Author Topic: Building OVITO from source  (Read 81 times)

mathewni

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Building OVITO from source
« on: March 07, 2019, 12:28:36 AM »
Hi,

I am trying to build a ‘basic’ OVITO (no video output, no netCDF, no hdf5) from source against the local python interpreter. My purpose is to be able to call OVITO from a python script. I am on Centos7.6, using g++ 6.4.0, Qt5.9.2, Boost 1.59, Python 3.5.4.

I got the source using
Code: [Select]
git clone https://gitlab.com/stuko/ovito.git ovito
The build compiles to 100% and I do not see errors. The log file from
Code: [Select]
make -j 8 “VERBOSE=1” is attached (see logmake.tar.gz).

Following this I tried a “
Code: [Select]
make install” and it failed with the following error (see attached loginstall):

Code: [Select]
[100%] Built target VoroTopPython_automoc
[100%] Built target VoroTopPython
Install the project...
-- Install configuration: "Release"
-- Installing: /home/mathewni/software/custom_ovito/ovito/build/./README.txt
-- Installing: /home/mathewni/software/custom_ovito/ovito/build/./LICENSE.txt
-- Installing: /home/mathewni/software/custom_ovito/ovito/build/./CHANGELOG.txt
CMake Error at src/3rdparty/netcdf_integration/cmake_install.cmake:42 (file):
  file INSTALL cannot find
  "/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libNetCDFIntegration.so".
Call Stack (most recent call first):
  src/3rdparty/cmake_install.cmake:42 (include)
  src/cmake_install.cmake:37 (include)
  cmake_install.cmake:53 (include)
I am trying to understand why it is complaining about ‘libNetCDFIntegration.so’ when I had set

Code: [Select]
OPTION(OVITO_BUILD_PLUGIN_NETCDFPLUGIN "Build the NetCDF plugin." "OFF")
in the upper-level CmakeLists.txt. My upper-level CmakeLists.txt is attached.

Please let me know if anyone has thoughts on what might be going wrong with the install (or my build). Thanks in advance.

Alexander Stukowski

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Re: Building OVITO from source
« Reply #1 on: March 07, 2019, 02:37:37 PM »
Hi,

First of all, let me mention that you should be able to run Ovito from inside the build directory. Thus, it may not really be necessary to first install it via "make install". Please try.

Now regarding your question: Even though its name may suggest otherwise, the "NetCDFPlugin" is not the only module that depends on the NetCDF/HDF5 libraries. The "CrystalAnalysis" plugin also requires the NetCDF/HDF5 libraries. Thus, unless you also set the "OVITO_BUILD_PLUGIN_CRYSTALANALYSIS" CMake variable to OFF, the build script will still try to build and install the "NetCDFIntegration" target, which in turn requires the NetCDF & HDF5 system libraries to be available on your system.

See this part of the CMake code:
https://gitlab.com/stuko/ovito/blob/master/src/3rdparty/CMakeLists.txt#L39-41

So one way to resolve your build problem is to disable the CrystalAnalysis plugin as well. You will then loose the Construct Surface Mesh and Dislocation Analysis modifiers though. I'm not sure if you need them.

I tried to build and install Ovito on my Ubuntu machine with OVITO_BUILD_PLUGIN_NETCDFPLUGIN set to OFF and OVITO_BUILD_PLUGIN_CRYSTALANALYSIS set to ON. This worked without problems. This suggests that the error you encountered is specific to the Centos environment. Is this why you had to disable the NetCDF plugin in the first place?

-Alex
« Last Edit: March 07, 2019, 02:42:18 PM by Alexander Stukowski »

mathewni

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Re: Building OVITO from source
« Reply #2 on: March 07, 2019, 02:48:50 PM »
Alex,

Thanks for your reply. I need the CrystalAnalysis plugin for dislocation analysis and I did not know that it uses the HDF5/NetCDF libraries. I disabled NetCDF, since it was mentioned as optional in the docs for building OVITO.

Thanks for trying those CMAKE options, and since it worked for you, it is likely that there are problems with my environment. I'll check a few things and get back on this.

