[Paraview] [Blog] Why is ParaView using all that memory?

[Ben Boeckel]

Hi,

I've written up a blog post on ParaView and memory usage[1]. If there
are any questions or things that need clarifications, feel free to let
me know.

--Ben

[1]http://www.kitware.com/blog/home/post/631
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Re: [Paraview] PV 4.1.0 ParaView-4.1.0-Linux-64bit/bin/paraview: cannot execute binary file

[Ben Boeckel]

On Sat, Mar 08, 2014 at 16:07:58 +0100, Stephen Wornom wrote:
 I have ubuntu as the operating system 
 
 ParaView-4.1.0-Linux-64bit/bin/paraview: cannot execute binary file 
 
 ls -al /home/stephen/ParaView-4.1.0-Linux-64bit/bin/paraview 
 -rwxr-xr-x 1 stephen stephen 79439 Jan 13 06:48 
 /home/stephen/ParaView-4.1.0-Linux-64bit/bin/paraview 
 
 home:file /home/stephen/ParaView-4.1.0-Linux-64bit/bin/paraview 
 /home/stephen/ParaView-4.1.0-Linux-64bit/bin/paraview: ELF 64-bit LSB 
 executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), 
 for GNU/Linux 2.6.0, not stripped 
 
 Anyone have an idea as to the problem? 

Is the filesystem mounted noexec?

--Ben
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Re: [Paraview] PV 4.1.0 ParaView-4.1.0-Linux-64bit/bin/paraview: cannot execute binary file

[Ben Boeckel]

On Sun, Mar 09, 2014 at 12:20:45 +0100, Stephen Wornom wrote:
 From: Ben Boeckel ben.boec...@kitware.com
  Is the filesystem mounted noexec?
 Not to my knowledge, how would I check?

The output of 'mount' will show the flags for mounted filesystems.

--Ben
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Re: [Paraview] missing python filters from python Shell

[Ben Boeckel]

On Wed, Mar 19, 2014 at 16:55:21 -0400, David E DeMarle wrote:
 Try this technique from Pat Marion.
   http://markmail.org/message/4kp7cxl2ani25cak
 It should give you access to most or all of VTK, not just the subset the
 ParaView exposes.

For those who would like to avoid 'exec', here's the equivalent using
__import__:

m = __import__('paraview.vtk.%s' % moduleName, globals(), locals())
try:
attrlist = m.__all__
except AttributeError:
attrlist = dir(m)
for attr in attrlist:
globals()[attr] = getattr(m, attr)

It doesn'appear that VTK sets __all__, so that should be able to be
removed.

--Ben
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Re: [Paraview] ParaView Digest, Vol 120, Issue 35

[Ben Boeckel]

On Tue, Apr 22, 2014 at 11:05:24 -0600, Jack Vant wrote:
 /usr/bin/ld: /cm/shared/apps/mvapich2/gcc/64/1.9/lib/libmpich.a(setbotf.o):
 relocation R_X86_64_32 against `mpifcmb2_' can not be used when making a
 shared object; recompile with -fPIC
^

 /cm/shared/apps/mvapich2/gcc/64/1.9/lib/libmpich.a: could not read symbols:
 Bad value
 
 collect2: ld returned 1 exit status
 
 make[2]: *** [lib/libvtkVPIC-pv4.1.so.1] Error 1
^^^

 Can someone translate for me?  Can I buy a vowel?  The google has run out
 of gas.

Your mvapich2 installation was not compiled with -fPIC
(position-independent code) which may not be mixed with code compiled
with -fPIC (which shared building enforces). Either compile a static
ParaView or get an mvapich2 built with -fPIC.

--Ben
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Re: [Paraview] ParaviewWeb Multiuser

[Ben Boeckel]

On Mon, May 19, 2014 at 16:03:49 +0200, Daniel Zuidinga wrote:
 'secret': 'katglrt54#%dfg',
 'user': 'sebastien.jourdain',
 'password': 'ousdfbdxldfgh',

Hmm...might want to change these if they're real?

--Ben
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Re: [Paraview] Linking Catalyst example samples with Catalyst

[Ben Boeckel]

On Fri, Jun 06, 2014 at 02:18:42 -0700, Praveen Narayanan wrote:
 I am examining the example code for catalyst from Andy Bauer’s git repository 
  
 (https://github.com/acbauer/CatalystExampleCode).
 
 I am trying to learn about the catalyst workflow before using it in my own in
 situ examples.

So, first, there is no requirement to use a Catalyst-the-build to use
Catalyst-the-coprocessing-API. Catalyst builds are meant for use where a
smaller ParaView is a better fit (super computing, lower memory
constraints, etc.). The naming is indeed confusing :( .

 python catalyze.py -i Editions/Base -o ../catalyst_src
 
 fatal: Not a git repository (or any of the parent directories): .git
 
 Error: Command '['git', 'rev-parse', '--show-toplevel']' returned non-zero 
 exit
 status 128

You can give `-r dir` to tell it the top-level of the source tree.
Without it, it will try and find the top-level using git, which won't
work for tarballs. I'll improve the error message.

 2)  I tried two of the catalyst sources
 
 a.  Base+python: This builds properly and links with the example code
 (CxxFullExample)
 
 b.  Base+essentials+extras+python: This also builds and links with the example
 code, but I get the following runtime error:

When do these errors pop up? The Catalyst build trees are slimmed down
ParaView builds and don't have everything under the sun included (e.g.,
animation classes are missing). If you need other classes, another
edition should be made to include the required classes and proxies.

 3)  The build base+python runs the example code, but does not connect with
 catalyst. Furthermore, upon running make test to test with the sample python
 script in ‘SampleScripts’ (which basically invokes CxxFullExample with the
 python script as an input argument, I get errors stating that it cannot load
 some vtk modules, which upon looking turn out not to be built at all

snip

 I would like to know what I am missing in these builds. It appears that some 
 of
 the vtk modules are not being built:
 
 Error: Could not import vtkCommonComputationalGeometryPython
 
 Error: Could not import vtkRenderingCorePython
 
 Error: Cannot import vtkPVServerManagerDefaultPython
 
 Error: Cannot import vtkPVServerManagerRenderingPython
 
 Error: Cannot import vtkPVAnimationPython

Catalyst builds do not build all ParaView modules, so some missing is
expected.

 What is the correct way to get a working run for the examples supplied. Also,
 how do we connect to catalyst after this?  My understanding is that we just
 load up paraview (4.1) and then the simulation would connect to catalyst after
 we hit ‘Connect to Catalyst’ and load up the ‘Coprocessing’ plugin. Does
 paraview have to be built from source?

The way I've done it is that the simulation loads up Catalyst (using
the vtkCPProcessor class). ParaView can create Python scripts for use
with vtkCPPythonScriptPipeline, but if there is a way to use
ParaView-the-application with in-situ runs, I don't know it. Andy?

 More specifically, is there a particular download version that might work, and
 what flags do we turn on in CMakeLists.txt? Is there any other set of examples
 (although I think the git examples demonstrate the workflow quite properly)
 that we could use to try catalyst?

From a full build, PARAVIEW_ENABLE_CATALYST=ON should be all that is
necessary. From a Catalyst build, the same should be sufficient, but for
any VTK or ParaView classes which you require, you will need to create
an edition to bring them in.

--Ben
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Re: [Paraview] dlclose assertion error with boost::regex

[Ben Boeckel]

On Fri, Jun 20, 2014 at 21:27:01 -0600, Andrew Ho wrote:
 The one thing I can do to get this message to go away is to change the
 target_link_libraries to INTERFACE, but then the code will crash on trying
 to run RequestData because it can't find the symbols.

This tells CMake that anything that links RegexProblem (via CMake code)
should link boost_regex as well (INTERFACE is like PUBLIC except it
isn't used by the library declaring the INTERFACE).

One of the things I'd watch for is whether any other code is using Boost
in the ParaView process (other plugins?) and making sure that *all* of
them use the *same* Boost install. If this doesn't happen, the headers
for one use may not line up with the library that is actually loaded and
can cause the linker to deallocate symbols which don't exist in the
Boost library that is actually loaded (of which only 1 is allowed per
process).

--Ben
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Re: [Paraview] compiling ParaView v4.2.0-RC1-75-gf64ee7a with -DModule_vtkIOXdmf3:BOOL=ON

[Ben Boeckel]

On Tue, Sep 16, 2014 at 16:22:38 +, Su, Simon M CTR USARMY ARL (US) wrote:
 I would like to test out the xdmf3 writer in ParaView 4.2 RC to see if the 
 file
 size is still increase 10 fold when saving pvd file to xmf format.
 
 However, when I configure ParaView v4.2.0-RC1-75-gf64ee7a with
 -DModule_vtkIOXdmf3:BOOL=ON
 
 cmake -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/home/simonsm/tools/
 paraview/paraview-v4.2.0-RC1-75-gf64ee7a_mesa -DPARAVIEW_ENABLE_PYTHON:BOOL=ON
 -DPARAVIEW_USE_MPI:BOOL=ON -DPARAVIEW_ENABLE_WEB:BOOL=OFF
 -DModule_vtkIOXdmf3:BOOL=ON ../ParaView-v4.2.0-RC1-75-gf64ee7a
 
 I got whole bunch of boost related cmake error with cmake version 3.0.0 and
 cmake version 2.8.12.2. Some of the error messages are included at the end of
 this email.
 
 I am able to compile RC1-22-g9ca4e44 version ok but without Module_vtkIOXdmf3
 set to ON. Is there anything on the boost side that I am not setting it right?
 I am compiling on RHEL 6.5 with boost-devel-1.41.0-18.el6.x86_64 installed.

Looks to be a CMake-ified boost. It worked here on Fedora with 1.54.0
(which I don't believe is built using CMake anymore). It seems that it
doesn't support multiple find_package calls. Try setting
Boost_NO_BOOST_CMAKE to ON to force the FindBoost.cmake logic to kick
in.

--Ben
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Re: [Paraview] Failure plotting cell labels

[Ben Boeckel]

On Sun, Sep 28, 2014 at 09:18:52 -0400, Bill Greene wrote:
 I'm trying to plot Cell labels in Paraview 4.1.0
 by defining a string array of cell data. However,
 I get an error in Find Data dialog when I try to select
 the cells. This very simple vtu file demonstrates the
 problem.
 
 Interestingly, when I attach a string array as point data
 in essentially the same way as I add the cell data, I don't
 have any problems plotting Point labels.
 
 If someone can tell me what I'm doing wrong, I would
 be most appreciative.

When selecting which labels to use, there's a gear icon towards the
right of the dialog for settings. In there, it has entries for the
format string to use for the labels. Currently, the default is:

%-#6.3g

which isn't that useful for string or integer arrays. Instead, if you
use:

%s

it appears to work here. What we should do is change the default format
string based on the array being used rather than just assuming
everything is floating point data. I'll file a bug for it.

It also appears that using an improper format string is an easy way to
make ParaView crash; I'll track that down now.

--Ben
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Re: [Paraview] PV 4.2.0 make install error (UNCLASSIFIED)

[Ben Boeckel]

On Tue, Sep 30, 2014 at 14:18:19 +, Su, Simon M CTR USARMY ARL (US) wrote:
 Any help is much appreciated.

I added the appdata stuff; looking into it.

--Ben
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Re: [Paraview] PV 4.2.0 make install error (UNCLASSIFIED)

[Ben Boeckel]

On Tue, Sep 30, 2014 at 11:03:56 -0400, Ben Boeckel wrote:
 On Tue, Sep 30, 2014 at 14:18:19 +, Su, Simon M CTR USARMY ARL (US) wrote:
  Any help is much appreciated.
 
 I added the appdata stuff; looking into it.

