Kernel Caching problem
We have developed an application in the MATLAB environment to apply statistical analysis to large ( ie: 200+ GB ) data sets. This application is a freely distributed research tool in the neuroscience field.
We have encountered a problem with the Linux ( and Mac ) kernel caching capacity. In the MATLAB environment, prior to allocating memory in variable space, the application determines if there is sufficient contiguous available memory, and returns an error if not. To ensure safety, only available memory is checked, and the kernel cache, though available, is disregarded.
During several phases of the processing, data is read from and written to disk multiple times. This consumes the kernel cache at an average rate of 500MB per operation, and quickly caches 20+GB on my test workstation, causing the application to return an 'out of memory' error (even though the cached memory is still available).
While I have operated in the past using various cache clearing operations ( such as sudo echo 3 | tee /proc/sys/vm/drop_caches ), this is not an entirely desirable option for distribution for several reasons.
1) not all potential users may be on the sudoers list
2) not all distributions will allow permissions to a sudo user for this operation
3) even if a sudo works, some operations may take as much as an hour to conclude, making it paramount for the researcher to be available to re-enter the password. As a full analysis may take 16-20 hours, this is not a feasible option.
What I think is needed is an ability to turn off or otherwise limit the kernel caching on an as needed basis. So far, I have found no options for this, other than rebuilding the kernel, an option most labs will not have available.
I will also be discussing this issue with the MATLAB developers team, though a proper resolution for public distribution may require action from both ends ( as well as ours ).
The manual released to the researcher community discusses this issue in depth, and offers some temporary mitigations, but it is quite inadequate to a full multi pass analysis. Additionally, while neuroscience researchers are quite brilliant in their own field, some aspects of computing just seem to fall short of comprehension to them.
Comments
-
Hi,
How do you handle your file writes? Have you considered using O_DIRECT within your output file handle? It is going to bypass linux buffering and cache and force DMA directly to physical memory.0 -
Hi Stefan
Nice tip!
Unfortunately, all of the I/O for the data files is handled by the MATLAB internals ( using the save/load commands ). While I could re-write the C and/or java code for file I/O of this nature, it would not really be worthwhile, as individual users would have to compile this, and not all labs would allow users to do that. Additionally, the MATLAB internal uses compression and versioning that would be different under different versions of MATLAB and environment.
I checked the settings and preferences within MATLAB to see if this option might have been available, but found nothing that would allow it. I will pass on to the MATLAB developers the suggestion to allow for the O_DIRECT setting in file save/load, if there was no specific reason for them not using it.0
Categories
- All Categories
- 50 LFX Mentorship
- 103 LFX Mentorship: Linux Kernel
- 553 Linux Foundation Boot Camps
- 296 Cloud Engineer Boot Camp
- 119 Advanced Cloud Engineer Boot Camp
- 52 DevOps Engineer Boot Camp
- 53 Cloud Native Developer Boot Camp
- 4 Express Training Courses
- 4 Express Courses - Discussion Forum
- 1.9K Training Courses
- 18 LFC110 Class Forum
- 6 LFC131 Class Forum
- 25 LFD102 Class Forum
- 150 LFD103 Class Forum
- 17 LFD121 Class Forum
- LFD137 Class Forum
- 61 LFD201 Class Forum
- LFD210 Class Forum
- LFD210-CN Class Forum
- 1 LFD213 Class Forum - Discontinued
- 128 LFD232 Class Forum
- LFD237 Class Forum
- 23 LFD254 Class Forum
- 598 LFD259 Class Forum
- 102 LFD272 Class Forum
- 1 LFD272-JP クラス フォーラム
- LFD273 Class Forum
- 2 LFS145 Class Forum
- 24 LFS200 Class Forum
- 739 LFS201 Class Forum
- 1 LFS201-JP クラス フォーラム
- 3 LFS203 Class Forum
- 69 LFS207 Class Forum
- 300 LFS211 Class Forum
- 54 LFS216 Class Forum
- 47 LFS241 Class Forum
- 41 LFS242 Class Forum
- 37 LFS243 Class Forum
- 11 LFS244 Class Forum
- 34 LFS250 Class Forum
- 1 LFS250-JP クラス フォーラム
- LFS251 Class Forum
- 140 LFS253 Class Forum
- LFS254 Class Forum
- 1K LFS258 Class Forum
- 10 LFS258-JP クラス フォーラム
- 92 LFS260 Class Forum
- 130 LFS261 Class Forum
- 32 LFS262 Class Forum
- 79 LFS263 Class Forum
- 15 LFS264 Class Forum
- 11 LFS266 Class Forum
- 17 LFS267 Class Forum
- 17 LFS268 Class Forum
- 23 LFS269 Class Forum
- 203 LFS272 Class Forum
- 1 LFS272-JP クラス フォーラム
- LFS281 Class Forum
- 221 LFW211 Class Forum
- 167 LFW212 Class Forum
- SKF100 Class Forum
- 902 Hardware
- 219 Drivers
- 74 I/O Devices
- 44 Monitors
- 115 Multimedia
- 209 Networking
- 101 Printers & Scanners
- 85 Storage
- 761 Linux Distributions
- 88 Debian
- 66 Fedora
- 15 Linux Mint
- 13 Mageia
- 24 openSUSE
- 141 Red Hat Enterprise
- 33 Slackware
- 13 SUSE Enterprise
- 356 Ubuntu
- 477 Linux System Administration
- 41 Cloud Computing
- 69 Command Line/Scripting
- Github systems admin projects
- 95 Linux Security
- 77 Network Management
- 108 System Management
- 49 Web Management
- 66 Mobile Computing
- 23 Android
- 29 Development
- 1.2K New to Linux
- 1.1K Getting Started with Linux
- 536 Off Topic
- 131 Introductions
- 216 Small Talk
- 21 Study Material
- 817 Programming and Development
- 275 Kernel Development
- 508 Software Development
- 928 Software
- 260 Applications
- 184 Command Line
- 3 Compiling/Installing
- 76 Games
- 316 Installation
- 59 All In Program
- 59 All In Forum
Upcoming Training
-
August 20, 2018
Kubernetes Administration (LFS458)
-
August 20, 2018
Linux System Administration (LFS301)
-
August 27, 2018
Open Source Virtualization (LFS462)
-
August 27, 2018
Linux Kernel Debugging and Security (LFD440)