--
Nithin

Alexander Stukowski

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Re: Building OVITO from source
« Reply #3 on: March 07, 2019, 03:16:25 PM »
The dependency of the CrystalAnalysis plugin on the NetCDF library has been introduced just recently, and only for an experimental feature that you don't need. If required, you can temporarily remove this dependency by removing the following lines from the CMake script:

https://gitlab.com/stuko/ovito/blob/master/src/plugins/crystalanalysis/CMakeLists.txt#L24
https://gitlab.com/stuko/ovito/blob/master/src/plugins/crystalanalysis/CMakeLists.txt#L70

And the three lines in the other CMake file linked in my post above.

-Alex

mathewni

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Re: Building OVITO from source
« Reply #4 on: March 07, 2019, 05:59:47 PM »
First of all, let me mention that you should be able to run Ovito from inside the build directory. Thus, it may not really be necessary to first install it via "make install". Please try.

That was one of my other questions. The docs mention that a successful build will result in /build/bin with the executable. That doesn't happen in my case either even though the build goes to 100% and no errors are reported. Please let me know if you have any thoughts on what might be the problem there.

The dependency of the CrystalAnalysis plugin on the NetCDF library has been introduced just recently, and only for an experimental feature that you don't need. If required, you can temporarily remove this dependency by removing the following lines from the CMake script:

https://gitlab.com/stuko/ovito/blob/master/src/plugins/crystalanalysis/CMakeLists.txt#L24
https://gitlab.com/stuko/ovito/blob/master/src/plugins/crystalanalysis/CMakeLists.txt#L70

And the three lines in the other CMake file linked in my post above.

I tried what you mentioned above - build goes to 100%, no /build/bin and when I try make install, it results in

Code: [Select]
-- Installing: /home/mathewni/software/custom_ovito/ovito/build/./CHANGELOG.txt
CMake Error at src/core/cmake_install.cmake:42 (file):
  file INSTALL cannot find
  "/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libCore.so".

I guess that something is seriously broken in the way I am trying to do this. Please let me know if you have any thoughts. Thanks, again.

Alexander Stukowski

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Re: Building OVITO from source
« Reply #5 on: March 07, 2019, 06:05:56 PM »
Please run just "make", not "make -j8". When doing a parallel build, error messages can easily get lost in the verbose console output. If you run just "make" to perform a serial build, any error messages should follow at the very end and should be easily visible.

I would find it very surprising if the build succeeds but there is no /bin/ovito executable being produced (unless you've set OVITO_BUILD_GUI to OFF for some reason).

mathewni

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Re: Building OVITO from source
« Reply #6 on: March 07, 2019, 08:47:37 PM »
unless you've set OVITO_BUILD_GUI to OFF for some reason.

That was the problem. I was under the impression that I can make an ovito(s) executable without the GUI. So now I do get an executable but it segfaults under execution. I put it through gdb (as suggested in a different thread) and the output is below:

Code: [Select]
GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-114.el7
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /home/mathewni/software/custom_ovito/ovito/build/bin/ovitos...(no debugging symbols found)...done.
(gdb) r
Starting program: /home/mathewni/software/custom_ovito/ovito/build/bin/ovitos -c pass
warning: the debug information found in "/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6.0.21" does not match "/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6" (CRC mismatch).

Missing separate debuginfo for /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6
Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/a5/3f2ebf5eaa52fa82ae3ed6317f5ee6646f83f6.debug
Missing separate debuginfo for /lib64/libssh.so.4
Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/de/f6a18eca4d6768e064dc9c21515c04d39e7d0f.debug
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-mathewni'
[New Thread 0x155541e0b700 (LWP 33576)]
ERROR: Failed to load native plugin library.
Library file: /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/CrystalAnalysis.so
Error: Cannot load library /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/CrystalAnalysis.so: (/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/CrystalAnalysis.so))
ERROR: Failed to load native plugin library.
Library file: /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/CrystalAnalysisGui.so
Error: Cannot load library /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/CrystalAnalysisGui.so: (/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/CrystalAnalysis.so))
ERROR: Failed to load native plugin library.
Library file: /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/CrystalAnalysisPython.so
Error: Cannot load library /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/CrystalAnalysisPython.so: (/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/CrystalAnalysis.so))
ERROR: Failed to load native plugin library.
Library file: /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Galamost.so
Error: Cannot load library /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Galamost.so: (/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Particles.so))
ERROR: Failed to load native plugin library.
Library file: /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/GalamostPython.so
Error: Cannot load library /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/GalamostPython.so: (/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Particles.so))
ERROR: Failed to load native plugin library.
Library file: /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Grid.so
Error: Cannot load library /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Grid.so: (/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Mesh.so))
ERROR: Failed to load native plugin library.
Library file: /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/GridGui.so
Error: Cannot load library /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/GridGui.so: (/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Mesh.so))
ERROR: Failed to load native plugin library.
Library file: /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/GridPython.so
Error: Cannot load library /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/GridPython.so: (/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Mesh.so))
ERROR: Failed to load native plugin library.
Library file: /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Mesh.so
Error: Cannot load library /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Mesh.so: (/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Mesh.so))
ERROR: Failed to load native plugin library.
Library file: /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/MeshGui.so
Error: Cannot load library /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/MeshGui.so: (/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Mesh.so))
ERROR: Failed to load native plugin library.
Library file: /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/MeshPython.so
Error: Cannot load library /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/MeshPython.so: (/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Mesh.so))
ERROR: Failed to load native plugin library.
Library file: /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Particles.so
Error: Cannot load library /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Particles.so: (/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Particles.so))
ERROR: Failed to load native plugin library.
Library file: /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/ParticlesGui.so
Error: Cannot load library /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/ParticlesGui.so: (/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Particles.so))
ERROR: Failed to load native plugin library.
Library file: /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/ParticlesPython.so
Error: Cannot load library /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/ParticlesPython.so: (/home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/plugins/Particles.so))

