To write output into a file, I come across with three methods. May I know which One is better to opt and How.
1) echo "some outputs" >> file.out
2) exec 3<> file.out
echo "some Outputs" >&3
exec 3<-&
3) echo "some outputs" | tee file.out
As I know file descriptor are handling by kernal, and It has to communicate to 3 tables, like File Descriptor table, file table, Inode table to access file info. But I see most of the programs uses File descriptors to handle files. I got few below mentioned questions.
Q1) How an Command works, Is it an complied code or "C" program or assembly code?
Q2) Is every Command takes different process?
Q3) What is the process behind re directors(<,>, >>,<< )?
Related
References
Fullcode of what will be discussed here:
https://github.com/djon2003/com.cyberinternauts.linux.backup
activateLogs question that solved how to log to file and screen: https://stackoverflow.com/a/70792273/214898
Limitation
Just a small reminder from the last question: this script is executed on limited environment, on a QNAP (NAS).
Background
I have a function that activate logging which now has three modes: SCREEN, DISK, BOTH. With some help (from the question of the link above), I achieve to make work the BOTH option. DISK & BOTH use a file descriptor numbered 3. The first is pointing to a file and the second to stdout.
On exit of my script (using trap), it detects if there were logged errors and send them via email.
Code
function sendErrorMailOnExit()
{
## If errors happened, then send email
local isFileDescriptor3Exist=$(command 2>/dev/null >&3 && echo "Y")
if [ "$isFileDescriptor3Exist" = "Y" ]; then
local logFile=$(readlink /proc/self/fd/3 | sed s/.log$/.err/)
local logFileSize=$(stat -c %s "$logFile")
if [ $logFileSize -gt 0 ]; then
addLog "N" "Sending error email"
local logFileName=$(basename "$logFile")
local logFileContent=$(cat "$logFile")
sendMail "Y" "QNAP - Backup error" "Error happened on backup. See log file $logFileName\n\nLog error file content:\n$logFileContent"
fi
fi
}
trap sendErrorMailOnExit EXIT
Problem
As you can see, this works well because the file descriptor #3 is using a file. But now, using the BOTH option, the file descriptor #3 is pointing to stdout and the file is written via tee. Hence my question, how could I get the location of the file of tee.
Why not only using a variable coming from my function activateLogs would you say? Because, this function relaunches the script to be able to get all the logs not caught before the function is called. Thus why using this method to retrieve the error file location.
Possible solutions, but not the best (I hope)
One way would be to pass the file location through a script
parameter, but I would prefer not do that if that can be avoid.
Another, would be to create a "fake" file descriptor #4 (probably my best solution up to now) that would always point to the file.
Does anyone have an idea?
I finally opted for the creation of a "fake" file descriptor #4 that does not nothing except pointing to the current log file.
Does stderr start out as a duplicate FD of stdout?
i.e. considering dup(2), is stderr initialized kind of like so?
int stderr = dup(stdout); // stdout = 1
In the BashGuide, there's a code example
$ grep proud file 'not a file' > proud.log 2> proud.log
The author states
We've created two FDs that both point to the same file, independently of each other. The results of this are not well-defined. Depending on how the operating system handles FDs, some information written via one FD may clobber information written through the other FD.
and further says
We need to prevent having two independent FDs working on the same destination or source. We can do this by duplicating FDs
So basically, 2 independent FDs on the same file = broken
Well, I know that stdout & stderr both point to my terminal by default. Since they can both function properly (i.e. i don't see mish-mashed output+error messages), does that mean that they're not independent FDs? And thus, stderr is a duplicate FD of stdout? (or vice versa)
No, stderr is not a duplicate of stdout.
They work in parallel, independent and asynchronously.
Which means that in a race condition, you might even 'mish-mash' as you say.
One practical difference is also that stderr output will be ignored when you pipe your output to a subsequent command:
Practical example:
$ cat tst.sh
#!/bin/bash
echo "written to stdout"
echo "written to stderr" 1>&2
exit 0
~$ ./tst.sh
written to stdout
written to stderr
~$ ./tst.sh | xargs -n1 -I{} echo "this came through the pipe:{}"
written to stderr
this came through the pipe:written to stdout
We have a tool for cutting adaptors https://github.com/vsbuffalo/scythe/blob/master/README.md and we wanted it to be used on all the files in the raw folder and make an output of each file separately as OUT+File Name.
Something is wrong with this script I wrote, because it doesn't take each file separately, and the whole thing doesn't work properly. It's gonna generateing empty file named OUT+files
Expected operation will looks:
take file1, use scythe on it, write output as OUTfile1
take file2 etc.
#!/bin/bash
FILES=/home/dave/raw/*
for f in $FILES
do
echo "Processing the $f file..."
