Invalid cross-device link (18) when saving a file on arch linux

I have installed matlab on arch linux. everything works fine, even simulink. I can also open files without a problem. But whenever i try to save a file, i get the error. I cant find anything about it online

Error writing file "[path]"Invalid cross-device link (18)".

Answer 1

[Joshua Ortiga]

I am also using Arch Linux and having the same problem as well. Unfortunately this is an issue that is currently only resolved by downgrading your kernel to <=Linux 5.18.9

See: https://bbs.archlinux.org/viewtopic.php?id=277970 and https://bbs.archlinux.org/viewtopic.php?pid=2051175#p2051175

[Paul]

I downgraded to LTS 5.15.58 and I'm still getting the error.

[Felix Van Oost]

Does anyone know if this issue is actively being looked into by MathWorks?

[Ali]

I reported this issue two weeks ago.

[LP]

Alos have error on 5.15.0-57-generic

Answer 2

[simone rotondi]

I had the same behaviour.

Anyway i have figured out that a big problem are the temp files, if i set the matlab tempdir to a file system different wrt btrfs or tempfs and the file is also in a different file system it works with no problem.

If the filesystem of the temp files or the files you are working with is btrfs with a newer kernel it wont work. i have tried also to disable the COW on the folder i was working but no improvement at all.

For instance to change the temp dir of matlab

clear all
tempdir
setenv('TMPDIR','FOLDER FROM NTFS,EXT4..')
clear all
tempdir 

and it should be fixed (for files not on btrfs)

[Ali]

Thanks, it works!

This solution solves the problem with .mlx files for me.

[Dimitris Kosmas]

This solved it for me as well. Together with this issue I posted about 4k scaling (link). One remark is that setting was not permanent for me (lost after restart). I had to define a TMP env variable and MATLAB can only see this when launched from terminal (not from a launcher).

[LP]

This did not work for me and i continue to get this problem with

MATLAB Version: 9.12.0.2039608 (R2022a) Update 5

[Phil]

Ensuring the TMPDIR is on the same partition as /home worked for me.

[FEDERICO]

Same for me, inside /home, works!

[FEDERICO]

Since It is needed to do it any time you open matlab.

Open (or create) startup.m in your userpath folder, with the following command:

edit(fullfile(userpath,'startup.m'))

And then place inside this file the following line (with the correct folder path):

setenv('TMPDIR','/home/youruser/yourtempdir');

Answer 3

[Jacek Jagosz]

To someone from Matlab, this is to help them fix this issue.

This seems to be the commit that introduced this issue, not only present in kernel 5.18 but even backported to 5.15 LTS https://git.kernel.org/pub/scm/linux/kernel/git/stable/linux.git/commit/?h=linux-5.15.y&id=4d5055873e24bba9e01b3b5d16790714b0d38533

Some other applications broke with this change, not just Matlab. For example qBittorrent, they discussed the whole issue here: https://github.com/qbittorrent/qBittorrent/issues/17352

And they fixed it in this particular commit: https://github.com/arvidn/libtorrent/pull/6965

Hope Matlab can introduce the same fix, and hope it finds its way to the new release.

Can I ping someone so this gets to someone from Mathworks, this could probably help them fix this issue.

[Walter Roberson]

@Jacek Jagosz

I opened a Support case and pointed to several postings, including your analysis here.

[Jacek Jagosz]

@Walter Roberson Could you check if this bug got fixed in R2022b Update 3 or maybe in the R2023a prerelease? I want to install a matlab release that is fully working.

[Walter Roberson]

@Jacek Jagosz

According to https://www.mathworks.com/support/bugreports/2856360 it is fixed in

• R2022a Update 6
• R2022b Update 4

I am not authorized to comment on pre-releases.

Answer 4

[Adrian Dummermuth]

I am getting this error while I try to save a .mlx file provided by the professor. I have write permissions in /tmp/ but I am not sure why saving the .mlx doesn't work but if I create a new file that works. Any suggestions?

