-topic and check the ParaView Wiki at: 
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Re: [Paraview] Building on Titan using ParaViewSuperbuild

2013-09-10 Thread Hong Yi

Thanks, Mark. It is good to know it is not only me having this problem. I found 
if I remove "-L/usr/lib64/gcc/x86_64-suse-linux/4.3  
-L/usr/x86_64-suse-linux/lib" from the build line, I can successfully build 
FortranCInterface. So the question now becomes how I can remove those two lib 
paths within CMake so that it can build FortranCInterface and set corresponding 
flags correctly. Let me know if anybody has some pointers on how to do that 
within CMake.

Thanks,
Hong

From: Vanmoer, Mark W [mailto:mvanm...@illinois.edu]
Sent: Tuesday, September 10, 2013 2:47 PM
To: Hong Yi; David E DeMarle; Vanmoer, Mark W
Cc: paraview@paraview.org
Subject: RE: [Paraview] Building on Titan using ParaViewSuperbuild

I have the same errors in my CMakeError.log, if I understand what's going on 
right, those symbols are defined in libgcc_s.so in the same directory, and so 
that lib isn't being linked?

Mark

From: Hong Yi [mailto:hon...@renci.org]
Sent: Tuesday, September 10, 2013 1:21 PM
To: David E DeMarle; Vanmoer, Mark W
Cc: paraview@paraview.org
Subject: RE: [Paraview] Building on Titan using ParaViewSuperbuild

Hi David,

I found FortranCInterface was not built even in the first TOOLS pass. Here are 
the errors I am getting from CMakeError.log:

-
/opt/gcc/4.7.2/bin/gfortran  CMakeFiles/FortranCInterface.dir/main.F.o 
CMakeFiles/FortranCInterface.dir/call_sub.f.o 
CMakeFiles/FortranCInterface.dir/call_mod.f90.o  -o FortranCInterface  
-L/usr/lib64/gcc/x86_64-suse-linux/4.3  -L/usr/x86_64-suse-linux/lib -rdynamic 
libsymbols.a libmyfort.a
/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64/libgfortran.so:
 undefined reference to `__gttf2@GCC_4.3.0'
/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64/libgfortran.so:
 undefined reference to `__netf2@GCC_4.3.0'
/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64/libgfortran.so:
 undefined reference to `__lttf2@GCC_4.3.0'
/usr/bin/ld: link errors found, deleting executable `FortranCInterface'
-

Could you confirm whether you are getting this error also for your superbuild 
on Titan? If you are not seeing these errors, could you confirm whether you are 
using the default gcc version 4.7.2 or some newer version?

Superbuild is able to build other libraries successfully for me on Titan except 
for this FortranCInterface problems, so I am hoping to confirm with you to see 
whether this is a specific problem on my part.

Thanks for all your help!

Hong

From: paraview-boun...@paraview.org 
[paraview-boun...@paraview.org] on behalf of David E DeMarle 
[dave.dema...@kitware.com]
Sent: Thursday, August 29, 2013 1:21 PM
To: Vanmoer, Mark W
Cc: paraview@paraview.org
Subject: Re: [Paraview] Building on Titan using ParaViewSuperbuild
Your tools build is pointing to the compiler wrapper that you normally would 
use to make code for the back end.
The tools build should just use plain old local gcc since we only build things 
at that point that run on the login node.

Try these setup scripts:
I source configtools.sh to set up my environment before I build the compile 
tools, and configcross.sh before before I cross compile ParaView.

configtools.sh
#use my own cmake, system one is too old
setenv PATH /autofs/na4_proj/csc035/demarle/pvdev/titan/cmake-build/bin:${PATH}
#switch compiler to compile code for front end
module unload PrgEnv-pgi
module load gcc
#configure settings for to build compile tools only
cmake \
  -DCROSS_BUILD_STAGE:STRING=TOOLS -Dcross_target:STRING=xk7_gnu \
  -DCMAKE_BUILD_TYPE:STRING=Release \
  -DBUILD_TESTING:BOOL=FALSE \
  -DParaView_FROM_GIT:BOOL=OFF \
  -DENABLE_paraview:BOOL=TRUE \
  -DENABLE_boost:BOOL=TRUE \
  -DENABLE_python:BOOL=TRUE \
  -DENABLE_portfwd:BOOL=FALSE \
  ../../ParaViewSuperbuild


