Since I installed according to the guide here on wsl2 ubuntu 20.04, I've been having errors related to libstc++.so.6, specifically GLIBCXX_3.4.26 not found (required by ...) where ... refers to different files within /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/ ending in .so, .so.1, .so.6 and so on (for instance, when running paraFoam the error would appear with respect to about 20 such files). I am able to successfully visualize the cavity tutorial (in paraview installation on windows).
I could get the errors to go away by doing what the user laborg suggested on Jan 4 for a similar problem with julia (see here), specifically copy libstdc++.so.6 from /usr/lib/x86_64-linux-gnu to /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/.
The questions is whether this copy-paste solution is recommended; will it come back and haunt me later? Is the libstdc++.so.6 from system installation going to be an issue if used in the lib64 folder of openfoam?
An additional info concerning openfoam installation, foamInstallationTest shows *not installed* errors against flex, wmake, gcc, g++, icoFoam and *critical error* for gcc, g++, icoFoam; but I as given here, foamInstallationTest is not meant for installation from the tar file. Openfoam installation seems to be alright based on the running of the cavity tutorial.
ok, please don't do copy past operation to solve this problem. The error means that you haven't installed the pre request libraries in your ubuntu. It seems that you have missed the first step in the tutorial.
It is not recommended but it will not hurt as long as the GLIBC versions returned from this command
strings /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/libstdc++.so.6 | grep GLIBC
are a subset of the GLIBC versions from this command.
strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBC
which was no doubt the case for your Ubuntu setup.
A less risky route would be to redirect the soft link /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/libstdc++.so.6 to point to your other libstdc++.so.6 (that way you retain both versions)
ln -sf /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/libstdc++.so.6
Then, if you hit an issue, you can always reset the link back to its original target. Of course /usr/lib/x86_64-linux-gnu/libstdc++.so.6 is itself a soft link, but you can point to it all the same or you can point to its target.
I believe the issue you are hitting is a derivative of the one mentioned here https://www.cfd-online.com/Forums/main/229027-persistence-glibcxx_3-4-26-not-found.html, which would point towards the fact that it is not an installation error on your part but an issue related to the packaging of the OpenFoam binaries. I agree it would screw up the wsl2 setup owing to the way OpenFoam prepends everything to paths. Of course the safest route is to compile from source using the Ubuntu system's gcc and thereby bypass the ThirdParty.
Seeing as you are using Ubuntu in the WSL instance, could also just install the Ubuntu package directly:
https://develop.openfoam.com/Development/openfoam/-/wikis/precompiled/debian
This problem comes from this line in the tutorial:
echo "source /opt/OpenFOAM/OpenFOAM-v2012/etc/bashrc" >> ~/.bashrc
This will point to OpenFOAM's libstdc++ everytime you open a terminal (or start a WSL2 session). If your workflow is not related to OpenFOAM, that can be an issue. If you remove or comment that line in your ~/.bashrc things should get back to normal. You can use nano in WSL2.
nano ~/.bashrc
Then comment:
#source /opt/OpenFOAM/OpenFOAM-v2012/etc/bashrc
However, as OpenFOAM uses that bashrc, you will need to source the OpenFOAM bashrc in each terminal before using openFOAM.
source /opt/OpenFOAM/OpenFOAM-v2012/etc/bashrc
My personal choice is to keep that line commented and, if I have a long work session using OpenFOAM, I just use nano to uncomment it, so every shell that I open works without sourcing again.
There are more elegant or complex approaches, but I prefer this one.
This answer should be valid with the 2006 version too, the link you shared points to 2012, so I guess they just updated the tutorial. If you installed 2006, just make sure when you source comment/uncomment to use the correct name.
In the same manner, if you followed another tutorial with another tool and sourced another library, you may experience issues.
Just start by taking a look at your bashrc and cleaning it.
Related
I am trying to use the latest version of the appImage-builder because appimages of my application built with the old version of appImage-builder do not run on ubuntu 22.04 anymore. So I got the order to try and see if it works with the new appImage-builder.
Currently (June 2022), only versions below 1.0 which are based on ubuntu 18.04 are available on docker (which we previously used to build our appimage).
The newer versions are available via github (https://github.com/AppImageCrafters/appimage-builder/releases).