Seems that the fact that ParaView's superbuild only builds the paraview
executable (which is tied to the appdata files) is controlled by whether
Qt is enabled in the superbuild and this wasn't used to expect the
appdata directory properly:

http://review.source.kitware.com/#/c/17283/

--Ben
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Re: [Paraview] PV 4.2.0 make install error (UNCLASSIFIED)

[Ben Boeckel]

On Tue, Sep 30, 2014 at 19:36:13 +, Su, Simon M CTR USARMY ARL (US) wrote:
 can I safely ignore the error? Can we assume the binary installation
 is complete? or are there additional installation steps after appdata
 step that is needed for a proper ParaView binary installation? If so,
 how do I get around it?

There are probably more files which need installed after the appdata,
but making the changes in the changeset should allow your make install
from the superbuild to complete fully. Once that happens, the install
should be fine.

--Ben
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Re: [Paraview] PV 4.2.0 make install error (UNCLASSIFIED)

[Ben Boeckel]

On Wed, Oct 01, 2014 at 17:15:34 +, Su, Simon M CTR USARMY ARL (US) wrote:
 I think your patch worked. Cmake not complaining all the way to the end.

The patch has been merged into master now.

--Ben
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Re: [Paraview] ParaView Superbuild - changing default Paraciew cmake option

[Ben Boeckel]

On Fri, Oct 17, 2014 at 15:18:00 +, Su, Simon M CTR USARMY ARL (US) wrote:
 CMake Warning:
   Manually-specified variables were not used by the project:
 
 Boost_NO_BOOST_CMAKE
 Module_vtkIOXdmf3
 
 How do I go around that?

The options need to be passed to the ParaView build itself, not the
superbuild. There's a cache option in the superbuild named
PV_EXTRA_CMAKE_ARGS which should contain
-DBoost_NO_BOOST_CMAKE:BOOL=ON -DModule_vtkIOXdmf3:BOOL=ON to pass it
to the ParaView build properly.

--Ben
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Re: [Paraview] ParaView Superbuild - changing default Paraciew cmake option

[Ben Boeckel]

On Fri, Oct 17, 2014 at 17:41:58 +, Su, Simon M CTR USARMY ARL (US) wrote:
 When I do both argument in the same -DPV_EXTRA_CMAKE_ARGS, cmake also didn't 
 like it.
 -DPV_EXTRA_CMAKE_ARGS=-DModule_vtkIOXdmf3:BOOL=ON 
 -DBoost_NO_BOOST_CMAKE:BOOL=ON 
 
 I am getting 
 CMake Warning:
   Manually-specified variables were not used by the project:
 
 PV_EXTRA_CMAKE_ARGS=-DModule_vtkIOXdmf3

Weird. It looks like the argument is being split at the colon? Playing
around with it a bit, it seems it's the shell's doing. Put the quotes
around the entire argument, not after the equals sign.

--Ben
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Re: [Paraview] ParaView Superbuild - changing default Paraciew cmake option

[Ben Boeckel]

On Mon, Oct 20, 2014 at 15:15:59 +, Su, Simon M CTR USARMY ARL (US) wrote:
 I ran cmake with
 
 -DPV_EXTRA_CMAKE_ARGS:STRING=-DModule_vtkIOXdmf3:BOOL=ON 
 -DBoost_NO_BOOST_CMAKE:BOOL=ON
 
 and check it with ccmake. Looks like -DModule_vtkIOXdmf3:BOOL=ON
 -DBoost_NO_BOOST_CMAKE:BOOL=ON made it into the variable
 PV_EXTRA_CMAKE_ARGS
 
 It appears :STRING does the trick.

Yep. This is a CMake parsing bug; the regular expression for this is too
greedy (it allows '=' in the variable name). Compare:

 -DPV_EXTRA_CMAKE_ARGS=-DModule_vtkIOXdmf3:BOOL=ON 
 -DBoost_NO_BOOST_CMAKE:BOOL=ON
|-| |--| 
|---|
variabletypevalue

versus:

 -DPV_EXTRA_CMAKE_ARGS:STRING=-DModule_vtkIOXdmf3:BOOL=ON 
 -DBoost_NO_BOOST_CMAKE:BOOL=ON
|-| || 
||
  variable   typevalue

this works:

 -DSOME_PATH=C:/path/to/file
|---| |-|
variable   value

because paths with '=' are very rare:

 -DSOME_PATH=C:/path/to/file/with/=/sign
|-| |-| |---|
  variable type value

--Ben
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[Paraview] [ANN] New 4.2.0 Release Binary for OS X 10.6 (Snow Leopard)

[Ben Boeckel]

Hi all,

We've tracked down the error with the Snow Leopard builds of ParaView
4.2.0 and new binaries have been uploaded to the website available
through the normal download page.

To ensure you have the new binary, the md5sum of the new dmg file is:

b1289277d12563321212ed83b70c2f20

The cause of the issue was that the machine building the binaries is a
newer OS X install which contains AVFoundation. This is detected and
linked to by FFmpeg automatically because it never received the proper
--sysroot flag for 10.6. FFmpeg now receives the proper CFLAGS and
LDFLAGS in the superbuild (which should be receiving a new tag in the
next day or two).

Thanks,

--Ben
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Re: [Paraview] ParaView Superbuild - changing default Paraciew cmake option

[Ben Boeckel]

On Mon, Oct 20, 2014 at 15:57:26 +, Su, Simon M CTR USARMY ARL (US) wrote:
 Unfortunately, when I checked the CMakeCache.txt in the directory
 paraview/src/paraview-build after the cmake ran, I am still finding

Sorry, this email went under my radar.

 //Request building vtkIOXdmf3
 Module_vtkIOXdmf3:BOOL=OFF
 
 and Boost_NO_BOOST_CMAKE is none existence in the  CMakeCache.txt
 
 I even tried both 
 -DPV_EXTRA_CMAKE_ARGS:STRING=-DModule_vtkIOXdmf3:BOOL=ON 
 -DBoost_NO_BOOST_CMAKE:BOOL=ON
 and 
 -DPV_EXTRA_CMAKE_ARGS:STRING=Module_vtkIOXdmf3:BOOL=ON 
 Boost_NO_BOOST_CMAKE:BOOL=ON
 
 thoughts?

Looking at the generated command line, it looks like the value is being
put in as a single argument. Try separating it with a ';' instead of a
space.

--Ben
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Re: [Paraview] 550 Neither MX nor MTA found for domain:paraview.org

[Ben Boeckel]

On Wed, Oct 29, 2014 at 12:36:35 +, Anton Shterenlikht wrote:
 Delivery to the following recipient failed permanently:
 
  paraview@paraview.org
 
 Technical details of permanent failure:
 Google tried to deliver your message, but it was rejected by the relay
 outbounds200.obsmtp.com by ou
 tbounds200.obsmtp.com. [207.126.147.11].
 
 The error that the other server returned was:
 550 Neither MX nor MTA found for domain:paraview.org - psmtp

Odd; works here (also worked inside the firewall this morning):

% dig -t MX paraview.org
;  DiG 9.9.6-RedHat-9.9.6-3.fc22  -t MX paraview.org
;; global options: +cmd
;; Got answer:
;; -HEADER- opcode: QUERY, status: NOERROR, id: 56901
;; flags: qr rd ra; QUERY: 1, ANSWER: 0, AUTHORITY: 1, ADDITIONAL: 1

;; OPT PSEUDOSECTION:
; EDNS: version: 0, flags:; udp: 4096
;; QUESTION SECTION:
;paraview.org.  IN  MX

;; AUTHORITY SECTION:
paraview.org.   3600IN  SOA dns1.name-services.com. 
info.name-services.com. 2002050701 10800 3600 604800 3600

;; Query time: 323 msec
;; SERVER: XXX.XXX.XXX.XXX#53(XXX.XXX.XXX.XXX)
;; WHEN: Wed Oct 29 19:09:02 EDT 2014
;; MSG SIZE  rcvd: 104

 Now sending via a different mailer.
 Hope this gets to the list

It was received :) .

--Ben
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Re: [Paraview] Compile error: unknown type name ‘sigjmp_buf’

[Ben Boeckel]

On Wed, Feb 18, 2015 at 12:52:30 -0500, John Moore wrote:
 H5JMP_BUF is not found in CMakeCache.txt, but H5_HAVE_SETJMP_H is, as shown
 below:

Ah, I see that H5JMP_BUF is defined at the top of the file, not by CMake
and is controlled by H5_HAVE_SIGSETJMP (empty on my Fedora install) or
H5_HAVE_SIGLONGJMP ('1' here) from the CMake cache file.

 //Have function setjmp
 H5_HAVE_SETJMP:INTERNAL=1
 //Have include
 sys/resource.h;sys/time.h;unistd.h;sys/ioctl.h;sys/stat.h;sys/socket.h;sys/types.h;stddef.h;setjmp.h
 H5_HAVE_SETJMP_H:INTERNAL=1
 
 I've tried to compile both with and without having HDF5 installed on my
 system, and both methods fail. I haven't tried -DVTK_USE_SYSTEM_HDF5=ON yet
 because I would like to be able to use the H5 included with VTK, if
 possible.

It is odd that it finds the header, but then (seems) to not include it.
Could you insert an #error or something in H5private.h in the same block
as #include setjmp.h to see if it is actually included?

--Ben
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Re: [Paraview] Compile error: unknown type name ‘sigjmp_buf’

[Ben Boeckel]

On Tue, Feb 17, 2015 at 15:14:13 -0500, John Moore wrote:
 I get the following error when compiling on Ubuntu 14.04
 
 /home/john/local/ParaView/4.3.1/ParaView-v4.3.1-source/VTK/ThirdParty/hdf5/vtkhdf5/src/H5detect.c:149:1:
 error: unknown type name ‘sigjmp_buf’
  static H5JMP_BUF jbuf_g;
 
 I've installed HDF5 and its development tools. Any idea how I can fix this?

You can pass -DVTK_USE_SYSTEM_HDF5=ON to use your installed HDF5, but it
looks like HDF5's configure checks are failing thinking it doesn't have
setjmp.h (H5_HAVE_SETJMP_H) while it does manage to find sigjmp_buf
(H5JMP_BUF). Are those H5* variables set in your CMakeCache.txt at all?

Thanks,

--Ben
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Re: [Paraview] [Paraview-developers] Super build Problem

[Ben Boeckel]

On Wed, Jan 28, 2015 at 13:01:30 -0700, Joshua Murphy wrote:
 I have posted this question once before, but everyone was probably
 busy with the 4.3.1 release… So here goes again.
 
 I am trying to build the superbuild on the NCAR visualization cluster
 Caldera for development work.  I need to build 4.1.0, as I have not
 yet had time to update my tools to the most recent release.
 
 When I attempt to build the superbuild, I get an error building
 Freetype (see below).
 
 I have not been able to figure out what is causing the build error.
 
 I am using the gnu/4.6.4 module, the cmake/3.0.2 module, and the
 gmake/4.1 module.
 
 If anyone can help, that would be great.

What branch of the superbuild are you using? Are you using the 4.1.0 tag
in the repository?

At a guess, it looks like the targets are out-of-order since it looks
like output directories aren't being created? Is this a parallel or
serial build?

--Ben
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Re: [Paraview] problem building ParaView Examples

[Ben Boeckel]

On Mon, Jan 12, 2015 at 10:47:16 -0800, Jeff Becker wrote:
 Yes. I turned that off, and now it builds fine. Thanks.

I'm tracking this part of it down; do you still have the CMakeCache.txt
related to this failure? If the current build is the same one as here
with just PARAVIEW_USE_UNIFIED_BINDINGS flipped, that will work.

Thanks,

--Ben
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Re: [Paraview] CPack issue with hdf5/libhdf5.settings

[Ben Boeckel]

On Tue, Feb 10, 2015 at 13:10:01 +0100, Christoph Grüninger wrote:
  How are you building the packages?
 
 with openSuse's buildservice. I branched the official ParaView
 package which is still ParaView 4.2 and tried to update it. After
 I replaced the sources and adjusted the spec file, I got the
 mentioned error.
 
