I have an embedded Linux system that uses ramdisk boot so it has run time no persistent storage available (it does have Flash to store kernel and ramdisk).
The only connectivity is RS-232 serial login console. So I am limited by what is provided by its built in busybox. I want to retrieve the ramdisk, modify it, and rewrite the ramdisk. The kernel does not have Flash filesystem support built-in. The ramdisk partition size is about 10 MBytes. When all files in the user directory are deleted, the free ramdisk size is about 14 MBytes.
The command dd is available so I can copy the ramdisk partition to the ramdisk, and can write to the flash from a ramdisk file. flashcp is also available.
So my problem is now how to receive and send binary files through the RS-232 serial console?
I research the followings and none is useful for me:
Linux command to send binary file to serial port with HW flow control? on stackoverflow
Binary data over serial terminal on stackoverflow
Transferring files using serial console on k.japko.eu
File transfer over a serial line on superuser.com
How to get file to a host when all you have is a serial console? on stackexchange
Mostly because x/y/zmodem are not available in the busybox.
Any idea? Thanks!
Per the request, here's what I should have included in the first place.
Available u-boot commands:
U-Boot >?
? - alias for 'help'
askenv - get environment variables from stdin
base - print or set address offset
bdinfo - print Board Info structure
boot - boot default, i.e., run 'bootcmd'
bootd - boot default, i.e., run 'bootcmd'
bootm - boot application image from memory
cmp - memory compare
coninfo - print console devices and information
cp - memory copy
crc32 - checksum calculation
crc32_chk_uimage- checksum calculation of an image for u-boot
echo - echo args to console
editenv - edit environment variable
env - environment handling commands
exit - exit script
false - do nothing, unsuccessfully
fatinfo - print information about filesystem
fatload - load binary file from a dos filesystem
fatls - list files in a directory (default /)
fatwrite- write file into a dos filesystem
go - start application at address 'addr'
gpio - input/set/clear/toggle gpio pins
help - print command description/usage
i2c - I2C sub-system
iminfo - print header information for application image
imxtract- extract a part of a multi-image
itest - return true/false on integer compare
loadb - load binary file over serial line (kermit mode)
loads - load S-Record file over serial line
loady - load binary file over serial line (ymodem mode)
loop - infinite loop on address range
md - memory display
mdc - memory display cyclic
mm - memory modify (auto-incrementing address)
mw - memory write (fill)
mwc - memory write cyclic
nm - memory modify (constant address)
printenv- print environment variables
reset - Perform RESET of the CPU
run - run commands in an environment variable
saveenv - save environment variables to persistent storage
saves - save S-Record file over serial line
setenv - set environment variables
sf - SPI flash sub-system
showvar - print local hushshell variables
sleep - delay execution for some time
source - run script from memory
sspi - SPI utility command
test - minimal test like /bin/sh
true - do nothing, successfully
usb - USB sub-system
usbboot - boot from USB device
version - print monitor, compiler and linker version
U-Boot >
Available busybox commands:
BusyBox v1.13.2 (2015-03-16 10:50:56 EDT) multi-call binary
Copyright (C) 1998-2008 Erik Andersen, Rob Landley, Denys Vlasenko
and others. Licensed under GPLv2.
See source distribution for full notice.
Usage: busybox [function] [arguments]...
or: function [arguments]...
BusyBox is a multi-call binary that combines many common Unix
utilities into a single executable. Most people will create a
link to busybox for each function they wish to use and BusyBox
will act like whatever it was invoked as!
Currently defined functions:
[, [[, addgroup, adduser, ar, ash, awk, basename, blkid,
bunzip2, bzcat, cat, chattr, chgrp, chmod, chown, chpasswd,
chroot, chvt, clear, cmp, cp, cpio, cryptpw, cut, date,
dc, dd, deallocvt, delgroup, deluser, df, dhcprelay, diff,
dirname, dmesg, du, dumpkmap, dumpleases, echo, egrep, env,
expr, false, fbset, fbsplash, fdisk, fgrep, find, free,
freeramdisk, fsck, fsck.minix, fuser, getopt, getty, grep,
gunzip, gzip, halt, head, hexdump, hostname, httpd, hwclock,
id, ifconfig, ifdown, ifup, inetd, init, insmod, ip, kill,
killall, klogd, last, less, linuxrc, ln, loadfont, loadkmap,
logger, login, logname, logread, losetup, ls, lsmod, makedevs,
md5sum, mdev, microcom, mkdir, mkfifo, mkfs.minix, mknod,
mkswap, mktemp, modprobe, more, mount, mv, nc, netstat,
nice, nohup, nslookup, od, openvt, passwd, patch, pidof,
ping, ping6, pivot_root, poweroff, printf, ps, pwd, rdate,
rdev, readahead, readlink, readprofile, realpath, reboot,
renice, reset, rm, rmdir, rmmod, route, rtcwake, run-parts,
sed, seq, setconsole, setfont, sh, showkey, sleep, sort,
start-stop-daemon, strings, stty, su, sulogin, swapoff,
swapon, switch_root, sync, sysctl, syslogd, tail, tar, tcpsvd,
tee, telnet, telnetd, test, tftp, tftpd, time, top, touch,
tr, traceroute, true, tty, udhcpc, udhcpd, udpsvd, umount,
uname, uniq, unzip, uptime, usleep, vconfig, vi, vlock,
watch, wc, wget, which, who, whoami, xargs, yes, zcat
In uboot you could use loady/loadx to get file from pc via uart.I usually use teraterm to send file.