Program received signal SIGSEGV, Segmentation fault.
0x000015553bb7c67d in ?? () from /projects/opt/centos7/anaconda3/lib/libQtGui.so.4
Missing separate debuginfos, use: debuginfo-install bzip2-libs-1.0.6-13.el7.x86_64 dbus-libs-1.10.24-12.el7.x86_64 elfutils-libelf-0.172-2.el7.x86_64 elfutils-libs-0.172-2.el7.x86_64 expat-2.1.0-10.el7_3.x86_64 fontconfig-2.13.0-4.3.el7.x86_64 freetype-2.8-12.el7_6.1.x86_64 glib2-2.56.1-2.el7.x86_64 glibc-2.17-260.el7_6.3.x86_64 graphite2-1.3.10-1.el7_3.x86_64 harfbuzz-1.7.5-2.el7.x86_64 keyutils-libs-1.5.8-3.el7.x86_64 krb5-libs-1.15.1-37.el7_6.x86_64 libICE-1.0.9-9.el7.x86_64 libSM-1.2.2-2.el7.x86_64 libX11-1.6.5-2.el7.x86_64 libXau-1.0.8-2.1.el7.x86_64 libXcursor-1.1.15-1.el7.x86_64 libXext-1.3.3-3.el7.x86_64 libXfixes-5.0.3-1.el7.x86_64 libXi-1.7.9-1.el7.x86_64 libXrender-0.9.10-1.el7.x86_64 libattr-2.4.46-13.el7.x86_64 libcap-2.22-9.el7.x86_64 libcom_err-1.42.9-13.el7.x86_64 libgcc-4.8.5-36.el7.x86_64 libgcrypt-1.5.3-14.el7.x86_64 libglvnd-1.0.1-0.8.git5baa1e5.el7.x86_64 libglvnd-glx-1.0.1-0.8.git5baa1e5.el7.x86_64 libgpg-error-1.12-3.el7.x86_64 libicu-50.1.2-17.el7.x86_64 libpng-1.5.13-7.el7_2.x86_64 libselinux-2.5-14.1.el7.x86_64 libuuid-2.23.2-59.el7.x86_64 libxcb-1.13-1.el7.x86_64 lz4-1.7.5-2.el7.x86_64 openssl-libs-1.0.2k-16.el7.x86_64 pcre-8.32-17.el7.x86_64 pcre2-utf16-10.23-2.el7.x86_64 qscintilla-2.8-1.el7.x86_64 qt5-qtbase-5.9.2-3.el7.x86_64 qt5-qtbase-gui-5.9.2-3.el7.x86_64 systemd-libs-219-62.el7_6.3.x86_64 xcb-util-0.4.0-2.el7.x86_64 xcb-util-image-0.4.0-2.el7.x86_64 xcb-util-keysyms-0.4.0-1.el7.x86_64 xcb-util-renderutil-0.3.9-3.el7.x86_64 xcb-util-wm-0.4.1-5.el7.x86_64 xz-libs-5.2.2-1.el7.x86_64 zlib-1.2.7-18.el7.x86_64
(gdb) bt
#0  0x000015553bb7c67d in ?? () from /projects/opt/centos7/anaconda3/lib/libQtGui.so.4
#1  0x000015553bb9e9a6 in ?? () from /projects/opt/centos7/anaconda3/lib/libQtGui.so.4
#2  0x0000000000000000 in ?? ()

