I am using seq2sparse to convert sequence files to sparse vectors. Is it normal for this to take so long? Mine has been stuck on a monitorAndPrintJob for thirty minutes now. It seems to be doing something because any attempt to do anything else on the machine is very very sluggish. But it'd be nice to know if I should stop it and try again or if I should just wait.
Here's the command I used:
mahout home/bin/mahout seq2sparse -o outputDirectory -i inputDirectory -ml 10 -ng 2 -seq
Should I tweak some of the switches to help it run more efficiently?
This is on one local machine. The sequence file is 151MB.
Edit: it is no longer sluggish to do other things, but htop shows java is doing things to do with hadoop and mahout so I guess I should leave it? It's been at this one part of the process for forty minutes now.
Edit 2: ah not to worry, I went out and came back and it had finished without crashing or anything. Cheers anyway if you read all this!
Related
I have a rather complex workflow with 750 samples and roughly 18.000 jobs, at first snakemake runs just fine but then after around 4.000 jobs it suddenly freezes and upon restart it hangs with "Select jobs to execute..." for 24h, after that I terminated it. The initial DAG building takes roughly 2-3 minutes, though.
When I run snakemake (v5.32.0 and v5.32.1) with the --verbose option, I get tons of lines similar to this one:
Cbc0010I After 600 nodes, 304 on tree, -52534.791 best solution, best possible -52538.194 (7.08 seconds
I tried to delete the .snakemake folder in the hope that something went riot there, but that wasn't the case, unfortunately. To me it seems that the CBC MILP Solver somehow does not converge, and it keeps going and going to bring the best and the best possible solution closer together!?
Now I do not have any idea anymore, how to proceed and fix the problem. My possible solutions are somehow to change the convergence criteria or the solver itself. In the manual I found the option --scheduler-ilp-solver but it has apparently only one option, the default COIN_CMD.
After terminating a (shorter) run, I get this verbose output
Result - User ctrl-cuser ctrl-c
Objective value: 52534.79114334
Upper bound: 52538.202
Gap: -0.00
Enumerated nodes: 186926
Total iterations: 1807277
Time (CPU seconds): 1181.97
Time (Wallclock seconds): 1188.11
Next I will try to limit the number of samples in the workflow and see if this has any impact (for other datasets with 500 samples, it ran without any problems (with snakemake version 5.24), but there the DAG building took some hours. Hence, I am not very eager to try the old version.)
So, any idea how to fix the problem is highly appreciated. Also, I do not even know, if this is a bug!?
EDIT Actually, I believe it is a bug in the current version, I downgraded Snakemake back to version 5.24, it created the DAG within 10 minutes and started to run the pipeline. So, apparently there is some bug with the latest version. I will make this an answer to my own question, as the downgrading to an older version solved the problem...
I also ran into this issue with a smaller workflow (~1500 jobs total) and snakemake version 6.0.2. About half the jobs had run when the workflow got stuck, and refused to run any more jobs. Looks like it's a problem specific to the ILP solver, because when I re-ran with --scheduler greedy, it worked fine.
Actually, I believe it is a bug in the current snakemake version, I downgraded Snakemake back to version 5.24, it created the DAG within 10 minutes and started to run the pipeline. So, apparently there is some bug with the latest version. I will make this an answer to my own question, as the downgrading to an older version solved the problem...
Is there a way to limit how many CPU cores Xcode can use to index code in the background?
I write code in emacs but I run my app from Xcode, because the debugger is pretty great. The problem is that in emacs I use rtags for indexing, which already needs a lot of CPU, and then Xcode wants to do the same. Basically whenever I touch a common header file, my computer is in big trouble...
I like this question, it presents hacky problem-solving :)
Not sure if this would work (not sure how to force Xcode to index) but here are some thoughts that might set you on the right track: there's a tool called cpulimit that you can use to slow down processes (it inserts a sleep or something into a given process, I used it when experimenting with mining crypto).
If you can figure out the process ID of the indexing daemon, maybe you can cpulimit it!
I'd start by running ps -A | grep -i xcode before and after indexing occurs to see what's changed (if anything), or using Activity Monitor to see what spikes (/Applications/Xcode10.1.app/Contents/SharedFrameworks/DVTSourceControl.framework/Versions/A/XPCServices/com.apple.dt.Xcode.sourcecontrol.WorkingCopyScanner.xpc/Contents/MacOS/com.apple.dt.Xcode.sourcecontrol.WorkingCopyScanner looks interesting)
There is a -i or --include-children param on cpulimit that should take care of this, but not sure how well it works in practice.
I made a script /usr/local/bin/xthrottle;
#!/bin/ksh
PID=$(pgrep -f Xcode | head -n 1)
sudo renice 10 $PID
You can play with the nice level, -20 is least nice, 20 is nicest for your neighbour processes.
I'm running a minecraft server on my linux box in a detached screen session. I'm not very fond of screen very much and would like to be able to constantly pipe the output of the server to a file(like a pipe) and pipe some input from a file to the server(so that I can input and output to the server from remote programs, like a python script). I'm not very experienced in bash, so could somebody tell me how to do this?
Thanks, NikitaUtiu.
It's not clear if you need screen at all. I don't know the minecraft server, but generally for server software, you can run it from a crontab entry and redirect output to log files.
