I wrote a simple bash script (in /homedir) to run an executable and then move the outputs to /workdir. I also made a soft link of /workdir named work to /homedir for me to switch easily between folders.
All steps are working well, except that an unspecified soft link named 'grids' is created in /workdir to itself. I can't delete it otherwise all outputs are gone as well.
How can this happen?
#!/bin/bash
cd ..
expname=`basename "$PWD"`
echo 'experiment name: '$expname
homedir=/home/b/b380963/icon_foehn/$expname/grids/
workdir=/work/bb1096/b380963/icon_foehn/$expname/grids/
if [ ! -d ${workdir} ]; then
mkdir -p ${workdir}
fi
cd $homedir
ln -s ${workdir} work
cd /home/b/b380963/nwp/dwd_icon_tools_v2/icontools/
./icongridgen --nml $homedir/gridgen_MCH_july.nml
mv ICON_1E_* $workdir/
mv base_grid* $workdir/
It's quite easy to see in your code:
workdir=/work/bb1096/b380963/icon_foehn/$expname/grids/
...
ln -s ${workdir} work
The command ln -s is the command, creating the symlink.
If you don't like the creation of that symlink, you might put that line in comment (don't delete it: in case you're not satisfied, it's easier to uncomment it).
You can solve your issue, using this command:
ln -sTf ...
This removes the existing destination files beforehand.
I don't work much with bash scripting and was trying to do something like this:
#!/bin/bash
wget https://johnvansickle.com/ffmpeg/builds/ffmpeg-git-i686-static.tar.xz
tar xvf ffmpeg-git-i686-static.tar.xz
cd ./ffmpeg-git-20210501-i686-static/
cp ./ffmpeg-git-20210501-i686-static/ffmpeg /etc/bin
Is there a variable or a way I can determine what that extracted folder is called during script execution. For example with bash completion at the command line I would use cd ./ffmpeg (since I know it starts with ffmpeg)
Make sense?
There is no way to know beforehand the directory structure, but you can use a wildcard in the copy command:
cp ./*/ffmpeg /etc/bin
Although, I do not recommend installing tarball extracted executable within /etc/bin.
I'd put a symbolic link inside /usr/local/bin/ instead:
#!/usr/bin/env sh
__opwd="$PWD"
trap 'cd "$__opwd"' EXIT ABRT INT
wget https://johnvansickle.com/ffmpeg/builds/ffmpeg-git-i686-static.tar.xz || exit 1
# Create place where to install the unpacked archive
mkdir -p '/opt/ffmpeg-git-i686-static' || exit 1
# Unpack the archive
cd '/opt/ffmpeg-git-i686-static' || exit 1
tar xf "$__opwd/ffmpeg-git-i686-static.tar.xz" || exit 1
# Create a symbolic link from the ffmpeg command into `/usr/local/bin/`
ln -sf /opt/ffmpeg-git-i686-static/*/ffmpeg /usr/local/bin/
I want to translate this bash-script intro a zsh-script. Hence I have no experience with this I hope I may get help here:
bash script:
SCRIPT_PATH="${BASH_SOURCE[0]}";
if([ -h "${SCRIPT_PATH}" ]) then
while([ -h "${SCRIPT_PATH}" ]) do SCRIPT_PATH=`readlink "${SCRIPT_PATH}"`; done
fi
pushd . > /dev/null
cd `dirname ${SCRIPT_PATH}` > /dev/null
SCRIPT_PATH=`pwd`;
popd > /dev/null
What I already know is that I can use
SCRIPT_PATH="$0"; to get the path were the script is located at. But then I get errors with the "readlink" statement.
Thanks for your help
Except for BASH_SOURCE I see no changes that you need to make. But what is the purpose of the script? If you want to get directory your script is located at there is ${0:A:h} (:A will resolve all symlinks, :h will truncate last path component leaving you with a directory name):
SCRIPT_PATH="${0:A:h}"
and that’s all. Note that original script has something strange going on:
if(…) and while(…) launch … in a subshell. You do not need subshell here, it is faster to do these checks using just if … and while ….
pushd . is not needed at all. While using pushd you normally replace the cd call with it:
pushd "$(dirname $SCRIPT_PATH)" >/dev/null
SCRIPT_PATH="$(pwd)"
popd >/dev/null
cd `…` will fail if … outputs something with spaces. It is possible for a directory to contain a space. In the above example I use "$(…)", "`…`" will also work.
You do not need trailing ; in variable declarations.