 By quickly scanning your spec file, I couldn't find the obvious
 difference causing my error.

You need to update %files to account for new files which are now
installed.

--Ben
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Re: [Paraview] CPack issue with hdf5/libhdf5.settings

[Ben Boeckel]

On Thu, Feb 12, 2015 at 06:45:47 +0100, Christoph Grüninger wrote:
 let me rephrase my question:
 Is it save to add /usr/share/cmake/hdf5/ within the ParaView package? Or
 would it affect a HDF5 package?

It would likely conflict with a native HDF5 package. Is there a reason
the system HDF5 isn't used?

 I am unsure, whether /usr/share/paraview/hdf5.setting wouldn't be safer.
 But I am alien to HDF5 and might be wrong.

Directory ownership in RPM isn't really straightforward or obvious all
the time :( . Fedora's guidelines are here:


https://fedoraproject.org/wiki/Packaging:Guidelines#File_and_Directory_Ownership

Here, I'd say the package you're making should own the directory and
hdf5.settings.

--Ben
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Re: [Paraview] EnSightReader: Change input file

[Ben Boeckel]

On Sat, Dec 20, 2014 at 10:09:46 +0100, Ian Krukow wrote:
 Then I switched to my desktop PC with Windows 7, where I set up the 
 building process. When I run the configuration in CMake, as soon as I 
 enable python, I get the error
 
 CMake Error at VTK/CMake/ExternalData.cmake:176 (add_test):
add_test given test NAME pvpythonPython-TestAnnotateAttributeData
which already exists in this directory.
 Call Stack (most recent call first):
VTK/CMake/vtkTestingMacros.cmake:431 (ExternalData_add_test)
CMake/ParaViewTestingMacros.cmake:44 (vtk_add_test_python)
Applications/ParaView/Testing/Python/CMakeLists.txt:82 
 (paraview_add_test_pvbatch)
 
 even without the patch. Can you tell me what to do about it?

The issue was fixed here:


https://github.com/Kitware/ParaView/commit/4d65c0684850b50442f7c1b60fb2ebf284931bcc

--Ben
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Re: [Paraview] Load text file delimited by tab

[Ben Boeckel]

On Tue, Nov 11, 2014 at 13:19:42 -0500, Utkarsh Ayachit wrote:
 Interesting! Alas, no, there isn't a direct way for setting this in
 the UI, currently.

A tab could be pasted into the field, I imagine (works here in other
fields).

--Ben
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Re: [Paraview] Superbuild and code changes

[Ben Boeckel]

On Fri, Mar 13, 2015 at 02:55:09 +, Scott, W Alan wrote:
 Is it possible to build ParaView with the superbuild, but change a few
 lines of code?  I want to comment out a few warnings.  These lines of
 source code keep getting written over.

You could apply a patch[1] (using an ExternalData step of which at
least Projects/apple/qt.cmake should have an example or two) or point
the superbuild to a different git repo with the patches applied. Without
looking, I can't remember the exact names of the cache variables, but
they're something like paraview_GIT_URL and paraview_GIT_HASH. Both
should be advanced variables on the master branch.

--Ben

[1]Due to the lack of a patch command on Windows, patch in superbuilds
usually means copy a file wholesale as a replacement.
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Re: [Paraview] Superbuild and code changes

[Ben Boeckel]

On Thu, Mar 12, 2015 at 23:18:54 -0400, Ben Boeckel wrote:
 Without looking, I can't remember the exact names of the cache
 variables, but they're something like paraview_GIT_URL and
 paraview_GIT_HASH.

They are PARAVIEW_GIT_REPOSITORY and PARAVIEW_GIT_TAG (which is any git
refname, not just a tag).

--Ben
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Re: [Paraview] [import error] Paraview Python on Windows

[Ben Boeckel]

[ Adding the list back to CC. ]

On Fri, May 01, 2015 at 15:55:26 +0200, Jonas Asche wrote:
 Thank you for the reply,
 Are you only using
 P:\ParaView 4.2.0\bin
 or do you link to other folders as well?

I ran with the following from Git bash (so that the environment was more
easily modified). All paths are relative to where ParaView was
extracted:


PYTHONPATH=lib/paraview-4.2;lib/paraview-4.2/site-packages;lib/paraview-4.2/site-packages/vtk
 PATH=$PATH;bin /c/Python27/python
 import vtk


If I didn't modify PATH, I got the same error you saw, so it seems to be
sufficient.

--Ben
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Re: [Paraview] [import error] Paraview Python on Windows

[Ben Boeckel]

On Fri, May 01, 2015 at 14:32:40 +0200, Jonas Asche wrote:
 Now i want to use those scripts on Windows 7 64bit. I downloaded
 ParaView-4.2.0-Windows-64bit
 and changed PythonPath and Path variable as described in this
 http://www.paraview.org/Wiki/ParaView/Python_Scriptingarticle:

Are you running python or pvpython?

 On Linux i have the following settings (i set them in .bashrc):
 PYTHONPATH:
 /sfw/paraview/ParaView-4.2.0-Linux-64bit-gl/lib/paraview-4.2:
 /sfw/paraview/ParaView-4.2.0-Linux-64bit-gl/lib/paraview-4.2/site-packages/:
 /sfw/paraview/ParaView-4.2.0-Linux-64bit-gl/lib/paraview-4.2:
 /sfw/paraview/ParaView-4.2.0-Linux-64bit-gl/lib/paraview-4.2/site-packages/vtk/:
 LD_LIBRARY_PATH:
 /sfw/paraview/ParaView-4.2.0-Linux-64bit-gl/lib/paraview-4.2/:

I assume this is working?

 Now i set Pythonpath in Windows to:
 (python location);
 P:\ParaView-4.2.0-Windows-64bit\lib\paraview-4.2;
 P:\ParaView-4.2.0-Windows-64bit\lib\paraview-4.2\site-packages\;
 P:\ParaView-4.2.0-Windows-64bit\lib\paraview-4.2;
 P:\ParaView-4.2.0-Windows-64bit\lib\paraview-4.2\site-packages\vtk\;
 And path to
 P:\ParaView-4.2.0-Windows-64bit\lib\paraview-4.2\;

I think this is supposed to be 'bin', not 'lib\paraview-4.2' since the
DLL files live there on Windows.

 I guess i am not using the proper path (i tried a whole bunch of different
 paths), can you send me a path that is working for you?

Using 'bin' seems to work here.

--Ben
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Re: [Paraview] vtk_use_system_protobuf

[Ben Boeckel]

On Thu, Apr 09, 2015 at 09:40:16 -0400, Ben Boeckel wrote:
 Doesn't seem so. Looks like ParaView will need changes for 2.6.0.
 Searching around, seems like the changes necessary for it are probably
 minor[1].

An attempt at this:

https://gitlab.kitware.com/paraview/paraview/merge_requests/52

This won't verify it works with 2.6.0 since we don't have any buildbot
machines with 2.6.0, so if you could test that this branch works for
you, that'd be great. Thanks,

--Ben
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Re: [Paraview] vtk_use_system_protobuf

[Ben Boeckel]

On Wed, Apr 08, 2015 at 19:36:28 -0700, Kevin Dean wrote:
 vtkPVMessage.proto:65:14: Message extensions cannot have required fields.
 vtkPVMessage.proto:68:14: Message extensions cannot have required fields.
 vtkPVMessage.proto:103:14: Message extensions cannot have required fields.
 vtkPVMessage.proto:104:14: Message extensions cannot have required fields.
 vtkPVMessage.proto:209:14: Message extensions cannot have required fields.
 vtkPVMessage.proto:222:14: Message extensions cannot have required fields.
 vtkPVMessage.proto:245:14: Message extensions cannot have required fields.
 vtkPVMessage.proto:246:14: Message extensions cannot have required fields.
 vtkPVMessage.proto:259:14: Message extensions cannot have required fields.
 make[2]: *** [ParaViewCore/ServerImplementation/Core/vtkPVMessage.pb.h]
 Error 1
 make[1]: ***
 [ParaViewCore/ServerImplementation/Core/CMakeFiles/protobuf_code_generation.dir/all]
 Error 2
 
 has anyone run into this problem? Might there be a work around?

Doesn't seem so. Looks like ParaView will need changes for 2.6.0.
Searching around, seems like the changes necessary for it are probably
minor[1].

--Ben

[1]https://github.com/rethinkdb/rethinkdb/issues/3137
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Re: [Paraview] Error building superbuild VS2010

[Ben Boeckel]

On Fri, Jul 31, 2015 at 16:34:49 +, Bruce Jones wrote:
 I am trying to build the superbuild for x64 on windows. I have configured
 everything with cmake (i have only selected ENABLE_paraview and ENABLE_qt)
 and am trying to do a release build. The build fails with,
 
 7  CMake Error at VTK/CMake/vtkModuleAPI.cmake:53 (message):
 7No such module: vtkCommonDataModel
 
 Any suggestions?

What CMake generator did you use? The superbuild is only tested with
Ninja on Windows:

C:\ REM Open a VS2010 x64 Command Tools Prompt
C:\ cmake -GNinja ../path/to/superbuild/source
C:\ REM Edit configuration in cmake-gui
C:\ ninja

Ninja is available from:

https://martine.github.io/ninja

if you do not have it already.

--Ben
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Re: [Paraview] Error building superbuild VS2010

[Ben Boeckel]

On Tue, Aug 04, 2015 at 00:55:16 +, Bruce Jones wrote:
 I followed your instructions and the build was successful in release mode.
 However, when I run the executable it crashes on load.
 
 Attempting to debug this I tried to build in debug mode using the same
 approach. Unfortunately the debug build fails with an error,
 
 qtmain.lib(qtmain_win.obj) : error LNK2038: mismatch detected for
 '_ITERATOR_DEBUG_LEVEL': value '0' doesn't match value '2' in
 paraview_main.cxx.obj
 MSVCRTD.lib(cinitexe.obj) : warning LNK4098: defaultlib 'msvcrt.lib'
 conflicts with use of other libs; use /NODEFAULTLIB:library
 bin\paraview.exe : fatal error LNK1319: 1 mismatches detected
 LINK Pass 1 failed. with 1319
 
 I am not sure why this is occurring.

This typically occurs because Qt is built in release while ParaView is
debug and the two can't mix on Windows. I'd recommend starting from a
completely clean build tree to avoid any lingering files and setting
CMAKE_BUILD_TYPE=Release.

--Ben
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Re: [Paraview] Qt

[Ben Boeckel]

On Sat, Jul 11, 2015 at 00:16:19 +, Scott, W Alan wrote:
 I notice that the Superbuild is running Qt 5.4.1.  Any idea where I
 can find the Windows installer (i.e., I don't want to build from
 source)?

Also, Qt5 is currently experimental in that it is known that there are
issues with it in some places. Qt4 is still the officially supported
version and is still in the superbuild.

--Ben
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Re: [Paraview] Qt

[Ben Boeckel]

On Sat, Jul 11, 2015 at 00:16:19 +, Scott, W Alan wrote:
 I notice that the Superbuild is running Qt 5.4.1.  Any idea where I
 can find the Windows installer (i.e., I don't want to build from
 source)?

Downloads are found here:

http://download.qt.io/archive/qt/5.4/5.4.1/

The superbuild is meant to run with MSVC2013, but I see that only
MSVC2013 has 64 bit and OpenGL support anyways with the prebuilt
binaries.

--Ben
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[Paraview] ANN: ParaView 5.0.0-RC1 is available for download

[Ben Boeckel]

Folks,

ParaView 5.0.0-RC1 is now available for download. Checkout the release
notes on the Kitware blog [1].

As always, we look forward to your feedback [2].

