I keep track of a cisco's UpTime.
sh ver shows me 1year 221 days
But when I want to get a sysuptime via snmpwalk I'm getting a response like:
snmpwalk -v1 -c public xxx.xxx.xxx.xxx 1.3.6.1.2.1.1.3
DISMAN-EVENT-MIB::sysUpTimeInstance = Timeticks: (776591904) 89 days, 21:11:59.04
OID=1.3.6.1.2.1.1.3 means sysUpTime in MIB.
Any ideas why it's different?
SNMP has its design limitation, as you discovered,
https://www.rfc-editor.org/rfc/rfc2578#page-24
The biggest value is about 1 year and 132 days. So in your case, 132 + 89 is roughly 221.
There is no way to fix such by design things, and you simply accept the fact.
Related
The issue / dilemma
I am currently busy creating a script to kickstart servers (with CentOS 6.x and CentOS 7.x) remotely. So far the script is working, but hangs on one minor thing. Well actually it does not hang, but it does not give detailed information about what is happening. In other words, I am not getting the correct information back in bash about the job being finished correctly.
I have tried various things, however it's hanging with the following message (which is being repeated endlessly):
servername is still installing and configuring packages...
PING 100.125.150.175 (100.125.150.175) 56(84) bytes of data.
64 bytes from 100.125.150.175: icmp_seq=1 ttl=63 time=0.152 ms
64 bytes from 100.125.150.175: icmp_seq=2 ttl=63 time=0.157 ms
64 bytes from 100.125.150.175: icmp_seq=3 ttl=63 time=0.157 ms
64 bytes from 100.125.150.175: icmp_seq=4 ttl=63 time=0.143 ms
64 bytes from 100.125.150.175: icmp_seq=5 ttl=63 time=0.182 ms
--- 100.125.150.175 ping statistics ---
5 packets transmitted, 5 received, 0% packet loss, time 120025ms
rtt min/avg/max/mdev = 0.143/0.158/0.182/0.015 ms
servername is still installing and configuring packages...
PING 100.125.150.175 (100.125.150.175) 56(84) bytes of data.
64 bytes from 100.125.150.175: icmp_seq=1 ttl=63 time=0.153 ms
64 bytes from 100.125.150.175: icmp_seq=2 ttl=63 time=0.132 ms
64 bytes from 100.125.150.175: icmp_seq=3 ttl=63 time=0.142 ms
etc....
So for some reason it does not contine to the next line of code or does the next action. Since it's only feedback to me (or another user), it's not a majorissue. But it would be nice to get this functional and providing (detailed) information back about the current progress or what the script/server is actually doing at the moment. This is not the case for the above (last) piece of code unfortunately.
This is the current code snippet I have (yes, it's a mess):
while true;
do
#ping -c3 -i3 $HWNODEIP > /dev/null
#ping -c5 -i30 $HWNODEIP > /dev/null
ping -c5 -i30 $HWNODEIP
if [ $? -eq 1 ] || [ $? -eq 2 ] || [ $? -eq 68 ]
then
echo -e " "
echo -e "Kickstart part II also done. $HOSTNAME will be rebooted one more time."
sleep 5
######return 0
echo -e " "
printf "%s" "Waiting for $HOSTNAME to come back online: "
while ! ping -c 1 -n -w 30 $HWNODEIP &> /dev/null
do
printf "%c" "."
#sleep 10
done
echo -e " "
echo -e "Reboot is done and $HOSTNAME is back online. Performing final check. Please wait..."
sleep 10
echo -e " "
sudo /usr/local/collectHWdata.pl $HWNODEIP
ssh root#$HWNODEIP "while ! test -e /root/kickstart-DONE; do sleep 3; done; echo KICKSTART IS DONE\!"
echo -e " "
exit
else
echo -e " "
echo -e "$HOSTNAME is still installing and configuring packages..."
fi
done
Sidenote: I removed > /dev/null #5 for debugging (not that it helped)
I am guessing I am using things incorrectly and I am by no means a experienced scripter; I can only do minor stuff, but ofcourse I am doing my best. I have been fooling around with this since last week and still no result on this part.
What am I trying to achieve?
