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Messages - Kevin

Pages: [1] 2
1
Support Forum / Re: Partial radial distribution function (RDF)
« on: October 23, 2018, 07:40:52 PM »
I needed this same functionality and tried myself with a problem.

Just noting that the file path has to be defined for the file name as well. (At least on mac)
Otherwise, the python script will complain that permission is denied.
I guess the default file path is somewhere writing permission is not given.

Thanks,
-Kyu

2
Support Forum / Re: which gcc is used to compile ovito?
« on: October 04, 2018, 07:41:08 AM »
Hello Dr.Stukowski,

I had other errors on this so I am reporting the issue here.

Note that I am running ovitos on remote cluster.

I used the following command to run ovitos as you directed:
Note that I added additional path (Qt5XcbQpa) to preload because I needed to log in with Xforwarding.
With Xforwarding on, ovitos complained that it was missing Qt5XcbQpa.
Code: [Select]
LD_PRELOAD=~/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/lib/libQt5DBus.so:~/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/lib/libQt5XcbQpa.so \
     ovitos2

But after enabling Xforwarding, a problem rises.

When I submit the ovitos job on computing nodes (non-interactively) as follows:
Code: [Select]
LD_PRELOAD=~/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/lib/libQt5DBus.so:~/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/lib/libQt5XcbQpa.so \
     ovitos2 -o cna.ovito \
                auto_movie.py

The error message is:
Code: [Select]
QXcbConnection: Could not connect to display 172.16.5.5:94.0


One thing I noticed is that
when I submit jobs and if the jobs run after I log off from the remote cluster, the error above is given.
But if I stay in the remote cluster then job runs to the end with the error message described below (xkbcommon problem).


Another thing I noticed is that,
when I run ovitos on interactive and non-interactive sessions on computing nodes,
the following error rises:  (Note this error does not rise on login node interactive session)
Code: [Select]
xkbcommon: ERROR: failed to add default include path /usr/share/X11/xkb
Qt: Failed to create XKB context!
Use QT_XKB_CONFIG_ROOT environmental variable to provide an additional search path, add ':' as separator to provide several search paths and/or make sure that XKB configuration data directory contains recent enough contents, to update please see http://cgit.freedesktop.org/xkeyboard-config/ .


Do you have any idea how to fix this?



3
Support Forum / can ovito movie rendering be paralleled?
« on: September 23, 2018, 08:37:38 AM »
Hello Dr.Stukowski,

I was just wondering if ovito movie rendering could be accelerated with multiple cores?

I tried with single core vs. multiple cores, and it seems like the movie rendering speed does not increase with the increase of core number.

Thanks,
Kyu

4
Support Forum / Re: which gcc is used to compile ovito?
« on: September 17, 2018, 08:00:40 PM »
1. Attached is the error evoked by running "LD_DEBUG=libs bin/ovitos".

2. Yes. With the preload command, the ovitos runs!!!

Thank you for your help!

-Kyu

5
Support Forum / Re: which gcc is used to compile ovito?
« on: September 17, 2018, 10:25:30 AM »
I put the file you gave under the following directory: "lib/ovito".

But note that under the "lib/ovito/lib" directory, the following files are included:
Code: [Select]
libQt5DBus.so    libQt5DBus.so.5.7    libQt5XcbQpa.so    libQt5XcbQpa.so.5.7
libQt5DBus.so.5  libQt5DBus.so.5.7.0  libQt5XcbQpa.so.5  libQt5XcbQpa.so.5.7.0
I think the file you uploaded in the previous comment is included in "lib/ovito/lib" directory.


Running  "QT_DEBUG_PLUGINS=1 bin/ovitos" results in the following error:

Code: [Select]
[kkim124@jhu.edu@bc-login01 ovito-2.9.0-x86_64]$ QT_DEBUG_PLUGINS=1 bin/ovitos
QFactoryLoader::QFactoryLoader() checking directory path "/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms" ...
QFactoryLoader::QFactoryLoader() looking at "/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqminimal.so"
Found metadata in lib /home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqminimal.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "minimal"
        ]
    },
    "className": "QMinimalIntegrationPlugin",
    "debug": false,
    "version": 329472
}


Got keys from plugin meta data ("minimal")
QFactoryLoader::QFactoryLoader() looking at "/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqoffscreen.so"
Found metadata in lib /home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqoffscreen.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "offscreen"
        ]
    },
    "className": "QOffscreenIntegrationPlugin",
    "debug": false,
    "version": 329472
}


Got keys from plugin meta data ("offscreen")
QFactoryLoader::QFactoryLoader() looking at "/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqxcb.so"
Found metadata in lib /home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqxcb.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "xcb"
        ]
    },
    "className": "QXcbIntegrationPlugin",
    "debug": false,
    "version": 329472
}


Got keys from plugin meta data ("xcb")
QFactoryLoader::QFactoryLoader() checking directory path "/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/bin/platforms" ...
loaded library "/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqminimal.so"
QLibraryPrivate::loadPlugin failed on "/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqminimal.so" : "Cannot load library /home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqminimal.so: (/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/bin/../lib/ovito/libQt5Core.so.5: version `Qt_5.9' not found (required by /software/centos7/lib64/libQt5DBus.so.5))"
This application failed to start because it could not find or load the Qt platform plugin "minimal"
in "".

Available platform plugins are: minimal, offscreen, xcb.

Reinstalling the application may fix this problem.
Aborted

-Kyu

6
Support Forum / Re: which gcc is used to compile ovito?
« on: September 17, 2018, 09:32:28 AM »
Thank you for the reply.

