I have a bash script that prints a line of text into a file, and then calls a second script that prints some more data into the same file. Lets call them script1.sh and script2.sh. The reason it's split into two scripts, is because I have different versions of script2.sh.
script1.sh:
rm -f output.txt
echo "some text here" > output.txt
source script2.sh
script2.sh:
./read_time >> output.txt
./run_program
./read_time >> output.txt
Variations on the three lines in script2.sh are repeated.
This seems to work most of the time, but every once in a while the file output.txt does not contain the line "some text here". At first I thought it was because I was calling script2.sh like this: ./script2.sh. But even using source the problem still occurs.
The problem is not reproducible, so even when I try to change something I don't know if it's actually fixed.
What could be causing this?
Edit:
The scripts are very simple. script1 is exactly as you see here, but with different file names. script 2 is what I posted, but then the same 3 lines repeated, and ./run_program can have different arguments. I did a grep for the output file, and for > but it doesn't show up anywhere unexpected.
The way these scripts are used is that script1 is created by a program (the only difference between the versions is the source script2.sh line. This script1.sh is then run on a different computer (linux on an FPGA actually) using ssh. Before that is done, the output file is also deleted using ssh. I don't know why, but I didn't write all of this. Also, I've checked the code running on the host. The only mention of the output file is when it is deleted using ssh, and when it is copied back to the host after the script1 is done.
Edit 2:
I finally managed to make the problem reproducible at a reasonable rate by stripping script2.sh of everything but a single line printing into the file. This also let me do the testing a bit faster. Once I had this I got the problem between 1 and 4 times for every 10 runs. Removing the command that was deleting the file over ssh before the script was run seems to have solved the problem. I will test it some more to be sure, but I think it's solved. Although I'm still not sure why it would be a problem. I thought that the ssh command would not exit before all the remove commands were executed.
It is hard to tell without seeing the real code. Most likely explanation is that you have a typo, > instead of >>, somewhere in one of the script2.sh files.
To verify this, set noclobber option with set -o noclobber. The shell will then terminate when trying to write to existing file with >.
Another possibility, is that the file is removed under certain rare conditions. Or it is damaged by some command which can have random access to it - look for commands using this file without >>. Or it is used by some command both as input and output which step on each other - look for the file used with <.
Lastly, you can have a racing condition with a command outputting to the file in background, started before that echo.
Can you grep all your scripts for 'output.txt'? What about scripts called inside read_time and run_program?
It looks like something in one of the script2.sh scripts must be either overwriting, truncating or doing a substitution on output.txt.
For example,there could be a '> output.txt' burried inside a conditional for a condition that rarely obtains. Just a guess, but it would explain why you don't always see it.
This is an interesting problem. Please post the solution when you find it!
Related
I have a bash script that executes a series of commands, some involving redirection. See cyrus-mark-ham-spam.
I want the script to have a test mode, where all the commands run are printed instead of executing them. As you can see, I have tried to do that by just putting "echo" on the front of each command in test mode.
Unfortunately this doesn't deal with redirection - any redirections are still done, so the program leaves lots of temp files littered about the place when run in test mode.
I have tried various ways to get round this, like quoting the whole command and passing it to a function that either prints it or runs it, but either the redirections work in test mode, or they don't work in run mode.
I thought this must have come up before, and wonder if there is a known solution which does not involve every command being repeated with an if TEST round the pair?
Please note, this is NOT a duplicate of show commands without executing them because neither that question, nor its answers, covers redirection (which is the essence of this question).
I see that it is not a duplicate but there is not general solution to this. You need to look at each command separately.
As long as the command doesn't use arguments enclosed in spaces, like
cmd -a -b -c > filename
, you can quote it:
echo 'cmd -a -b -c > filename'
But real life code is more complex, sure.
echo: write error: Bad file descriptor
Throughout my code (through several bash scripts) I encounter this error. It happens when I'm trying to write or append to a (one) file.
LOGRUN_SOM_MUT_ANA=/Volumes/.../logRUN_SOMATIC_MUT_ANA
I use the absolute path for this variable and I use the same file for each script that is called. The file has a bunch of lines just like this. I use the import '.' on each script to get it.
echo "debug level set for $DEBUG_LEVEL" >> ${LOGRUN_SOM_MUT_ANA}
Worth noting:
It typically happens AFTER the FIRST time I write to it.
I read about files 'closing' themselves and yielding this error
I am using the above line in one script, and then calling another script.
I'd be happy to clarify anything.
For others encountering the same stupid error under cygwin in a script that works under a real Linux: no idea why, but it can happen:
1) after a syntax error in the script
2) because cygwin bash wants you to replace ./myScript.sh with . ./myScript.sh (where dot is the bash-style include directive, aka source)
I figured it out, the thumb drive I'm using is encrypted. It outputs to /tmp/ so it's a permission thing. That's the problem!
My Makefile look something like this:
setsid ./CppServer>daemon.log 2>&1 &
echo $!>daemon.pid
What I expect it to do is to store the PID of my_awesome_script in corresponding file. However there's nothing there. So where's the problem?
If your makefile really looks like this you will get an error, because I don't see any actual make syntax, just shell syntax. However, my crystal ball tells me that these two lines might be part of the recipe for a rule. If they are, you should realise how make executes recipes; for each line a separate subshell is created, in which that line's command is executed independently: your two commands don't know anything about each other's environment. If you want two commands to be executed in the same subshell, you should issue them as one line (using line continuation characters if necessary), or use make's ONESHELL directive.