then make

configcross.sh
#use my own cmake, system one is too old
setenv PATH /autofs/na4_proj/csc035/demarle/pvdev/titan/cmake-build/bin:${PATH}
#switch compiler to compile code for back end
module unload PrgEnv-pgi
module unload gcc
module load PrgEnv-gnu
#not sure why module load wasn't sufficient, but ended up needing to force
#cmake to choose the right compiler
setenv CC /opt/cray/xt-asyncpe/5.17/bin/cc
setenv CXX /opt/cray/xt-asyncpe/5.17/bin/CC
#configure settings to cross compile python, (mesa - implied), and paraview
cmake \
  -DCROSS_BUILD_STAGE:STRING=CROSS -Dcross_target:STRING=xk7_gnu \
  -DCMAKE_BUILD_TYPE:STRING=Release \
  -DBUILD_TESTING:BOOL=TRUE \
  -DParaView_FROM_GIT:BOOL=OFF \
  -DENABLE_paraview:BOOL=TRUE \
  -DENABLE_python:BOOL=TRUE \
  ../../ParaViewSuperbuild

then make again


David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Tue, Aug 27, 2013 at 4:26 PM, Vanmoer, Mark W 
mailto:mvanm...@illinois.edu>> wrote:
Hi, I'm trying to follow the advice on building

Re: [Paraview] Errors when linking catalyst in ParaView version 4.0.1 to, simulation code on Titan (Hong Yi)

2013-09-10 Thread Vanmoer, Mark W

Hi Hong,

Can you share all of the CMake variables regarding Fortran and Phasta 
Coprocessing you might have hand set during the superbuild process? I'm trying 
to compare to a successful non-superbuild Fortran copro install on my 
workstation.