1. For your information, yes, I am running on remote server without active X forwarding.

2. On ovito-2.9.0 version, I ran "QT_DEBUG_PLUGINS=1 bin/ovitos" and the outputs are as follows:

Code: [Select]
[kkim124@jhu.edu@bc-login03 ovito-2.9.0-x86_64]$ QT_DEBUG_PLUGINS=1 bin/ovitos
QFactoryLoader::QFactoryLoader() checking directory path "/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms" ...
QFactoryLoader::QFactoryLoader() looking at "/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqminimal.so"
Found metadata in lib /home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqminimal.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "minimal"
        ]
    },
    "className": "QMinimalIntegrationPlugin",
    "debug": false,
    "version": 329472
}


Got keys from plugin meta data ("minimal")
QFactoryLoader::QFactoryLoader() looking at "/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqoffscreen.so"
Found metadata in lib /home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqoffscreen.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "offscreen"
        ]
    },
    "className": "QOffscreenIntegrationPlugin",
    "debug": false,
    "version": 329472
}


Got keys from plugin meta data ("offscreen")
QFactoryLoader::QFactoryLoader() looking at "/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqxcb.so"
Found metadata in lib /home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqxcb.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "xcb"
        ]
    },
    "className": "QXcbIntegrationPlugin",
    "debug": false,
    "version": 329472
}


Got keys from plugin meta data ("xcb")
QFactoryLoader::QFactoryLoader() checking directory path "/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/bin/platforms" ...
loaded library "/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqminimal.so"
QLibraryPrivate::loadPlugin failed on "/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqminimal.so" : "Cannot load library /home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platforms/libqminimal.so: (/home-net/home-3/kkim124@jhu.edu/opt/ovito/ovito-2.9.0-x86_64/bin/../lib/ovito/libQt5Core.so.5: version `Qt_5.9' not found (required by /software/centos7/lib64/libQt5DBus.so.5))"
This application failed to start because it could not find or load the Qt platform plugin "minimal"
in "".

Available platform plugins are: minimal, offscreen, xcb.

Reinstalling the application may fix this problem.
Aborted


Thank you for your prompt and detailed explanation.
-Kyu

7
Support Forum / Re: which gcc is used to compile ovito?
« on: September 16, 2018, 07:43:50 PM »
Yes of course. I forgot to do this for the most recent version for ovito 3.

My problem is solved but I will report findings that you may find helpful just in case.


Initially I had some problems running ovitos version 2.9.0 and version 3.0.0_dev101 due to the dependencies problem (It ran fine before on centOS 6.9). But this error doesn't happen with the newest development version (ovito 3.0.0_dev234). But even though the ovitos runs in dev234 version with gcc/4.8.5, it is still complaining the dependency problem.


Note that I am using centOS 7.5.
Note that all the errors discussed below are still invoked even though "libstdc++.so.6.0.21" and "libstdc++.so.6" are put in the appropriate directory as you mentioned in your previous reply.

First, on dev234 version, upon checking the dependencies of "libqminimal.so" on the following directory :
Code: [Select]
ovito-3.0.0-dev234-x86_64/lib/ovito/plugins_qt/platforms,
the error invoked was as follows:

Code: [Select]
ldd libqminimal.so
ldd: warning: you do not have execution permission for `./libqminimal.so'
./libqminimal.so: /software/centos7/lib64/libQt5Core.so.5: version `Qt_5.10' not found (required by ./libqminimal.so)
./libqminimal.so: /software/centos7/lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by ./libqminimal.so)
linux-vdso.so.1 =>  (0x00007fffc7194000)
libfreetype.so.6 => /software/centos7/lib64/libfreetype.so.6 (0x00007f2e8bafd000)
libfontconfig.so.1 => /software/centos7/lib64/libfontconfig.so.1 (0x00007f2e8b8c0000)
libQt5Gui.so.5 => /software/centos7/lib64/libQt5Gui.so.5 (0x00007f2e8b40a000)
libQt5Core.so.5 => /software/centos7/lib64/libQt5Core.so.5 (0x00007f2e8af60000)
libGL.so.1 => /software/centos7/lib64/libGL.so.1 (0x00007f2e8acee000)
libpthread.so.0 => /software/centos7/lib64/libpthread.so.0 (0x00007f2e8aad2000)
libstdc++.so.6 => /software/centos7/lib64/libstdc++.so.6 (0x00007f2e8a7cb000)
libm.so.6 => /software/centos7/lib64/libm.so.6 (0x00007f2e8a4c9000)
libgcc_s.so.1 => /software/centos7/lib64/libgcc_s.so.1 (0x00007f2e8a2b3000)
libc.so.6 => /software/centos7/lib64/libc.so.6 (0x00007f2e89ee6000)
libexpat.so.1 => /software/centos7/lib64/libexpat.so.1 (0x00007f2e89cbc000)
libpng15.so.15 => /software/centos7/lib64/libpng15.so.15 (0x00007f2e89a91000)
libharfbuzz.so.0 => /software/centos7/lib64/libharfbuzz.so.0 (0x00007f2e8982e000)
libz.so.1 => /software/centos7/lib64/libz.so.1 (0x00007f2e89618000)
libsystemd.so.0 => /software/centos7/lib64/libsystemd.so.0 (0x00007f2e893e7000)
libicui18n.so.50 => /software/centos7/lib64/libicui18n.so.50 (0x00007f2e88fe8000)
libicuuc.so.50 => /software/centos7/lib64/libicuuc.so.50 (0x00007f2e88c6f000)
libicudata.so.50 => /software/centos7/lib64/libicudata.so.50 (0x00007f2e8769b000)
libpcre2-16.so.0 => /software/centos7/lib64/libpcre2-16.so.0 (0x00007f2e8742f000)
libdl.so.2 => /software/centos7/lib64/libdl.so.2 (0x00007f2e8722b000)
libgthread-2.0.so.0 => /software/centos7/lib64/libgthread-2.0.so.0 (0x00007f2e87029000)
libglib-2.0.so.0 => /software/centos7/lib64/libglib-2.0.so.0 (0x00007f2e86d15000)
/lib64/ld-linux-x86-64.so.2 (0x00007f2e8bda3000)
libxcb-dri3.so.0 => /software/centos7/lib64/libxcb-dri3.so.0 (0x00007f2e86b12000)
libxcb-xfixes.so.0 => /software/centos7/lib64/libxcb-xfixes.so.0 (0x00007f2e8690a000)
libxcb-present.so.0 => /software/centos7/lib64/libxcb-present.so.0 (0x00007f2e86707000)
libxcb-sync.so.1 => /software/centos7/lib64/libxcb-sync.so.1 (0x00007f2e86500000)
libxshmfence.so.1 => /software/centos7/lib64/libxshmfence.so.1 (0x00007f2e862fd000)
libglapi.so.0 => /software/centos7/lib64/libglapi.so.0 (0x00007f2e860cd000)
libselinux.so.1 => /software/centos7/lib64/libselinux.so.1 (0x00007f2e85ea6000)
libXext.so.6 => /software/centos7/lib64/libXext.so.6 (0x00007f2e85c94000)
libXdamage.so.1 => /software/centos7/lib64/libXdamage.so.1 (0x00007f2e85a91000)
libXfixes.so.3 => /software/centos7/lib64/libXfixes.so.3 (0x00007f2e8588b000)
libX11-xcb.so.1 => /software/centos7/lib64/libX11-xcb.so.1 (0x00007f2e85689000)
libX11.so.6 => /software/centos7/lib64/libX11.so.6 (0x00007f2e8534b000)
libxcb.so.1 => /software/centos7/lib64/libxcb.so.1 (0x00007f2e85123000)
libxcb-glx.so.0 => /software/centos7/lib64/libxcb-glx.so.0 (0x00007f2e84f08000)
libxcb-dri2.so.0 => /software/centos7/lib64/libxcb-dri2.so.0 (0x00007f2e84d03000)
libXxf86vm.so.1 => /software/centos7/lib64/libXxf86vm.so.1 (0x00007f2e84afd000)
libdrm.so.2 => /software/centos7/lib64/libdrm.so.2 (0x00007f2e848ec000)
libgraphite2.so.3 => /software/centos7/lib64/libgraphite2.so.3 (0x00007f2e846be000)
libcap.so.2 => /software/centos7/lib64/libcap.so.2 (0x00007f2e844b9000)
librt.so.1 => /software/centos7/lib64/librt.so.1 (0x00007f2e842b1000)
liblzma.so.5 => /software/centos7/lib64/liblzma.so.5 (0x00007f2e8408b000)
liblz4.so.1 => /software/centos7/lib64/liblz4.so.1 (0x00007f2e83e76000)
libgcrypt.so.11 => /software/centos7/lib64/libgcrypt.so.11 (0x00007f2e83bf5000)
libgpg-error.so.0 => /software/centos7/lib64/libgpg-error.so.0 (0x00007f2e839f0000)
libresolv.so.2 => /software/centos7/lib64/libresolv.so.2 (0x00007f2e837d7000)
libdw.so.1 => /software/centos7/lib64/libdw.so.1 (0x00007f2e83590000)
libpcre.so.1 => /software/centos7/lib64/libpcre.so.1 (0x00007f2e8332e000)
libXau.so.6 => /software/centos7/lib64/libXau.so.6 (0x00007f2e8312a000)
libattr.so.1 => /software/centos7/lib64/libattr.so.1 (0x00007f2e82f25000)
libelf.so.1 => /software/centos7/lib64/libelf.so.1 (0x00007f2e82d0d000)
libbz2.so.1 => /software/centos7/lib64/libbz2.so.1 (0x00007f2e82afd000)

The reason why I ended up checking the dependencies of libqminimal.so is as follows.
On ovito 2.9.0 or ovitos 3.0.0_dev_101 version, I had some errors regarding dependencies of minimal plugin. (again, this didn't happen in centOS 6.9, but happens in centOS 7.5)

When I try to run ovitos,
the error invoked was as follows:

Code: [Select]
This application failed to start because it could not find or load the Qt platform plugin "minimal"
in "".

Available platform plugins are: minimal, offscreen, xcb.