I can see
Code: [Select]
`GLIBCXX_3.4.22' not found I understand that my libstdc++ is old and copying the two files in https://ovito.org/download/2.9.0/ does not help as it appears to have only up to GLIBCXX_3.4.21 (found using strings). Is that leading to the SEGFAULT?

mathewni

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Re: Building OVITO from source
« Reply #7 on: March 07, 2019, 10:13:00 PM »
Sorry, please ignore the GDB part of the previous post. I had not loaded the correct gcc module (which I had used to build). With the correct module loaded, gdb gives the following:

Code: [Select]
[mathewni@darwin-fe1 bin]$ gdb --args ovitos -c "pass"
GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-114.el7
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /home/mathewni/software/custom_ovito/ovito/build/bin/ovitos...(no debugging symbols found)...done.
(gdb) r
Starting program: /home/mathewni/software/custom_ovito/ovito/build/bin/ovitos -c pass
warning: File "/projects/opt/centos7/gcc/6.4.0/lib64/libstdc++.so.6.0.22-gdb.py" auto-loading has been declined by your `auto-load safe-path' set to "$debugdir:$datadir/auto-load:/usr/bin/mono-gdb.py".
To enable execution of this file add
add-auto-load-safe-path /projects/opt/centos7/gcc/6.4.0/lib64/libstdc++.so.6.0.22-gdb.py
line to your configuration file "/home/mathewni/.gdbinit".
To completely disable this security protection add
set auto-load safe-path /
line to your configuration file "/home/mathewni/.gdbinit".
For more information about this security protection see the
"Auto-loading safe path" section in the GDB manual.  E.g., run from the shell:
info "(gdb)Auto-loading safe path"
Missing separate debuginfo for /lib64/libssh.so.4
Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/de/f6a18eca4d6768e064dc9c21515c04d39e7d0f.debug
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-mathewni'
[New Thread 0x155541e0e700 (LWP 21956)]
Missing separate debuginfo for /lib64/libmuparser.so.2
Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/f1/e1392b1c17e021b565214114c277baac4f3b2a.debug

Program received signal SIGSEGV, Segmentation fault.
0x00001555384c667d in ?? () from /projects/opt/centos7/anaconda3/lib/libQtGui.so.4
Missing separate debuginfos, use: debuginfo-install bzip2-libs-1.0.6-13.el7.x86_64 dbus-libs-1.10.24-12.el7.x86_64 elfutils-libelf-0.172-2.el7.x86_64 elfutils-libs-0.172-2.el7.x86_64 expat-2.1.0-10.el7_3.x86_64 fontconfig-2.13.0-4.3.el7.x86_64 freetype-2.8-12.el7_6.1.x86_64 glib2-2.56.1-2.el7.x86_64 glibc-2.17-260.el7_6.3.x86_64 graphite2-1.3.10-1.el7_3.x86_64 harfbuzz-1.7.5-2.el7.x86_64 keyutils-libs-1.5.8-3.el7.x86_64 krb5-libs-1.15.1-37.el7_6.x86_64 libICE-1.0.9-9.el7.x86_64 libSM-1.2.2-2.el7.x86_64 libX11-1.6.5-2.el7.x86_64 libXau-1.0.8-2.1.el7.x86_64 libXcursor-1.1.15-1.el7.x86_64 libXext-1.3.3-3.el7.x86_64 libXfixes-5.0.3-1.el7.x86_64 libXi-1.7.9-1.el7.x86_64 libXrender-0.9.10-1.el7.x86_64 libattr-2.4.46-13.el7.x86_64 libcap-2.22-9.el7.x86_64 libcom_err-1.42.9-13.el7.x86_64 libgcrypt-1.5.3-14.el7.x86_64 libglvnd-1.0.1-0.8.git5baa1e5.el7.x86_64 libglvnd-glx-1.0.1-0.8.git5baa1e5.el7.x86_64 libgpg-error-1.12-3.el7.x86_64 libicu-50.1.2-17.el7.x86_64 libpng-1.5.13-7.el7_2.x86_64 libselinux-2.5-14.1.el7.x86_64 libuuid-2.23.2-59.el7.x86_64 libxcb-1.13-1.el7.x86_64 lz4-1.7.5-2.el7.x86_64 openssl-libs-1.0.2k-16.el7.x86_64 pcre-8.32-17.el7.x86_64 pcre2-utf16-10.23-2.el7.x86_64 qscintilla-2.8-1.el7.x86_64 qt5-qtbase-5.9.2-3.el7.x86_64 qt5-qtbase-gui-5.9.2-3.el7.x86_64 systemd-libs-219-62.el7_6.3.x86_64 xcb-util-0.4.0-2.el7.x86_64 xcb-util-image-0.4.0-2.el7.x86_64 xcb-util-keysyms-0.4.0-1.el7.x86_64 xcb-util-renderutil-0.3.9-3.el7.x86_64 xcb-util-wm-0.4.1-5.el7.x86_64 xz-libs-5.2.2-1.el7.x86_64 zlib-1.2.7-18.el7.x86_64
(gdb) bt
#0  0x00001555384c667d in ?? () from /projects/opt/centos7/anaconda3/lib/libQtGui.so.4
#1  0x00001555384e89a6 in ?? () from /projects/opt/centos7/anaconda3/lib/libQtGui.so.4
#2  0x0000000000000000 in ?? ()