The process should be this:
run loady in uboot
use teraterm send data
the file is transfer to you device's memory located in 0x01000000.
Independently I found a way to upload binary files through the Linux console and I'll document the steps here in case others find it useful since I had a hard time looking for this information on the net.
Here's the theory: change the console mode to raw so all the binary traffic are't interpretted as console command, e.g. ctrl-C. Turn off echo so it doesn't add extra serial traffic. Run tar to accept input from the stdin. Since ctrl-C won't work, and tar won't know when to terminate, use a background task to kill the login shell so you can login again to do your staff.
Steps:
Create a script to run in the background. Change myvar variable so it kills the login shell after the transfer is complete. Currently 120 corresponds to 1200 seconds, sufficient for a 10 MBytes file. In addition edit the 808 to match your login shell PID:
create bg file:
myvar=120
while [ $myvar -gt 0 ]
do
myvar=$(( $myvar-1 ))
echo -e " $myvar \n"
ls -l
sleep 10
done
kill -9 808
Launch the script in the background:
in console type:
source ./bg &
Use stty to change console to raw mode and do not echo
in console type:
stty raw -echo
Start tar to untar stdin. Note: I have to use ctrl-J since no longer work after the stty command
in console type and ends with ctrl-j, not :
tar zx -f - 1> 1.log 2> 2.log
Start Teraterm to send binary file
Wait for completion and the new login prompt
I forgot I asked this question. I figured out how to make ssh connection which in turn allows many more things to be done more easily. Of course it requires sshd in addition to nc and stty so you are out of luck if these are not available on your embedded Linux. I have tried it several times and it seems to work well, allowing multiple ssh sessions to be established, and mc to transfer files.
You will need two shell sessions on the host computer, one to loop the serial port to socket, and the other for the ssh, and more if you want to establish more ssh sessions.
First you need to setup the serial port. The '--noreset' option for picocom does this:
sudo picocom --noreset -b 115200 -e b /dev/ttyUSB3
Quit picocom once this is done (^B^X to exit).
Next we need to verify that the line endings are not translated or else ssh won't work. In the first shell run:
cat /dev/ttyUSB3 | hexdump -C
In the second shell run:
echo "echo -e \"LFLF\\n\\nCRCR\\r\\rEND\"" > /dev/ttyUSB3
You may see that \n (0x0A) is translated to \r\n (0x0D0x0A)
Use stty to set raw mode without echo and you should see no more translation:
echo "stty raw -echo" > /dev/ttyUSB3
echo "echo -e \"LFLF\\n\\nCRCR\\r\\rEND\"" > /dev/ttyUSB3
Finally in the first shell run nc to funnel local traffic between the serial port and ssh socket:
cat /dev/ttyUSB3 | nc -l -p 2222 > /dev/ttyUSB3
and funnel remote serial traffic to sshd:
echo "while true ; do nc localhost 22 ; done" > /dev/ttyUSB3
and connect ssh with port forwarding:
ssh -vvv root#localhost -p 2222 -L 0.0.0.0:22022:localhost:22
you can make more ssh connections simultaneously:
ssh -vvv root#localhost -p 22022
if you use mc, you can connect to it so you can easily browse the remote file system and copy files:
sh://root#localhost:22022
Last words: nc strips the TCP headers so the ssh packets are no checksumed and are not retried. If there were data error, the connection will break. If you remember your login shell PID, you can kill it and login again, otherwise you have to reboot. The '-vvv' flag for the ssh is for debugging.
I am using Sungrid6.2u5 ,I am trying to submit some jobs on 4 hosts, I need to run 50 jobs using all the 4 hosts but I want to inform the SGE that I want only 5 jobs to be run on the 4th host at any given time,how do I do that?
I am new to SunGrid.Could any one please point me to the SGE basics,I mean where do I get started?