Reinstalling the application may fix this problem.
Aborted

So I went to the following directory
Code: [Select]
ovito-2.9.0-x86_64/lib/ovito/plugins_qt/platformsand checked the dependencies as follows:
Code: [Select]
ldd libqminimal.so
The error invoked was as follows:
Code: [Select]
ldd: warning: you do not have execution permission for `./libqminimal.so'
./libqminimal.so: /software/centos7/lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by ./libqminimal.so)
linux-vdso.so.1 =>  (0x00007ffd74549000)
libfontconfig.so.1 => /software/centos7/lib64/libfontconfig.so.1 (0x00007f088336f000)
libfreetype.so.6 => /software/centos7/lib64/libfreetype.so.6 (0x00007f08830c9000)
libQt5DBus.so.5 => /software/centos7/lib64/libQt5DBus.so.5 (0x00007f0883721000)
libXrender.so.1 => /software/centos7/lib64/libXrender.so.1 (0x00007f0882ebe000)
libXext.so.6 => /software/centos7/lib64/libXext.so.6 (0x00007f0882cac000)
libX11.so.6 => /software/centos7/lib64/libX11.so.6 (0x00007f088296e000)
libQt5Gui.so.5 => /software/centos7/lib64/libQt5Gui.so.5 (0x00007f08824b8000)
libQt5Core.so.5 => /software/centos7/lib64/libQt5Core.so.5 (0x00007f088200e000)
libGL.so.1 => /software/centos7/lib64/libGL.so.1 (0x00007f0881d9c000)
libpthread.so.0 => /software/centos7/lib64/libpthread.so.0 (0x00007f0881b80000)
libstdc++.so.6 => /software/centos7/lib64/libstdc++.so.6 (0x00007f0881879000)
libm.so.6 => /software/centos7/lib64/libm.so.6 (0x00007f0881577000)
libgcc_s.so.1 => /software/centos7/lib64/libgcc_s.so.1 (0x00007f0881361000)
libc.so.6 => /software/centos7/lib64/libc.so.6 (0x00007f0880f94000)
libexpat.so.1 => /software/centos7/lib64/libexpat.so.1 (0x00007f0880d6a000)
libdbus-1.so.3 => /software/centos7/lib64/libdbus-1.so.3 (0x00007f0880b1a000)
libxcb.so.1 => /software/centos7/lib64/libxcb.so.1 (0x00007f08808f2000)
libdl.so.2 => /software/centos7/lib64/libdl.so.2 (0x00007f08806ee000)
libpng15.so.15 => /software/centos7/lib64/libpng15.so.15 (0x00007f08804c3000)
libharfbuzz.so.0 => /software/centos7/lib64/libharfbuzz.so.0 (0x00007f0880260000)
libz.so.1 => /software/centos7/lib64/libz.so.1 (0x00007f088004a000)
libsystemd.so.0 => /software/centos7/lib64/libsystemd.so.0 (0x00007f087fe19000)
libicui18n.so.50 => /software/centos7/lib64/libicui18n.so.50 (0x00007f087fa1a000)
libicuuc.so.50 => /software/centos7/lib64/libicuuc.so.50 (0x00007f087f6a1000)
libicudata.so.50 => /software/centos7/lib64/libicudata.so.50 (0x00007f087e0cd000)
libpcre2-16.so.0 => /software/centos7/lib64/libpcre2-16.so.0 (0x00007f087de61000)
libgthread-2.0.so.0 => /software/centos7/lib64/libgthread-2.0.so.0 (0x00007f087dc5f000)
libglib-2.0.so.0 => /software/centos7/lib64/libglib-2.0.so.0 (0x00007f087d94b000)
/lib64/ld-linux-x86-64.so.2 (0x00007f08835ac000)
libxcb-dri3.so.0 => /software/centos7/lib64/libxcb-dri3.so.0 (0x00007f087d748000)
libxcb-xfixes.so.0 => /software/centos7/lib64/libxcb-xfixes.so.0 (0x00007f087d540000)
libxcb-present.so.0 => /software/centos7/lib64/libxcb-present.so.0 (0x00007f087d33d000)
libxcb-sync.so.1 => /software/centos7/lib64/libxcb-sync.so.1 (0x00007f087d136000)
libxshmfence.so.1 => /software/centos7/lib64/libxshmfence.so.1 (0x00007f087cf33000)
libglapi.so.0 => /software/centos7/lib64/libglapi.so.0 (0x00007f087cd03000)
libselinux.so.1 => /software/centos7/lib64/libselinux.so.1 (0x00007f087cadc000)
libXdamage.so.1 => /software/centos7/lib64/libXdamage.so.1 (0x00007f087c8d9000)
libXfixes.so.3 => /software/centos7/lib64/libXfixes.so.3 (0x00007f087c6d3000)
libX11-xcb.so.1 => /software/centos7/lib64/libX11-xcb.so.1 (0x00007f087c4d1000)
libxcb-glx.so.0 => /software/centos7/lib64/libxcb-glx.so.0 (0x00007f087c2b6000)
libxcb-dri2.so.0 => /software/centos7/lib64/libxcb-dri2.so.0 (0x00007f087c0b1000)
libXxf86vm.so.1 => /software/centos7/lib64/libXxf86vm.so.1 (0x00007f087beab000)
libdrm.so.2 => /software/centos7/lib64/libdrm.so.2 (0x00007f087bc9a000)
libXau.so.6 => /software/centos7/lib64/libXau.so.6 (0x00007f087ba96000)
libgraphite2.so.3 => /software/centos7/lib64/libgraphite2.so.3 (0x00007f087b868000)
libcap.so.2 => /software/centos7/lib64/libcap.so.2 (0x00007f087b663000)
librt.so.1 => /software/centos7/lib64/librt.so.1 (0x00007f087b45b000)
liblzma.so.5 => /software/centos7/lib64/liblzma.so.5 (0x00007f087b235000)
liblz4.so.1 => /software/centos7/lib64/liblz4.so.1 (0x00007f087b020000)
libgcrypt.so.11 => /software/centos7/lib64/libgcrypt.so.11 (0x00007f087ad9f000)
libgpg-error.so.0 => /software/centos7/lib64/libgpg-error.so.0 (0x00007f087ab9a000)
libresolv.so.2 => /software/centos7/lib64/libresolv.so.2 (0x00007f087a981000)
libdw.so.1 => /software/centos7/lib64/libdw.so.1 (0x00007f087a73a000)
libpcre.so.1 => /software/centos7/lib64/libpcre.so.1 (0x00007f087a4d8000)
libattr.so.1 => /software/centos7/lib64/libattr.so.1 (0x00007f087a2d3000)
libelf.so.1 => /software/centos7/lib64/libelf.so.1 (0x00007f087a0bb000)
libbz2.so.1 => /software/centos7/lib64/libbz2.so.1 (0x00007f0879eab000)

