So, I have a scientific server with a HDD and a SSD hard drive.
Where for computations involving lot's of data reading/writing a user can use the SSD but all the home directories are on the HDD.
Is there an automatic way to redirect the output of any program writing on the SSD to the home directory of the user running the program if the SSD is full?
If the best solution is to write my own script, then what is the best way to determine if the SSD runs out of space?
My OS is Ubuntu 18.04 LTS
In short, I do not think there is such a thing and I do believe that you should implement a bash script that checks (my tool of choice would simply be df) that there is enough space for you to run the next computation run before actually doing it. Maybe you should pre-allocate the space you intend to use, if possible, to avoid other concurrent runs to crash/run out of space? Maybe you should have an automated procedure to clean up some space?
Obviously, you could have the ssd available on some mountpoint in /home/, and then periodically check with a cron job whether it is full. And the maybe unmount it and send a warning mail. This will sort of do what you want. Sort of. But what happens then when also the HDD gets full? Watch out- these kind of problems can easily cause a server to crash, or otherwise experience issues.
This looks like a problem you might partially solve/mitigate by e.g., using a quota scheme (that is, limiting the amount of space that each user can allocate) or better yet by using a dedicated system for queueing jobs and allocating resources.
Does Linux need a writeable file system to function correctly? I'm just running a very simple init programme. Presently I'm not mounting any partitions. The Kernel has mounted the root partition as read-only. Is Linux designed to be able run with just a read-only file system as long as I stick to mallocs, readlines and text to standard out (puts), or does Linux require a writeable file system in-order even to perform standard text input and output?
I ask because I seem to be getting kernel panics and complaints about the stack. I'm not trying to run a useful system at the moment. I already have a useful system on another partition. I'm trying to keep it as simple as possible so as I can fully understand things before adding in an extra layer of complexity.
I'm running a fairly standard x86-64 desktop.
No, writable file system is not required. It is theoretically possible to run GNU/Linux with the only read-only file system.
In practice you probably want to mount /proc, /sys, /dev, possibly /dev/pts to everything work properly. Note that even some bash commands requires writable /tmp. Some other programs - writable /var.
You always can mount /tmp and /var as ramdisk.
Yes and No. No it doesn't need to be writeable if it did almost nothing useful.
Yes, you're running a desktop so it's needed to be writeable.
Many processes actually need a writeable filesystem as many system calls can create files. e.g. Unix Domain Sockets can create files.
Also many applications write into /var, and /tmp
The way to get around this is to mount the filesystem read/only and use a filesystem overlay to overlay an in memory filesystem. That way, the path will be writable but they go to ram and any changes are thrown away on reboot.
See: overlayroot
No it's not required. For example as most distributions have a live version of Linux for booting up for a cd or usb disk with actually using and back end hdd.
Also on normal installations, the root partitions are changed to read-only when there are corruptions on the disk. This way the system still comes up as read-only partition.
You need to capture the vmcore and the stack trace of the panic form the dmesg output to analyse further.
I'm creating a web application running on a Linux server. The application is constantly accessing a 250K file - it loads it in memory, reads it and sends back some info to the user. Since this file is read all the time, my client is suggesting to use something like memcache to cache it to memory, presumably because it will make read operations faster.
However, I'm thinking that the Linux filesystem is probably already caching the file in memory since it's accessed frequently. Is that right? In your opinion, would memcache provide a real improvement? Or is it going to do the same thing that Linux is already doing?
I'm not really familiar with neither Linux nor memcache, so I would really appreciate if someone could clarify this.
Yes, if you do not modify the file each time you open it.
Linux will hold the file's information in copy-on-write pages in memory, and "loading" the file into memory should be very fast (page table swap at worst).
Edit: Though, as cdhowie points out, there is no 'linux filesystem'. However, I believe the relevant code is in linux's memory management, and is therefore independent of the filesystem in question. If you're curious, you can read in the linux source about handling vm_area_struct objects in linux/mm/mmap.c, mainly.
As people have mentioned, mmap is a good solution here.
But, one 250k file is very small. You might want to read it in and put it in some sort of memory structure that matches what you want to send back to the user on startup. Ie, if it is a text file an array of lines might be a good choice, etc.
The file should be cached, but make sure the noatime option is set on the mount, otherwise the access time will attempt to be saved to the file, invalidating the cache.
Yes, definitely. It will keep accessed files in memory indefinitely, unless something else needs the memory.
You can control this behaviour (to some extent) with the fadvise system call. See its "man" page for more details.
A read/write system call will still normally need to copy the data, so if you see a real bottleneck doing this, consider using mmap() which can avoid the copy, by mapping the cache pages directly into the process.
I guess putting that file into ramdisk (tmpfs) may make enough advantage without big modifications. Unless you are really serious about response time in microseconds unit.
I am interested to know how the file system data structures are handled when suspending to disk.
I am wondering if it is possible to hibernate and then switch a disk (physically) and then resume. My guess is that all of the inodes in memory for hibernation would be invalid. Is there any way to refresh the inode data or any place in the Kernel source I could look that might provide an example?
It is not possible for me to umount the disk, I am curious what options are available to me.
I think one thing you can do is this:
boot on disk 1, hibernate.
Change to disk 2, and press the power button. The computer will boot again (not wake up).
hibernate on disk 2.
Switch to disk 1, and it has a better chance to wake up successfully.
When you remove it when should down, the hibernate image does not fit any longer to the configuration, as the swap does not happen when the system either can notice it or it doesnt care (because its really off). Maybe you are lucky, but I wont risk it. Many people dont know it, but SATA (and Linux) are capable of hot swap - maybe its an option for you to remove the old disk and connect a new one after you came back from hibernate.
Is it possible to 'hibernate' a process in linux?
