MATLAB 2017b freezes on Ubuntu 17.10: memory issue?

Hi,

I recently installed MATLAB2017b on a machine with 32 GB RAM (+32GB of swap) running Ubuntu 17.10 in order to run some computations that require a decent amount of memory. After running parts of the code MATLAB freezes (and with it the whole system). No error message is displayed, the computer just crashes and a hard restart is the only thing I can do. I was able to pin down the exact line at which MATLAB freezes. Before that line is executed my system indicator shows that I'm using 25 GB RAM. Since that specific line creates another large object, I'm assuming that the reason for the freeze is some kind of memory issue.

I'm puzzled by this behavior since, on my iMac running OS X and MATLAB 2016b with only 16GB RAM the exact same code runs without any problems.

Does anybody know what the problem with my code/MATLAB under Linux is? Is there anything I can do to make the code run on the Ubuntu machine?

Thank you very much!

Stefan

[Walter Roberson]

I wonder... does the Linux machine just happen to have an AMD Jaguar class of CPU ?

[Stefan Weiergraeber]

The Linux machine has an i7-7700, 3.60GHz, which is also more powerful than what I have on the iMac where everything works fine.

[Walter Roberson]

On the Linux machine, have you configured the preference for maximum array size?

... not that it should crash if you use an array too large.

A question at this point would be whether triggering swapping is what is crashing the system. You should be able to test that with a couple of lines of MATLAB.

[Stefan Weiergraeber]

Preferences for array sizes are set exactly as on my Mac. Indeed, it looks like triggering swapping crashes the system. As soon as the workspace becomes too large for the physical RAM, the problem occurs. Any ideas on how to fix this?

[Walter Roberson]

Would your swap partition happen to be encrypted?

https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1647400

[Stefan Weiergraeber]

Yes, the swap partition is encrypted. This sounds like there's nothing I can do about this at this point?

[Walter Roberson]

Looks to me that your options include:

• changing your MATLAB pref so as to prevent arrays that big so at least the entire system does not hang; or
• moving your swap to a non-encrypted partition

One thing I am not clear about though: when you run on your Unbuntu system, and when you run on OS-X, are you running with the same datasets on Linux, or with larger ones (or with some setting that deliberately causes it to use more memory) ?

[Stefan Weiergraeber]

Thanks a lot: Moving the swap to a nonencrypted partition solved the problem, at least for now. MATLAB does not freeze anymore when swap is triggered. However, I get an out-of-memory error now. What confuses me is that the exact same code with exactly the same data runs smoothly on my Mac with 16GB only. I need to run the code for a large range of parameter values, and I wanted to use the Linux machine for that after having developed the code on Mac.

Is there a fundamental difference in how MATLAB's OS x and Linux versions differ when it comes to memory? Could it be that Linux-MATLAB simply does not use the swap?

[Walter Roberson]

OS-X's libmalloc might not be the same as the libmalloc that is used on that particular version of Ubuntu: it is not uncommon for different versions of Unix to prefer different allocation strategies.

For example in traditional Unix systems, it was quite fragile to ever execute a sbrk() that released memory that had been allocated at a previous time, as it was difficult to track whether there were any remaining "live" references to memory within a previously allocated segment. These days it is much more common to use allocation strategies that can give memory back to the OS.

Also, traditional libmalloc did not have any "safeguard" areas between allocated ranges, so if a program happened to overwrite the end of an array, it was common for it to end up trashing something else that might happen to be a pointer, resulting in random memory locations being affected. A more modern libmalloc would be more protective against these kinds of errors.

As far as I know, Linux MATLAB will happily use swap -- the encrypted swap problem was an OS bug.

[Stefan Weiergraeber]

Moving the swap file to an non-encrypted partition solved the problem! Thank you!

[Guillaume R]

Hello, this is also happening to me, my swap folder is encrypted but I do not wish to disable encryption for obvious security reasons. Is there any other option to solve this problem ? For me the freeze is only on Matlab, not on the whole system though, so it could be a different issue but I don’t know where to start looking.

[Walter Roberson]

Please read through https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1647400 . It is a confirmed Linux bug, and fixes for it have been released. You should follow the "Continued at" link at the end too as the fix for this problem triggers other related but distinct issues so you need multiple fixes.