This happens with gcc/4.8.5, so I tried ldd again with gcc/5.5.0 loaded.
In this case the error is not invoked as follows, indicating all the dependencies are met:
Code: [Select]
ldd: warning: you do not have execution permission for `./libqminimal.so'
linux-vdso.so.1 =>  (0x00007ffe41566000)
libfontconfig.so.1 => /software/centos7/lib64/libfontconfig.so.1 (0x00007fc58ab14000)
libfreetype.so.6 => /software/centos7/lib64/libfreetype.so.6 (0x00007fc58a86e000)
libQt5DBus.so.5 => /software/centos7/lib64/libQt5DBus.so.5 (0x00007fc58aec6000)
libXrender.so.1 => /software/centos7/lib64/libXrender.so.1 (0x00007fc58a663000)
libXext.so.6 => /software/centos7/lib64/libXext.so.6 (0x00007fc58a451000)
libX11.so.6 => /software/centos7/lib64/libX11.so.6 (0x00007fc58a113000)
libQt5Gui.so.5 => /software/centos7/lib64/libQt5Gui.so.5 (0x00007fc589c5d000)
libQt5Core.so.5 => /software/centos7/lib64/libQt5Core.so.5 (0x00007fc5897b3000)
libGL.so.1 => /software/centos7/lib64/libGL.so.1 (0x00007fc589541000)
libpthread.so.0 => /software/centos7/lib64/libpthread.so.0 (0x00007fc589325000)
libstdc++.so.6 => /software/apps/compilers/gcc/5.5.0/lib64/libstdc++.so.6 (0x00007fc588fa9000)
libm.so.6 => /software/centos7/lib64/libm.so.6 (0x00007fc588ca7000)
libgcc_s.so.1 => /software/apps/compilers/gcc/5.5.0/lib64/libgcc_s.so.1 (0x00007fc588a90000)
libc.so.6 => /software/centos7/lib64/libc.so.6 (0x00007fc5886c3000)
libexpat.so.1 => /software/centos7/lib64/libexpat.so.1 (0x00007fc588499000)
libdbus-1.so.3 => /software/centos7/lib64/libdbus-1.so.3 (0x00007fc588249000)
libxcb.so.1 => /software/centos7/lib64/libxcb.so.1 (0x00007fc588021000)
libdl.so.2 => /software/centos7/lib64/libdl.so.2 (0x00007fc587e1d000)
libpng15.so.15 => /software/centos7/lib64/libpng15.so.15 (0x00007fc587bf2000)
libharfbuzz.so.0 => /software/centos7/lib64/libharfbuzz.so.0 (0x00007fc58798f000)
libz.so.1 => /software/centos7/lib64/libz.so.1 (0x00007fc587779000)
libsystemd.so.0 => /software/centos7/lib64/libsystemd.so.0 (0x00007fc587548000)
libicui18n.so.50 => /software/centos7/lib64/libicui18n.so.50 (0x00007fc587149000)
libicuuc.so.50 => /software/centos7/lib64/libicuuc.so.50 (0x00007fc586dd0000)
libicudata.so.50 => /software/centos7/lib64/libicudata.so.50 (0x00007fc5857fc000)
libpcre2-16.so.0 => /software/centos7/lib64/libpcre2-16.so.0 (0x00007fc585590000)
libgthread-2.0.so.0 => /software/centos7/lib64/libgthread-2.0.so.0 (0x00007fc58538e000)
libglib-2.0.so.0 => /software/centos7/lib64/libglib-2.0.so.0 (0x00007fc58507a000)
/lib64/ld-linux-x86-64.so.2 (0x00007fc58ad51000)
libxcb-dri3.so.0 => /software/centos7/lib64/libxcb-dri3.so.0 (0x00007fc584e77000)
libxcb-xfixes.so.0 => /software/centos7/lib64/libxcb-xfixes.so.0 (0x00007fc584c6f000)
libxcb-present.so.0 => /software/centos7/lib64/libxcb-present.so.0 (0x00007fc584a6c000)
libxcb-sync.so.1 => /software/centos7/lib64/libxcb-sync.so.1 (0x00007fc584865000)
libxshmfence.so.1 => /software/centos7/lib64/libxshmfence.so.1 (0x00007fc584662000)
libglapi.so.0 => /software/centos7/lib64/libglapi.so.0 (0x00007fc584432000)
libselinux.so.1 => /software/centos7/lib64/libselinux.so.1 (0x00007fc58420b000)
libXdamage.so.1 => /software/centos7/lib64/libXdamage.so.1 (0x00007fc584008000)
libXfixes.so.3 => /software/centos7/lib64/libXfixes.so.3 (0x00007fc583e02000)
libX11-xcb.so.1 => /software/centos7/lib64/libX11-xcb.so.1 (0x00007fc583c00000)
libxcb-glx.so.0 => /software/centos7/lib64/libxcb-glx.so.0 (0x00007fc5839e5000)
libxcb-dri2.so.0 => /software/centos7/lib64/libxcb-dri2.so.0 (0x00007fc5837e0000)
libXxf86vm.so.1 => /software/centos7/lib64/libXxf86vm.so.1 (0x00007fc5835da000)
libdrm.so.2 => /software/centos7/lib64/libdrm.so.2 (0x00007fc5833c9000)
libXau.so.6 => /software/centos7/lib64/libXau.so.6 (0x00007fc5831c5000)
libgraphite2.so.3 => /software/centos7/lib64/libgraphite2.so.3 (0x00007fc582f97000)
libcap.so.2 => /software/centos7/lib64/libcap.so.2 (0x00007fc582d92000)
librt.so.1 => /software/centos7/lib64/librt.so.1 (0x00007fc582b8a000)
liblzma.so.5 => /software/centos7/lib64/liblzma.so.5 (0x00007fc582964000)
liblz4.so.1 => /software/centos7/lib64/liblz4.so.1 (0x00007fc58274f000)
libgcrypt.so.11 => /software/centos7/lib64/libgcrypt.so.11 (0x00007fc5824ce000)
libgpg-error.so.0 => /software/centos7/lib64/libgpg-error.so.0 (0x00007fc5822c9000)
libresolv.so.2 => /software/centos7/lib64/libresolv.so.2 (0x00007fc5820b0000)
libdw.so.1 => /software/centos7/lib64/libdw.so.1 (0x00007fc581e69000)
libpcre.so.1 => /software/centos7/lib64/libpcre.so.1 (0x00007fc581c07000)
libattr.so.1 => /software/centos7/lib64/libattr.so.1 (0x00007fc581a02000)
libelf.so.1 => /software/centos7/lib64/libelf.so.1 (0x00007fc5817ea000)
libbz2.so.1 => /software/centos7/lib64/libbz2.so.1 (0x00007fc5815da000)