Also stay tuned to the Kitware Blog [3] for upcoming features and
enhancements to ParaView, ParaView Catalyst, ParaViewWeb and much
more!

- The ParaView team

[1] http://kitware.com/blog/home/post/998
[2] http://paraview.uservoice.com
[3] http://www.kitware.com/blog/
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Re: [Paraview] Paraview 4.4.0 build error with osmesa on RHEL cluster at LLNL

[Ben Boeckel]

On Fri, Oct 30, 2015 at 18:22:01 +, Cook, Rich wrote:
> I'm seeing an error when trying to build the latest Paraview using
> osmesa:
> 
> The configuration step goes OK.  In particular note that I set
> -DOPENGL_glu_LIBRARY:FILEPATH=/usr/lib64/libGLU.so

I think with OSMesa, this should be empty. Here is what our superbuild
sets when using osmesa:

  -DOPENGL_INCLUDE_DIR:PATH=
  -DOPENGL_xmesa_INCLUDE_DIR:PATH=
  -DOPENGL_gl_LIBRARY:FILEPATH=
  -DOPENGL_glu_LIBRARY:FILEPATH=
  -DOSMESA_INCLUDE_DIR:PATH=/include
  -DOSMESA_LIBRARY:FILEPATH=/lib/libOSMesa.so

Where  is /usr on a system-installed mesa. You can also use
libOSMesa.a for a static mesa.

--Ben
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Re: [Paraview] numpy build issues

[Ben Boeckel]

On Fri, Oct 16, 2015 at 18:44:40 +, Scott, W Alan wrote:
> I am having issues getting ParaView, remote cluster, working with my
> own build of Python and numpy.  Obviously, I don't have root on these
> clusters, and I want to use my own Python.  (Clusters often have 10
> year old python.)
> 
> From the following, it appears I am missing a libgfortran.so.1.  Any
> idea why numpy wants Fortran, where it should be found and what I did
> wrong?   Any idea what I should do to fix it?

You can get numpy to not use fortran with:

python setup.py build --fcompiler=no

It will use Fortran by default though. It is strange that a Fortran
compiler was found, but the libraries are not in a standard location…

--Ben
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Re: [Paraview] Successful SuperBuild on OSX 10.11?

[Ben Boeckel]

On Wed, Oct 07, 2015 at 00:23:45 +0100, Mathew Guilfoyle wrote:
> I have just upgraded to OS X 10.11 and am now unable to build Paraview
> 
> I had successfully built the Suepbuild 4.4.0 on OS X 10.10 using my
> installed Qt4.8 (I was unable to build against the Qt that comes with
> the SuperBuild.
> 
> Qt 4.8 is not compatible with the latest OS X, hence I’ve installed
> Qt5.5.  However, even building Paraview against the installed Qt5.5
> now fails.  The primary error seems to be:  

Qt5 is not supported in ParaView fully yet. Qt 5.6 will have the
necessary patches.

> CMake Error at 
> /Builds/ParaView/Build/paraview/src/paraview/CMake/generate_proxydocumentation.cmake:20
>  (message):
>   No xmlpatterns executable was defined!!!
> 
> Any ideas how to fix this?

There's a "patch" in the superbuild[1] which adds '10' to the list of
versions it can detect. Adding '11' there might help you get further.

Or are the Qt issues deeper?

--Ben

[1]Projects/patches/qt4.src.plugins.bearer.corewlan.corewlan.pro
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Re: [Paraview] No module named paraview...

[Ben Boeckel]

On Wed, Sep 09, 2015 at 09:18:26 +0800, Ruggiero Guida wrote:
> I am trying to run paraview scripts from the command line without using the
> specific pvpython from paraview (this one works).

Look at the paths in the output of:

>>> import sys
>>> sys.path

from pvpython. You may be missing some paths (there are 4 or 5 IIRC, but
the paraview.app packaging may reduce that).

> Mac OS X 10.10.5

...

> export
> LD_LIBRARY_PATH="/Applications/paraview.app/Contents/Libraries:/Applications/paraview.app/Contents/Python/paraview:/Applications/paraview.app/Contents/Python/vtk:/Applications/paraview.app/Contents/Python/paraview"

OS X uses 'DYLD_LIBRARY_PATH', not 'LD_LIBRARY_PATH'. You should only
need to use the '/Applications/paraview.app/Contents/Libraries'[1] path
for this.

--Ben

[1]And possibly its paraview-4.3 subdirectory, though I forget if that
exists in the .app or not…
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Re: [Paraview] /usr/bin/paraview not packaged with CPack in Paraview 4.3.1 Superbuild

[Ben Boeckel]

On Mon, Sep 14, 2015 at 02:00:22 +, Anthony Crognale wrote:
> After enabling qt and recompiling after a clean, I receive the following 
> error:

"make clean" isn't really reliable in a superbuild. I usually do "rm -rf
*/"[1] in the build tree to keep the cache but kill any state related to
the build.

> .obj/release-shared/qpnghandler.o: In function 
> `QPngHandlerPrivate::readPngHeader()':
> qpnghandler.cpp:(.text+0xb4f): undefined reference to `png_set_longjmp_fn'
> .obj/release-shared/qpnghandler.o: In function 
> `QPngHandlerPrivate::readPngImage(QImage*)':
> qpnghandler.cpp:(.text+0xdbd): undefined reference to `png_set_longjmp_fn'
> .obj/release-shared/qpnghandler.o: In function 
> `QPNGImageWriter::writeImage(QImage const&, int, QString const&, int, int)':
> qpnghandler.cpp:(.text+0x1a0c): undefined reference to `png_set_longjmp_fn'
> collect2: error: ld returned 1 exit status
> make[4]: *** [../../lib/libQtGui.so.4.8.6] Error 1
> Makefile:1073: recipe for target '../../lib/libQtGui.so.4.8.6' failed
> make[3]: *** [sub-gui-make_default-ordered] Error 2
> Makefile:382: recipe for target 'sub-gui-make_default-ordered' failed
> CMake Error at /home/acrognale/paraview/build/pv-qt-build.cmake:26 (message):
> 
> Any thoughts?

Are you using a system libpng? What version is it?

--Ben

[1]More surgical is "rm -rf install/ */src/*-stamp/*-install", but this
still has cases where it is insufficient.
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Re: [Paraview] /usr/bin/paraview not packaged with CPack in Paraview 4.3.1 Superbuild

[Ben Boeckel]

On Sun, Sep 13, 2015 at 21:35:20 -0400, Ben Boeckel wrote:
> I think qt was renamed to qt4 after 4.3.1 was released

Just looked; this is indeed new for 4.4.0.

--Ben
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Re: [Paraview] /usr/bin/paraview not packaged with CPack in Paraview 4.3.1 Superbuild

[Ben Boeckel]

On Mon, Sep 14, 2015 at 14:15:26 +, Anthony Crognale wrote:
> I had been using the system libpng version 1.2.52, but it appears
> `png_set_longjmp_fn` was not introduced until 1.6, so I tried building
> libpng 1.6.18 from source last night, which then allows Paraview to
> continue building with qt enabled, however, when running the built
> version, I get:
> 
> libpng warning: Application built with libpng-1.4.8 but running with
> 1.6.18
> 
> So it appears that there is some other version of libpng (maybe
> bundled in the superbuild?) that it was using to build.

Yeah, it looks like it built against the superbuild's libpng and running
against the one you grabbed. Other than a compiler and things like libc
or OpenGL, the superbuild *should* be providing everything it needs (and
it is not regularly tested against other external dependency versions).

> Should I turn off use_system_png? Turn off ENABLE_png? Something else?

Using the superbuild-provided png would probably be best
(-DUSE_SYSTEM_png=OFF -DENABLE_png=ON). However, it seems that removing
the 1.6.18 libpng should fix the warning.

--Ben
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Re: [Paraview] /usr/bin/paraview not packaged with CPack in Paraview 4.3.1 Superbuild

[Ben Boeckel]

On Mon, Sep 14, 2015 at 00:55:42 +, Anthony Crognale wrote:
> /usr/bin/paraview is not in this list, nor the other binaries that I
> would expect when it is built.

Usually means Qt wasn't enabled.

> I've attached my CMakeCache.txt to this email as it would be rather
> large to paste.
> 
> Any thoughts?



> //Request to build project qt
> ENABLE_qt:BOOL=OFF
> 
> //No help, variable specified on the command line.
> ENABLE_qt4:UNINITIALIZED=ON

It looks like you're not enabling Qt. I think qt was renamed to qt4
after 4.3.1 was released (when we tried using qt5, but we will have to
wait until at least 5.5.1 for some bugs). I'll check tomorrow when we
did the rename, but setting ENABLE_qt should work (check the list of
enabled projects during configure).

--Ben
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Re: [Paraview] /usr/bin/paraview not packaged with CPack in Paraview 4.3.1 Superbuild

[Ben Boeckel]

On Mon, Sep 14, 2015 at 21:41:09 +, Anthony Crognale wrote:
> Looks like building for release worked properly, the resulting
> Paraview runs fine now.
> 
> Thanks much for your help!

Great!

FYI, the release mode improvments are here:

https://gitlab.kitware.com/paraview/paraview-superbuild/merge_requests/50

--Ben
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Re: [Paraview] /usr/bin/paraview not packaged with CPack in Paraview 4.3.1 Superbuild

[Ben Boeckel]

On Mon, Sep 14, 2015 at 19:05:27 +, Anthony Crognale wrote:
> Another quick follow up (sorry!) 
> 
> [pid   360] 
> stat("/home/acrognale/paraview/build/qt/src/qt/src/3rdparty/libpng", 
> {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
> [pid   360] openat(AT_FDCWD, 
> "/home/acrognale/paraview/build/qt/src/qt/src/3rdparty/libpng", 
> O_RDONLY|O_NONBLOCK|O_DIRECTORY|O_CLOEXEC) = 6
> [pid   360] 
> stat("/home/acrognale/paraview/build/qt/src/qt/src/3rdparty/libpng/RCS", 
> 0x7ffed1fed140) = -1 ENOENT (No such file or directory)
> [pid   360] 
> stat("/home/acrognale/paraview/build/qt/src/qt/src/3rdparty/libpng/SCCS", 
> 0x7ffed1fed130) = -1 ENOENT (No such file or directory)
> [pid   360] 
> stat("/home/acrognale/paraview/build/qt/src/qt/src/3rdparty/libpng/pnglibconf.h",
>  {st_mode=S_IFREG|0644, st_size=6329, ...}) = 0
> [pid   360] 
> stat("/home/acrognale/paraview/build/qt/src/qt/src/3rdparty/libpng/pngconf.h",
>  {st_mode=S_IFREG|0644, st_size=21404, ...}) = 0
> [pid   373] stat("/home/acrognale/paraview/build/install/lib/libpng.so", 
> 0x7fffc4b213f0) = -1 ENOENT (No such file or directory)
> [pid   373] open("/home/acrognale/paraview/build/install/lib/libpng.so", 
> O_RDONLY) = -1 ENOENT (No such file or directory)
> [pid   373] stat("/home/acrognale/paraview/build/install/lib/libpng.a", 
> 0x7fffc4b21430) = -1 ENOENT (No such file or directory)
> [pid   373] open("/home/acrognale/paraview/build/install/lib/libpng.a", 
> O_RDONLY) = -1 ENOENT (No such file or directory)
> [pid   373] stat("/home/acrognale/paraview/build/install/lib/libpng.so", 
> 0x7fffc4b213f0) = -1 ENOENT (No such file or directory)
> [pid   373] open("/home/acrognale/paraview/build/install/lib/libpng.so", 
> O_RDONLY) = -1 ENOENT (No such file or directory)
> [pid   373] stat("/home/acrognale/paraview/build/install/lib/libpng.a", 
> 0x7fffc4b21430) = -1 ENOENT (No such file or directory)
> [pid   373] open("/home/acrognale/paraview/build/install/lib/libpng.a", 
> O_RDONLY) = -1 ENOENT (No such file or directory)
> 
> It seems to not be finding libpng.so even though it exists as a symbolic link 
> to libpng14d.so.14.8.0, which does indeed exist.
> 
> Thoughts?

