I have a very large tar file(>1GB) that needs to be checked out and is a precondition for executing any tests.
I cannot have dedicated build server for my tests since tests are going to be executed on slave machines which are disposable.
Checking out a file(>1GB) is not optimal since in this case test execution time would increase because of precondition.What is the best optimal way of solving this problem?
I would dedicate a location on the slaves for that file.
Then in your tests, check if the file is in that location. If not, check it out and move it there. Since this location is outside your normal work area it won't get cleaned, and the file will stay there for the next test execution to use, and you won't need to check it out again.
Of course if the file changes you have to clear those caches. A first option would be to do this manual, alternative you can create a hash of the file and keep that hash in the cash and in your version control. You would then compare only the hashes, and only if those change you would check out the file.
Of course this requires that you have the ability to checkout all the rest of your code without the big file. How to do that obviously depends on the version control system in use.
Related
Are there guidelines regarding how to share a Snakemake workflow among multiple users on the same data under Linux, or is the whole thing considered bad practice?
Let me explain in case it's not clear:
Suppose user A executes a workflow in directory dir/. Assume the workflow terminates successfully, and he/she then properly sets file/directory permissions recursively on all output and intermediate files and the .snakemake/ subdirectory for other users to read/write, of course.
User B subsequently navigates to dir/, adds input files to the workflow, then executes it. Can anything go wrong?
TL;DR: I'm asking about non-concurrent execution of the same workflow by distinct users on the same system, and on the same data on disk. Is Snakemake designed for such use cases?
It's possible to run snakemake --nolock which will prevent locking of the directory, so multiple runs can be made from inside the same directory. However, without lock, there's now an opening for errors due to concurrent runs trying to modify the same files. It's probably OK, if you are certain that this will be avoided, e.g. if you are in constant communication with another user about which files will be modified.
An alternative option is to create a third directory/path, and put all the data there. This way you can work from separate directories/path and avoid costly recomputes.
I would say that from the point of view of snakemake, and workflow management in general, it's ok for user B to add or update input files and re-run the pipeline. After all, one of the advantages of a workflow management system is to update results according to new input. The problem is that user A could find her results updated without being aware of it.
From the top of my head and without more detail this is what I would suggest. Make snakemake read the list of input files from a table (pandas comes in handy for this) or from some configuration file. Keep this sample sheet under version control (with git/github) together with the Snakefile and other source code.
When users update the working directory with new files, they will also need to update the sample sheet in order for snakemake to "see" the new input and other users will know about it via version control. I prefer this setup over dumping files in a directory and letting snakemake process whatever is in there.
We have a legacy COBOL application based on OpenVMS for-which we do not have a clear idea of configuration. In this context, by "configuration" I am talking about:
Which executable files comprise the application;
Which pristine source files correspond to which executable files.
It may seem odd that 1 above is something that is not known, but over time what has happened is that executables have "come and gone" (and many still remain used). The knowledge of which executable files constitute the application as it exists today is not known since knowledge of which executables are no longer required has been lost in time. In practical terms, the team faithfully compiles all source code files and deploy the resultant executables despite the fact that there are obviously programs that are no longer used.
It goes without saying that there is no formal configuration management process and the source code is not kept in a version control system. Since the application runs on OpenVMS, the corresponding Files-11-based file system keeps older versions of files (including source files) and this has long been the excuse for not putting the application source into a version control system (despite the reasons for using a VCS extending far beyond merely having a record of previous versions).
There are a number of ways in which the configuration can be determined, of course, but I'd like to start with a first "small step", that is: determine the set of executables that comprise the application. At this point I should mention that the executable components of the application are not limited to OpenVMS images, but also DCL command files. I would like to:
Log all invocations of images that reside in a certain directory or set of directories;
Log all invocations of command files that reside in a certain directory or set of directories.
If we run this logging on our production system over an extended period of time, say two months, we can get a pretty good idea of what the application comprises. Together with user consultation, we'll be able to confirm the need for the executable files that aren't being called.
I think I have an idea of how to do 1 above, although I'm not sure of the specifics, that is, use SET/AUDIT. The second part, at this stage, I have no idea of how to do.
So, the main criterion for this effort is that as little of the existing system be affected in order to gain the above information. Due to the question mark around the configuration (and the complete lack of automated tests), changing anything is a nerve-wracking undertaking.
Using operating-system-level services like SET/AUDIT would allow one to get to know what's being run without the need to change source and/or recompile anything. So, my question is a multi-parter:
Is this the optimal way to do this on OpenVMS?
What would I need to do to restrict SET/AUDIT to only monitor images in a particular directory?
