Problems with Qt 5.14.2 during building visIt in Ubuntu 20

[fernest0]

Hi!

I'm making a first attempt to install visIt in my pc.
My environment is:

No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 20.04.4 LTS
Release:	20.04
Codename:	focal 

gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Following the manual I'm running
$ ./build_visit3_3_0 --makeflags -j4 --tarball visit3_3_0.linux-x86_64-ubuntu20.tar.g

The compilation fails because is unable to build Qt. The full log file is attached.
And the screen prints are:

Processing bsd license.
[build_visit invocation arguments] --makeflags -j4 --tarball visit3_3_0.linux-x86_64-ubuntu20.tar.gz
[build_visit build mode ] Release
g++ version 9.4.0 9 9 9 9.4.0 9.4.0
Fortran support for thirdparty libraries disabled.
enabling any dependent libraries
initializing module variables
initialize module variables for cmake
initialize module variables for python
initialize module variables for qt
initalizing qt vars
initialize module variables for qwt
initialize module variables for vtk
initalizing vtk vars
initialize module variables for zlib

Checking for files . . .
Checking for cmake-3.18.2
Checking for python-3.7.7
Checking for qt-5.14.2
Checking for qwt-6.1.2
Checking for vtk-8.1.0
Checking for zlib-1.2.11
Found existing GIT visit directory, using that . . .
Checking optional 3rd party libs
building required libraries
cmake already installed, skipping
checking if python is installed
python already installed, skipping
Building Qt (~60 minutes)
Unzipping/Untarring qt-everywhere-src-5.14.2.tar.xz . . .
Patching qt . . .
Patching qt 5.14.2 for numeric-limits
Patching qt 5.14.2 for Linux and OpenGL
Configuring Qt5: 
Building Qt5 . . . (~60 minutes)
Qt5 build failed. Giving up
Unable to build or install Qt. Bailing out.

I took a look to Qt requirements such as here, here and #12371 (comment).

At this point any help would be much appreciated.
Thanks in advance!

build_visit3_3_0_log.txt

[alexmyczko]

@fernest0 did you meanwhile try to build it on 22.04?

[fernest0]

Hi Alex!

No, I haven't because I didn't upgrade my system yet.

I did try to build the visIt release 3.2.2 with the same problem.

[biagas]

For visit 3.3.0, try adding --qt510 as an option when calling build_visit3_3_0, in order to have the build script build qt 5.10.1 instead of qt 5.14.2.

[alexmyczko]

@fernest0 thanks for the reminder for me to test this on 22.04. actually i have quite some users of visit, and plan to continue trying to work on https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=395573

@biagas is it impossible to use a system provided installed later version of qt with visit 3.3.0? debian prefers to link dynamically against well maintained software packages, and to not bundle libraries with software (but keep them separate). past years. it was always a problem for me packaging visit mainly because visit was using versions of vtk, that debian didn't have (too old, or too new), i need to check what is the current state. and i believe a lot of visit users (and debian as well as ubuntu users) would profit having this software at their fingertips of apt install visit...

[biagas]

@alexmyczko You can build VisIt against a system version of Qt. If it is not a version we have tested, there are no guarantees that it will be compatible with the VTK needed for VisIt, or if VisIt will compile cleanly or run correctly with it.

As for VTK, it is much harder to use a system version, especially if it is newer than what VisIt currently supports (mainly due to API changes). System versions may also not be built with the same settings that VisIt requires. We currently support VTK-8.1.0 (with patches we apply during a build). We are adding support for VTK-9.1.0, but the work on this is not yet completed.

[alexmyczko]

@biagas Thanks for the information, unfortunately, Debian sid (aka unstable) only has these:

apt-cache search ^vtk |grep ^vtk
vtk-dicom-tools - DICOM for VTK - tools
vtk7 - Binaries for VTK7
vtk7-doc - VTK class reference documentation
vtk7-examples - VTK examples
vtk9 - Binaries for VTK9
vtk9-doc - VTK class reference documentation
vtk9-examples - VTK examples
vtkdata - Example data for VTK

Is there a way to see or get notified when vtk-9.1.0 is supported?