Ooh. Are you compiling in Debug mode (empty is also usually "Debug") for
CMAKE_BUILD_TYPE? I don't think that's ever been tested. I'll add a
patch to have it default to Release.

--Ben
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Re: [Paraview] /usr/bin/paraview not packaged with CPack in Paraview 4.3.1 Superbuild

[Ben Boeckel]

On Mon, Sep 14, 2015 at 19:29:58 +, Anthony Crognale wrote:
> I was indeed compiling in Debug mode! Is there a different recommended
> way to compile the application in debug mode then?

Not cleanly. I can add a flag for that as well.

Currently, once ParaView is done configuring, stop the build, edit
paraview/src/paraview-build/CMakeCache.txt to have
CMAKE_BUILD_TYPE:STRING=Debug (though RelWithDebInfo is probably
sufficient and not dog slow), and then continue the build at the
top-level again.

--Ben
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Re: [Paraview] Direct link to ParaView sources not working with wget

[Ben Boeckel]

On Mon, Sep 28, 2015 at 07:22:52 +, Schlottke-Lakemper, Michael wrote:
> Thanks for the quick fix! I still end up with a file named
> "download.php?submit=Download=v4.4=source=all=ParaView-v4.4.0-source.tar.gz”
> (and that can be fixed using "-O filename”), but at least the
> downloading works ;)

The wget tool also has the `--content-disposition` option which will use
the server-recommended filename.

--Ben
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Re: [Paraview] QT5/libxcb on RHEL5

[Ben Boeckel]

On Wed, Sep 23, 2015 at 16:46:51 +, Angelini, Richard C (Rick) CIV USARMY 
RDECOM ARL (US) wrote:
> I’m doing some test build of PV 4.4.0, and if I try to build using
> QT5, I need to have access to the libxcb libraries.It doesn’t look
> like there’s an RPM for this for RHEL5 .Can the Superbuild script
> be tweaked to pick up the sources for this dependent library and build
> it if it can’t find it on the system? Otherwise, at least on
> RHEL5, I’ll need to download/build outside of the Superbuild?

Qt5 needs a newer libxcb than is shipped on some of these older distros
(1.2? I'd have to double check). For example, Debian Etch'n'half (yes,
Debian 4) which we use to build the current binaries cannot build it.
And a newer libxcb needs a newer X than is availble tooi and that
certainly isn't going to be added to the superbuild :) . I would expect
RHEL5 to have similar problems (RHEL6 would be better).

Besides that, there is a known bug in Qt5 which makes user interaction
painful on X. Basically, mouse events aren't collapsed, so every mouse
event has a render call in between. It's basically unusable. There is a
patch which got merged in for 5.6.0, but that hasn't had a release yet.

--Ben
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Re: [Paraview] rpath error when compiling ParaView 5.0

[Ben Boeckel]

On Sat, Dec 05, 2015 at 20:53:49 +0200, Armin Wehrfritz wrote:
> I'm building ParaView (version 5.0 RC1) for openSUSE Tumbleweed (using
> gcc 5.2.1) and get an error related to rpath (see below). I cannot say
> much more about this, since don't really understand what's going wrong here.
> 
> Does anybody have some hints how to solve this?

Are you giving any rpath-related settings to CMake? What is the
configure line?

> Please let me know if you need more information.

What version of CMake are you using?

--Ben
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Re: [Paraview] OpenGL Backend Identification

[Ben Boeckel]

On Mon, Dec 07, 2015 at 14:49:51 -0500, Tim Thirion wrote:
> I'm looking to provide run-time identification of the current OpenGL
> backend in use. Some questions:
> 
> 1. VTK #defines VTK_OPENGL2, but ParaView #defines VTKGL2. Is there a
> particular reason we have both?

VTK used to have both. VTKGL2 should be migrated to VTK_OPENGL2 (as VTK
did).

> 2. Is there an ideal place to define such a constant? Perhaps on the render
> window?

The About dialog has a list of information already (versions of Python,
matplotlib, numpy, Qt, etc.).

--Ben
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Re: [Paraview] Paraview v5.0.0-RC1 with OpenGL2 backend not running using OSMESA v10.5.5

[Ben Boeckel]

On Thu, Dec 10, 2015 at 17:20:35 +0100, Albina, Frank wrote:
> Thank you for the reply. My idea was to run PV-5.0.0-RC1 in parallel on our 
> cluster, 
> therefore the need to recompile as the binaries do not usually ship with this 
> feature
>  and I guess that you do not necessarily know either which parallel 
> communication 
> library is going to be used  on the end user's compute platform.
> 
> If the binaries ship with SWR using prebuilt mesa  binaries, is there any 
> documentation
> on how to build the mesa binaries with SWR support? I might eventually figure 
> it out by
> myself (or not) but I would be grateful for any hints.

Here's the relevant subset of the Dockerfile Utkarsh used:

#--
WORKDIR /opt/tools/src/openswr-mesa
RUN git clone https://github.com/OpenSWR/openswr-mesa.git src-avx2 --depth 1 -b 
11.0-openswr
WORKDIR /opt/tools/src/openswr-mesa/src-avx2
RUN scons build=release texture_float=yes swr_arch=core-avx2 libgl-xlib

WORKDIR /opt/tools/mesa-swr-avx2
RUN cp 
/opt/tools/src/openswr-mesa/src-avx2/build/linux-x86_64/gallium/targets/libgl-xlib/libGL.so.1.5
 . && \
ln -s libGL.so.1 libGL.so && \
ln -s libGL.so.1.5 libGL.so.1

#--
WORKDIR /opt/tools/src/openswr-mesa
RUN git clone https://github.com/OpenSWR/openswr-mesa.git src-avx --depth 1 -b 
11.0-openswr

WORKDIR /opt/tools/src/openswr-mesa/src-avx
RUN scons build=release texture_float=yes swr_arch=avx libgl-xlib

WORKDIR /opt/tools/mesa-swr-avx
RUN cp 
/opt/tools/src/openswr-mesa/src-avx/build/linux-x86_64/gallium/targets/libgl-xlib/libGL.so.1.5
 . && \
ln -s libGL.so.1 libGL.so && \
ln -s libGL.so.1.5 libGL.so.1

--Ben
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Re: [Paraview] Differences between OpenGL and OpenGL2 versions of ParaView

[Ben Boeckel]

On Wed, Dec 16, 2015 at 13:22:09 -0600, Adam Lyon wrote:
> I'm curious as to why I didn't have any of these problems in v4.4 -- or is
> this two path multiblock rendering code all new for v5?  Thanks again!! --

4.4 defaults to the OpenGL1 backend (glBegin/glEnd); 5.0 is using the
OpenGL2 backend (shaders and VBOs).

--Ben
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Re: [Paraview] Paraview v5.0.0-RC1 with OpenGL2 backend not running using OSMESA v10.5.5

[Ben Boeckel]

On Thu, Dec 10, 2015 at 09:18:44 -0500, Ken Martin wrote:
> people on this list are more familiar with the specifics of setting up SWR
> and Mesa on a cluster but I wanted to at least give you a quick response to
> let you know we are working on it :-)

The binaries built by our buildbots (and uploaded to the website) have
SWR available using prebuilt mesa binaries. If you have AVX CPU
extensions available, passing:

--mesa-swr-avx

should enable it. There's also --mesa-swr-avx2 if you have AVX2
extensions available.

--Ben
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Re: [Paraview] OpenGL Backend Identification

[Ben Boeckel]

On Thu, Dec 10, 2015 at 09:29:27 -0500, Ken Martin wrote:
> Maybe vtkRenderingOpenGLConfigure.h ?
> 
> That header is configured from a .in file for both the old and new backend.
> We could define VTK_OPENGL2 in that header and applications could include
> it as needed.  That header appears to get installed. The only issue I see
> is that if someone built VTK with no rendering then that header file might
> not exist.

The library to link to doesn't either for that matter…

> Does that work? If so I can put the VTK_OPENGL2 definition in there.

It looks like a good location to me.

--Ben
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Re: [Paraview] OpenGL Backend Identification

[Ben Boeckel]

On Thu, Dec 10, 2015 at 10:08:14 -0500, David E DeMarle wrote:
> And it should appear in a wrapped class so that we can get it at runtime
> from python.

In that case, there should probably be an enum in RenderingCore:

enum vtkRenderingBackend {
...
};

class vtkRenderingSomething {
static vtkRenderingBackend getRenderingBackend();
};

--Ben
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Re: [Paraview] How to stop a paraview python script on error (try-catch-ing) ?

[Ben Boeckel]

On Sat, Jan 02, 2016 at 16:12:49 +0100, houssen wrote:
> How to stop a paraview python script on error (try-catch-ing) ?
> 
> I have a filter (which calls vtkErrorMacro when an error occurs). I 
> have a python script that uses this filter from paraview: how to stop 
> this script when an error occurs ? I tried to add "try/except" in core 
> part of the script but it does not work as expected (keep running, don't 
> stop).

VTK errors are not Python exceptions, so there's nothing to catch. See
this post from David Gobbi:

http://public.kitware.com/pipermail/vtkusers/2012-June/074703.html

--Ben
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Re: [Paraview] What is the difference between pvbatch and pvpython ?

[Ben Boeckel]

On Thu, Jan 07, 2016 at 16:50:16 +0100, houssen wrote:
> What is the difference between pvbatch and pvpython ? (general purpose 
> question)
> 
> My understanding is that one can always use python scripts (from 
> paraview, pvbatch, pvpython), paraview has the GUI, pvbatch is "paraview 
> in batch mode" (that is paraview without the gui). But what is the 
> purpose of pvpython ? When is it needed to use pvbatch or pvpython 
> instead of the other one ? Or what can do pvbatch that pvpython can not 
> do ?

pvbatch and pvpython are both ParaView-aware Python interpreters (sets
sys.path to work with ParaView). pvbatch is the MPI-enabled version of
pvpython.

--Ben
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Re: [Paraview] passing argument to pvpython script

[Ben Boeckel]

On Wed, Nov 25, 2015 at 15:11:43 +0300, Gena Bug wrote:
> And this works fine untill I tried new version. In 5rc1 I always get 
> Segmentation Fault:
> Error running 
> "~/ParaView-5.0.0-RC1-Qt4-OpenGL2-Linux-64bit/lib/paraview-5.0/pvpython" 
> "myscript.py" "filename"Segmentation fault
> 
> Seems, sys module couldn't be imported... Is it problem with rc-version? 
> How can I correctly pass arguments to a script?

What distro? I ran into something with similar symptoms and fixed it
here (no one else could reproduce it, so we didn't delay RC1 for it):

https://gitlab.kitware.com/paraview/paraview/merge_requests/478

Do the lastest binaries work for you?


http://www.paraview.org/paraview-downloads/download.php?submit=Download=nightly=all=all=ParaView-5.0.0-RC1-18-g7560de5-Qt4-OpenGL2-Linux-64bit.tar.gz

Thanks,

--Ben
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Re: [Paraview] ParaView 5.0.0-RC1: two minor problems

[Ben Boeckel]

On Fri, Nov 20, 2015 at 11:23:02 -0500, Hom Nath Gharti wrote:
> In Linux 64-bit binary
> 1) error while loading shared libraries: libbz2.so.1.0: cannot open
> shared object file: No such file or directory
> 
> ln -s /lib64/libbz2.so.1 libbz2.so.1.0 fixed the problem.

Hmm, interesting. It seems to be popping into binaries and back out
randomly. RC1 doesn't have it, RC1+5 and RC1+7 (5 and 7 commits later)
has the .so (but not the .1.0 version), and the RC1+10 and RC1+16
binaries don't have it again. I'll try and take a look today or early
next week.