However, I seem to be unable to execute:
appimage-builder --generate
or
appimage-builder --recipe AppImageBuilder.yml
Is there any documentation available on how to correctly use the .appimage version of appImage-builder? All I could find in https://appimage-builder.readthedocs.io/en/latest/ seems to refer to the docker version or a manually built version of appImage-builder.
Depending on the error message you get, there could be a couple of issues at play here.
If you got an error related to FUSE, then you need to install the libfuse2 package with apt install libfuse2. AppImages rely on libfuse2, but Ubuntu has stopped including it since 22.04, in favor of libfuse3.
If you get an error related to "file not found", then it could be that you do not have AppImageLauncher installed. Sadly, with type 2 AppImages the design decision was taken to modify the ELF header of the executable with 3 magic bytes at offset 8 of the executable. This means that Linux linkers will not run the file. AppImageLauncher actually copies the file to a temporary directory and zeroes out the magic number in order to be able to execute it.
A good starting point for debugging issues like this is to run the strace command, which will let you see which system call likely cause the error. Keep in mind that if you try to execute a file and you get File not found, it might mean that the linker specified by the file can not be found on the system or the ELF header is not valid. You can also run the executable by using the linker directly, which might give you more clues. For example with: /lib64/ld-linux-x86-64.so.2 <NAME-OF-YOUR-EXECUTABLE>.
Situation
Software author wants to add zsh completion to his project. Has written completion script, works.
Needs to figure out where under $CMAKE_INSTALL_PREFIX to install so it gets found by default.
Problem
Testing Fedora 34 against Ubuntu 20.04, it was found that the only common member of $fpath is /usr/local/share/zsh/site-functions; none of the /usr/share fpaths overlap. Especially, Ubuntu does not read /usr/share/zsh/site-functions.
So, I can't just install into $CMAKE_INSTALL_PREFIX/share/zsh/site-functions, because that only works for $CMAKE_INSTALL_PREFIX==/usr/local, but not later in packaging ($CMAKE_INSTALL_PREFIX==/usr). I'd argue this is a Ubuntu inconsistency, but that doesn't effectively matter.
Question
Is there a sensible way to figure out at CMake time where to put completion scripts?
Note that CMake is not usually run from zsh, so checking $fpath is not an option.
$CMAKE_INSTALL_PREFIX/share/zsh/site-functions is the right place.
It is the same with man pages, info pages, pkg-config path, binaries and libraries and whatever else. On a default install, man will only look in predefined places like /usr/share/man and /usr/local/share/man.
If someone decides to install to /opt/gnuradio or whatever, it is then also their responsibility to ensure that they set $PATH, $MANPATH $INFOPATH and whatever else accordingly. It is the same for $fpath. The best software can do is ensure that they stick to established conventions and not to spew files elsewhere on the filesystem outside of $PREFIX.
If Ubuntu wants to be clever and invent their own vendor-completion directories then a consequence of that is that is that they need to patch everything they package that includes a zsh completion. That's their problem because they created the problem for themselves.
I am trying to build my software using cygwin-x86(32 bit version) on Windows-7.
Cygwin-x64(64 bit) works perfectly fine on the same machine. I want to build 32-bit executable.
Whenever I try cygwin-x86, I get the following errors:
[main] make 7780 child_info_fork::abort:
C:\cygwin\bin\cygiconv-2.dll: Loaded to different address:
parent(0x440000) != child(0x5F0000) make: fork: Resource temporarily
unavailable
I have checked this thread Cygwin Error
I have already tried everything mentioned in there, but I still continue to face the same issue.
Whenever i try /usr/bin/rebaseall -v or cd /usr/bin && ./rebaseall -v as mentioned in the step 7 of the accepted answer in the above mentioned thread, I get this error:
/usr/x86_64-pc-cygwin/sys-root/usr/bin/cygvtv_stubs-0.dll: skipped
because wrong machine type.
/usr/x86_64-pc-cygwin/sys-root/usr/bin/cygz.dll: skipped because wrong
machine type. Segmentation fault (core dumped)
I get this wrong machine type error for a lot of other .dll's as well.
As mentioned earlier I have cygwin-64 installed on my machine & working as expected. But while running rebaseall it is somehow looking for x86-64-pc-cygwin instead of 32 bit version.
The thread is obsolete.
run /usr/bin/rebase-trigger, close all cygwin processes and run again setup-x86.exe. Also without installing anything will execute a rebase for you.
You can also specify the option full.