Running on Pop!_OS 22.04 LTS

Linux pop-os 5.19.0-76051900-generic #202207312230~1660780566~22.04~9d60db1 SMP PREEMPT_DYNAMIC Thu A x86_64 x86_64 x86_64 GNU/Linux

Unable to save file ex_1_1_tmp.mlx.
java.lang.RuntimeException: Internal Exception in writing MLX file : Could not commit changes: copy failed: fl:filesystem:SystemError: /tmp/.ed28-df99-8888-aaaa.tmp Invalid cross-device link

[Adrian Dummermuth]

I have worked around it with saving it as a normal .m file and working on it like that.

Assupiton from my side is, that there is an unterlying issue in saving compressed files such as .mlx

[Ali]

I have the same problem on Ubuntu 22.04.1 LTS (kernel: Ubuntu 5.15.0-48.54-generic 5.15.53).

When I try to save the mlx-file I get this error and Matlab creates a file in the current directory like this: ".xxxx-xxxx-xxxx-xxxx.tmp".

[Youp Lamb]

i also get the tmp file in the directory

[Maciej]

You can save the .mlx file to your /tmp directory, and then move the file to your prefferred location. It is a poor workaround, though.

Answer 5

[Carlos Planelles Otero]

I have same issue on Pop!_OS 22.04, saving as a .m file works fine but not .mlx.

Answer 6

[Lennart Guderian]

Hey guys,

this issue has been bugging me too (on Garuda (Arch) Linux) and I just wanted to share a solution I came up with that doesn't require you to downgrade your kernel since that was something I wasn't really excited about. Thank you @simone rotondi for the information about the filesystem being the issue in conjunction with the temp dir!

Since on my main hard drive I have a btrfs, I just formatted a small USB-Stick with FAT, named it matlab, created a tmp and set the TMPDIR var to point to it (`/run/media/uname/matlab/tmp`). Then I save all matlab files on this usb stick - works like a charm. Surely not optimal (looking forward to a soon fix from the MathWorks Team) but for me that was the more chill option than downgrading and version locking my kernel.

Hope it helps someone!

Cheers

[Rishab Kumar]

Could you send the CLI commands with which you set the TMPDIR var pointer

[Lennart Guderian]

The command to use in Matlab is setenv('TMPDIR','FOLDER FROM NTFS,EXT4..')as you can see in Simone's answer above. In Matlab there is a startup script you can write that is run automatically when you open the program, if you add this line in there, it will be set automatically on every start and the problem is solved (if you also have your external storage device with FAT filesystem connected).

Answer 7

[Eugene Feinberg]

After wasting (I hate to admit it) a few days trying to find a complete workaround to varients of this issue, I found that the root cause for me is the old version of the Java JRE that Mathworks packages with R2022b. Replacing the JRE with a newer version fixes every instance of the copy_file_range cross device problem (temporary directory, simulink saving issues, Xilinx blockset compile).

Process:

• Download and untar or install java from https://www.java.com/en/download/manual.jsp
• In the matlab install directory, rename R2022b/sys/java/jre/glnxa64 to R2022b/sys/java/glnxa64.orig
• In the R2022b/sys/java/jre directory create a symlink to the download jre named glnxa64. There should now be a glnxa64/bin/java pointing to the new java binary.

The shipping version with R2022b update 2 is from January 2019

java version "1.8.0_202"
Java(TM) SE Runtime Environment (build 1.8.0_202-b08)
Java HotSpot(TM) 64-Bit Server VM (build 25.202-b08, mixed mode)

After installing the newer version

java version "1.8.0_351"
Java(TM) SE Runtime Environment (build 1.8.0_351-b10)
Java HotSpot(TM) 64-Bit Server VM (build 25.351-b10, mixed mode)

[simone rotondi]

Hi, i thought this was a cool solution but i didnt manage to fix the problem.

I'm on fedora 37 and Matlab 2022b update1

I tried this trick with both the java oracle libraries and the openjdk libs .. but both of them didnt solved the error. (anyway i'll keep using it)

'Java 1.8.0_352-b08 with Red Hat, Inc. OpenJDK 64-Bit Server VM mixed mode'

'Java 1.8.0_351-b10 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode'

This could be totally my fault and i hope it is. I'll keep trying , thanks anyway!