Please let me know if you have thoughts on what might be going on. Thanks.

Alexander Stukowski

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Re: Building OVITO from source
« Reply #8 on: March 08, 2019, 08:35:26 AM »
There seems to be a problem with the library "/projects/opt/centos7/anaconda3/lib/libQtGui.so.4" from the Anaconda distribution. Is this the right installation of the Qt 5.x libraries that you intended to use? I can't tell for sure from the error message, but at least I can imagine that this crash results from a conflict between several Qt5 installations present on your system. Perhaps Ovito was compiled against a different Qt version than the one being loaded at runtime. Please attach the CMakeCache.txt file from your build directory. Then I will take a look at your build configuration.

mathewni

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Re: Building OVITO from source
« Reply #9 on: March 11, 2019, 11:31:57 PM »
There seems to be a problem with the library "/projects/opt/centos7/anaconda3/lib/libQtGui.so.4" from the Anaconda distribution. Is this the right installation of the Qt 5.x libraries that you intended to use?

In fact, no. Not sure why /projects/opt/centos7/anaconda3/lib/libQtGui.so.4 is creating a problem.
I am using the python that comes in the anaconda3 distribution, though. My cmake is below:

Code: [Select]
cmake -DOVITO_BUILD_DOCUMENTATION=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/home/mathewni/software/custom_ovito/ovito/build -DPYTHON_EXECUTABLE=/projects/opt/centos7/anaconda3/bin/python -DPYTHON_INCLUDE_DIR=/projects/opt/centos7/anaconda3/include/python3.5m -DPYTHON_LIBRARY=/projects/opt/centos7/anaconda3/lib/libpython3.5m.so -DBOOST_ROOT=/projects/opt/centos7/boost/1.59.0/ -DCMAKE_CXX_COMPILER=/projects/opt/centos7/gcc/6.4.0/bin/g++ -DCMAKE_C_COMPILER=/projects/opt/centos7/gcc/6.4.0/bin/gcc -DCMAKE_PREFIX_PATH=/usr/include/qt5/ ../

ldd ovitos produces:

Code: [Select]
linux-vdso.so.1 =>  (0x00007ffc0b43a000)
libGui.so => /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libGui.so (0x0000147cc0466000)
libOpenGLRenderer.so => /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libOpenGLRenderer.so (0x0000147cc01ee000)
libCore.so => /home/mathewni/software/custom_ovito/ovito/build/lib/ovito/libCore.so (0x0000147cbfe2e000)
libQt5Concurrent.so.5 => /lib64/libQt5Concurrent.so.5 (0x0000147cc0a37000)
libQt5Widgets.so.5 => /lib64/libQt5Widgets.so.5 (0x0000147cbf7c5000)
libQt5Gui.so.5 => /lib64/libQt5Gui.so.5 (0x0000147cbf30f000)
libQt5Network.so.5 => /lib64/libQt5Network.so.5 (0x0000147cc08ae000)
libQt5Core.so.5 => /lib64/libQt5Core.so.5 (0x0000147cbee65000)
libstdc++.so.6 => /projects/opt/centos7/gcc/6.4.0/lib64/libstdc++.so.6 (0x0000147cbeae5000)
libm.so.6 => /lib64/libm.so.6 (0x0000147cbe7e3000)
libgcc_s.so.1 => /projects/opt/centos7/gcc/6.4.0/lib64/libgcc_s.so.1 (0x0000147cbe5cc000)
libc.so.6 => /lib64/libc.so.6 (0x0000147cbe1ff000)
libGL.so.1 => /lib64/libGL.so.1 (0x0000147cbdf73000)
libssh.so.4 => /lib64/libssh.so.4 (0x0000147cbdd02000)
libz.so.1 => /lib64/libz.so.1 (0x0000147cbdaec000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x0000147cbd8d0000)
libpng15.so.15 => /lib64/libpng15.so.15 (0x0000147cbd6a5000)
libharfbuzz.so.0 => /lib64/libharfbuzz.so.0 (0x0000147cbd408000)
libssl.so.10 => /lib64/libssl.so.10 (0x0000147cbd196000)
libcrypto.so.10 => /lib64/libcrypto.so.10 (0x0000147cbcd35000)
libsystemd.so.0 => /lib64/libsystemd.so.0 (0x0000147cbcb04000)
libicui18n.so.50 => /lib64/libicui18n.so.50 (0x0000147cbc705000)
libicuuc.so.50 => /lib64/libicuuc.so.50 (0x0000147cbc38c000)
libicudata.so.50 => /lib64/libicudata.so.50 (0x0000147cbadba000)
libpcre2-16.so.0 => /lib64/libpcre2-16.so.0 (0x0000147cbab4e000)
libdl.so.2 => /lib64/libdl.so.2 (0x0000147cba94a000)
libgthread-2.0.so.0 => /lib64/libgthread-2.0.so.0 (0x0000147cba748000)
libglib-2.0.so.0 => /lib64/libglib-2.0.so.0 (0x0000147cba432000)
/lib64/ld-linux-x86-64.so.2 (0x0000147cc083b000)
libGLX.so.0 => /lib64/libGLX.so.0 (0x0000147cba200000)
libX11.so.6 => /lib64/libX11.so.6 (0x0000147cb9ec2000)
libXext.so.6 => /lib64/libXext.so.6 (0x0000147cb9cb0000)
libGLdispatch.so.0 => /lib64/libGLdispatch.so.0 (0x0000147cb99fa000)
librt.so.1 => /lib64/librt.so.1 (0x0000147cb97f2000)
libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2 (0x0000147cb95a5000)
libkrb5.so.3 => /lib64/libkrb5.so.3 (0x0000147cb92bc000)
libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x0000147cb9089000)
libcom_err.so.2 => /lib64/libcom_err.so.2 (0x0000147cb8e85000)
libfreetype.so.6 => /lib64/libfreetype.so.6 (0x0000147cb8bc6000)
libgraphite2.so.3 => /lib64/libgraphite2.so.3 (0x0000147cb8998000)
libcap.so.2 => /lib64/libcap.so.2 (0x0000147cb8793000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x0000147cb856c000)
liblzma.so.5 => /lib64/liblzma.so.5 (0x0000147cb8346000)
liblz4.so.1 => /lib64/liblz4.so.1 (0x0000147cb8131000)
libgcrypt.so.11 => /lib64/libgcrypt.so.11 (0x0000147cb7eb0000)
libgpg-error.so.0 => /lib64/libgpg-error.so.0 (0x0000147cb7cab000)
libresolv.so.2 => /lib64/libresolv.so.2 (0x0000147cb7a92000)
libdw.so.1 => /lib64/libdw.so.1 (0x0000147cb7843000)
libpcre.so.1 => /lib64/libpcre.so.1 (0x0000147cb75e1000)
libxcb.so.1 => /lib64/libxcb.so.1 (0x0000147cb73b9000)
libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x0000147cb71a9000)
libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x0000147cb6fa5000)
libbz2.so.1 => /lib64/libbz2.so.1 (0x0000147cb6d95000)
libattr.so.1 => /lib64/libattr.so.1 (0x0000147cb6b90000)
libelf.so.1 => /lib64/libelf.so.1 (0x0000147cb6978000)
libXau.so.6 => /lib64/libXau.so.6 (0x0000147cb6774000)


I have also attached the CMakeCache.txt file. Thanks a lot for all the help.