Thanks,
Mark

> -Original Message-
> From: paraview-boun...@paraview.org [mailto:paraview-
> boun...@paraview.org] On Behalf Of Hong Yi
> Sent: Monday, September 09, 2013 12:06 PM
> To: Benson Muite; paraview@paraview.org
> Subject: Re: [Paraview] Errors when linking catalyst in ParaView version 4.0.1
> to, simulation code on Titan (Hong Yi)
> 
> Thanks for the useful info, Benson. I did what you suggested and now
> superbuild can find MPI_FORTRAN. However,
> FortranCInterface_GLOBAL_FOUND variable is zero, so I still got the warning
> "No FortranCInterface mangling known for coprocessorinitialize" during the
> build. Did you get that error also? I have not found where
> FortranCInterface_GLOBAL_FOUND variable is set in CMake yet, so have no
> exact clue on why this variable is zero (i.e., why FortranCInterface_GLOBAL is
> not found). Have to dig in deeper to see what else I need to set for
> superbuild to find FortranCInterface, but let me know if you or anybody else
> in the list have some suggestions on what to look for to resolve this issue.
> 
> Thanks and regards,
> 
> Hong
> 
> From: paraview-boun...@paraview.org [paraview-boun...@paraview.org]
> on behalf of Benson Muite [benson_mu...@yahoo.com]
> Sent: Saturday, September 07, 2013 4:55 AM
> To: paraview@paraview.org
> Subject: Re: [Paraview] Errors when linking catalyst in ParaView version 4.0.1
> to, simulation code on Titan (Hong Yi)
> 
> Hi Hong Yi,
> 
> I got a similar error. One way to is to find the paths for the mpi libraries 
> on
> titan directly - do module show cray_mpich for the mpich version in your gcc
> environment. When you run ccmake, toggle to the advanced configuration
> and enter the paths directly. You will need to manually add all the statically
> linked libraries. To put in more than one library on the same line, you will
> need to separate the paths by semicolons.
> 
> Regards,
> Benson
> 
> On 07/09/2013 09:08, paraview-requ...@paraview.org wrote:
> >
> >
> > --
> >
> > Message: 1
> > Date: Fri, 6 Sep 2013 21:27:23 +
> > From: Hong Yi 
> > Subject: Re: [Paraview] Errors when linking catalyst in ParaView
> >   version 4.0.1 to simulation code on Titan
> > To: David E DeMarle , Andy Bauer
> >   
> > Cc: "paraview@paraview.org" 
> > Message-ID:
> >
> > <65F8B323A072504ABFC5D3D8751910514FEB3E51@MAIL-
> MBX2.ad.renci.org>
> > Content-Type: text/plain; charset="windows-1252"
> >
> > Hi Andy, David,
> >
> > I used GCC to build both ParaView and simulation code. The problem is
> with ParaView's superbuild not being able to find MPI_Fortran on Titan. I got
> the following messages during superbuild:
> >
> > --
> > Could NOT find MPI_Fortran (missing:  MPI_Fortran_LIBRARIES
> > MPI_Fortran_INCLUDE_PATH)
> >
> > No FortranCInterface mangling known for coprocessorinitialize
> >
> > ...
> >
> > --
> >
> > I then tried to add "ftn" into FindMPI.cmake, but got the message "Unable
> to determine MPI from MPI driver /opt/cray/xt-asyncpe/5.17/bin/ftn" prior
> to those MPI_Fortran errors. I looked at ftn wrapper but could not
> determine the mpi Fortran executable, either. Let me know if you have ideas
> on how to make superbuild to find MPI_Fortran.
> >
> > Many thanks,
> >
> > Hong
> >
> > 
> > From: David E DeMarle [dave.dema...@kitware.com]
> > Sent: Friday, September 06, 2013 4:21 PM
> > To: Andy Bauer
> > Cc: Hong Yi; paraview@paraview.org
> > Subject: Re: [Paraview] Errors when linking catalyst in ParaView
> > version 4.0.1 to simulation code on Titan
> >
> > The Superbuild on cray uses the backend flavor of the GCC compiler
> (xk7_gcc target). I haven't made an xk7_pgi target yet.
> >
> > David E DeMarle
> > Kitware, Inc.
> > R&D Engineer
> > 21 Corporate Drive
> > Clifton Park, NY 12065-8662
> > Phone: 518-881-4909
> >
> >
> > On Fri, Sep 6, 2013 at 4:07 PM, Andy Bauer
> mailto:andy.ba...@kitware.com>> wrote:
> > Hi Hong,
> >
> > This Fortran/C mangling issue is a bit tricky. It has to be done during the
> configuration process because the C and Fortran compilers won't necessarily
> know how to properly mangle the function names. The thing is that it the
> configuration process depends on using the same compilers as any other
> code that links to the generated libraries. You can check out Bill Hoffman's
> blog at http://www.kitware.com/blog/home/post/231 which explains this
> issue and how CMake handles it. Now if ParaView Catalyst was built with GCC
> and you built your simulation code with PGI, for example, then it wouldn't
> surprise me that this issue crops up. What compilers did you use for your
> ParaView

Re: [Paraview] Building on Titan using ParaViewSuperbuild

2013-09-10 Thread Vanmoer, Mark W

I have the same errors in my CMakeError.log, if I understand what's going on 
right, those symbols are defined in libgcc_s.so in the same directory, and so 
that lib isn't being linked?

Mark

From: Hong Yi [mailto:hon...@renci.org]
Sent: Tuesday, September 10, 2013 1:21 PM
To: David E DeMarle; Vanmoer, Mark W
Cc: paraview@paraview.org
Subject: RE: [Paraview] Building on Titan using ParaViewSuperbuild

Hi David,

I found FortranCInterface was not built even in the first TOOLS pass. Here are 
the errors I am getting from CMakeError.log:

-
/opt/gcc/4.7.2/bin/gfortran  CMakeFiles/FortranCInterface.dir/main.F.o 
CMakeFiles/FortranCInterface.dir/call_sub.f.o 
CMakeFiles/FortranCInterface.dir/call_mod.f90.o  -o FortranCInterface  
-L/usr/lib64/gcc/x86_64-suse-linux/4.3  -L/usr/x86_64-suse-linux/lib -rdynamic 
libsymbols.a libmyfort.a
/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64/libgfortran.so:
 undefined reference to `__gttf2@GCC_4.3.0'
/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64/libgfortran.so:
 undefined reference to `__netf2@GCC_4.3.0'
/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64/libgfortran.so:
 undefined reference to `__lttf2@GCC_4.3.0'
/usr/bin/ld: link errors found, deleting executable `FortranCInterface'
-

Could you confirm whether you are getting this error also for your superbuild 
on Titan? If you are not seeing these errors, could you confirm whether you are 
using the default gcc version 4.7.2 or some newer version?