The server is rebooted after the selected CentOS version, creating partitions and setting up the network. This all works. The above snippet is after that reboot. Now it will install packages I selected, configure various things (like Nagios) and install/compile certain PERL modules. And a few other minor things.
This is done correctly in the background. I wanted to make the script (the above piece of code) that the server is still busy with installing things and such. Since I lack the knowledge to do that, I decided for a different approach; check if the server is online (in other words that it's still installing). As long as the server is online, it's still installing/configuring things obviously. After that is done, the server will reboot once more to perform the final 2 commands (as seen in my snippet). However (here is the problem) it never does those commands, though the kickstart is completely done.
So I am guessing I am doing something wrong and even might messed up things (or got confused by doing so). Maybe someone has an idea, solution or a completely different approach to tackle and fix this problem (or at least I hope so).
Other things I have tried so far? Well I tried a various of ping commands and I also tried nc (netcat) but also without a good result. I every single time hit a brick wall with the last 2 commands and it keeps pinging instead of showing that the kickstart was done... I think I have spend several hours (since last week) on this already without getting anywhere.
So I am hoping someone can take a look at this and tell me what I am doing wrong and maybe there is a better approach (other than pinging a server) to see if it's still busy. Maybe a (remote) check on yum, perl or a service, so that the script knows it's still busy.
Sorry for the long post, but I know when I provide as much information as possible including code examples and results, this is more "appreciated". So I am hoping I provided adequate information. If not, let me know. I will try to add as much information as I can. As always I am always willing to learn or change my approach.
Thank you already for reading my post!
As noted in the comments under the question:
The server may already be rebooted by the time ping -c5 -i30 $HWNODEIP finishes. The command sends 5 packets (-c flag), waiting 30 seconds between each packet (-i interval flag). So thats's 5*30 = 150 seconds, which is a bit more than 2 minutes. A server could reboot just fine within 2 minutes, especially if there's SSD in use. So try lowering the total time it would take this command to complete.
[ $? -eq 68 ] is probably unnecessary. $HWNODEIP is just ip address, and exit code 68 is for domain name not being resolved, which doesn't apply to IP addresses.
The if statement could be simplified to
if ! ping -c5 -i30 "$HWNODEIP"
These are minor suggestions,probably not bulletproof. As confirmed by OP in the comments, lowering interval helps. There's other small improvements that could be done (like quoting variables), but that's outside the scope of the question, so I'll leave it for now.
I have a fairly large query running on Clickhouse. The problem is when running on localhost using cmd line it takes about 0.7 sec to complete. This is consistently fast. Issue is when querying from C# / HTTP / Postman. Here it takes about 10 times to return the data. (the size is about 3-4mb) so I dont think its a size issue.
I have tried to monitor network latency, but nothing to notice here.
On the host it works like a charm, but outside it does not :(.... what to do.
I exptect the latency to be a few 100 ms, but turns out to be 7 sec :/
check timings with curl https://clickhouse.yandex/docs/en/interfaces/http/
https://stackoverflow.com/a/22625150
and compare local vs remote
CH HTTP usually provides almost the same performance as TCP and HTTP could be faster for small resultsets (like 10 rows)
Again. The problem is not the HTTP.
Example:
time clickhouse-client -q "select number, arrayMap(x->sipHash64(number,x), range(10)) from numbers(10000)" >native.out
real 0m0.034s
time curl -S -o http.out 'http://localhost:8123/?query=select%20number%2C%20arrayMap(x-%3EsipHash64(number%2Cx)%2C%20range(10))%20from%20numbers(10000)'
real 0m0.017s
ls -l http.out native.out
2108707 Oct 1 16:17 http.out
2108707 Oct 1 16:17 native.out
10 000 rows - 2Mb
HTTP is faster 0.017s VS 0.034s
Canada -> Germany (openvpn)
time curl -S -o http.out 'http://user:xxx#cl.host.x:8123/?query=select%20number%2C%20arrayMap(x-%3EsipHash64(number%2Cx)%2C%20range(10))%20from%20numbers(10000)'
real 0m1.619s
ping cl.host.x
PING cl.host.x (10.253.52.6): 56 data bytes
64 bytes from 10.253.52.6: icmp_seq=0 ttl=61 time=131.710 ms
64 bytes from 10.253.52.6: icmp_seq=1 ttl=61 time=133.711 ms
When i run this command on my VPS:
netstat -n|grep :80|cut -c 45-|cut -f 1 -d ':'|sort|uniq -c|sort -nr|more
i get this result:
207 222.73.144.194
89 191.96.249.54
58 191.96.249.53
21 2400
15 51.255.64.23
6 143.137.103.251
3 103.27.72.36
1 89.180.150.168
1 66.102.7.137
1 5.189.170.167
1 191.181.39.208
1 183.2.246.218
I think this command is showing the number of connections per IP to port 80.