Thanks for the report,

--Ben
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Re: [Paraview] [Non-DoD Source] ANN: ParaView 5.0.0-RC1 is available for download

[Ben Boeckel]

On Wed, Jan 13, 2016 at 16:50:59 +, Angelini, Richard C (Rick) CIV USARMY 
RDECOM ARL (US) wrote:
> Has anyone tried or been able to build ParaView 5.0 on RHEL5?Looks
> like there may be compiler dependencies which exclude a successful build
> on RHEL5?  So far, I’ve not had any luck …..

Doesn't Red Hat provide a gcc44 package? Or was that EPEL?

--Ben
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Re: [Paraview] ANN: ParaView 5.1.0-RC1 available for download

[Ben Boeckel]

On Mon, Jun 13, 2016 at 12:11:29 -0400, 曹智选 wrote:
> It turned out that the operating system on my machine does not have the
> library: GLIBCXX_3.4.15. And the linux system on my machine does not allow
> me upgrading the library to GLIBCXX_3.4.15.
> Is there any other way that I can still use the new version of paraview
> without GLIBCXX_3.4.15? I only want to use the SPH interpolation feature of
> the new paraview.

This is a "symbol version". It basically means that your libstdc++ is
too old for the build we created. What Linux distribution and version
are you using?

--Ben
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Re: [Paraview] Required CMake version 3.5

[Ben Boeckel]

On Wed, Jun 22, 2016 at 05:21:33 +0200, Christoph Grüninger wrote:
> thanks for link to the developer mailing list discussion. I think CMake 3.3 
> is better then
> 3.5, because at least the last Leap 42.1 release provides that.
> I patched ParaView to require CMake 3.0 and it builds fine. I will package 
> ParaView 5.1
> that way and hope you reduce the requirement to CMake 3.3 for the next time.

I think the easiest way to check this would be to set the minimum to 3.3
and run against 3.5 to see if any POLICY warnings are triggered for the
way openSUSE builds ParaView. If they are, the old version is probably
silently doing something wrong.

--Ben
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Re: [Paraview] Required CMake version 3.5

[Ben Boeckel]

On Fri, Jun 24, 2016 at 15:50:45 +0200, Christoph Grüninger wrote:
> I don't think it is a good idea to ask for the latest version. Only 
> developers like us have
> a current version of CMake installed. From already released distributions 
> nobody
> provides CMake 3.5.

My thought here is that building ParaView is much harder than CMake, so
it's not a super high barrier to require a custom-built CMake to build a
custom ParaView build.

> > Though I question the distro update policies surrounding where ParaView
> > is aggressively pushed forward when CMake isn't. CMake is *much* better
> > with its backwards compatibility, but I guess it's down to maintainer
> > style to some extent.
> 
> Sorry, there is a misunderstanding. We provide packages for already released
> distributions. We cannot change the CMake version shipped with them. By
> requesting a too recent version, there won't be updated versions of
> ParaView for users of released openSuses any more.
> I know they can download the binaries you provide or get a more recent
> CMake and compile it themselves. You have to weight your inconveniences
> against the ones of your users.

Ah, so this is more like a PPA? Yeah, I guess overriding the CMake from
those wouldn't be a great thing to recommend.

Talking with Utkarsh, we can move the version down since that's our
actual minimum version. However, if things get added to ParaView's build
that require newer CMake support, bumping the minimum version would not
be a huge blocker.

--Ben
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Re: [Paraview] Required CMake version 3.5

[Ben Boeckel]

On Fri, Jun 24, 2016 at 09:28:29 -0400, Jim wrote:
> Can you let me know how it goes?  I just pulled the latest versions of 
> Paraview & cmake and want to build under VS2015. I'm going to work on it 
> over the weekend. If you're doing the same, I could use any 
> configuration tricks you discover.

I thought we had a VS2015 dashboard, but I see it is just VS2013
(thinking back, probably because there isn't a Qt4 build against 2015 on
that machine). They're not that different for setup though. I'll look at
getting the other Windows machine onto the dashboard setup here today.

I don't expect any issues, but if you find any, feel free to email the
list or open issues.

Thanks,

--Ben
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Re: [Paraview] Required CMake version 3.5

[Ben Boeckel]

On Fri, Jun 24, 2016 at 00:25:00 +0200, Cory Quammen wrote:
> @Utkarsh, any foreseeable problems reducing the CMake required version to 3.3?

I think we'll want 3.5 in the (hopefully) near future, so if
distributions don't have a new enough CMake, they can patch it down to
3.3 in the meantime. A comment might be worthwhile.

Though I question the distro update policies surrounding where ParaView
is aggressively pushed forward when CMake isn't. CMake is *much* better
with its backwards compatibility, but I guess it's down to maintainer
style to some extent.

> @Ben, I assume all the dashboard machines are running CMake 3.5. Do
> you think we should downgrade one to CMake 3.3?

I was actually going to upgrade them to 3.6's rc today to test it out.

--Ben
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Re: [Paraview] [Non-DoD Source] ANN: ParaView 5.0.0-RC1 is available for download

[Ben Boeckel]

On Wed, Jan 13, 2016 at 18:50:21 +, Angelini, Richard C (Rick) CIV USARMY 
RDECOM ARL (US) wrote:
> gcc on our RHEL5 systems is 4.1 and seemingly cannot be upgraded.

I think there is also a "gcc44" package which contains a gcc4.4 binary
(and is parallel installable). But I don't remember if it is Red
Hat-provided or EPEL which did so.

--Ben
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Re: [Paraview] compiling mdf error

[Ben Boeckel]

On Tue, Feb 02, 2016 at 10:06:25 +, mersad mostaghimi via ParaView wrote:
> Dear Cory Quammenthe first problem is solved but there is an other
> problem  which is again an MD5 problem. this time is in VTK
> installation during installing Paraview from source files.

If you don't need testing data, you can disable it with:

-DBUILD_TESTING:BOOL=OFF

or toggling it in either ccmake or cmake-gui.

--Ben
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Re: [Paraview] Troubles building mathstuf/qhull subproject using PV 4.4.0 superbuild with Intel >14.x compilers

[Ben Boeckel]

On Tue, Jan 19, 2016 at 19:05:38 -0700, Giovanni A. Cone wrote:
> I'm attempting to get PV 4.4.0 builds of Paraview 
> against Intel 14 and 15 on our HPC systems.  One item that 
> some users have asked us for was the Cosmotools integration. 
> This ultimately needs the Qhull library to be built.  Builds 
> against GCC 4.8.2 went through without a hitch.  However the 
> Intel builds all failed with an odd cryptic syntax error 
> message that I do not fully comprehend (sorry I'm still 
> stuck in Fortranistan).
> 
> Building CXX object 
   ^^^

See below.

> CMakeFiles/qhullcpp.dir/src/libqhullcpp/Coordinates.cpp.o
> In file included from 
> /tmp/conega/BUILD/lightshow/paraview-4.4.0-osmesa/intel-15_openmpi-1.6.5/BUILD01/qhull/src/qhull/src/libqhull/poly2.c(16):
> /tmp/conega/BUILD/lightshow/paraview-4.4.0-osmesa/intel-15_openmpi-1.6.5/BUILD01/qhull/src/qhull/src/libqhull/qhull_a.h(106):
>  
> warning #77: this declaration has no storage class or type 
> specifier
>template 
>^
> 
> In file included from 
> /tmp/conega/BUILD/lightshow/paraview-4.4.0-osmesa/intel-15_openmpi-1.6.5/BUILD01/qhull/src/qhull/src/libqhull/poly2.c(16):
> /tmp/conega/BUILD/lightshow/paraview-4.4.0-osmesa/intel-15_openmpi-1.6.5/BUILD01/qhull/src/qhull/src/libqhull/qhull_a.h(106):
>  
> error: expected a ";"
>template 
> ^
>  From what little I understand of C and C++, I believe that 
> "templates" are a C++ construct.  I'm thinking the Intel 
> compiler is attempting to digest the above as "straight-up 
> C" and failing.

Marked above, it is compiling as C++, but it appears that it is trying
to parse template as an identifier rather than a keyword. My guess is
that it is something like:

struct foo {
int member;
} // no semicolon
template ...

which parses into a function returning a foo struct (declared there as
well) named 'template'.

> The error messages put the blame on 
> QHULL_SRC_ROOT/src/libqhull/qhull_a.h  around line 105
> 
> I then decided to snoop on github.com for another qhull 
> repo.  I found one
> at
> 
> https://github.com/qhull/qhull
> 
>  From which I believe the "https://github.com/mathstuf/qhull 
> next branch" repo that Paraview wants to use was forked from.

Not originally, but it is now that qhull has moved from sourceforge to
github (it was originally forked from George Zegaris' clone which he
mirrored from sourceforge to github, but I recently re-forked the proper
repo).

> Point being that the mainline non-forked Qhull has something 
> different in the preprocessor conditional surrounding the 
> above offensive line of source:
> 
> #if defined(__cplusplus) && defined(__INTEL_COMPILER) && 
> !defined(QHULL_OS_WIN)
> 
> while the mathstuf/qhull repo DOES NOT have the above 
> "defined(__cplusplus)" preproc conditional.

My 'next' branch is based off an old release, so differences to upstream
are not surprising.

> I tested to see if the addition would at least allow the 
> 'mathstuf/qhull next branch' source to properly build with 
> Intel 14 and 15.  It got about to 36% and then failed with 
> the error message:

All my branch does is fix an Xcode compilation errors where std::
iterator tags are forward declared improperly.

> In file included from 
> /tmp/conega/qhull_SRC/src/libqhullcpp/QhullIterator.h(13),
> from /tmp/conega/qhull_SRC/src/libqhullcpp/Coordinates.h(13),
> from /tmp/conega/qhull_SRC/src/libqhullcpp/Coordinates.cpp(11):
> /tmp/conega/qhull_SRC/src/libqhull/qhull_a.h(106): error: 
> this declaration may not have extern "C" linkage
>template 
>^

It appears that something is doing

extern "C" {
#include "qhull.h"
}

which won't work since qhull is a C++ header. Are there any 'extern "C"'
bits around? Passing -E (or whatever Intel's equivalent is) to dump the
preprocessed source would help to see. The __cplusplus check may be
guarding against that line in upstream.

> So at least the conditional helped a bit for what I believe 
> is the "straight up C" part of the build.
> 
> 
> I'll CC the author of the fork Ben Boeckel about this.

That's me too :) . Seems I forgot to change the author setting for that
clone :/ . Rewrote the commit with the proper email.

--Ben
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Re: [Paraview] [EXTERNAL] Symbol WinMain missing when compiling with Visual Studio

[Ben Boeckel]

On Thu, Jun 30, 2016 at 19:20:58 +, Scott, W Alan wrote:
> Try building without Ninja?  If that also fails, I could try a build
> of my own.  Haven't done so in 6 months, but it seems to work.
> 
> By the way, what version of Visual Studio?

Also relevant: version of CMake and Qt.

--Ben
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Re: [Paraview] Query on ccmake for building Paraview

[Ben Boeckel]

On Wed, Feb 08, 2017 at 02:10:27 -0500, Bishwajit Dutta wrote:
> I had the below query. Thanks to pls help out.
> 
> I wanted to build Paraview 4.0.1 source on my 64 bit ubuntu system. I need
> to
> configure options to build with mesa and I read that this is to be done
> with ccmake.
> 
> Now I compiled cmake 2.8.8 and 3.7.0 but I cannot see any ccmake getting
> compiled in bin folder.
> Thanks for letting me know a proper version of cmake which has ccmake.

You need to set BUILD_CursesDialog=ON.