Superbuild is able to build other libraries successfully for me on Titan except 
for this FortranCInterface problems, so I am hoping to confirm with you to see 
whether this is a specific problem on my part.

Thanks for all your help!

Hong

From: paraview-boun...@paraview.org 
[paraview-boun...@paraview.org] on behalf of David E DeMarle 
[dave.dema...@kitware.com]
Sent: Thursday, August 29, 2013 1:21 PM
To: Vanmoer, Mark W
Cc: paraview@paraview.org
Subject: Re: [Paraview] Building on Titan using ParaViewSuperbuild
Your tools build is pointing to the compiler wrapper that you normally would 
use to make code for the back end.
The tools build should just use plain old local gcc since we only build things 
at that point that run on the login node.

Try these setup scripts:
I source configtools.sh to set up my environment before I build the compile 
tools, and configcross.sh before before I cross compile ParaView.

configtools.sh
#use my own cmake, system one is too old
setenv PATH /autofs/na4_proj/csc035/demarle/pvdev/titan/cmake-build/bin:${PATH}
#switch compiler to compile code for front end
module unload PrgEnv-pgi
module load gcc
#configure settings for to build compile tools only
cmake \
  -DCROSS_BUILD_STAGE:STRING=TOOLS -Dcross_target:STRING=xk7_gnu \
  -DCMAKE_BUILD_TYPE:STRING=Release \
  -DBUILD_TESTING:BOOL=FALSE \
  -DParaView_FROM_GIT:BOOL=OFF \
  -DENABLE_paraview:BOOL=TRUE \
  -DENABLE_boost:BOOL=TRUE \
  -DENABLE_python:BOOL=TRUE \
  -DENABLE_portfwd:BOOL=FALSE \
  ../../ParaViewSuperbuild

then make

configcross.sh
#use my own cmake, system one is too old
setenv PATH /autofs/na4_proj/csc035/demarle/pvdev/titan/cmake-build/bin:${PATH}
#switch compiler to compile code for back end
module unload PrgEnv-pgi
module unload gcc
module load PrgEnv-gnu
#not sure why module load wasn't sufficient, but ended up needing to force
#cmake to choose the right compiler
setenv CC /opt/cray/xt-asyncpe/5.17/bin/cc
setenv CXX /opt/cray/xt-asyncpe/5.17/bin/CC
#configure settings to cross compile python, (mesa - implied), and paraview
cmake \
  -DCROSS_BUILD_STAGE:STRING=CROSS -Dcross_target:STRING=xk7_gnu \
  -DCMAKE_BUILD_TYPE:STRING=Release \
  -DBUILD_TESTING:BOOL=TRUE \
  -DParaView_FROM_GIT:BOOL=OFF \
  -DENABLE_paraview:BOOL=TRUE \
  -DENABLE_python:BOOL=TRUE \
  ../../ParaViewSuperbuild

then make again

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Tue, Aug 27, 2013 at 4:26 PM, Vanmoer, Mark W 
mailto:mvanm...@illinois.edu>> wrote:
Hi, I'm trying to follow the advice on building ParaView on Titan using the 
ParaViewSuperbuild method from an earlier discussion in June.