How would I log command file invocation without changing the .COM source files?
What should I expect in terms of performance degradation as a result of logging such information?
Ad 2., 3.
I would try security auditing with ACLs. From a a privileged account, something like ...
Make sure ACL auditing is enabled:
$ show audit
should show
System security audits currently enabled for:
...
ACL
...
If it doesn't, enable it with
$ set audit/audit/enable=acl
and then you may want to disable it when you are done with
$ set audit/audit/disable=acl
Set audit ACLs on all the wanted files:
$ set sec/acl=(audit=security,access=success+execute) [.app]*.com
$ set sec/acl=(audit=security,access=success+execute) [.app]*.exe
and you may want to delete the ACLs when you are done with
$ set security/acl=(audit=security,access=success+execute)/delete [.app]*.com
$ set security/acl=(audit=security,access=success+execute)/delete [.app]*.exe
You can check what ACLs are set with:
$ show security [.app]*.*
Run you application ...
Get the results from the audit file
$ analyze/audit [vms$common.sysmgr]security.audit$journal/sel=access=execute/full/since=17:00/out=app.log
Check your report for your files:
$ pipe type app.log |search sys$pipe "File name", ,"Access requested"
File name: _EMUVAX$DUA0:[USER.APP]NOW.COM;1
Access requested: READ,EXECUTE
Auditable event: Object access
File name: _EMUVAX$DUA0:[USER.APP]ECHO.EXE;1
Access requested: READ,EXECUTE
$
Sorry, I have no answer for 1. and 4.
It would help to know the OpenVMS Version (e.g. 6.2, 7.3-2, 8.4...) and the architecture (Vax, Alpha,Itanium).
Recent OpenVMS versions have great sda extensions
http://h71000.www7.hp.com/doc/84final/6549/6549pro_ext1.html
or
http://de.openvms.org/Spring2009/05-SDA_EXTENSIONS.pdf
such as LNM to check the logical names used by a process, PCS for PC sampling of a process, FLT to check the faulting behavior of applications, RMS for RMS data structures, PERF only for Itanium performance tracing, PROCIO for the reads and writes for all files opened by a process
Post a
dir sys$share:*sda.exe
so that we know which Sda extensions are available for you.
You can always check what a process with a pid of 204002B4 does with
$ ana/sys
set proc/id=204020b4
sh process /channel
exam #pc
and repeat while the process moves on.
I'm trying to configure a set of build configurations in TeamCity 6 and am trying to model a specific requirement in the cleanest possible manner way enabled by TeamCity.
I have a set of acceptance tests (around 4-8 suites of tests grouped by the functional area of the system they pertain to) that I wish to run in parallel (I'll model them as build configurations so they can be distributed across a set of agents).
From my initial research, it seems that having a AcceptanceTests meta-build config that pulls in the set of individual Acceptance test configs via Snapshot dependencies should do the trick. Then all I have to do is say that my Commit build config should trigger AcceptanceTests and they'll all get pulled in. So, lets say I also have AcceptanceSuiteA, AcceptanceSuiteB and AcceptanceSuiteC
So far, so good (I know I could also turn it around the other way and cause the Commit config to trigger AcceptanceSuiteA, AcceptanceSuiteB and AcceptanceSuiteC - problem there is I need to manually aggregate the results to determine the overall success of the acceptance tests as a whole).
The complicating bit is that while AcceptanceSuiteC just needs some Commit artifacts and can then live on it's own, AcceptanceSuiteA and AcceptanceSuiteB need to:
DeploySite (lets say it takes 2 minutes and I cant afford to spin up a completely isolated one just for this run)
Run tests against the deployed site
The problem is that I need to be able to ensure that:
the website only gets configured once
The website does not get clobbered while the two suites are running
If I set up DeploySite as a build config and have AcceptanceSuiteA and AcceptanceSuiteB pull it in as a snapshot dependency, AFAICT:
a subsequent or parallel run of AcceptanceSuiteB could trigger another DeploySite which would clobber the deployment that AcceptanceSuiteA and/or AcceptanceSuiteB are in the middle of using.
While I can say Limit the number of simultaneously running builds to force only one to happen at a time, I need to have one at a time and not while the dependent pieces are still running.
Is there a way in TeamCity to model such a hierarchy?
EDIT: Ideas:-
A crap solution is that DeploySite could set a 'in use flag' marker and then have the AcceptanceTests config clear that flag [after AcceptanceSuiteA and AcceptanceSuiteB have completed]. The problem then becomes one of having the next DeploySite down the pipeline wait until said gate has been opened again (Doing a blocking wait within the build, doesnt feel right - I want it to be flagged as 'not yet started' rather than looking like it's taking a long time to do something). However this sort of stuff a flag over here and have this bit check it is the sort of mutable state / flakiness smell I'm trying to get away from.
