Oneapi fatal error: compare: No such file or directory after system restart - tbb

I have a project been working on for my research for over a year, Oneapi have been integrated for way longer than 6months, everything working and all. Yesterday I updated some test code, and ran the tests, nothing out of normal. Today I restarted my machine (Ubuntu 20.04.2 LTS, 64bits) for updates, and now when I try to compile the project it gives:
In file included from /opt/intel/oneapi/tbb/2021.2.0/env/../include/oneapi/tbb/enumerable_thread_specific.h:26,
from /opt/intel/oneapi/tbb/2021.2.0/env/../include/oneapi/tbb/combinable.h:22,
from /opt/intel/oneapi/tbb/2021.2.0/env/../include/oneapi/tbb.h:35,
from ...file name omitted for privacy...
/opt/intel/oneapi/tbb/2021.2.0/env/../include/oneapi/tbb/concurrent_vector.h:33:10: fatal error: compare: No such file or directory
33 | #include <compare>
| ^~~~~~~~~
compilation terminated.
This only happened after system restart (possibly broke some links?) and only happens in files that require concurrent_vector.h
Ideally I'd prefer a fix that won't require reinstall of oneapi, apt-get update followed by apt-get upgrade didn't fix it, neither did restarting the system again.

Just ran into the same thing. It looks as if TBB automatically includes <compare> if you are compiling with -std=c++20:
https://github.com/oneapi-src/oneTBB/blob/9e15720bc7744f85dff611d34d65e9099e077da4/include/oneapi/tbb/detail/_config.h#L253
#define __TBB_CPP20_COMPARISONS_PRESENT __TBB_CPP20_PRESENT
GCC only added the compare header in libstdc++-10.
To me, this looks like a bug in TBB. I opened an issue here.
As a hotfix, I was able to downgrade my project to C++17. If that is not an option, you could consider copying detail/_config.h, defining __TBB_CPP20_COMPARISONS_PRESENT 0 in your copy and including it before you include any TBB header. The include guards should make sure that your version supersedes the broken TBB version.

Related

Deployement Qt error [duplicate]