[biagas]

@fernest0 I took another look at your log file and the error message when building QT, and believe it may be related to this ticket filed with Qt.

Do you have CPATH defined in your environment? What are its contents? If the contents begin with ':', try removing that leading ':' and re-running build_visit3_3_0 (remove any untarred Qt source or build directories for best results).

[fernest0]

Hi @biagas ! I'm sorry for the delay.

• About the CPATH theory.
  Yes, I have a CPATH defined in my .bashrc file. Typing echo $CPATH in the console gives
  :/opt/hdf5/1.10.7/include:/home/ernesto/programas/hypre-2.9.0b/src/hypre/include
  Y could move forward with the building commenting those lines out in the .bashrc file.
  I need that CPATHs in my .bashrc file but I couldn't play deleting the colon symbols.

• About compiling qt5.10.1 instead of qt-5.14.2: #Problems with Qt 5.14.2 during building visIt in Ubuntu 20 #17976 (comment)
  helps me to move forward in the building.
  Just in case the log file of the failed building with qt-5.14.2 is attached where the problem is not clear.
  build_visit3_3_0_qt-5.14.2_log.txt

Currently problem
I think that I'm close. During the final part of building VisIt appeared the problem
"/usr/bin/ld: ../../../lib/libavtquery_ser.so: undefined reference to `shm_open'"
The log file is attached. Any idea of how to solve this problem?
build_visit3_3_0_log.txt

====
On the other hand, here I have to say something that may be important. I began using the building command
./build_visit3_3_0 --qt510 --tarball visit3_3_0.linux-x86_64-ubuntu20.tar.gz --makeflags -j4
obtaining the following error

Building VisIt (~50 minutes) 
Unzipping/untarring visit3_3_0.linux-x86_64-ubuntu20.tar.gz . . . 
Building VisIt in visit3_3_0.linux-x86_64-ubuntu20/build . . . 
Configuring VisIt . . . 
VisIt configuration failed.

because of the untar-folder name of visit3_3_0.linux-x86_64-ubuntu20.tar.gz instead of being visit3_3_0.linux-x86_64-ubuntu20
was just visit3_3_0.linux-x86_64, so the "Building VisIt in visit3_3_0.linux-x86_64-ubuntu20/build" failed because the folder didn't exist.
After that I re-ran the building script as
./build_visit3_3_0 --qt510 --tarball visit3.3.0.tar.gz --makeflags -j4
obtaining the above-attached log file (build_visit3_3_0_log.txt)

[biagas]

  I need that CPATHs in my .bashrc file but I couldn't play deleting the colon symbols.

You should only try deleting the leading colon, so that CPATH reads:
/opt/hdf5/1.10.7/include:/home/ernesto/programas/hypre-2.9.0b/src/hypre/include

Currently problem I think that I'm close. During the final part of building VisIt appeared the problem "/usr/bin/ld: ../../../lib/libavtquery_ser.so: undefined reference to `shm_open'" The log file is attached. Any idea of how to solve this problem? build_visit3_3_0_log.txt

Take a look at visit3.3.0/build/avt/Queries/CMakeFiles/avtquery_ser.dir/link.txt
See if '-lrt' is listed in there somewhere.
If it is listed, then there may be something missing from your system. Take a look at the packages we add to our Ubuntu 20 container. It lists everything we need for building VisIt successfully.

If '-lrt' is not listed, (and you feel like experimenting) try modifying visit3.3.0/avt/Queries/CMakeLists.txt so that the TARGET_LINK_LIBRARIES commands like like this (addition of -lrt at end):

TARGET_LINK_LIBRARIES(avtquery_ser visitcommon avtmath avtshapelets avtexpressions_ser avtfilters_ser visit_vtk -lrt)
TARGET_LINK_LIBRARIES(avtquery_par visitcommon avtmath avtshapelets avtexpressions_par avtfilters_par visit_vtk -lrt)

Then run 'make' from visit3.3.0/build.