When I run make in the "TOOLS" directory I get the following error:

[ 66%] Building CXX object 
Utilities/ProcessXML/CMakeFiles/kwProcessXML.dir/ProcessXML.cxx.o
Linking CXX executable ../../bin/vtkkwProcessXML-pv4.0
/usr/bin/ld: attempted static link of dynamic object 
`../../lib/libvtkCommonCore-pv4.0.so.1'
collect2: error: ld returned 1 exit status
make[6]: *** [bin/vtkkwProcessXML-pv4.0] Error 1
make[5]: *** [Utilities/ProcessXML/CMakeFiles/kwProcessXML.dir/all] Error 2
make[4]: *** [CMakeFiles/pvCompileTools.dir/rule] Error 2
make[3]: *** [pvCompileTools] Error 2
CMake Error at 
/ccs/home/vanmoer/builds/superbuild/tools-build/pv-paravie

Re: [Paraview] Building on Titan using ParaViewSuperbuild

2013-09-10 Thread Hong Yi

Hi David,

I found FortranCInterface was not built even in the first TOOLS pass. Here are 
the errors I am getting from CMakeError.log:

-
/opt/gcc/4.7.2/bin/gfortran  CMakeFiles/FortranCInterface.dir/main.F.o 
CMakeFiles/FortranCInterface.dir/call_sub.f.o 
CMakeFiles/FortranCInterface.dir/call_mod.f90.o  -o FortranCInterface  
-L/usr/lib64/gcc/x86_64-suse-linux/4.3  -L/usr/x86_64-suse-linux/lib -rdynamic 
libsymbols.a libmyfort.a
/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64/libgfortran.so:
 undefined reference to `__gttf2@GCC_4.3.0'
/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64/libgfortran.so:
 undefined reference to `__netf2@GCC_4.3.0'
/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64/libgfortran.so:
 undefined reference to `__lttf2@GCC_4.3.0'
/usr/bin/ld: link errors found, deleting executable `FortranCInterface'
-

Could you confirm whether you are getting this error also for your superbuild 
on Titan? If you are not seeing these errors, could you confirm whether you are 
using the default gcc version 4.7.2 or some newer version?

Superbuild is able to build other libraries successfully for me on Titan except 
for this FortranCInterface problems, so I am hoping to confirm with you to see 
whether this is a specific problem on my part.

Thanks for all your help!

Hong


From: paraview-boun...@paraview.org [paraview-boun...@paraview.org] on behalf 
of David E DeMarle [dave.dema...@kitware.com]
Sent: Thursday, August 29, 2013 1:21 PM
To: Vanmoer, Mark W
Cc: paraview@paraview.org
Subject: Re: [Paraview] Building on Titan using ParaViewSuperbuild

Your tools build is pointing to the compiler wrapper that you normally would 
use to make code for the back end.
The tools build should just use plain old local gcc since we only build things 
at that point that run on the login node.

Try these setup scripts:
I source configtools.sh to set up my environment before I build the compile 
tools, and configcross.sh before before I cross compile ParaView.

configtools.sh
#use my own cmake, system one is too old
setenv PATH /autofs/na4_proj/csc035/demarle/pvdev/titan/cmake-build/bin:${PATH}
#switch compiler to compile code for front end
module unload PrgEnv-pgi
module load gcc
#configure settings for to build compile tools only
cmake \
  -DCROSS_BUILD_STAGE:STRING=TOOLS -Dcross_target:STRING=xk7_gnu \
  -DCMAKE_BUILD_TYPE:STRING=Release \
  -DBUILD_TESTING:BOOL=FALSE \
  -DParaView_FROM_GIT:BOOL=OFF \
  -DENABLE_paraview:BOOL=TRUE \
  -DENABLE_boost:BOOL=TRUE \
  -DENABLE_python:BOOL=TRUE \
  -DENABLE_portfwd:BOOL=FALSE \
  ../../ParaViewSuperbuild


then make

configcross.sh
#use my own cmake, system one is too old
setenv PATH /autofs/na4_proj/csc035/demarle/pvdev/titan/cmake-build/bin:${PATH}
#switch compiler to compile code for back end
module unload PrgEnv-pgi
module unload gcc
module load PrgEnv-gnu
#not sure why module load wasn't sufficient, but ended up needing to force
#cmake to choose the right compiler
setenv CC /opt/cray/xt-asyncpe/5.17/bin/cc
setenv CXX /opt/cray/xt-asyncpe/5.17/bin/CC
#configure settings to cross compile python, (mesa - implied), and paraview
cmake \
  -DCROSS_BUILD_STAGE:STRING=CROSS -Dcross_target:STRING=xk7_gnu \
  -DCMAKE_BUILD_TYPE:STRING=Release \
  -DBUILD_TESTING:BOOL=TRUE \
  -DParaView_FROM_GIT:BOOL=OFF \
  -DENABLE_paraview:BOOL=TRUE \
  -DENABLE_python:BOOL=TRUE \
  ../../ParaViewSuperbuild