I found this online,
Beginner's Guide to Sun Grid Engine 6.2 by Daniel Templeton
but apparently this is intended for system administrators ,I am just a normal user who is trying to understand the SGE features.
Thanks,
If you should not run more than 5 jobs on 4th node (let's call it computer04), probably, it is not capable of running something more. In general, you are encouraged to specify amount of resources for you job properly to prevent cores overload and out-of-memory situation.
If you have totally 20 Gb on computer04 and your job uses 5 Gb, you can limit all your jobs to 5Gb memory usage:
qsub -l vmem=5G my_work
The similar holds for disk amount:
qsub -l fsize=10G my_work
I found it is possible to run job on specific host with -l -h= option.
qsub -l -h=computer04 -l vmem=5G my_work
for 5 jobs. Then use
qsub -l vmem=5G my_work
for other 45 jobs.
(More dirty way)
You could do it without memory/disk restrictions:
qsub -l -h=computer04 my_work # 5 jobs
qsub -l -h="!computer04" my_work # for 45 jobs
If you have different queues or resources, and you could use them for different jobs. E.g., you have queue_4 that runs everything on computer04, and queue_main that is linked with other computers, then, you do
qsub -q queue_4 my_work
for 5 jobs, and
qsub -q queue_main my_work
for other jobs.
UPD on comment:
It is possible to force SGE denial of more than X jobs for user/host. It should be done by queue administrator.
qconf -arqs
{
name max_jobs_per_computer04
description "maximal number of jobs for user1 on computer04 restricted to 5!"
enabled TRUE
limit users user1 hosts computer04 to slots=5
}
If you want to restrict your user only in submitting jobs of some kind for computer04, you need to define complex parameter as shown here.
I'm running some slightly unreliable software on some instances in an instance group. The software is installed and run by a startup script, and most of the time it works without issue, but about ~10% of the new instances run out of memory and crash due to some sort of memory leak in the software. I can't get this leak fixed myself, so in the meantime, I've been checking the instances every few hours and killing any that show an idle CPU (the software consumes all available CPU power normally).
However, I'm using preemptible instances, and they can be killed off and restarted at any time, leaving dead instances running whenever I'm not actively monitoring them. After a day of leaving things unattended, I usually see ~80-85% CPU usage in the dashboard, the rest of which is wasted.
Is there any automated way I can kill off these dead instances? Restarting them is already handled by the instance group.
The following worked for me. It's a bash script which uses the uptime UNIX command to check whether the 15-minute average load on the CPU is below a threshold, and automatically shuts down the system if this is true on ten consecutive checks. You need to run this within your VM instance.
Credit, and more detailed explanation: Rohit Rawat's blog.
#!/bin/bash
threshold=0.4
count=0
while true
do
load=$(uptime | sed -e 's/.*load average: //g' | awk '{ print $3 }')
res=$(echo $load'<'$threshold | bc -l)
if (( $res ))
then
echo "Idling.."
((count+=1))
fi
echo "Idle minutes count = $count"
if (( count>10 ))
then
echo Shutting down
# wait a little bit more before actually pulling the plug
sleep 300
sudo poweroff
fi
sleep 60
done
It seems like there are two parts to this question:
Identifying dead instances.
Killing off those instances.
In terms of identifying dead instances, one way to do this would be to have a separate, management instance that does not run this software and that keeps tabs on the other instances. For example, it could do this by periodically sending a health request to the various instances and marking non-responsive instances or instances reporting an overly high CPU usage as unhealthy.
Once your management instance has identified the unhealthy instances that need to be reset, you should be able to reset those other instances using the API (I'm guessing the reset command) or by executing the same operation using the gcloud commandline tool.
I wish I could add this as a comment to viswajithiii answer but I'm just shy of the reputations necessary to comment.
I found the static threshold variable to be inappropriate when I am using cloud VM's with variable numbers of cpu's as the output of uptime scales with the number of CPU's as discussed here.
My updated script adds two lines below the threshold assignment to scale the threshold by the number of cpu's. This allows me to set a percentage cpu utilization that will work across VM's with different numbers of cpu's.
Otherwise, the script is the same as viswajithiii's.
#!/bin/bash
threshold=0.4
n_cpu=$( grep 'model name' /proc/cpuinfo | wc -l )
threshold=$( echo $n_cpu*$threshold | bc )
count=0
while true
do
load=$(uptime | sed -e 's/.*load average: //g' | awk '{ print $3 }')
res=$(echo $load'<'$threshold | bc -l)
if (( $res ))
then
echo "Idling.."
((count+=1))
fi
echo "Idle minutes count = $count"
if (( count>10 ))
then
echo Shutting down
# wait a little bit more before actually pulling the plug
sleep 300
sudo poweroff
fi
sleep 60
done
This works without bc (not in GCP Container OS) using viswajithiii's answer and this post:
How can I replace 'bc' tool in my bash script?