Is this a DDoS atack?
Have you check another aspect (eg. cpu load, network throughput to specific ip(s) using iftop or iptraf)? If there's normal, maybe it's just web/http scanner to your web.
If you're use nginx, you can use limit_conn module, to queue the rest of ip(s) if didn't obey your policy.
Need to recruit the help of any budding bioinformaticians that are lurking in the shadows here.
I am currently in the process of formatting some .fasta files for use in a set of grouping programs but I cannot for the life of me get them to work. First things first, all the files have to have a 3 or 4 character name such as the following:
PP41.fasta
PP59.fasta
PPBD.fasta
...etc...
The files must have headers for each gene sequence that look like so: >xxxx|yyyyyyyyyy where xxxx is the same 3 or 4 letter 'taxon' identifier as the file names I put above and yyyyyyy is a numerical identifier for each of the proteins within each of the taxons (the pipe symbol can also be replaced with an _ as below). I then cat all of these in to one file which has a header that looks correct like so:
>PP49_00001
MIENFNENNDMSDMFWEVEKGTGEVINLVPNTSNTVQPVVLMRLGLFVPTLKSTKRGHQG
EMSSMDATAELRQLAIVKTEGYENIHITGARLDMDNDFKTWVGIIHSFAKHKVIGDAVTL
SFVDFIKLCGIPSSRSSKRLRERLGASLRRIATNTLSFSSQNKSYHTHLVQSAYYDMVKD
TVTIQADPKIFELYQFDRKVLLQLRAINELGRKESAQALYTYIESLPPSPAPISLARLRA
RLNLRSRVTTQNAIVRKAMEQLKGIGYLDYTEIKRGSSVYFIVHARRPKLKALKSSKSSF
KRKKETQEESILTELTREELELLEIIRAEKIIKVTRNHRRKKQTLLTFAEDESQ*
>PP49_00002
MQNDIILPINKLHGLKLLNSLELSDIELGELLSLEGDIKQVSTGNNGIVVHRIDMSEIGS
FLIIDSGESRFVIKAS*
Next step is to construct a blast database which I do as follows, using the formatdb tool of NCBI Blast:
formatdb -i allproteins.fasta -p T -o T
This produces a set of files for the database. Next I conduct an all-vs-all BLAST of the concatenated proteins against the database that I made of them like so, which outputs a tabular file which I suspect is where my issues are beginning to arise:
blastall -p blastp -d allproteins.fasta -i allproteins.fasta -a 6 -F '0 S' -v 100000 -b 100000 -e 1e-5 -m 8 -o plasmid_allvall_blastout
These files have 12 columns and look like the below. It appears correct to me, but my supervisor suspects the error is in the blast file - I don't know what I'm doing wrong however.
PP49_00001 PP51_00025 100.00 354 0 0 1 354 1 354 0.0 552
PP49_00001 PP49_00001 100.00 354 0 0 1 354 1 354 0.0 552
PP49_00001 PPTI_00026 90.28 288 28 0 1 288 1 288 3e-172 476
PP49_00001 PPNP_00026 90.28 288 28 0 1 288 1 288 3e-172 476
PP49_00001 PPKC_00016 89.93 288 29 0 1 288 1 288 2e-170 472
PP49_00001 PPBD_00021 89.93 288 29 0 1 288 1 288 2e-170 472
PP49_00001 PPJN_00003 91.14 79 7 0 145 223 2 80 8e-47 147
PP49_00002 PPTI_00024 100.00 76 0 0 1 76 1 76 3e-50 146
PP49_00002 PPNP_00024 100.00 76 0 0 1 76 1 76 3e-50 146
PP49_00002 PPKC_00018 100.00 76 0 0 1 76 1 76 3e-50 146
SO, this is where the problems really begin. I now pass the above file to a program called orthAgogue which analyses the paired sequences I have above using parameters laid out in the manual (still no idea if I'm doing anything wrong) - all I know is the several output files that are produced are all just nonsense/empty.
