I have seen, I think, a file that is actively written to by some program on a NFS share be full of null bytes before the data was actually available. I think I could rationalize that with: Whatever wrote to the file allocated the file first and then filled in the data, and I just happened to read the file before tha actual data was available.
@Kusalananda well it's unlikely here, I have a python script using inotify and psutil to watch some program activity and wrote it out to a csv. It's very unlikely that someone tries to read/modify the data at the same time.
but I'll make a new run to check what happened strange to get thos nullbyte in middle of a file
@Kusalananda thanks for the edit although I wanted to avoid using the POSIX classes since I find them ugly and cumbersome and I was pretty sure we only needed to deal with a space. But if I use [:space:] at the beginning, I also need to use it after the .com.
I don't know ho this could have happen I'm going to do a rerun to see if it's just a random mistake in the distributed FS or my python monitoring script doing some bullshit randomly. it seems very strange to me
well I do not administrate the storage cluster and those file are a bit old, if this error happen again I'll consider doing so. But it's the one and only time I notice that. It's probably an epiphenomenon
@RuiFRibeiro well according to my workflow I really do not understand how a race condition could occur. But that's probably an epiphenomenon race condition indeed :D
:D this is a very complex movement it's very controversial topic with anyone here. I doubt any people outside of France as most people inside the country already do not understand :D
I like it though, I didn't though such a movement would birth from the poorest but I'm glad something is finally happening in France I would be glad to see more similar movement all over the world. I see this movement as an anti capitalism system (and it's a good thing IMO) but that's my point of view only and everybody sees what he want to see in this movement. It's composed of so many political apolitical smaller group that it's basically impossible to define
@Kiwy My first take on it was "they don't like taxes, they must be right-leaning activists". Now it seems it's mostly about throwing tantrums in as many ways as possible.
@Kusalananda well I first was thinking the same though now there's real discussion between several movement inside the same movement. and basically all the rage against a lot of recent laws voted mostly to make economy more Liberalism
what is complex is that there's extrem left and right in the same boat :D and regular left and right and centrist and apolitical people. but I feel like there's a rage against a lot of liberalism law voted the last 10 years.
@Kusalananda Oh, come on, you could teach them something!
And don't diss bioinformaticans' knowledge of awk. I may have mentioned my PhD supervisor had actually written one of the first gene prediction algorithms and had implemented the entire thing in awk.
The thing would read through an entire genome, apply Markov chain models and predict genes. In awk!
@terdon Awk is a really useful tool, no worries. I just now wrote an awk script for a colleague to split fasta sequences on runs of "N" (I previously did the opposite, to create contigs out of sequences in such a way that they were packed in a particular manner, with gaps of these Ns).
No, it's just that most of the time, with shell scripting and awk programming (and even Perl and Python) courses, the tutors will teach students bad behaviour, out of ignorance.
"Just do for fasta in $(cat fastafile.fa); do echo $fasta | grep ..." etc.
Obviously, these tutors may well be good ones. I don't know them. They are local sysops.
@StephenKitt I had trouble understanding them almost any time I read them, but I think I have a problem here with APT, I should look for "apt cache" in Google I guess because it seems to go beyond Ansible (I never used apt-get cache or apt cache).
I have a long list of read IDs of interest to me in a file called read_names.txt. it is simply in the format:
m54197_180831_211346/4981510/ccs
m54197_180831_211346/6226723/ccs
m54197_180831_211346/6619607/ccs
...
etc where these are the actual read names from a fastq file. I am then trying to ...
thanks terdon, I will keep this in mind and find the better ways to handle this in the future. I use this method quite often so that is great for me to know! — d_kennetzDec 6 at 21:51
@JohnDoea look closely at the Ansible directive; what does it say exactly?
user141350
"apt: update_cache=yes", but what is update cache? I don't think someone updates something when the data is taken from a cache, a cache stores something old, not something new (that's how I see it).
user141350
4:38 PM
Maybe it means the updated data is cached somewhere?
@JohnDoea you’re still not reading the description of the update_cache parameter. I’ll give you a hint: it’s the section which has update_cache in the “Parameter” column.
Yes, I saw it earlier (I meant this one actually, sorry, it was confusing to me).
I assume they say "equivalent" because Ansible translates "old" codes to their community-derived up2date equivalents if the original codes themselves change,
but I still miss the relation to the "caching" concept of computing... Why should the old code be cached, just as history?
update
update is used to resynchronize the package index files from their sources. The indexes of available
packages are fetched from the location(s) specified in /etc/apt/sources.list. For example, when
using a Debian archive, this command retrieves and scans the Packages.gz files, so that information
about new and updated packages is available. An update should always be performed before an upgrade
or dist-upgrade. Please be aware that the overall progress meter will be incorrect as the size of
user141350
I think my description describes what's usually happens per that man description but I still miss what's caching has to do with it. Either the list is up2date or it doesn't... No?... Well, I assume maybe not.
user141350
I am sorry, maybe I should ask an SE question about this, I feel bad you maybe bother explaining this to me here personally, dear Stephen.
@JohnDoea The apt system has a local list (a cache) of available packages and that is where it looks to see what package versions are available. The apt-get update command does not update existing packages. It doesn't change any software installed. All it does is download a new (updated) list of available software. That means that next time you run apt-get WHATEVER, the list (cache) will have been updated and you know it is, well, up to date.
This is why you run apt-ge update && apt-get upgrade: the first command, update, will update the list of available package versions and the second command, upgrade will actually upgrade all packages to the newest version available.
@StephenKitt yes I know it is a list which apt update (or apt-get update) updates but that software based on it isn't upgraded until apt upgrade or apt-get upgrade are done... I just didn't call it a "cache". Thank you for all the help. I should re-read the answer you posted soon.
@PrabhjotSingh Hi. Was just replying to your email. My mother is also a bit in and out. I don't know which theory this makes more likely. I.e. she isn't consistently out.
@PrabhjotSingh Re the hospital medical thing, you saw the email I sent, right?
I mean, I forwarded it to you.
I got a rather unhelpful reply back from i-probono. Reads like it was written by a robot.
@PrabhjotSingh You don't understand what? I just said I don't know what you do - professionally. Or to put it differently - what do you do professionally?
Requirement:
1) 11 subnets needed given IP 172.16.0.0
2) Packet of each subnet should not step into another subnet, given a single router connecting all 11 subnets
Solution:
• First octet says that this is Class A
• Network ID is 172.16 and Host ID is 0.0
• Defa...
I have a long list of read IDs of interest to me in a file called read_names.txt. it is simply in the format:
m54197_180831_211346/4981510/ccs
m54197_180831_211346/6226723/ccs
m54197_180831_211346/6619607/ccs
...
etc where these are the actual read names from a fastq file. I am then trying to ...
Requirement:
1) 11 subnets needed given IP 172.16.0.0
2) Packet of each subnet should not step into another subnet, given a single router connecting all 11 subnets
Solution:
• First octet says that this is Class A
• Network ID is 172.16 and Host ID is 0.0
• Defa...