I wrote application for linux which uses Qt5.
But when I am trying to launch it on the linux without Qt SDK installed, the output in console is:
Failed to load platform plugin "xcb". Available platforms are:
How can I fix this? May be I need to copy some plugin file?
When I use ubuntu with Qt5 installed, but I rename Qt directory, the same problem occurs. So, it uses some file from Qt directory...
UPDATE:
when I create in the app dir "platforms" folder with the file libqxcb.so, the app still doesnot start, but the error message changes:
Failed to load platform plugin "xcb". Available platforms are:
xcb
How can this happen? How can platform plugin be available but can't be loaded?
Use ldd (man ldd) to show shared library dependencies. Running this on libqxcb.so
.../platforms$ ldd libqxcb.so
shows that xcb depends on libQt5DBus.so.5 in addition to libQt5Core.so.5 and libQt5Gui.so.5 (and many other system libs). Add libQt5DBus.so.5 to your collection of shared libs and you should be ready to move on.
As was posted earlier, you need to make sure you install the platform plugins when you deploy your application. Depending on how you want to deploy things, there are two methods to tell your application where the platform plugins (e.g. platforms/plugins/libqxcb.so) are at runtime which may work for you.
The first is to export the path to the directory through the QT_QPA_PLATFORM_PLUGIN_PATH variable.
QT_QPA_PLATFORM_PLUGIN_PATH=path/to/plugins ./my_qt_app
or
export QT_QPA_PLATFORM_PLUGIN_PATH=path/to/plugins
./my_qt_app
The other option, which I prefer is to create a qt.conf file in the same directory as your executable. The contents of which would be:
[Paths]
Plugins=/path/to/plugins
More information regarding this can be found here and at using qt.conf
I tried to start my binary, compiled with Qt 5.7, on Ubuntu 16.04 LTS where Qt 5.5 is preinstalled. It didn't work.
At first, I inspected the binary itself with ldd as was suggested here, and satisfied all "not found" dependencies. Then this notorious This application failed to start because it could not find or load the Qt platform plugin "xcb" error was thrown.
How to resolve this in Linux
Firstly you should create platforms directory where your binary is, because it is the place where Qt looks for XCB library. Copy libqxcb.so there. I wonder why authors of other answers didn't mention this.
Then you may want to run your binary with QT_DEBUG_PLUGINS=1 environment variable set to check which dependencies of libqxcb.so are not satisfied. (You may also use ldd for this as suggested in the accepted answer).
The command output may look like this:
me#xerus:/media/sf_Qt/Package$ LD_LIBRARY_PATH=. QT_DEBUG_PLUGINS=1 ./Binary
QFactoryLoader::QFactoryLoader() checking directory path "/media/sf_Qt/Package/platforms" ...
QFactoryLoader::QFactoryLoader() looking at "/media/sf_Qt/Package/platforms/libqxcb.so"
Found metadata in lib /media/sf_Qt/Package/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")
loaded library "/media/sf_Qt/Package/platforms/libqxcb.so"
QLibraryPrivate::loadPlugin failed on "/media/sf_Qt/Package/platforms/libqxcb.so" : "Cannot load library /media/sf_Qt/Package/platforms/libqxcb.so: (/usr/lib/x86_64-linux-gnu/libQt5DBus.so.5: version `Qt_5' not found (required by ./libQt5XcbQpa.so.5))"
This application failed to start because it could not find or load the Qt platform plugin "xcb"
in "".
Available platform plugins are: xcb.
Reinstalling the application may fix this problem.
Aborted (core dumped)
Note the failing libQt5DBus.so.5 library. Copy it to your libraries path, in my case it was the same directory where my binary is (hence LD_LIBRARY_PATH=.). Repeat this process until all dependencies are satisfied.
P.S. thanks to the author of this answer for QT_DEBUG_PLUGINS=1.
I tried the main parts of each answer, to no avail. What finally fixed it for me was to export the following environment variables:
LD_LIBRARY_PATH=/usr/local/lib:~/Qt/5.9.1/gcc_64/lib
QT_QPA_PLATFORM_PLUGIN_PATH=~/Qt/5.9.1/gcc_64/plugins/
Ubuntu 16.04 64bit.
I got the problem for apparently no reasons. The night before I watched a movie on my VideoLan instance, that night I would like to watch another one with VideoLan. VLC just didn't want to run because of the error into the question.
I google a bit and I found the solution it solved my problem: from now on, VLC is runnable just like before. The solution is this comand:
sudo ln -sf /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/ /usr/bin/
I am not able to explain what are its consequencies, but I know it creates some missing symbolic link.
Since version 5, Qt uses a platform abstraction system (QPA) to abstract from the underlying platform.
The implementation for each platform is provided by plugins. For X11 it is the XCB plugin. See Qt for X11 requirements for more information about the dependencies.
There might be many causes to this problem. The key is to use
export QT_DEBUG_PLUGINS=1
before you run your Qt application. Then, inspect the output, which will point you to the direction of the error. In my case it was:
Cannot load library /opt/nao/plugins/platforms/libqxcb.so: (/opt/nao/bin/../lib/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/x86_64-linux-gnu/libpng16.so.16))
But that is solved in different threads. See for instance https://stackoverflow.com/a/50097275/2408964.
Probably this information will help. I was on Ubuntu 18.04 and when I tried to install Krita, using the ppa method, I got this error:
This application failed to start because it could not find or load the Qt platform plugin "xcb" in "".
Available platform plugins are: linuxfb, minimal, minimalegl, offscreen, wayland-egl, wayland, xcb.
Reinstalling the application may fix this problem.
Aborted
I tried all the solutions that I found in this thread and other webs without any success.
Finally, I found a post where the author mention that is possible to activate the debugging tool of qt5 using this simple command:
export QT_DEBUG_PLUGINS=1
After adding this command I run again krita I got the same error, however this time I knew the cause of that error.
libxcb-xinerama.so.0: cannot open shared object file: No such file or directory.
This error prevents to the "xcb" to load properly. So, the solution will be install the `libxcb-xinerama.so.0" right? However, when I run the command:
sudo apt install libxcb-xinerama
The lib was already installed. Now what Teo? Well, then I used an old trick :) Yeah, that one --reinstall
sudo apt install --reinstall libxcb-xinerama
TLDR: This last command solved my problem.
I ran into a very similar problem with the same error message. First, debug some by turning on the Qt Debug printer with the command line command:
export QT_DEBUG_PLUGINS=1
and rerun the application. For me this revealed the following:
"Cannot load library /home/.../miniconda3/lib/python3.7/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so: (libxkbcommon-x11.so.0: cannot open shared object file: No such file or directory)"
"Cannot load library /home/.../miniconda3/lib/python3.7/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so: (libxkbcommon-x11.so.0: cannot open shared object file: No such file or directory)"
Indeed, I was missing libxkbcommon-x11.so.0 and libxkbcommon-x11.so.0. Next, check your architecture using dpkg from the linux command line. (For me, the command "arch" gave a different and unhelpful result)
dpkg --print-architecture #result for me: amd64
I then googled "libxkbcommon-x11.so.0 ubuntu 18.04 amd64", and likewise for libxkbcommon-x11.so.0, which yields those packages on packages.ubuntu.com. That told me, in retrospect unsurprisingly, I'm missing packages called libxkbcommon-x11-0 and libxkbcommon0, and that installing those packages will include the needed files, but the dev versions will not. Then the solution:
sudo apt-get update
sudo apt-get install libxkbcommon0
sudo apt-get install libxkbcommon-x11-0
So, I spent about a day trying to figure out what was the issue; tried all the proposed solutions, but none of that worked like installing xcb libs or exporting Qt plugins folder. The solution that suggested to use QT_DEBUG_PLUGINS=1 to debug the issue didn't provide me a direct insight like in the answer - instead I was getting something about unresolved symbols within Qt5Core.
That gave me a hint, though: what if it's trying to use different files from different Qt installations? On my machine I had standard version installed in /home/username/Qt/ and some local builds within my project that I compiled by myself (I have other custom built kits as well in other locations). Whenever I tried to use any of the kits (installed by Qt maintenance tool or built by myself), I would get an "xcb error".
The solution was simple: provide the Qt path through CMAKE_PREFIX_PATH and not though Qt5_DIR as I did, and it solved the problem. Example:
cmake .. -DCMAKE_PREFIX_PATH=/home/username/Qt/5.11.1/gcc_64
I faced the same problem when after installing Viber. It had all required qt libraries in /opt/viber/plugins/.
I checked dependencies of /opt/viber/plugins/platforms/libqxcb.so and found missing dependencies. They were libxcb-render.so.0, libxcb-image.so.0, libxcb-icccm.so.4, libxcb-xkb.so.1
So I resolved my issue by installing missing packages with this libraries:
apt-get install libxcb-xkb1 libxcb-icccm4 libxcb-image0 libxcb-render-util0
I like the solution with qt.conf.
Put qt.conf near to the executable with next lines:
[Paths]
Prefix = /path/to/qtbase
And it works like a charm :^)
For a working example:
[Paths]
Prefix = /home/user/SDKS/Qt/5.6.2/5.6/gcc_64/
The documentation on this is here: https://doc.qt.io/qt-5/qt-conf.html
All you need to do is
pip uninstall PyQt5
and
conda install pyqt
Most of the problem of pyqt can be fixed by this simplest solution.
In my case, I needed to deploy two Qt apps on an Ubuntu virtualbox guest. One was command-line ("app"), the other GUI_based ("app_GUI").
I used "ldd app" to find out what the required libs are, and copied them
to the Ubuntu guest.
While the command-line executable "app" worked ok, the GUI-based executable crashed, giving
the "Failed to load platform plugin "xcb" error. I checked ldd for libxcb.so, but this too had no missing dependencies.
The problem seemed to be that while I did copy all the right libraries I accidentally had copied also libraries that were already present at the guest system.. meaning that (a) they were unnecessary to copy them in the first place and (b) worse, copying them produced incompatibilities between the install libraries.
Worse still, they were undetectable by ldd like I said..
The solution? Make sure that you copy libraries shown as missing by ldd and absolutely no extra libraries.
In my case missing header files were the reason libxcb was not built by Qt. Installing them according to https://wiki.qt.io/Building_Qt_5_from_Git#Linux.2FX11 resolved the issue:
yum install libxcb libxcb-devel xcb-util xcb-util-devel mesa-libGL-devel libxkbcommon-devel
Folks trying to get this started on Ubuntu 20.04 please try to run this and see if this solves the problem. This worked for me
sudo apt-get update -y
sudo apt-get install -y libxcb-xinerama0
I link all Qt stuff statically to the generic Linux builds of my open source projects. It makes life a bit easier. You just need to build static versions of Qt libraries first. Of course this cannot be applied to closed source software due to licensing issues. The deployment of Qt5 apps on Linux is currently a bit problematic, because Ubuntu 12.04, for example, doesn't have Qt5 libraries in the package repositories.
I had this problem, and on a hunch I removed the Qt Configs from my environment. I.e.,
rm -rf ~/.config/Qt*
Then I started qtcreator and it reconfigured itself with the existing state of the machine. It no longer remembered where my projects were, but that just meant I had to browse to them "for the first time" again.
But more importantly it built itself a coherent set of library paths, so I could rebuild and run my project executables again without the xcb or qxcb libraries going missing.
I faced the same situation, but on a Ubuntu 20.04 VM.
TL;DR: Check file permissions.
What I did:
I copied the Qt libs required to /usr/local/lib/x86_64-linux-gnu/ and added it to LD_LIBRARY_PATH
I copied the platforms folder from Qt to my application directory and added it to QT_PLUGIN_PATH
I ran ldd on the executable and in the offending libqxcb.so (ldd libqxcb.so), and it complains about some dependencies although ldconfig listed them as found.
linux-vdso.so.1 (0x00007ffee19af000)
libQt5XcbQpa.so.5 => not found
libfontconfig.so.1 => /lib/x86_64-linux-gnu/libfontconfig.so.1 (0x00007f7cb18fb000)
libfreetype.so.6 => /lib/x86_64-linux-gnu/libfreetype.so.6 (0x00007f7cb183c000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f7cb1820000)
libQt5Gui.so.5 => /usr/local/lib/x86_64-linux-gnu/libQt5Gui.so.5 (0x00007f7cb0fd4000)
libQt5DBus.so.5 => not found
I used export QT_DEBUG_PLUGINS=1 for further info. It complains about missing files, although they are there.
What I found:
For some reason, when copying to the VM through the shared folder the files permissions were not the correct ones.
Thus, I ran: sudo chmod 775 * on the libs and voilà.
I solved the issue through this https://github.com/NVlabs/instant-ngp/discussions/300
pip uninstall opencv-python
pip install opencv-python-headless
This seems to have been a problem with the cv2 Python package and how it loops in Qt
sudo ln -sf /usr/lib/...."adapt-it"..../qt5/plugins/platforms/ /usr/bin/
It creates the symbolic link it's missed. Good for QT ! Good for VLC !!