But, when I try to run ovitos, it still gives the following error:

Code: [Select]
This application failed to start because it could not find or load the Qt platform plugin "minimal"
in "".

Available platform plugins are: minimal, offscreen, xcb.

Reinstalling the application may fix this problem.
Aborted


Thanks,
Kyu


8
Support Forum / which gcc is used to compile ovito?
« on: September 16, 2018, 07:59:42 AM »
Hello Dr.Stukowski,


Is gcc 5.1 used to compile linux version of ovito? (That was the only update that you wrote on the update info page (https://ovito.org/index.php/about/version-history).

I am using gcc 4.8.5 in centOS 7.5, and "ovitos" is complaining as follows:
Code: [Select]
./ovitos: /software/centos7/lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by ./ovitos)

It looks like gcc 4.8.5 does not have CXXABI_1.3.9, and I was wondering what gcc version I should be using to use ovitos. (But before the supercomputer server updated to centOS 7.5 from 6.9, it worked fine with 4.8.5.)



Thanks,
Kyu

9
Support Forum / Re: rendering quality
« on: May 07, 2018, 04:24:41 AM »
Hi Dr.Stukowski,

You indicated that I could change the zoom level with Viewport.fov attribute, but I am not sure how this changes the zoom level.

Doesn't Viewport.fov attribute change the angle of the camera, not the zoom level?

-Kyu

10
Support Forum / Re: viewport
« on: April 25, 2018, 06:04:43 PM »
Yes, zoom_all was what I meant to say. I should have clarified a little more when I asked the question. Thanks for clarifying.

I will report what I did wrong as follows in case other users encounter similar mistake:

So, zoom_all() has to be used after setting the viewing direction and the FOV angle.
1. set up viewing direction and FOV angle
2. zoom_all()

I used in the reverse order;
1. zoom_all()  #this sets up viewing position so that all system is viewed in current viewing direction and FOV angle.
2. set up viewing direction and FOV angle  #changing viewing direction and FOV angle here would result in previously set viewing position in step 1 obsolete.

Thanks again,
-Kyu

11
Support Forum / Re: viewport
« on: April 19, 2018, 12:42:29 AM »
I actually have an additional question.

Is there a way to access how how GUI version of OVITO's 'Perspective' viewport calculates its 'View position', 'View direction', and 'View angle' ?

Thank you,
Kyu

12
Support Forum / Re: viewport
« on: April 18, 2018, 11:08:24 PM »
Thank you so much.
This was exactly what I was looking for.
I can't believe I missed that part of the documentation, and only focused on scripting documentation.
Thanks again.

- Kyu

13
Support Forum / viewport
« on: April 17, 2018, 06:17:45 AM »
Hello Dr.Stukowski and OVITO users,

I am trying to output a movie in python scripting. I found there are three parameters I can adjust, but have struggled to really understand what the parameters actually do. Three parameters are as follows:
1. fov
2. camera_pos
3. camera_dir

Could anyone help me adjust the parameters so that I can mimic the 'Perspective' viewport as in GUI? (see attached image)

- Kyu

14
Support Forum / rendering quality
« on: March 11, 2018, 11:15:00 PM »
Hello OVITO users,


I am using 'TachyonRenderer' to output a movie from dump files. (TachyonRenderer is used because I am outputting movie on the remote cluster, so openGL doesn't work)

As you can see from the attached file, quality of the picture is low. This happens so because I am using very big simulation box (3200 angstrom in x direction). Is there a way to increase the definition of the movie?



-Kyu


15
Support Forum / how to import_file with specified dump files
« on: February 25, 2018, 07:32:53 AM »
Hello everyone,

Is there a way to import only the dump files that I want?

I know combining 'wildcard character' and 'multiple_frames' option would allow OVITO to import multiple frames as follows:
Code: [Select]
import_file("dump.200.*",  multiple_frames = True)
However, let's say one has dump files called dump.0000, dump.0001, dump.0002, dump.0003.
And one only wants OVITO to import all the frames only in dump.0000 and dump.0001, excluding dump.0002 and dump.0003.

If anyone has encountered a problem like this and figured out how to do so,
please share your solution.