--Ben
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Re: [Paraview] Windows plugin compatibility with Paraview

[Ben Boeckel]

On Wed, Jan 25, 2017 at 11:08:00 -0600, Chris Marsh wrote:
> I would like to build and make available a pre-compiled windows binary for
> a filter I have developed. I would like to avoid the (windows) user having
> to compile the filter as well as paraview. Therefore I am wondering what
> compiler is used to produce the official Paraview builds so-as to avoid ABI
> issues with my pre-compiled .dll. Is there anything else I need to be aware
> of?

We use Visual Studio 2013 Community to build the binaries from the
superbuild:

https://gitlab.kitware.com/paraview/paraview-superbuild

If you want to be compatible with the paraview.org downloads, there are
two packages built, one with MPI and one without. You can see the
command lines used to build the superbuild here:

https://open.cdash.org/viewConfigure.php?buildid=4740356 (no MPI)
https://open.cdash.org/viewConfigure.php?buildid=4740247 (with MPI)

Only MSMPI is supported (but cannot be redistributed, so we rely on it
being available on the target machine already).

If you want to build your own package with the plugin pre-packaged, you
can use the documentation here:

https://gitlab.kitware.com/paraview/paraview-superbuild/#external-plugins

to support building your plugin and then extract it from the install/
tree and distribute it to your users. We currently do not ship an SDK
for Windows, so it is easiest to build 5.2.0 locally and then
redistribute your plugin (though building your own package is also
easy). Note that your plugin is built as part of ParaView in this
configuration, so there is no need to do a `find_package(ParaView)`. You
can see how the PointSpritePlugin deals with this here:


https://gitlab.kitware.com/paraview/paraview/blob/4897676d1cdc764f933a9fac22149dadf6dd5cb2/Plugins/PointSprite/CMakeLists.txt#L14

--Ben
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Re: [Paraview] [Non-DoD Source] Re: Superbuild repo change?

[Ben Boeckel]

On Wed, Feb 22, 2017 at 13:10:04 +, Angelini, Richard C (Rick) CIV USARMY 
RDECOM ARL (US) wrote:
> Cory - so I did a “git pull” and “git submodule update” in my existing
> paraview-superbuild repository directory and that 5.3.0-RC1 information
> was not in the versions.cmake file. I did a clean “git clone” and I
> then received the correct files.I’m not a git expert - so I’m not
> sure why I had to do a clean “git clone”.   I thought I “git pull” should
> have done a proper update.  I must be missing something with my
> repository update commands …..

What is the output of the following commands:

  - git config branch.master.remote
  - git remote show $output_from_previous_command
  - git remote show origin

--Ben
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Re: [Paraview] PVSB 5.2: missing modules and plugins after "make install"

[Ben Boeckel]

On Fri, Feb 17, 2017 at 13:17:37 +, Michel Rasquin wrote:
> Has anybody already tested successfully PVSB 5.2 from the install
> directory without loosing plugins and other module down the road?

Oh, running from the install directory? That's not really fully
supported. The reason is that we have 3 places ParaView ends up during
the superbuild:

  - the build tree
  - the install tree
  - the package

Getting it to work in all three on all platforms is not really feasible,
so we prioritize them as:

  - the package (because this has to work)
  - the build tree (so that tests can be run)
  - the install tree

It is best to make the package (ctest -R cpack-paraview-TGZ) and then
either run from _CPack_Packages/... or extract the generated tarball
somewhere else and run that. There is also `make install`, which should
also work just fine (it basically just does the packaging step to a
given directory and then doesn't actually make the package).

--Ben
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Re: [Paraview] Compiling Paraview 5.2 GCC 4.8 vtkOpenGLRenderWindow.cxx, line 641

[Ben Boeckel]

On Tue, Feb 21, 2017 at 17:57:37 +0100, Nabil Ghodbane wrote:
> many thanks for the prompt reply. I should have hit the toggle option :).

It's fine, that bug is elusive and a pain to deal with.

> No i did not give it a try yet. I will try it and send feedback (I am using
> miniconda)
> Does this mean that using non embedded python is still experimental ?

Using a system Python is fine, it's just that the one in the superbuild
hasn't been bumped.

--Ben
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Re: [Paraview] Compiling Paraview 5.2 GCC 4.8 vtkOpenGLRenderWindow.cxx, line 641

[Ben Boeckel]

> > On Tue, Feb 21, 2017 at 9:25 AM, Nabil Ghodbane
> >  wrote:
> > > OK many thanks,; I am trying to use the Superbuild now.
> > > I can see that it is downloading Python 2.7.11. Is there a particular
> > reason
> > > to use this version instead of the 2.7.12?

Haven't gotten around to updating to 2.7.12 (we're behind in updating
dependencies).

On Tue, Feb 21, 2017 at 16:18:48 +0100, Nabil Ghodbane wrote:
> ok thanks for the hint. I obviously missed this point. I will try again.
> I tried with the Python which is downloaded by the Paraview builder and i
> am hiting a new issue about libQtLucene.so
> Is this a known issue ?

There's a flag qt4_WORK_AROUND_BROKEN_ASSISTANT_BUILD you can set (it's
marked as advanced, so it is hidden by default). Details are here if
you're interested:


https://gitlab.kitware.com/paraview/common-superbuild/blob/master/projects/qt4.common.cmake#L5

--Ben
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Re: [Paraview] Compiling Paraview 5.2 GCC 4.8 vtkOpenGLRenderWindow.cxx, line 641

[Ben Boeckel]

On Wed, Feb 22, 2017 at 09:37:47 +0100, Nabil Ghodbane wrote:
> - I am requesting USE_SYSTEM_hdf5 = OFF
> but looking as you suggested in superbuild/paraview/build/CMakeCache.txt, I
> can see that VTK_USE_SYSTEM_HDF5:BOOL=TRUE
> Shouldn't this be FALSE ?

>From ParaView's point of view, it is using a "system" HDF5, but it is
being provided by the superbuild itself. It looks like it is finding the
superbuild's HDF5, so something else is going wrong here :( .

> Find attached, the CMakeCache.txt, How can I workaround this issue?

It will need investigation. I'll try and get to it this week.

> Find below some additional informations:
> -  it works on Ubuntu (I tried my own Python), but I need to stick to an
> older glibc :(
> - on a Debian node, it fails if I use my local Python installation, while
> trying to compile numpy: "/usr/lib/python2.7/distutils/sysconfig.py"

More information is needed to help with this.

--Ben
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Re: [Paraview] ParaView 5.3.0 Release Candidate 1 binaries are available for download

[Ben Boeckel]

On Tue, Feb 14, 2017 at 10:04:50 -0500, Utkarsh Ayachit wrote:
> Chuck, is this a CMake version related issue? Ufuk, which cmake
> version are you using?

It likely is. VTK is now using CMake's C++11 support detection and older
versions of CMake do not have the required bits for Intel 16. These
appear to have been introduced in 3.8.0, but may have been in 3.7.0 (I'm
not completely sure).

--Ben
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Re: [Paraview] PVSB 5.2: missing modules and plugins after "make install"

[Ben Boeckel]

On Sat, Feb 11, 2017 at 17:48:27 -0500, Cory Quammen wrote:
> Will updating to the current superbuild master address the missing
> plugins issue Michel is seeing? It looks like there have been some
> minor changes on plugin handling in linux since
> 4ec37480a6f1ad39c9aa3168c2f0e6a1b0147b16.

Yes, it's possible. If you look at the output of the packaging step,
there is probably some set of system libraries being pulled into the
package which should not be there.

--Ben
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Re: [Paraview] (no subject)

[Ben Boeckel]

On Mon, Feb 13, 2017 at 14:16:03 -0500, Bishwajit Dutta wrote:
> http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download=b10bd3f7136ef809f1df7ad5c94c553f=MD5
> ("Couldn't connect to server")
> 
> http://www.paraview.org/files/ExternalData/MD5/b10bd3f7136ef809f1df7ad5c94c553f
> ("Couldn't connect to server")

This indicates that you can't contact the host. Does it work if you
change the URLs to use `https` in CMake/vtkExternalData.cmake?

> Also I wanted to run a paraview python script with CPU acceleration. Will
> this compilation generate
> pvpython and can I pass it  --mesa-llvm for running the script (I assume by
> default it will use GPU acceleration as I have NVIDIA GPU on my system)?

5.0.0 did not have support for that flag (I think). That flag also
assumes certain things about the way ParaView was built (namely that
Mesa is available under `lib/paraview-5.x/mesa`).

--Ben
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Re: [Paraview] [Non-DoD Source] Re: Superbuild repo change?

[Ben Boeckel]

On Thu, Feb 16, 2017 at 16:53:55 +, Angelini, Richard C (Rick) CIV USARMY 
RDECOM ARL (US) wrote:
> Fabian - thank you - that was enough of a hint to get me over the hump.
> Switched my build to qt5 AND based on some information from a previous
> email thread, I added the following to my CMAKE command:
> 
> -DCMAKE_OSX_SDK="macosx10.9" \
> -DCMAKE_OSX_SYSROOT="/Applications/Xcode.app/Contents/Developer/Platforms/M
> acOSX.platform/Developer/SDKs/MacOSX10.9.sdk"

That shouldn't be necessary for Qt5 (though if it works, that's great).

--Ben
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Re: [Paraview] Superbuild repo change?

[Ben Boeckel]

On Wed, Feb 15, 2017 at 13:50:13 +, Angelini, Richard C (Rick) CIV USARMY 
RDECOM ARL (US) wrote:
> I did a fresh pull of the ParaView superbuild repository, and now I can’t do
> a clean build of PV 5.2.0 on my Mac (OSX 10.9.5).
> 
> First, I had to remove the entries for “qt” and “scipy" in the
> CMakeLists.txt:

You need to run `git submodule update` to update the common-superbuild
bits.

> After removing those entries, the cmake completes and the build starts and
> passes out in qt4. 
> I’m not sure why it’s complaining about OS X 10.7 or later?)

What version of Xcode are you using?

--Ben
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Re: [Paraview] [Non-DoD Source] Re: Superbuild repo change?

[Ben Boeckel]

On Fri, Feb 17, 2017 at 12:43:17 +, Angelini, Richard C (Rick) CIV USARMY 
RDECOM ARL (US) wrote:
> Cmake was complaining about CMAKE_OSX_SDK not being set …
> I’m not sure if I needed to set both variables, but I recalled seeing this
> in a mail thread, so I just set it!   8-)

Ah, then you just set it to what you had. That's fine :) . I just saw
"10.9" and assumed you were setting it to an older version.

--Ben
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Re: [Paraview] packing superbuild 5.2 fails on openSUSE due to ldconfig

[Ben Boeckel]

On Tue, Jan 17, 2017 at 11:19:40 +0100, Fabian Wein wrote:
> ldconfig is on openSUSE and Ubuntu /sbin/ldconfig but sbin in on 
> openSUSE not in the user path. For me a link in $HOME/bin helped but 
> maybe using the full path
> would work on all unix systems?!

I guess we'll go with the full path. PR is making its way to the
superbuild via:

https://gitlab.kitware.com/paraview/common-superbuild/merge_requests/136

Thanks,

--Ben
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Re: [Paraview] Issues viewing PV5.0.0 Filters/Alphabetical submenu

[Ben Boeckel]

On Tue, Feb 28, 2017 at 19:02:50 +0900, kenichiro yoshimi wrote:
> Has this issue been resolved?
> 
> I think that this might be caused by a bug in Qt 4.8.6:
> https://bugreports.qt.io/browse/QTBUG-54921

I think we came to the same conclusion. Windows has used Qt4 4.8.4 since
then to avoid the issue. However, as Cory said, Qt5 is now in use, so
the bug might have been avoided that way now.