Just like 'hibernate' in laptop, I would to write all the memory used by a process to disk, free up the RAM. And then later on, I can 'resume the process', i.e, reading all the data from memory and put it back to RAM and I can continue with my process?
I used to maintain CryoPID, which is a program that does exactly what you are talking about. It writes the contents of a program's address space, VDSO, file descriptor references and states to a file that can later be reconstructed. CryoPID started when there were no usable hooks in Linux itself and worked entirely from userspace (actually, it still does work, depending on your distro / kernel / security settings).
Problems were (indeed) sockets, pending RT signals, numerous X11 issues, the glibc caching getpid() implementation amongst many others. Randomization (especially VDSO) turned out to be insurmountable for the few of us working on it after Bernard walked away from it. However, it was fun and became the topic of several masters thesis.
If you are just contemplating a program that can save its running state and re-start directly into that state, its far .. far .. easier to just save that information from within the program itself, perhaps when servicing a signal.
I'd like to put a status update here, as of 2014.
The accepted answer suggests CryoPID as a tool to perform Checkpoint/Restore, but I found the project to be unmantained and impossible to compile with recent kernels.
Now, I found two actively mantained projects providing the application checkpointing feature.
The first, the one I suggest 'cause I have better luck running it, is CRIU
that performs checkpoint/restore mainly in userspace, and requires the kernel option CONFIG_CHECKPOINT_RESTORE enabled to work.
Checkpoint/Restore In Userspace, or CRIU (pronounced kree-oo, IPA: /krɪʊ/, Russian: криу), is a software tool for Linux operating system. Using this tool, you can freeze a running application (or part of it) and checkpoint it to a hard drive as a collection of files. You can then use the files to restore and run the application from the point it was frozen at. The distinctive feature of the CRIU project is that it is mainly implemented in user space.
The latter is DMTCP; quoting from their main page:
DMTCP (Distributed MultiThreaded Checkpointing) is a tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications. It operates directly on the user binary executable, without any Linux kernel modules or other kernel modifications.
There is also a nice Wikipedia page on the argument: Application_checkpointing
The answers mentioning ctrl-z are really talking about stopping the process with a signal, in this case SIGTSTP. You can issue a stop signal with kill:
kill -STOP <pid>
That will suspend execution of the process. It won't immediately free the memory used by it, but as memory is required for other processes the memory used by the stopped process will be gradually swapped out.
When you want to wake it up again, use
kill -CONT <pid>
The more complicated solutions, like CryoPID, are really only needed if you want the stopped process to be able to survive a system shutdown/restart - it doesn't sound like you need that.
Linux Kernel has now partially implemented the checkpoint/restart futures:https://ckpt.wiki.kernel.org/, the status is here.
Some useful information are in the lwn(linux weekly net):
http://lwn.net/Articles/375855/ http://lwn.net/Articles/412749/ ......
So the answer is "YES"
The issue is restoring the streams - files and sockets - that the program has open.
When your whole OS hibernates, the local files and such can obviously be restored. Network connections don't, but then the code that accesses the internet is typically more error checking and such and survives the error conditions (or ought to).
If you did per-program hibernation (without application support), how would you handle open files? What if another process accesses those files in the interim? etc?
Maintaining state when the program is not loaded is going to be difficult.
Simply suspending the threads and letting it get swapped to disk would have much the same effect?
Or run the program in a virtual machine and let the VM handle suspension.
Short answer is "yes, but not always reliably". Check out CryoPID:
http://cryopid.berlios.de/
Open files will indeed be the most common problem. CryoPID states explicitly:
Open files and offsets are restored.
Temporary files that have been
unlinked and are not accessible on the
filesystem are always saved in the
image. Other files that do not exist
on resume are not yet restored.
Support for saving file contents for
such situations is planned.
The same issues will also affect TCP connections, though CryoPID supports tcpcp for connection resuming.
I extended Cryopid producing a package called Cryopid2 available from SourceForge. This can
migrate a process as well as hibernating it (along with any open files and sockets - data
in sockets/pipes is sucked into the process on hibernation and spat back into these when
process is restarted).
The reason I have not been active with this project is I am not a kernel developer - both
this (and/or the original cryopid) need to get someone on board who can get them running
with the lastest kernels (e.g. Linux 3.x).
The Cryopid method does work - and is probably the best solution to general purpose process
hibernation/migration in Linux I have come across.
The short answer is "yes." You might start by looking at this for some ideas: ELF executable reconstruction from a core image (http://vx.netlux.org/lib/vsc03.html)
As others have noted, it's difficult for the OS to provide this functionality, because the application needs to have some error checking builtin to handle broken streams.
However, on a side note, some programming languages and tools that use virtual machines explicitly support this functionality, such as the Self programming language.
This is sort of the ultimate goal of clustered operating system. Mathew Dillon puts a lot of effort to implement something like this in his Dragonfly BSD project.
adding another workaround: you can use virtualbox. run your applications in a regular virtual machine and simply "save the machine state" whenever you want.
I know this is not an answer, but I thought it could be useful when there are no real options.
if for any reason you don't like virtualbox, vmware and Qemu are as good.
Ctrl-Z increases the chances the process's pages will be swapped, but it doesn't free the process's resources completely. The problem with freeing a process's resources completely is that things like file handles, sockets are kernel resources the process gets to use, but doesn't know how to persist on its own. So Ctrl-Z is as good as it gets.
There was some research on checkpoint/restore for Linux back in 2.2 and 2.4 days, but it never made it past prototype. It is possible (with the caveats described in the other answers) for certain values of possible - I you can write a kernel module to do it, it is possible. But for the common value of possible (can I do it from the shell on a commercial Linux distribution), it is not yet possible.
There's ctrl+z in linux, but i'm not sure it offers the features you specified. I suspect you asked this question since it doesn't