-Kevin

16
Support Forum / Re: How to calculate max and min of cluster's position
« on: February 14, 2018, 09:00:46 PM »
I just wanted to add why I decided to add clustering feature when identifying stackingfault width.
This was a safety feature that will exclude some of the HCP structures randomly appearing from thermal fluctuation.

-Kevin

17
Support Forum / Re: How to calculate max and min of cluster's position
« on: February 13, 2018, 06:41:08 PM »
Yes definitely, it's always nice to have someone look at my code.

Yes, I don't know why I decided to use clustering when there is going to be only 1 cluster. Thanks for pointing that out.

-Kevin

18
Support Forum / How to calculate max and min of cluster's position
« on: February 13, 2018, 04:49:58 AM »
Hello everyone,

I figured out this problem after writing all the question and right before submitting it,
but I will just post this anyways with the working code in case someone finds helpful.

Following is the code that identifies a cluster of HCP atoms, extracts only the atoms in the cluster, and calculates maximum and minimum x-position of this cluster.

Essentially I was trying to find the stackingfault width of a dissociated dislocation.

Code: [Select]
from ovito.io import *
from ovito.modifiers import *
import numpy

node = import_file("dump.200.*",
                   multiple_frames = True)
# Modifiers                                                                                                 
# Modifier 1: CNA                                                                                           
node.modifiers.append(CommonNeighborAnalysisModifier())

# Modifier 2: Select HCP (dislocation)                                                                     
node.modifiers.append(SelectExpressionModifier
                      (expression = 'StructureType==2'))
# Modifier 3: Cluster HCP                                                                                   
node.modifiers.append(ClusterAnalysisModifier
                      (cutoff=3.5,
                       only_selected = True))
# Modifier 4: Select cluster 0, which doesn't belong to any cluster.                                                                           
node.modifiers.append(SelectExpressionModifier
                      (expression = 'Cluster==0'))
# Modifier 5: Delete cluster 0                                                                                       
node.modifiers.append(DeleteSelectedParticlesModifier())

#Each particle's Position.X in addition to cluster id                                                                   
#can be outputted to xyz format file as follows:                                                           
export_file(node, "1xyz", "xyz",
            columns = ["Cluster", "Position.X"])

# BUT, I wanted to have access to position data in this script level
# to calculate Min and Max values of Position.X
# All particle_properties that belong to 'deleted_particles' seem
# to get deleted
data = node.compute()
cluster = data.particle_properties['Cluster'].array #this is not necessary
pos = data.particle_properties['Position'].array
xpos = pos[:,0]
leading = max(xpos)
trailing= min(xpos)


PS. Just in case someone new to OVITO finds this post and is trying to understand better way of manipulating clustering feature, I found the following post helpful:
http://forum.ovito.org/index.php?topic=118.msg222#msg222
(Note that the post was written 2017 Feb, and note the version of OVITO by then.)

19
Support Forum / Re: source, output attributes
« on: February 11, 2018, 02:26:33 AM »
Thank you for the reply.
I came up with one additional question as follows:

Code: [Select]
# Note                                                                         
# :This works with ovito 3.0.0                                                 

from ovito.io import *
from ovito import dataset
from ovito.modifiers import *
import numpy

node = import_file("dump.200.*",
                   multiple_frames = True)
# Modifiers                                                                     
# Modifier 1: CNA                                                               
node.modifiers.append(CommonNeighborAnalysisModifier
                      (mode=CommonNeighborAnalysisModifier.Mode.FixedCutoff,
                       cutoff=3.5))
# Modifier 2: Selection                                                         
node.modifiers.append(SelectExpressionModifier
                      (expression = 'StructureType==3'))


print(node.source.attributes['Timestep'])
print(node.compute(3).attributes['Timestep'])
print(dataset.anim.current_frame)
dataset.anim.current_frame=3   
node.compute()
print(dataset.anim.current_frame)
print(node.source.attributes['Timestep'])

The results from the last 6 lines of the code are as follows:
print(node.source.attributes['Timestep'])           => 0   [This is OK]
print(node.compute(3).attributes['Timestep'])    => 7500  [This is OK]
print(dataset.anim.current_frame)                    => 0  [This is OK]
dataset.anim.current_frame=3
node.compute()
print(dataset.anim.current_frame)                     => 3  [This is OK]
print(node.source.attributes['Timestep'])            => 0  [This should be 7500]

Quote
node.source is the cache for the current animation time, which is controlled by the global ovito.dataset.anim.current_frame setting (basically the time slider in the GUI). This setting is not affected when you call node.compute(3). Thus, you'll still find data for the current animation time (frame 0) in that input cache.

According to the quote above, I expect the last line of the code to print 7500 instead of 0. Could you explain why this prints 0?

UPDATE
1. this happens only when previous node.compute(3) is there.
If 'frame1' in node.compute(frame1) (6th line from the bottom) and
'frame2' in dataset.anim.current_frame = frame2  (4th line from the bottom) is different, this behavior is not observed.

2. node.source seems to update only after both 'current_frame' has changed and node.compute() has been used.

20
Support Forum / source, output attributes
« on: February 10, 2018, 06:45:37 AM »
Dear Dr.Stukowski,

I observed a weird behavior in both OVITO 2.9.0 and 3.0.0, so I report it here.

The following code reads in two files(dump.200.0000 and dump.200.0001).
Each timestep is incremented by 2500.
So, node.compute(3) should result in timestep 7500.