then make again


David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909


On Tue, Aug 27, 2013 at 4:26 PM, Vanmoer, Mark W 
mailto:mvanm...@illinois.edu>> wrote:
Hi, I'm trying to follow the advice on building ParaView on Titan using the 
ParaViewSuperbuild method from an earlier discussion in June.

When I run make in the "TOOLS" directory I get the following error:

[ 66%] Building CXX object 
Utilities/ProcessXML/CMakeFiles/kwProcessXML.dir/ProcessXML.cxx.o
Linking CXX executable ../../bin/vtkkwProcessXML-pv4.0
/usr/bin/ld: attempted static link of dynamic object 
`../../lib/libvtkCommonCore-pv4.0.so.1'
collect2: error: ld returned 1 exit status
make[6]: *** [bin/vtkkwProcessXML-pv4.0] Error 1
make[5]: *** [Utilities/ProcessXML/CMakeFiles/kwProcessXML.dir/all] Error 2
make[4]: *** [CMakeFiles/pvCompileTools.dir/rule] Error 2
make[3]: *** [pvCompileTools] Error 2
CMake Error at 
/ccs/home/vanmoer/builds/superbuild/tools-build/pv-paraview-build.cmake:26 
(message):
  Failed!!!


make[2]: *** [paraview/src/paraview-stamp/paraview-build] Error 1

I don't see a BUILD_SHARED that I can toggle. All of the 
CMAKE_SHARED_LINKER_FLAGS* vars are empty, if those are related.

Any suggestions?

Thanks,
Mark



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Re: [Paraview] Errors when linking catalyst in ParaView version 4.0.1 to, simulation code on Titan (Hong Yi)

2013-09-10 Thread Hong Yi

Hi Mark,

I just added the following:

--
list(APPEND PARAVIEW_OPTIONS 
"-DMPI_Fortran_COMPILER:FILEPATH=/opt/cray/xt-asyncpe/5.17/bin/ftn")
list(APPEND PARAVIEW_OPTIONS 
"-DMPI_Fortran_INCLUDE_PATH:FILEPATH=/opt/cray/mpt/5.6.3/gni/mpich2-gnu/47/include")
list(APPEND PARAVIEW_OPTIONS 
"-DMPI_Fortran_LIBRARIES:FILEPATH=/opt/cray/mpt/5.6.3/gni/mpich2-gnu/47/lib/libfmpich.a;/opt/cray/mpt/5.6.3/gni/mpich2-gnu/47/lib/libmpichf90.a")
--

While looking into the CMakeError.log, I found there are a few related 
undefined reference errors during the final linking stages when linking 
FortranCInterface, hence FortranCInterface got dropped in both tools and cross 
stages. I am trying to play with some options and rebuilt everything. 

By the way, have you been able to successfully superbuild paraview with 
FortranCInterface/FortranCMangling built also successfully on Titan? If so, 
could you share what additional options you have added into 
ParaViewDefaults.cmake to have them build successfully?

Thanks,
Hong 


From: Vanmoer, Mark W [mvanm...@illinois.edu]
Sent: Tuesday, September 10, 2013 11:34 AM
To: Hong Yi; paraview@paraview.org
Subject: RE: [Paraview] Errors when linking catalyst in ParaView version 4.0.1 
to, simulation code on Titan (Hong Yi)

Hi Hong,

Can you share all of the CMake variables regarding Fortran and Phasta 
Coprocessing you might have hand set during the superbuild process? I'm trying 
to compare to a successful non-superbuild Fortran copro install on my 
workstation.