Command looks like so:
orthAgogue -i plasmid_allvsall_blastout -t 0 -p 1 -e 5 -O .
Any and all ideas welcome! (Hope I've covered everything - sorry about the long post!)
EDIT Never did manage to find a solution to this. Had to use an alternative piece of software. If admins wish to close this please do, unless it is worth having open for someone else (though I suspect its a pretty niche issue).
Discovered this issue (of orthAgogue) first today:
though my reply may be old, I hope it may help future users;
issue is due to a missing parameter: seems like you forgot to specify the separator: -s '_', ie, the following set of command-line parameters should do the trick*:
orthAgogue -i plasmid_allvsall_blastout -t 0 -p 1 -e 5 -O -s '_'
(* Under the assumption that your input-file is a tabular-seperated file of columns.)
A brief update after comment made by Joe:
In brief, the problem described in the intiail error report (by Joe) is (in most cases) not a bug. Instead it is one of the core properties of the Inparanoid algorithm which orthAgogue implements: if your ortholog-result-file is empty (though constructed), this (in most cases) implies that there are no reciprocal best match between a protein-pair from two different taxa/species.
One (of many) explanations for this could be that your blastp-scores are too similar, a case where I would suggest a combined tree-based/homology clustering as in TREEFAM.
Therefore, when I receive your data, I'll send it to one of the biologists I'm working with, with goal of identifying the tool proper for your data: hope my last comment makes your day ;)
Ole Kristian Ekseth, developer of orthAgogue
I recently hooked up an APC battery backup to one of my servers, I installed the powerchute agent on the server and have verified that I can remotely access the agent and the APC through the agent.
I am trying to get my Cacti install to retrieve my APC data, and everything is working except that it is returning "Result from SNMP not valid. Partial Result: U" and I suspect it is do to the SNMP problem I am having. How can I fix it so the MIB works with the instance number?
From the command line I can successfully GET other OIDs.
----WORKS----
$ snmpget -v1 -cpublic 192.168.1.2 .1.3.6.1.2.1.1.3.0
iso.3.6.1.2.1.1.3.0 = Timeticks: (140629508) 16 days, 6:38:15.08
From the command line I can snmpwalk the powerchute MIB as long as I do not add the final instance number. Adding the instance number causes nothing to be returned.
----WORKS----
$ snmpwalk -v1 -cpublic 192.168.1.2 .1.3.6.1.4.1.318.1.1.1.2.2.3
iso.3.6.1.4.1.318.1.1.1.2.2.3.0 = Timeticks: (72000) 0:12:00.00
----FAILS----
$ snmpwalk -v1 -cpublic 192.168.1.2 .1.3.6.1.4.1.318.1.1.1.2.2.3.0
$
However I can not snmpget any of the powerchute OIDs with or without the instance number.
----FAILS----
$ snmpget -v1 -cpublic 192.168.1.2 .1.3.6.1.4.1.318.1.1.1.2.2.3.0
Error in packet
Reason: (noSuchName) There is no such variable name in this MIB.
Failed object: iso.3.6.1.4.1.318.1.1.1.2.2.3.0
----FAILS----
$ snmpget -v1 -cpublic 192.168.1.2 .1.3.6.1.4.1.318.1.1.1.2.2.3
Error in packet
Reason: (noSuchName) There is no such variable name in this MIB.
Failed object: iso.3.6.1.4.1.318.1.1.1.2.2.3
The fact that snmpwalk returns an OID that you consequently cannot snmpget indicates a bug in the SNMP agent of the device you are accessing.
As frustrating as this is it isn't uncommon, even in enterprise equipment. I've encountered SNMP agent bugs in Cisco and Nortel telecommunications equipment costing hundreds of thousands of dollars.
You do have a work-around. Consider writing a BASH script to snmpwalk the desired value and scrape the result. And tell Cacti to use your custom script instead of accessing via SNMP directly.