Additional note:
The most likely cause of fork problems on 32 bit system are too many programs and libraries installed.
for example:
/usr/x86_64-pc-cygwin/sys-root/usr/bin/cygz.dll
belongs to cygwin64-zlib a cross library for building cygwin64 programs from cygwin32. Do you really need it ? If not, as I suspect, remove all cywgin64 packages .
The problem can also be triggered by an anti-virus program. (I saw it happening with Avast.) You can test if this is the cause by disabling it.
Could also be caused by this update
https://support.microsoft.com/en-us/help/4561616/windows-10-update-kb4561616
You can also kill each of the latest process of ash, dash or bash that was forked, setup.exe will simply skip this script and continue with the rest.
I had to kill about 10-20 of them, mostly in latex postinstall scripts.
For me, the solution was to remove the .new file extention of the libs from c:\cygwin64\bin\
I had the same problem using git. various dlls depending on the git command used where included in the error message stating that it was loaded to "different adress".
In fact a corporate antivirus or a loaded program had probably prevent un update during the rebase phase while installing a new program (git-svn in my case)
some required libraries where not installed but cleverly left in the target with the .new file extention.
I just had to remove the .new extention (and rename the original lib to .old) to solve the problem.
In my case the list of lib involved was:
cygcrypto-1.1.dll
cyggcc_s-seh-1.dll
cygintl-8.dll
cygwin1.dll
I'm trying get Homebrew working with Xcode Command Line Tools, and they seem to be having it out with each other... In the words of Rodney King, "Can't we all just get along?"
For some background, when I first got my Mac about a year ago, I had no idea what I was doing. I was also using macports, which was, as the Homebrew website seems to be cognizant, driving me to become a raging alcoholic. As a result, my /usr/local directory got wayyy f-ed up. Eventually, gcc and g++ stopped working, and a lot of other things were breaking. So I did a clean install of OS X, and I want my shiny new installation to stay a little more organized.
Now, I've installed Apple's Command Line Tools, and all the binaries/libraries/etc have ended up in /usr/local. That's fine, but then I try to install homebrew, and it's also putting everything in the /usr/local/ directory. When I run the command
brew doctor
I get the following output (actually, this is just a snippet, but it captures the general spirit of what Homebrew is telling me):
Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected static libraries:
/usr/local/lib/libatomic.a
/usr/local/lib/libgfortran.a
/usr/local/lib/libgmp.a
/usr/local/lib/libgomp.a
/usr/local/lib/libitm.a
/usr/local/lib/libmpc.a
/usr/local/lib/libmpfr.a
/usr/local/lib/libquadmath.a
/usr/local/lib/libssp.a
/usr/local/lib/libssp_nonshared.a
/usr/local/lib/libstdc++.a
/usr/local/lib/libsupc++.a
I thought I might place Homebrew in a different directory; however, the Homebrew documentation specifically warned against this. They say:
"Do yourself a favor and install to /usr/local. Some things may not build when installed elsewhere. One of the reasons Homebrew just works relative to the competition is because we recommend installing to /usr/local. Pick another prefix at your peril!"
The whole point is that I don't want to bother with micro-managing every package I install, and I don't want my filesystem to become an ungodly mess either. Anyone have any suggestions? Do I move command line tools to a different directory and add this to my $PATH? Any tips would be much appreciated.
It's a warning, and the message says why. If you later want to install a Homebrew formula that installs one of those files, it will fail, because it will decline to overwrite those files, and then you will have to delete those files, as the message says.
Specifically, those files appear to belong to an installation of gcc. You might want to research or try to remember why that was installed there. It's probably OK to just delete them and install gcc from Homebrew if you need it.
It's late and I should go to bed and maybe that's why I can't figure this out. I'm on a fedora-13 machine and I just ran
yum install gambit-c
I installed it because I want to follow along in a schemed text book.
but now that it's installed, how do I start the scheme interpreter??
It looks from the RPM listing that the binaries are named gsi, gsix, and gsc, all in /usr/bin. I suspect that gsi is the interpreter.
For more details, there's also the manual entry for gsi.
BTW: I don't know about the Fedora RPM, but I found that the Ubuntu repository's Gambit-C was quite outdated (4.0-ish), with missing features like simple compilation of stand-alone executables. The most recent version is 4.6. If your RPM's version is a few decimal places behind, I'd suggest just installing from source; it's a pretty standard configure -> make -> make install sequence. Just remember the following option when running configure:
./configure --enable-single-host
This speeds things up quite a bit.