==== On the other hand, here I have to say something that may be important. I began using the building command ./build_visit3_3_0 --qt510 --tarball visit3_3_0.linux-x86_64-ubuntu20.tar.gz --makeflags -j4 obtaining the following error

visit3_3_0.linux-x86_64-ubuntu20.tar.gz is a binary tarball, you would use it to install the pre-built verison of VisIt, not to build VisIt from sources.

If you wanted to try it you would download the visit-install3_3_0 script and follow Installing on Linux instructions.

[fernest0]

Take a look at visit3.3.0/build/avt/Queries/CMakeFiles/avtquery_ser.dir/link.txt See if '-lrt' is listed in there somewhere. If it is listed, then there may be something missing from your system. Take a look at the packages we add to our Ubuntu 20 container. It lists everything we need for building VisIt successfully.

'-lrt' isn't listed in there.

If '-lrt' is not listed, (and you feel like experimenting) try modifying visit3.3.0/avt/Queries/CMakeLists.txt so that the TARGET_LINK_LIBRARIES commands like like this (addition of -lrt at end):

TARGET_LINK_LIBRARIES(avtquery_ser visitcommon avtmath avtshapelets avtexpressions_ser avtfilters_ser visit_vtk -lrt)
TARGET_LINK_LIBRARIES(avtquery_par visitcommon avtmath avtshapelets avtexpressions_par avtfilters_par visit_vtk -lrt)

So I followed this suggestion to add '-lrt' in the TARGET_LINK_LIBRARIES statements and made a run make in visit3.3.0/build. The run seemly reached at the end well. See the attached file
run_make.txt
Unfortunately when I execute ./visit VisIt doesn't open the window viewer and I face with the message:

Running: gui -dv
Running: viewer -dv -geometry 1097x777+503+54 -borders 26,4,4,4 -shift 0,0 -preshift 4,26 -defer -host 127.0.0.1 -port 5600
/home/ernesto/visit3.3.3-qt510/visit3.3.0/build/exe/viewer: error while loading shared libraries: libvtkRenderingOpenGL2-8.1.so.1: cannot open shared object file: No such file or directory

which make think that something went wrong during the built.
I took a look at the Ubuntu 20 container and my system has everything install from there.

Any opinion about it?

Thank you!

[brugger1]

I've actually run into that recently when trying to run VisIt from a build using build/bin/visit on Ubuntu20. I believe we aren't setting an RPATH properly. There are a couple of ways to fix this.

1. You can add the path to the VTK8.1 lib directory to your LD_LIBRARY_PATH. This is something along the lines of third_party/vtk/8.1.0/linux-x86_64_gcc_7.5/lib where you would need to add the rest of the path before third_party and the version of gcc may be something other than 7.5.

2. You can do a make -j 4 package, then untar the resulting tar file, and then run VisIt out of that installation.

[fernest0]

Well, @brugger1 you made me realise I had made a mistake. During the run make in visit3.3.0/build I had just run make instead of make package.
Now seems that VisIt's built is right. Bravo! I could lunch the GUI and made a few visualisations. Thank you very much!

To give the next step I would like to ask about building options. As I'm manly interested in viewing FLASH-formatted data (an hdf5 flavour) and this was just my first attempt building VisIt from source using
./build_visit3_3_0 --qt510 --tarball visit3.3.0.tar.gz --makeflags -j4
I expect that next time building with --hdf5 I'll be able to open FLASH data. Am I right or will I need to add another building option such as --flash?

Finally, I'm thinking to build as:
./build_visit3_3_0 --qt510 --mpich --mesagl --fortran --python --hdf5 --vtk --silo --prefix /opt/visit --tarball visit3.3.0.tar.gz --makeflags -j4

Any tip to take into account?