Answer 8

[Eugene Feinberg]

I have the same problem on 22.04.1 LTS. MATLAB is installed on a different volume than /tmp. An strace shows the pattern below. By creating a temporary directory on the same disk volume that matlab is installed on and running matlab with the TMP variable set to that directory the error is resolved but that seems like a bad solution.

[pid 38662] openat(AT_FDCWD, "/opt/MATLAB/R2022b/toolbox/simulink/blocks/obsolete/simulink_need_slupdate.mdl", O_RDONLY|O_CLOEXEC) = 948
[pid 38662] fstat(948, {st_mode=S_IFREG|0444, st_size=164480, ...}) = 0
[pid 38662] openat(AT_FDCWD, "/tmp/.d1ee-e4b5-3401-aa22.tmp_extracted_package_simulink_need_slupdate.mdl/_mwopc_packageCopy.txt", O_WRONLY|O_CREAT|O_EXCL|O_TRUNC|O_CLOEXEC, 0100644) = 950
[pid 38662] fstat(950, {st_mode=S_IFREG|0644, st_size=0, ...}) = 0
[pid 38662] copy_file_range(948, NULL, 950, NULL, 164480, 0) = -1 EXDEV (Invalid cross-device link)

Answer 9

[simone rotondi]

On fedora 36 with btrfs file system there is the same error both in R2022a and in R2022b.

Linux 5.18.9 is the last one working well but is now 4 months old and from 5.18.10 to 5.19.12 the problem persists.

Everytime i have to save a slx file it gives me

Error writing file "[path]/name.slx": Failed to close the package: "Collegamento tra dispositivi non valido (18)".

Where "Collegamento tra dispositivi non valido" means "Invalid cross link device"

[Paul]

I should mention that I am also using BTRFS so it's probably an issue with matlab and BTRFS specifically rather than the kernel version or distro.

[simone rotondi]

Yes, my SO is on btrfs but i am editing the files on a shared drive formatted with ntfs. Everywhere (but not /tmp) i edit simulink files with a newer kernel i see this problem.

[simone rotondi]

Anyway i have figured out that a big problem are the temp files, if i set the matlab tempdir to a file system different wrt btrfs or tempfs and the file is also in a different file system it works with no problem.

If the filesystem of the temp files or the files you are working with is btrfs with a newer kernel it wont work. i have tried also to disable the COW on the folder i was working but no improvement at all.

For instance to change the temp dir of matlab

clear all
tempdir
setenv('TMPDIR','FOLDER FROM NTFS,EXT4..')
clear all
tempdir 

and it should be fixed (almost)

[Valeria Fedeli]

@simone rotondi how do I create a folder from NTFS or ext4? I'm working on Fedora 36 too.

[Walter Roberson]

@Valeria Fedeli

You would need to have a partition available on a hard disk or SSD or flash drive (such as USB stick). The command line command that would be used at the Linux console would be mkfs -- see https://www.howtogeek.com/443342/how-to-use-the-mkfs-command-on-linux/

If I recall correctly there is a GUI available that will invoke the command on your behalf, but it has been several years since I last booted Linux so unfortunately I do not know where the GUI would be located.

[simone rotondi]

@Valeria Fedeli

If you are on Fedora36 i would just recommend to go back to kernel 5.18.9

You can download and install it with

mkdir KernDown
cd KernDown
koji download-build kernel-5.18.9-200.fc36
sudo dnf install ./kernel-*

and lock it with

sudo dnf versionlock add kernel-5.18.9-200.fc36

then unlock when the problem will be fixed whith

sudo dnf versionlock delete kernel-5.18.200.fc36

Otherwise you should follow @Walter Roberson advice

Answer 10

[FEDERICO]

SOLUTION, LATEST KERNEL, MATLAB R2022b

Make sure to chose a TMPDIR inside your /home partition:

Since It is needed to do it any time you open matlab.

Open (or create) startup.m in your userpath folder, with the following command:

edit(fullfile(userpath,'startup.m'))

And then place inside this file the following line (with the correct folder path):

setenv('TMPDIR','/home/youruser/yourtempdir');