EDIT 2: if I could programmatically alter the agent configuration, I could set Agent Requirements to require InUse=false and then set the flag when a deploy starts and clear it after the tests have run
Seems you go look on the Jetbrains Devnet and YouTrack tracker first and remember to use the magic word clobber in your search.
Then you install groovy-plug and use the StartBuildPrecondition facility
To use the feature, add system.locks.readLock. or system.locks.writeLock. property to the build configuration.
The build with writeLock will only start when there are no builds running with read or write locks of the same name.
The build with readLock will only start when there are no builds running with write lock of the same name.
therein to manage the fact that the dependent configs 'read' and the DeploySite config 'writes' the shared item.
(This is not a full productised solution hence the tracker item remains open)
EDIT: And I still dont know whether the lock should be under Build Parameters|System Properties and what the exact name format should be, is it locks.writeLock.MYLOCKNAME (i.e., show up in config with reference syntax %system.locks.writeLock.MYLOCKNAME%) ?
Other puzzlers are: how does one manage giving builds triggered by build completion of a writeLock task read access - does the lock get dropped until the next one picks up (which would allow another writer in) - or is it necessary to have something queue up the parent and child dependency at the same time ?
I'm running a very computationally intensive scientific job that spits out results every now and then. The job is basically to just simulate the same thing a whole bunch of times, so it's divided among several computers, which use different OSes. I'd like to direct the output from all these instances to the same file, since all the computers can see the same filesystem via NFS/Samba. Here are the constraints:
Must allow safe concurrent appends. Must block if some other instance on another computer is currently appending to the file.
Performance does not count. I/O for each instance is only a few bytes per minute.
Simplicity does count. The whole point of this (besides pure curiosity) is so I can stop having every instance write to a different file and manually merging these files together.
Must not depend on the details of the filesystem. Must work with an unknown filesystem on an NFS or Samba mount.
The language I'm using is D, in case that matters. I've looked, there's nothing in the standard lib that seems to do this. Both D-specific and general, language-agnostic answers are fully acceptable and appreciated.
Over NFS you face some problems with client side caching and stale data. I have written an OS independent lock module to work over NFS before. The simple idea of creating a [datafile].lock file does not work well over NFS. The basic idea to work around it is to create a lock file [datafile].lock which if present means file is NOT locked and a process that wants to acquire a lock renames the file to a different name like [datafile].lock.[hostname].[pid]. The rename is an atomic enough operation that works well enough over NFS to guarantee exclusivity of the lock. The rest is basically a bunch of fail safe, loops, error checking and lock retrieval in case the process dies before releasing the lock and renaming the lock file back to [datafile].lock
The classic solution is to use a lock file, or more accurately a lock directory. On all common OSs creating a directory is an atomic operation so the routine is:
try to create a lock directory with a fixed name in a fixed location
if the create failed, wait a second or so and try again - repeat until success
write your data to the real data file
delete the lock directory
This has been used by applications such as CVS for many years across many platforms. The only problem occurs in the rare cases when your app crashes while writing and before removing the lock.
Why not just build a simple server which sits between the file and the other computers?
Then if you ever wanted to change the data format, you would only have to modify the server, and not all of the clients.
In my opinion building a server would be much easier than trying to use a Network file system.
Lock File with a twist
Like other answers have mentioned, the easiest method is to create a lock file in the same directory as the datafile.
Since you want to be able to access the same file over multiple PC the best solution I can think of is to just include the identifier of the machine currently writing to the data file.
So the sequence for writing to the data file would be:
Check if there is a lock file present
If there is a lock file, see if I'm the one owning it by checking that its content has my identifier.
If that's the case, just write to the data file then delete the lock file.
If that's not the case, just wait a second or a small random length of time and try the whole cycle again.
If there is no lock file, create one with my identifier and try the whole cycle again to avoid race condition (re-check that the lock file is really mine).
Along with the identifier, I would record a timestamp in the lock file and check whether it's older than a given timeout value.
If the timestamp is too old, then assume that the lock file is stale and just delete it as it would mea one of the PC writing to the data file may have crashed or its connection may have been lost.
Another solution
If you are in control the format of the data file, could be to reserve a structure at the beginning of the file to record whether it is locked or not.
If you just reserve a byte for this purpose, you could assume, for instance, that 00 would mean the data file isn't locked, and that other values would represent the identifier of the machine currently writing to it.
Issues with NFS
OK, I'm adding a few things because Jiri Klouda correctly pointed out that NFS uses client-side caching that will result in the actual lock file being in an undetermined state.