The variable you're trying to use prints the pid of the last program run in the background. It is correctly written as echo $! > filename.extension. But since you are running it in the foregorund you have two choices. Run it in the background by appending an & to the end of the line ./script_to_run &, or you can have the script itself print to file the pid of the currently running process by using echo $$ > filename.extension (inside the script). Here is a link that might help you http://tldp.org/LDP/abs/html/internalvariables.html
UPDATE: this is a repost of How to make shell scripts robust to source being changed as they run
This is a little thing that bothers me every now and then:
I write a shell script (bash) for a quick and dirty job
I run the script, and it runs for quite a while
While it's running, I edit a few lines in the script, configuring it for a different job
But the first process is still reading the same script file and gets all screwed up.
Apparently, the script is interpreted by loading each line from the file as it is needed. Is there some way that I can have the script indicate to the shell that the entire script file should be read into memory all at once? For example, Perl scripts seem to do this: editing the code file does not affect a process that's currently interpreting it (because it's initially parsed/compiled?).
I understand that there are many ways I could get around this problem. For example, I could try something like:
cat script.sh | sh
or
sh -c "`cat script.sh`"
... although those might not work correctly if the script file is large and there are limits on the size of stream buffers and command-line arguments. I could also write an auxiliary wrapper that copies a script file to a locked temporary file and then executes it, but that doesn't seem very portable.
So I was hoping for the simplest solution that would involve modifications only to the script, not the way in which it is invoked. Can I just add a line or two at the start of the script? I don't know if such a solution exists, but I'm guessing it might make use of the $0 variable...
The best answer I've found is a very slight variation on the solutions offered to How to make shell scripts robust to source being changed as they run. Thanks to camh for noting the repost!
#!/bin/sh
{
# Your stuff goes here
exit
}
This ensures that all of your code is parsed initially; note that the 'exit' is critical to ensuring that the file isn't accessed later to see if there are additional lines to interpret. Also, as noted on the previous post, this isn't a guarantee that other scripts called by your script will be safe.
Thanks everyone for the help!
Use an editor that doesn't modify the existing file, and instead creates a new file then replaces the old file. For example, using :set writebackup backupcopy=no in Vim.
How about a solution to how you edit it.
If the script is running, before editing it, do this:
mv script script-old
cp script-old script
rm script-old
Since the shell keep's the file open as long as you don't change the contents of the open inode everything will work okay.
The above works because mv will preserve the old inode while cp will create a new one. Since a file's contents will not actually be removed if it is opened, you can remove it right away and it will be cleaned up once the shell closes the file.
According to the bash documentation if instead of
#!/bin/bash
body of script
you try
#!/bin/bash
script=$(cat <<'SETVAR'
body of script
SETVAR)
eval "$script"
then I think you will be in business.
Consider creating a new bang path for your quick-and-dirty jobs. If you start your scripts with:
#!/usr/local/fastbash
or something, then you can write a fastbash wrapper that uses one of the methods you mentioned. For portability, one can just create a symlink from fastbash to bash, or have a comment in the script saying one can replace fastbash with bash.
If you use Emacs, try M-x customize-variable break-hardlink-on-save. Setting this variable will tell Emacs to write to a temp file and then rename the temp file over the original instead of editing the original file directly. This should allow the running instance to keep its unmodified version while you save the new version.
Presumably, other semi-intelligent editors would have similar options.
A self contained way to make a script resistant to this problem is to have the script copy and re-execute itself like this:
#!/bin/bash
if [[ $0 != /tmp/copy-* ]] ; then
rm -f /tmp/copy-$$
cp $0 /tmp/copy-$$
exec /tmp/copy-$$ "$#"
echo "error copying and execing script"
exit 1
fi
rm $0
# rest of script...
(This will not work if the original script begins with the characters /tmp/copy-)
(This is inspired by R Samuel Klatchko's answer)
To process a bunch of data and get it ready to be inserted into our database, we generate a bunch of shell scripts. Each of them has about 15 lines, one for each table that the data is going. One a recent import batch, some of the import files failed going into one particular table. So, I have a bunch of shell scripts (about 600) where I need to comment out the first 7 lines, then rerun the file. There are about 6000 shell scripts in this folder, and nothing about a particular file can tell me if it needs the edit. I've got a list of which files that I pulled from the database output.
So how do I write a bash script (or anything else that would work better) to take this list of file names and for each of them, comment out the first 7 lines, and run the script?
EDIT:
#!/usr/bin/env sh
cmd1
cmd2
cmd3
cmd4
cmd5
cmd6
cmd7
cmd8
Not sure how readable that is. Basically, the first 7 lines (not counting the first line) need to have a # added to the beginning of them. Note: the files have been edited to make each line shorter and partially cut off copying out of VIM. But in the main part of each file, there is a line starting with echo, then a line starting with sqlldr
Using sed, you can specify a line number range in the file to be changed.
#!/bin/bash
while read line
do
# add a comment to beginning of lines 1 - 7 and rename the script
sed '3,9 s/^/#/' $line > $line.new
exec $line.new
done < "filelist.txt"
You may wish to test this before running it on all of those scripts...
EDIT: changed the lines numbers to reflect comments.
Roughly speaking:
#!/bin/sh
for file in "$#"
do
out=/tmp/$file.$$
sed '2,8s/^/#/' < $file > $out
$SHELL $out
rm -f $out
done
Assuming you don't care about checking for race conditions etc.
ex seems made for what you want to do.
For instance, for editing one file, with a here document:
#!/bin/sh
ex test.txt << END
1,12s/^/#/
wq
END
That'll comment out the first 12 lines in "test.txt". For your example you could try "$FILE" or similar (including quotes!).
Then run them the usual way, i.e. ./"$FILE"
edit: $SHELL "$FILE" is probably a better approach to run them (from one of the above commenters).
Ultimately you're going to want to use the linux command sed. Whatever logic you need to place in the script, you know. But your script will ultimately call sed. http://lowfatlinux.com/linux-sed.html