How to include additional directories when configuring makefiles

I'm trying to compile geany-plugins-1.28. The debugger plugin (the only one I need) gives the error:
debug.c:53:21: fatal error: vte/vte.h: No such file or directory
#include <vte/vte.h>
Clearly it needs to know where this file is located to compile. I found the vte.h file in the src directory of the main program geany-1.28. When running
sudo ./configure cflags=-I/home/pi/Desktop/geany-1.28/src
I get the same error about the missing header later trying to compile the debugger plugin.
I ran
./configure --help
to get all the flag options. The output is here
How do I get this to configure correctly so that it compiles. I need to compile the debugger version 1.28 myself because apt only installs 1.24 which I think has a bug because it crashes when I run my code with the error:
close failed in file object destructor:
sys.execpthook is missing
lost sys.stderr
CFLAGS is case-sensitive environment variable, so you should set it before running configure, not try to pass it as a command line argument. This variant:
$ export CFLAGS=-I/home/pi/Desktop/geany-1.28/src
$ ./configure
leaves CFLAGS set for current shell until you leave it. While this:
$ CFLAGS=-I/home/pi/Desktop/geany-1.28/src ./configure
sets variable only for current command, i.e. configure.
Some other issues:
You do not need sudo to configure and make. It is also unnecessary for make install if you set PREFIX to a path you have privileges to write to.
Does plugin's build system also builds all it's dependencies? If not, you may face linker errors a bit later.
Update:
I have tried to build debugger plugin and got rid of your error. It seems that vte.h coming with Geany is it's intrinsic, while the plugin requires full-featured file from the library. So I just installed vte and vte-devel from repos. Nevertheless, I got some other unrelated errors coming from Glib. I will not continue my attempts to build all this right now. Hope my effort will be helpful at least a little.
As in this answer stated, vte.h is not the file you are looking for. Install libvte(-dev) package on your system and rerun configure.
Just for the record: vte.h on Geany is a dummy to allow Geany to kind of dynamical enable vte or disable it depending on vte is installed on the system or not.