/home/deve/scythe/scythe -a /home/dev/scythe/illumina_adapters.fa -o "OUT"+$f $f
done
Additionally, I noticed (testing for a single file) that the script uses only one core out of 130 available. Is there any way to improve it?
There is no string concatenation operator in shell. Use juxtaposition instead; it's "OUT$f", not "OUT"+$f.
I am working on a tiny Raspberry Pi cluster (4 pis). I have 3 Raspberry Pi nodes that will be leaving a message in a message.txt file on the head Pi. The head Pi will be in a loop checking the message.txt file to see if it has any lines. When it does I want to lock the file and then extract the info I need. The problem I am having is that I need to do multiple commands. The only ways I have found that allows multiple commands look like this...
(
flock -s 200
# ... commands executed under lock ...
) 200>/var/lock/mylockfile
The problem with this way is that it uses a sub shell. The problem with that is that I have "job" files labeled job_1 job_2 etc..... that I want to be able to use a counter with. If I place the increment of the counter in the subshell it will be considered only in the scope of the subshell. If I pull the incrementation out there is a chance that another pi will add an entry before I increment the counter and lock the file.
I have heard talk that there is a way to lock the file and run multiple commands and flow control and then unlock it all using flock. I have not seen any good examples though.
Here is my current code.
# Now go into loop to send out jobs as pis ask for more work
while [ $jobsLeftCount -gt 0 ]
do
echo "launchJobs.sh: About to check msg file"
msgLines=$(wc -l < $msgLocation)
if [ $msgLines ]; then
#FIND WAY TO LOCK FILE AND DO THAT HERE
echo "launchJobs.sh: Messages found. Locking message file to read contents"
(
flock -e 350
echo "Message Received"
while read line; do
#rename file to be sent to node "job"
mv $jobLocation$jobName$jobsLeftCount /home/pi/algo2/Jobs/job
#transfer new job to each script that left a message
scp /home/pi/algo2/Jobs/job pi#192.168.0.$line:/home/pi/algo2/Jobs/
jobsLeftCount=$jobsLeftCount-1;
echo $line
done < $msgLocation
#clear msg file
>$msgLocation
#UNLOCK MESG FILE HERE
) 350>>$msgLocation
echo "Head node has $jobsLeftCount remaining"
fi
#jobsLeftCount=$jobsLeftCount-1;
#echo "here is $jobsLeftCount file"
done
If the sub-shell environment is not acceptable, use braces in place of parentheses to group the commands:
{
flock -s 200
# ... commands executed under lock ...
} 200>/var/lock/mylockfile
This runs the commands executed under lock in a new I/O context, but does not start a sub-shell. Within the braces, all the commands executed will have file descriptor 200 open to the locked lock file.
I'm trying to redirect(?) my standard error/output to a text file.
I did my research, but for some reason the online answers are not working for me.
What am I doing wrong?
cd /home/user1/lists/
for dir in $(ls)
do
(
echo | $dir > /root/user1/$dir" "log.txt
) > /root/Desktop/Logs/Update.log
done
I also tried
2> /root/Desktop/Logs/Update.log
1> /root/Desktop/Logs/Update.log
&> /root/Desktop/Logs/Update.log
None of these work for me :(
Help please!
Try this for the basics:
echo hello >> log.txt 2>&1
Could be read as: echo the word hello, redirecting and appending STDOUT to the file log.txt. STDERR (file descriptor 2) is redirected to wherever STDOUT is being pointed. Note that STDOUT is the default and thus there is no "1" in front of the ">>". Works on the current line only.
To redirect and append all output and error of all commands in a script, put this line near the top. It will be in effect for the length of the script instead of doing it on each line:
exec >>log.txt 2>&1
If you are trying to obtain a list of the files in /home/user1/lists, you do not need a loop at all:
ls /home/usr1/lists/ >Update.log
If you are attempting to run every file in the directory as an executable with a newline as its input, and collect the output from all these programs in Update.log, try this:
for file in /home/user1/lists/*; do
echo | "$file"
done >Update.log
(Notice how we avoid the useless use of ls and how there is no redirection inside the loop.)
If you want to create an empty file called *.log.txt for each file in the directory, you would do
for file in /home/user1/lists/*; do
touch "$(basename "$file")"log.txt
done
(Using basename to obtain the file name without the directory part avoids the cd but you could do it the other way around. Generally, we tend to avoid changing the directory in scripts, so that the tool can be run from anywhere and generate output in the current directory.)
If you want to create a file containing a single newline, regardless of whether it already exists or not,
for file in /home/user1/lists/*; do
echo >"$(basename "$file")"log.txt
done
In your original program, you redirect the echo inside the loop, which means that the redirection after done will not receive any output at all, so the created file will be empty.
These are somewhat wild guesses at what you might actually be trying to accomplish, but should hopefully help nudge you slightly in the right direction. (This should properly be a comment, I suppose, but it's way too long and complex.)