--Ben
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Re: [Paraview] [vtkusers] Testing ITK/VTK/PV contributions with (kitware) Gitlab-CI

[Ben Boeckel]

On Thu, Sep 08, 2016 at 12:36:40 +0200, Grothausmann, Roman Dr. wrote:
> Just getting to know Gitlab-CI, I am wondering whether it is possible to test 
> contributions to ITK/VTK/PV with Gitlab-CI from gitlab.com or 
> gitlab.kitware.com. As far as I understand, this basically needs runners, in 
> this case specific to ITK/VTK/PV. Since kitware has done CI even before the 
> use 
> of gitlab, I wonder if the former testing environments are available for use 
> with Gitlab-CI and if so how to use them.

We're (VTK and ParaView) using buildbot to manage our testing. The
number of settings we test across machines is hard to specify in YAML
files (machines also have different settings based on what you're
testing, e.g., load up a different compiler or Qt4 or Qt5 and the paths
they live in, etc.). We're working on improving the hardware situation
buildbot is currently in; things should be getting better over the next
few months on that front.

> For example, none of my contributions to the ITK/VTK/Midas Journals got into 
> the 
> testing phase even though marked for testing during submission. So a 
> possibility 
> to use Gitlab-CI to test the compilation and to run the project test would be 
> really great, especially for continued development and testing on other OSs.
> Specifically, for e.g. testing my FacetAnalyser contribution 
> (http://www.midasjournal.org/browse/publication/951 
> https://gitlab.com/romangrothausmann/FacetAnalyser) I would need a runner 
> environment with PV, VTK and ITK ideally for Linux, MacOS and Windows.

ITK is using Gerrit and Jenkins, not Gitlab.

--Ben
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Re: [Paraview] [vtk-developers] Which Compilers and Operating Systems to you require for VTK and / ParaView?

[Ben Boeckel]

On Mon, Sep 26, 2016 at 14:01:38 -0400, Chuck Atkins wrote:
> Just as a follow-up, I will be leaving this survey open all week and stop
> accepting responses on Friday, October 30.

I assume you mean September 30?

--Ben
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Re: [Paraview] Building ParaView v5.1.2 on Linux from source with support for GPU and SWR.

[Ben Boeckel]

On Wed, Sep 28, 2016 at 17:54:53 +0200, Albina, Frank wrote:
> I had to recompile from scractch, which took a bit of time. Actually,
> the GNU compiler requirement is coming from building the OSPRAY
> project, as shown hereafter:
> 
> [...]
> CMake Error at cmake/gcc.cmake:48 (MESSAGE):
>   GCC version 4.8.0 or greater is required to build OSPRay.
> Call Stack (most recent call first):
>   cmake/ospray.cmake:97 (INCLUDE)
>   common/CMakeLists.txt:17 (CONFIGURE_OSPRAY)

This makes sense; ospray requires C++11 support for which GCC 4.8 was
the first release with viable support (4.7.x had some, but not enough).

> If the new superbuild has support for building mesa 12.0.3, I would be
> interested in trying this out. Are there any instructions I can follow
> to do that?

It's on my list to improve docs here. I'd welcome feedback where the
existing docs are deficient (they're in README.md on the master branch)
so I can improve those parts.

> My intention is to compile paraview without GUI to run it in batch on
> our cluster. This is the main reason why I am using a specific test
> suite to check the performance of mesa-llvm vs. mesa-swr vs. GPU. At
> the moment, on CPUs supporting AVX2 instruction set, mesa-swr shows a
> very decent performance. Hence, my interest also to try out the latest
> mesa 12.0.3 version, which I have downloaded today and started
> compiling. In this regard, do you have any configuration options you
> can share for use in offscreen mode? If this is handled already by the
> latest superbuild version, then please disregard the questions above.

Chuck (Cc'd) does this quite a bit. There are scripts he has committed
which are used to build for specific platforms which you may be able to
start using, but he's the best source of instructions for those.

--Ben
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Re: [Paraview] Building ParaView v5.1.2 on Linux from source with support for GPU and SWR.

[Ben Boeckel]

On Wed, Sep 28, 2016 at 10:06:15 +0200, Albina, Frank wrote:
> In this regard, I would like to point out a few things I have found
> while performing the build process on the aforementioned Linux
> distribution. Note that my incentive is to help improve the ParaView
> software suite as well as helping others to be able to build and use
> the software.

Thanks for the feedback. Responses inline.

> 2. You definitely need cmake at least cmake v3.5 (and not v3.3) to
> compile ParaView from SuperBuild.

Ah, ParaView is 3.3, but the superbuild is 3.5. As a heads up, the new
superbuild which will be used for ParaView 5.2 will require at least
3.6.1.

> 3. You need a GNU compiler v4.8.0 or above to build. My Linux
> distribution comes with gcc v4.7.2. Fortunately, I had gcc v4.9.2
> installed with which I could perform a successful build.

What subproject required this?

> 4. Dependencies such libsz, libxml, libbzip2 are built and stored
> in the /install/lib64 directory on my platform. This creates
> linking issues which I could partly resolve by pushing the missing
> libraries into the /install/lib directory. This is not ideal
> but could be solved by forcing the lib directory to
> /install/lib using the --libdir option.

Hrm. I'm on Fedora (which also uses lib64) and though I had gotten all
the lib64-isms out of the superbuild. Maybe I had missed some before
5.1.2 (the superbuild now uses common infrastructure shared between
other similar superbuilds).

> 5. The vistrails plugin cannot be built. After 3 attempts, the git
> clone from https://kwgitlab.kitware.com/paraview/vistrails.git fails.
> Either the link is wrong or the server is unreachable.

vistrails should be hidden behind a "USE_NONFREE_COMPONENTS" flag.
vistrails (and acusolve) are not FOSS, so their git repos are on our
internal server.

> 6. The mesa libraries are pre-compiled and downloaded to
> /mesa-downloads. They are unpacked and moved into the ParaView
> installation directory when performing “make install”. These libraries
> are dating from May 3rd, hence prior to the release of Mesa 12.0 which
> embeds OpenSWR as a build option. Is there a way to build new libGL.so
> and libOSMesa.so libraries based on Mesa3D v12.0 and replace the
> currently pre-compiled binaries? If so,what are the typical
> configuration options used in this case?

The new superbuild has support for building mesa 12.0.3 as part of the
build. We used prebuilt binaries before because our build machine was
Debian 6 which was not easily capable of compiling the LLVM -> Mesa
chain without a self-compiled compiler and such, so it was built once
and that was it. I think it did contain SWR since it was a git snapshot.
Utkarsh?

--Ben
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Re: [Paraview] ParaView 5.2 Release Candidate 2 available for download

[Ben Boeckel]

On Thu, Oct 20, 2016 at 15:13:51 +0300, Gena Bug via ParaView wrote:
> Now, with RC2, fontconfig warns me about blank section:
> 
> Fontconfig warning: line 160: blank doesn't take any effect anymore. 
> please remove it from your fonts.conf

We're now using a newer fontconfig, so the fontconfig may be newer than
your system, so this is just fontconfig being more pedantic than your
distro. Looking at fontconfig, there's no environment variable to
suppress these warnings.

> However, that all -- no more new folder "fontconfig" in the running 
> directory. Thank you, that was really annoying!
> 
> Also, lib-dynload is still missing in the lib/python2.7

Ah, the superbuild didn't get bumped for that fix yet. I'll do that
today.

--Ben
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Re: [Paraview] ParaView 5.2 Release Candidate 2 available for download

[Ben Boeckel]

On Fri, Oct 21, 2016 at 10:31:00 -0400, David Thompson wrote:
> Your attempt to set CMAKE_OSX_SDK=10.12 was probably on the superbuild
> project, and it is not passed to the Qt subproject as QT_MAC_SDK. Try
> passing the proper value to CMAKE_OSX_SDK (i.e., the full path which
> is usually
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk)
> and see if the superbuild properly determines the value of
> QMAKE_MAC_SDK from that.

No, CMAKE_OSX_SDK is the name of the SDK. The path is CMAKE_OSX_SYSROOT.

--Ben
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Re: [Paraview] ParaView 5.2 Release Candidate 2 available for download

[Ben Boeckel]

On Thu, Oct 20, 2016 at 16:03:05 +0200, Fabian Wein wrote:
> Are you interested in superbuild tests, too? Or do you want to skip
> that issue for the time 5.2 is released?

We're interested :) .

> On macOS 10.12 Sierra I have problems building qt5:

Hmm, we haven't done 10.12 yet; upgrading it usually breaks things :( .

> superbuild fails with the output below but building qt5 manually seems
> to work (at least it builds for a longer time up to now)

We don't build the Qt5 bits yet for ParaView, but it is used with other
projects. (Though even for Qt4 is built once and reused to avoid an
extra 45+ minutes per build.)

Please open an issue here:

https://gitlab.kitware.com/paraview/common-superbuild

to help track this.

> On Linux (openSUSE tumbleweed with gcc 6.2.1) hdf5 fails the rest is still 
> building …

Could you post a bug at the same place for this? I use 6.2.1 from Fedora
and HDF5 is fine here. More details would be nice too.

Thanks,

--Ben
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[Paraview] [ANN] Dropping 32bit binaries for 5.3 and beyond

[Ben Boeckel]

Hi,

We're planning on dropping 32bit binaries (currently only provided on
Windows) for post-5.2 development.

Any objections?

--Ben
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Re: [Paraview] ParaView 5.2 Release Candidate 1 available for download

[Ben Boeckel]

On Wed, Oct 12, 2016 at 16:05:28 +0200, Albina, Frank wrote:
> Issue being configuration messages.

Oh, you're compiling 5.1.2 with the new superbuild; yes, that'd have the
same thing. I'll look to see if there's a way to get FONTCONFIG_PATH
default to the right place. Thanks for the hint.

--Ben
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Re: [Paraview] ParaView 5.2 Release Candidate 1 available for download

[Ben Boeckel]

On Tue, Oct 11, 2016 at 23:30:16 +0300, Gena Bug via ParaView wrote:
> I've just tried the 5.2rc and noticed this in the console:
> 
> $ Fontconfig error: "/etc/fonts/conf.d/10-scale-bitmap-fonts.conf", line 
> 72: non-double matrix element
> Fontconfig error: "/etc/fonts/conf.d/10-scale-bitmap-fonts.conf", line 
> 72: non-double matrix element
> Fontconfig warning: "/etc/fonts/conf.d/10-scale-bitmap-fonts.conf", line 
> 80: saw unknown, expected number

This is due to the way we now package fontconfig. We used to have it
just use the (non-existent) config files from the package, so you got
crappy fonts usually. Now, we use the system configuration and you
should get the same fonts as the system, but it seems that we probably
need to update our fontconfig. Other than that, the messages are
harmless as far as we've been able to tell.

> And a fontconfig folder is created in the run directory with a bunch of 
> cache-files.

Yeah, not sure how to fix this; I had tried putting them into /var/cache
like the system, but it seems that that flag is insufficient :( .

--Ben
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Re: [Paraview] ParaView 5.2 Release Candidate 1 available for download

[Ben Boeckel]

On Wed, Oct 12, 2016 at 15:36:24 +0200, Albina, Frank wrote:
> I have been having similar issue when compiling ParaView 5.1.2 from
> source with QT4 support, which depends on the fontconfig project. 
> I could get rid of it by setting FONTCONFIG_PATH to /etc/fonts on my
> system.

"Issue" being the crappy font rendering or the configuration messages?

--Ben
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Re: [Paraview] ParaView 5.2 Release Candidate 1 available for download

[Ben Boeckel]

On Wed, Oct 12, 2016 at 10:42:43 -0400, Ben Boeckel wrote:
> Oh, you're compiling 5.1.2 with the new superbuild; yes, that'd have the
> same thing. I'll look to see if there's a way to get FONTCONFIG_PATH
> default to the right place. Thanks for the hint.

Looks like updating to the latest fontconfig release solves the problem
with both the config file warnings and the cache files being dropped in
the wrong place; rc2 should be better.

--Ben
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