make: *** [install] Error 1

I have a problem with installing old software developed in 1995 for Linux.
My operating system is Cent Os. and I got some errors as below when I tried to follow the program instruction. I still do not know what the problems are....
sometimes the clock skew error messages show up but frequently it does not come up.
Waiting for expert's help
igrf]$ make
make: Warning: File igrf' has modification time 98 s in the future
make:igrf' is up to date.
make: warning: Clock skew detected. Your build may be incomplete.
igrf]$ make install
make: Warning: File igrf' has modification time 94 s in the future
install -c /home/hj/master/mag/bin -m 755 ./igrf
install: omitting directory/home/hj/master/mag/bin'
make: * [install] Error 1
Thanks!!
I installed the old version of libpcap-1.0.0 on Ubuntu 18.04 from the source, but this was not successful, as it does not fit my version of Ubuntu and gives a make error: *** [install] Error 1.
Instead this tar.gz archive i used the usual command in the terminal:
sudo apt install libpcap-dev # the problem is solved
It is possible that there is incompatibility of archives to new versions of Ubuntu.
It is also possible to find missing dependencies, check this:
IMPORTANT: There is enough information about this error; please do not post anything unless there is a specific review!
make install --touch
What can i do to help find dependencies. All of these workarounds are specific to one configuration or another. Therefore, it makes sense to track other issues as a separate bug instead of continuing to use one bug report for each issue. To make sure we focus on bugs that affect testers, Q_A_ asks reporters to feel free to post fixes and commits. The answer was very focused on the lack of specific dependencies. It will automatically collect and attach updated debug information to your report. Please add them for the feisty to help muffle the compilation issue. Maybe even backport fixes for the dapper and edgy ones?
Initially when compiling mongoose i used the helper:
make --touch
и был вывод:
touch vc98
touch vc2017
touch mingw
touch mingw++
touch linux
touch fuzzer
touch fuzz
Then i installed the missing dependencies:
sudo apt install fuzz libfuzzer-10-dev ocaml-mingw-w64-x86-64 vc-dev
...and still not all, then i had to use install (using reportdependencies the current behavior is unexpected and unsatisfactory):
I have output for mongoose:
touch linux-libs
touch install
Reportdependencies doesn't handle this very well.
In this case, linux-libs (install is omitted) points to some missing libraries. And this:
sudo apt install liblinux-pid-perl
I had an equivalent problem in the past. It is tied to the timestamps of (some) files. You should try to use the command "touch" on the concerned files. This will update the time stamps of those files.
I hope this will make the trick.

Operation not permitted when running a Haskell program on OS X

I am writing my first Haskell program, a web application based on the Yesod framework.
I compiled the code using cabal configure && cabal build. When I try to run the executable, I get the following error:
-bash: dist/build/MyApp/MyApp: Operation not permitted
I installed the 64-bit Haskell platform (2012.2.0.0) on OS X Mountain Lion. I had originally installed the 32-bit version, but got the same error, so I uninstalled it and tried the 64-bit version.
The application compiles and links with no errors or warnings.
I even tried the fix described in http://reviews.cnet.com/8301-13727_7-57374676-263/workarounds-for-quarantine-bug-in-os-x-lion/, but it made no difference.
UPDATE: The plot thickens. The source tree is actually on an encrypted sparse bundle (all of my source code is). When I copy the tree to my home directory, it compiles and runs.
The mount command does not show the noexec option:
/dev/disk2s9 on /Volumes/Personal (hfs, local, nodev, nosuid, journaled, noowners, quarantine, mounted by grk)
I'm not sure about the quarantine option, but I suspect it comes from Symantec Endpoint Protection (required by my employer). I'll try disabling it for the sparse bundle.
I found the answer at the sister site apple.stackexchange.com: https://apple.stackexchange.com/questions/64456/mount-is-adding-a-quarantine-flag-causing-bin-bash-bad-interpreter-operatio
The sparse bundle is actually marked with the quarantine flag. I unmounted the volume and removed the quarantine with the following command:
xattr -d com.apple.quarantine Personal.sparsebundle
then remounted. Problem solved.

installing gcc 4.2.4

I want to install gcc 4.2.4 on a linux x86_64, intel cpu with 2 cores, in a not default path.
I downloaded the code via svn and configured from a build directory with
../gcc_424/configure --prefix=/scratch/user/local/gcc-424 --with-local-prefix=/scratch/user/local/include
then in the build directory
make
when I run
make install
I get the error
/bin/sh: line 3: cd: ./fixincludes: No such file or directory
I am a little bit lost with what I should do now, any help?
Although untested (because it's fairly old), EasyBuild should be able to build GCC 4.2 without much trouble.
Just use one of the available example easyconfigs for GCC (the non ClooG-PPL ones), adjust the version number, and run the EasyBuild install command specifying that easyconfig file.
No root priveleges required, and EasyBuild takes care of all the nasty stuff.

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