It also appends the history list to file before poweroff. I set my threshold very low, but the load is showing 0.00 even when I'm editing files via cli. Might work better if instance is under heavy load.
#!/bin/bash
threshold=10
count=0
while true
do
load=$(uptime | sed -e 's/.*load average: //g' | awk '{ print $3 }')
load2=$(awk -v a="$load" 'BEGIN {print a*100}')
echo $load2
if [ $load2 -lt $threshold ]
then
echo "Idling.."
((count+=1))
fi
echo "Idle minutes count = $count"
if (( count>10 ))
then
echo Shutting down
# wait a little bit more before actually pulling the plug
sleep 300
history -a
sudo poweroff
fi
sleep 60
done
That's not working for my low cpu, but this seems too:
#!/bin/bash
threshold=1
count=0
while true
do
load=$(awk '{u=$2+$4; t=$2+$4+$5; if (NR==1){u1=u; t1=t;} else print ($2+$4-u1) * 1000 / (t-t1); }' <(grep 'cpu ' /proc/stat) <(sleep 1;grep 'cpu ' /proc/stat))
load2=$(printf "%.0f\n" $load)
echo $load
echo $load2
if [[ $load2 -lt $threshold ]]
then
echo "Idling.."
((count+=1))
fi
echo "Idle minutes count = $count"
if (( count>10 ))
then
echo Shutting down
# wait a little bit more before actually pulling the plug
sleep 300
history -a
sudo poweroff
fi
sleep 60
done
It only works with both echo loads for some reason.
credits:
How to get overall CPU usage (e.g. 57%) on Linux
https://unix.stackexchange.com/questions/89712/how-to-convert-floating-point-number-to-integer
FYI: according to here, GCP monitoring agent is not available for N type instances: Google Cloud Platform: how to monitor memory usage of VM instances
Put this in a startup script in /etc/my_init.d and make it executable:
sudo mkdir /etc/my_init.d
sudo mv autooff.sh /etc/my_init.d/autooff.sh
sudo chmod 755 /etc/my_init.d/autooff.sh
Actually, that's being deleted. Instead add to Custom Metadata in Edit for the instance: startup-script and #! /bin/bash \n~./autooff.sh
I have a very large .csv file, and I'm loading it into mysql with the LOAD DATA INFILE command. Because it takes so long, I'd like to see how far along the upload has progressed.
I've tried 2 methods so far-
First I simply did a SELECT COUNT(*) command to see how many rows had been inserted as the upload was in progress, but that always returns a count of 0.
Second, I tried SHOW PROCESSLIST and saw simply how long the query has been running. sometimes the status says 'freeing data' or something to that effect.
Does anyone know a good way to track the progress of a LOAD DATA INFILE command? Also, does anyone know how to track the insertion rate?
Thanks
On Linux you can print info about file descriptor (ls -l /proc//fd), and file position reader (cat /proc//fdinfo). So:
Find mysqld pid (in this example: 1234):
$ ps -ef | grep mysqld
mysql 1234 1 0 feb12 ? 00:00:55 /usr/sbin/mysqld
Find file descriptor number of your loaded file (in this example: 45):
$ sudo ls -l /proc/1234/fd
lr-x------ 1 root root 64 Feb 13 10:56 45 -> /var/lib/mysql/db/Loaded_file.txt
Print info about that file descriptor and check number of bytes already read (in this example: 494927872):
$ cat /proc/1234/fdinfo/45
pos: 494927872
flags: 0100000
You can compare this progress indicator (in bytes) to the actual file size being loaded.
Instead of step 1 and 2, you can also use 'lsof' command:
$ lsof /var/lib/mysql/db/Loaded_file.txt | grep mysql
COMMAND PID USER FD TYPE DEVICE SIZE/OFF NODE NAME
mysqld 1234 youknowwho 45r REG 252,0 190312 5505353 /var/lib/mysql/db/Loaded_file.txt
From http://www.stephenchu.com/2008/12/speed-up-your-mysql-data-load.html, you can use the SHOW INNODB STATUS IF your table is Innodb type, which you didn't happen to mention.
The page I linked to also has some good tuning suggestions to improve your overall performance with loading data in this manner.
Couple of approaches here...
set session transaction isolation level read uncommitted; Then count(*) will work
select
rows_read as 'Read',
round((rows_read/{linecount})*100, 2) as 'Complete',
round(time/60, 2) as 'Elapsed',
round(time * 100 / round((rows_read/<line count>)*100, 2) / 60, 2) as 'ETA'
from INFORMATION_SCHEMA.PROCESSLIST
where id = <id>;