Thanks,
Mark

> -Original Message-
> From: paraview-boun...@paraview.org [mailto:paraview-
> boun...@paraview.org] On Behalf Of Hong Yi
> Sent: Monday, September 09, 2013 12:06 PM
> To: Benson Muite; paraview@paraview.org
> Subject: Re: [Paraview] Errors when linking catalyst in ParaView version 4.0.1
> to, simulation code on Titan (Hong Yi)
>
> Thanks for the useful info, Benson. I did what you suggested and now
> superbuild can find MPI_FORTRAN. However,
> FortranCInterface_GLOBAL_FOUND variable is zero, so I still got the warning
> "No FortranCInterface mangling known for coprocessorinitialize" during the
> build. Did you get that error also? I have not found where
> FortranCInterface_GLOBAL_FOUND variable is set in CMake yet, so have no
> exact clue on why this variable is zero (i.e., why FortranCInterface_GLOBAL is
> not found). Have to dig in deeper to see what else I need to set for
> superbuild to find FortranCInterface, but let me know if you or anybody else
> in the list have some suggestions on what to look for to resolve this issue.
>
> Thanks and regards,
>
> Hong
> 
> From: paraview-boun...@paraview.org [paraview-boun...@paraview.org]
> on behalf of Benson Muite [benson_mu...@yahoo.com]
> Sent: Saturday, September 07, 2013 4:55 AM
> To: paraview@paraview.org
> Subject: Re: [Paraview] Errors when linking catalyst in ParaView version 4.0.1
> to, simulation code on Titan (Hong Yi)
>
> Hi Hong Yi,
>
> I got a similar error. One way to is to find the paths for the mpi libraries 
> on
> titan directly - do module show cray_mpich for the mpich version in your gcc
> environment. When you run ccmake, toggle to the advanced configuration
> and enter the paths directly. You will need to manually add all the statically
> linked libraries. To put in more than one library on the same line, you will
> need to separate the paths by semicolons.
>
> Regards,
> Benson
>
> On 07/09/2013 09:08, paraview-requ...@paraview.org wrote:
> >
> >
> > --
> >
> > Message: 1
> > Date: Fri, 6 Sep 2013 21:27:23 +
> > From: Hong Yi 
> > Subject: Re: [Paraview] Errors when linking catalyst in ParaView
> >   version 4.0.1 to simulation code on Titan
> > To: David E DeMarle , Andy Bauer
> >   
> > Cc: "paraview@paraview.org" 
> > Message-ID:
> >
> > <65F8B323A072504ABFC5D3D8751910514FEB3E51@MAIL-
> MBX2.ad.renci.org>
> > Content-Type: text/plain; charset="windows-1252"
> >
> > Hi Andy, David,
> >
> > I used GCC to build both ParaView and simulation code. The problem is
> with ParaView's superbuild not being able to find MPI_Fortran on Titan. I got
> the following messages during superbuild:
> >
> > --
> > Could NOT find MPI_Fortran (missing:  MPI_Fortran_LIBRARIES
> > MPI_Fortran_INCLUDE_PATH)
> >
> > No FortranCInterface mangling known for coprocessorinitialize
> >
> > ...
> >
> > --
> >
> > I then tried to add "ftn" into FindMPI.cmake, but got the message "Unable
> to determine MPI from MPI driver /opt/cray/xt-asyncpe/5.17/bin/ftn" prior
> to those MPI_Fortran errors. I looked at ftn wrapper but could not
> determine the mpi Fortran executable, either. Let me know if you have ideas
> on how to make superbuild to find MPI_Fortran.
> >
> > Many thanks,
> >
> > Hong
> >
> > 
> > From: David E DeMarle [

[Paraview] build failure

Re: [Paraview] Building on Titan using ParaViewSuperbuild

Re: [Paraview] Building on Titan using ParaViewSuperbuild

[Paraview] Bug Report

Re: [Paraview] Building on Titan using ParaViewSuperbuild

Re: [Paraview] Errors when linking catalyst in ParaView version 4.0.1 to, simulation code on Titan (Hong Yi)

Re: [Paraview] Building on Titan using ParaViewSuperbuild

Re: [Paraview] Building on Titan using ParaViewSuperbuild

Re: [Paraview] Errors when linking catalyst in ParaView version 4.0.1 to, simulation code on Titan (Hong Yi)

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