Assuming your server kills itself at midnight sunday night, (we can discuss changing this if restarting 1x per week is too little or too much OR you require ad-hoc restarts), but for a basic idea of what to do, here is a crontab entry that starts the server each monday at 1 minute after midnight.
01 00 * * 1 dtTm=`/bin/date +\%Y\%m\%d.\%H\%M\%S`; export dtTm; { /usr/bin/mineserver -o ..... your_options_to_run_mineserver_here ... ; } > /tmp/mineserver_trace_log.${dtTm} 2>&1
consult your man page for crontab to confirm that day-of-week ranges are 0-6 (0=Sunday), and change the day-of-week value if 0!=Sunday.
Normally I would break the code up so it is easier to read, but for crontab entries, each entry has to be all on one line, (with some weird exceptions) AND usually a limit of 1024b-8K to how long the line can be. Note that the ';' just before the closing '}' is super-critical. If this is left out, you'll get un-deciperable error messages, or no error messages at all.
Basically, you're redirecting any output into a file (including std-err output). Now you can do a lot of stuff with the output, use more or less to look at the file, grep ERR ${logFile}, write scripts that grep for error messages and then send you emails that errors have been found, etc, etc.
You may have some sys-admin work on your hands to get the mineserver user so it can run crontab entries. Also if you're not comfortable using the vi or emacs editors, creating a crontab file may require help from others. Post to superuser.com to get answers for problems you have with linux admin issues.
Finally, there are two points I'd like to make about dated logfiles.
Good: a. If you app dies, you never have to rerun it to then capture output and figure out why something has stopped working. For long running programs this can save you a lot of time. b. keeping dated files gives you the ability to prove to you, your boss, others, that It used to work just fine, see here are the log files. c. Keeping the log files, assuming there is useful information in them, gives you the opportunity to mine those files for facts. I.E. : program used to take 1 sec for processing, now it is taking 1 hr, etc etc.
Bad: a. You'll need to set up a mechanism to sweep old log files, otherwise at some point everything will have stopped, AND when you finally figure out what the problem was, you discover that your /tmp OR whatever dir you chose to use IS completely full.
There is a self-maintaining solution to using dates on the logfiles I can tell you about if you find this approach useful. It will take a little explaining, so I don't want to spend the time writing it up if you don't find the crontab solution useful.
I hope this helps!
I have a Perl script that runs via a system() command from C. On a specific site (SunOS 5.10), when that script is run, it nearly always takes 6 seconds or more. On other sites, it runs pretty much instantly (0.1s). If I run the script manually, i.e. not from the C code, it also runs instantly. I eventually tracked the slowness down (by spitting out the time a whole bunch in a lot of different places), to a single require line. The file that it is requiring is another Perl script we wrote. The script consists of a single require (this file here), 3 scalars that are assigned integer values, and a handful of time/date conversion routines. The file ends with a 1;. That single require appears to take as much as 6 seconds on occasion, but as I said, not always even on the same machine. I'm absolutely stumped here. My only last thought is to turn on profiling, but the site doesn't have Devel::Profiler and my only other option (that I know of) would be to add it to the Perl command which would require me altering and recompiling the C code (doable but non-trivial).
Anybody have ANY idea what could be going on here? I don't think I can/want to put the entire date.pl that is being required, but it's pretty much exactly as I described; I could answer any questions about it that you have.
Thanks in advance.
You might be interested in A Timely Start by Jean-Louis Leroy. He had a similar problem and tracked it down to a long and deep module search path where perl usually found the modules in the last entries in #INC.
Six seconds is a long time. Have you checked what your network is doing during this?
My first thought was that spawning the new process when using the system() command could be the problem, but six seconds is too long.
I don't know much about perl, but I could imagine that for any reason, the access of the time module could invoke a call to a network time server. Just to get synchronized. Maybe this takes so long or maybe it is getting a time out.
It could be that this only happens for a newly spawned process -- hence only when you use the system() command.
just wild guessing...
So, this does nothing to answer your question directly, but please tell me that you're not actually running on perl 4? Assuming you're on perl 5, you could remove the entire file and replace the require with use POSIX qw(ctime) to get the version that comes with Perl.
If you do have to support perl4, I'll merely grumble something about version 5 being fifteen years old now and go away. :)
I'm working on a system with four logical CPS (two dual-core CPUs if it matters). I'm using make to parallelize twelve trivially parallelizable tasks and doing it from cron.
The invocation looks like:
make -k -j 4 -l 3.99 -C [dir] [12 targets]
The trouble I'm running into is that sometimes one job will finish but the next one won't startup even though it shouldn't be stopped by the load average limiter. Each target takes about four hours to complete and I'm wondering if this might be part of the problem.
Edit: Sometimes a target does fail but I use the -k option to have the rest of the make still run. I haven't noticed any correlation with jobs failing and the next job not starting.
I'd drop the '-l'
If all you plan to run the the system is this build I think the -j 4 does what you want.
Based on my memory, if you have anything else running (crond?), that can push the load average over 4.
GNU make ref
Does make think one of the targets is failing? If so, it will stop the make after the running jobs finish. You can use -k to tell it to continue even if an error occurs.
#BCS
I'm 99.9% sure that the -l isn't causeing the problem because I can watch the load average on the machine and it drops down to about three and sometimes as low as one (!) without starting the next job.