A few ways to solve this issue:
mount the NFS directory with the noac or sync options. This is easy but doesn't completely guarantee data consistency between client and server though so there may still be issues although in your case it may be OK.
Open the lock file or data file using the O_DIRECT, the O_SYNC or O_DSYNC attributes. This is supposed to disable caching altogether.
This will lower performance but will ensure consistency.
You may be able to use flock() to lock the data file but its implementation is spotty and you will need to check if your particular OS actually uses the NFS locking service. It may do nothing at all otherwise.
If the data file is locked, then another client opening it for writing will fail.
Oh yeah, and it doesn't seem to work on SMB shares, so it's probably best to just forget about it.
Don't use NFS and just use Samba instead: there is a good article on the subject and why NFS is probably not the best answer to your usage scenario.
You will also find in this article various methods for locking files.
Jiri's solution is also a good one.
Basically, if you want to keep things simple, don't use NFS for frequently-updated files that are shared amongst multiple machines.
Something different
Use a small database server to save your data into and bypass the NFS/SMB locking issues altogether or keep your current multiple data files system and just write a small utility to concatenate the results.
It may still be the safest and simplest solution to your problem.
I don't know D, but I thing using a mutex file to do the jobe might work. Here's some pseudo-code you might find useful:
do {
// Try to create a new file to use as mutex.
// If it's already created, it will throw some kind of error.
mutex = create_file_for_writing('lock_file');
} while (mutex == null);
// Open your log file and write results
log_file = open_file_for_reading('the_log_file');
write(log_file, data);
close_file(log_file);
close_file(mutex);
// Free mutex and allow other processes to create the same file.
delete_file(mutex);
So, all processes will try to create the mutex file but only the one who wins will be able to continue. Once you write your output, close and delete the mutex so other processes can do the same.
It's a very common scenario: some process wants to drop a file on a server every 30 minutes or so. Simple, right? Well, I can think of a bunch of ways this could go wrong.
For instance, processing a file may take more or less than 30 minutes, so it's possible for a new file to arrive before I'm done with the previous one. I don't want the source system to overwrite a file that I'm still processing.
On the other hand, the files are large, so it takes a few minutes to finish uploading them. I don't want to start processing a partial file. The files are just tranferred with FTP or sftp (my preference), so OS-level locking isn't an option.
Finally, I do need to keep the files around for a while, in case I need to manually inspect one of them (for debugging) or reprocess one.
I've seen a lot of ad-hoc approaches to shuffling upload files around, swapping filenames, using datestamps, touching "indicator" files to assist in synchronization, and so on. What I haven't seen yet is a comprehensive "algorithm" for processing files that addresses concurrency, consistency, and completeness.
So, I'd like to tap into the wisdom of crowds here. Has anyone seen a really bulletproof way to juggle batch data files so they're never processed too early, never overwritten before done, and safely kept after processing?
The key is to do the initial juggling at the sending end. All the sender needs to do is:
Store the file with a unique filename.
As soon as the file has been sent, move it to a subdirectory called e.g. completed.
Assuming there is only a single receiver process, all the receiver needs to do is:
Periodically scan the completed directory for any files.
As soon as a file appears in completed, move it to a subdirectory called e.g. processed, and start working on it from there.
Optionally delete it when finished.
On any sane filesystem, file moves are atomic provided they occur within the same filesystem/volume. So there are no race conditions.
Multiple Receivers
If processing could take longer than the period between files being delivered, you'll build up a backlog unless you have multiple receiver processes. So, how to handle the multiple-receiver case?
Simple: Each receiver process operates exactly as before. The key is that we attempt to move a file to processed before working on it: that, and the fact the same-filesystem file moves are atomic, means that even if multiple receivers see the same file in completed and try to move it, only one will succeed. All you need to do is make sure you check the return value of rename(), or whatever OS call you use to perform the move, and only proceed with processing if it succeeded. If the move failed, some other receiver got there first, so just go back and scan the completed directory again.
If the OS supports it, use file system hooks to intercept open and close file operations. Something like Dazuko. Other operating systems may let you know about file operations in anoter way, for example Novell Open Enterprise Server lets you define epochs, and read list of files modified during an epoch.
Just realized that in Linux, you can use inotify subsystem, or the utilities from inotify-tools package
File transfers is one of the classics of system integration. I'd recommend you to get the Enterprise Integration Patterns book to build your own answer to these questions -- to some extent, the answer depends on the technologies and platforms you are using for endpoint implementation and for file transfer. It's a quite comprehensive collection of workable patterns, and fairly well written.