Since node.compute() should cache the most recent compute to the node.output field,
expected outputs for the last 3 lines of the codes are as follows:
0        => node.source.attributes['Timestep']   
7500  => node.output.attributes['Timestep']
7500  => theOutput.attributes['Timestep']

However, the outputs from 2.9.0 version are as follows:
7500  => (source should remain at the timestep 0)
7500
7500


*I was going to say 3.0.0 version also behaves weirdly as follwos,
*but I guess 3.0.0 version doesn't have output field anymore.
Also, the outputs from 3.0.0 version are as follows:
0
0    =>(I don't think the most recent compute is cached into output field)
7500


Code: [Select]
from ovito.io import *
from ovito import dataset
from ovito.modifiers import *
import numpy

node = import_file("dump.200.*",
                   multiple_frames = True)
# Modifiers                                                                     
# Modifier 1: CNA                                                               
node.modifiers.append(CommonNeighborAnalysisModifier
                      (mode=CommonNeighborAnalysisModifier.Mode.FixedCutoff,
                       cutoff=3.5))
# Modifier 2: Selection                                                         
node.modifiers.append(SelectExpressionModifier
                      (expression = 'StructureType==3'))

theOutput=node.compute(3)
print(node.source.attributes['Timestep'])
print(node.output.attributes['Timestep'])
print(theOutput.attributes['Timestep'])

21
Support Forum / Accessing ovito source for histogram
« on: February 09, 2018, 08:23:10 PM »
Dear Dr.Stukowski,

I want to access how OVITO GUI works when it outputs histogram data.
Specifically, I want to figure out what the output format is. It is because the last floating number of histogram data in the following has one less decimal, and I couldn't mimic this behavior in my scripting version of histogram output. (I am trying to implement automated testing between data outputted from GUI and data from scripting.)

I was able to locate histogram_modifier.py here:
/Applications/Ovito_3.0.0.app/Contents/Resources/python/ovito/modifiers/stdmod/histogram_modifier.py
but this file only specifies how histogram data is created.

Code: [Select]
# Position.X histogram (bin size: 2.01018)
1.09469 2
3.10487 1
5.11505 1
7.12524 0
9.13542 0
11.1456 1
13.1558 1
15.166 1

Thank you,
Kevin

22
Support Forum / Re: Box size in Ovito scripting
« on: February 09, 2018, 05:43:27 PM »
Ahh I see. I just have to use the cell vector anyways. (Since Ovito GUI provides 'Width', 'Length' and 'Height' of box, I thought there may be a function that retrieves the box size, which I couldn't locate on the OVITO documentation. I guess the GUI provides box sizes using by calculating elements in the cell vector.)

PS. By the way, I think the cell origin has to be considered to get the exact box size(unless it's 0).

Thank you again for answering this somewhat trivial question.

23
Support Forum / Re: Box size in Ovito scripting
« on: February 09, 2018, 04:53:14 PM »
Thank you for the reply.


Yes I could use cell vector and then calculate box size using elements in the cell vector as follows:
I was just wondering if there is a function that directly retrieves box size rather than cell vector.


Code: [Select]
cell = node.source.cell                                               
cellSize = cell.matrix
boxLo = cellSize[2][3]                                         
boxHi = cellSize[2][2]                                 
boxSize = boxHi - boxLo 

24
Support Forum / Box size in Ovito scripting
« on: February 08, 2018, 03:33:32 AM »
Dear Dr. Stukowski,

Attached is the image of 'Simulation cell' panel from ovito.
It seems like there is no function(?) to access Box sizes of simulation cell on scripting.
I could calculate this from "Cell geometry" but was wondering if there is a function to retrieve box size directly since it is offered in the OVITO GUI.

-Kevin

25
Support Forum / Re: histogram over all frames
« on: February 05, 2018, 06:20:51 PM »
1st node.compute() right after CNA modifier, and 2nd node.compute() after histogram modifier also does not trigger the error.

Since this issue is resolved in 3.0.0 version of OVITO, it may not be important issue, but I just wanted to refer this issue in case this matters to the developers.

Thanks again for the help.

26
Support Forum / Re: ovito on Linux
« on: February 02, 2018, 10:06:49 PM »
Nevermind.
Changing name of 'ovitos' works.
So, I changed 'ovitos' to 'ovitos3', and it still works.

27
Support Forum / ovito on Linux
« on: February 02, 2018, 08:07:54 PM »
Ovito executable file on linux seems to be not a 'stand-alone' executable. So if I move 'ovitos' executable to '~/bin', ovitos wouldn't work.

I am currently using both 2.9.0 and 3.0.0 version, and am trying to find a way to run both versions of 'ovitos'.

I could add the ovito directory to $PATH environment, but then ovitos (2.9.0) and ovitos(3.0.0) will not be distinguished. Is there a way to distinguish two versions of ovitos with different name? (Would it be possible to change the name of 'ovitos' to 'ovitos3')

28
Support Forum / Re: installing two versions of OVITO
« on: February 01, 2018, 09:13:46 PM »
I downloaded again with Chrome and Safari, and installed it again, but it still gives the same error.

I am using mac, and I have 2.9.0 version installed (and changed the name of application "Ovito" to "Ovito_2.9.0"). Then I installed newer version (3.0.0), and it still gives the same error.

I could still run ovito using terminal command, but I just wanted to report the problem.

29
Support Forum / Re: installing two versions of OVITO
« on: February 01, 2018, 05:55:15 PM »
I think there is something wrong with Ovito 3.0.0 installation file for mac.

Attached is the error shown after installing and running the Ovito 3.0.0

30
Support Forum / installing two versions of OVITO
« on: February 01, 2018, 03:07:21 PM »
Hello Dr. Stukowski,

Is it possible to install both OVITO 2.9.0 and 3.0.0 on mac?
I currently have 2.9.0 version on my mac, but I believe installing 3.0.0 would delete 2.9.0.
Would it be possible to keep both?

Bests,
Kevin

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