There is readlink -f that will resolve all symlinks thus you may consider reducing original script to SCRIPT_PATH="$(dirname $(readlink -f "${BASH_SOURCE[0]}"))" (the behavior may change as your script seems to resolve symlinks only in last component): this is bash equivalent to ${0:A:h}.
if [ -h "$SCRIPT_PATH" ] is redundant since while body with the same condition will not be executed unless script path is a symlink.
readlink $SCRIPT_PATH will return symlink relative to the directory containing $SCRIPT_PATH. Thus original script cannot possibly used to resolve symlinks in last component.
There is no ; between if(…) and then. I am surprised bash accepts this.
All of the above statements apply both to bash and zsh.
If resolving only symlinks only in last component is essential you should write it like this:
SCRIPT_PATH="$0:a"
function ResolveLastComponent()
{
pushd "$1:h" >/dev/null
local R="$(readlink "$1")"
R="$R:a"
popd >/dev/null
echo $R
}
while test -h "$SCRIPT_PATH" ; do
SCRIPT_PATH="$(ResolveLastComponent "$SCRIPT_PATH")"
done
.
To illustrate 7th statement there is the following example:
Create directory $R/bash ($R is any directory, e.g. /tmp).
Put your script there without modifications, e.g. under name $R/bash/script_path.bash. Add line echo "$SCRIPT_PATH" at the end of it and line #!/bin/bash at the start for testing.
Make it executable: chmod +x $R/bash/script_path.bash.
Create a symlink to it: cd $R/bash && ln -s script_path.bash link.
cd $R
Launch $R/bash/1. Now you will see that your script outputs $R while it should output $R/bash like it does when you launch $R/bash/script_path.bash.
I have many tar.bz2 files in a directory, and would like to extract them to another directory.
Here is my bash script:
for i in *.tar.bz2 do;
sudo tar -xvjf $i.tar.bz2 -C ~/myfiles/
done
It doesn't work. How can I make it work? Thanks!
Your variable $i contains the entire file name (as you have applied the regex *.tar.bz2). So inside your for loop you don't need to attach the extension.
Try:
for i in *.tar.bz2; do
sudo tar -xvjf "$i" -C ~/myfiles/
done
You also have ; misplaced.
I am using make and tar to backup. When executing makefile, tar command shows file changed as we read it. In this case,
the tar package is ok when the warning comes up
but it stops the tar command for the following backup
the file showing the warning in fact doesn't change -- it is really strange that the warning comes up
the files showing the warning come up randomly, I mean, everytime I run my makefile, the files showing the warning are different
--ignore-failed-read doesn't help. I am using tar 1.23 in MinGW
I just changed my computer to WIN7 64 bit. The script works well in old WIN7 32 bit. But the tar version is not as new as the 1.23.
How can I stop the tar's warning to stop my backup following the warning?
Edit-2: it might be the reason
As I said above, the bash shell script worked well in my old computer. Comparing with the old computer, the msys version is different. So is the version of tar command. In the old computer, tar is 1.13.19 and it is 1.23 in the new computer. I copied the old tar command without copying its dependency msys-1.0.dll to the new computer and renamed it tar_old. And I also updated the tar command in the shell script and run the script. Then everything is ok. So, it seemed that the problem is the tar command. I am sure that there is no any file changed when taring. Is it a bug for tar command in new version? I don't know.
Edit-1: add more details
The backup is invoked by a bash shell script. It scans the target directory and builds makefile then invokes make to use tar command for backup. Followed is a typical makefile built by the bash shell script.
#--------------------------------------------
# backup VC
#--------------------------------------------
# the program for packing
PACK_TOOL=tar
# the option for packing tool
PACK_OPTION=cjvf
# M$: C driver
WIN_C_DIR=c:
# M$: D driver
WIN_D_DIR=d:
# M$: where the software is
WIN_PRG_DIR=wuyu/tools
# WIN_PRG_DIR=
# where to save the backup files
BAKDIR=/home/Wu.Y/MS_bak_MSYS
VC_FRAMEWORK=/home/Wu.Y/MS_bak_MSYS/tools/VC/VC_framework.tar.bz2
VC_2010=/home/Wu.Y/MS_bak_MSYS/tools/VC/VC_2010.tar.bz2
.PHONY: all
all: $(VC_FRAMEWORK) $(VC_2010)
$(VC_FRAMEWORK): $(WIN_C_DIR)/$(WIN_PRG_DIR)/VC/Framework/*
#$(PACK_TOOL) $(PACK_OPTION) "$#" --ignore-failed-read /c/$(WIN_PRG_DIR)/VC/Framework
$(VC_2010): $(WIN_C_DIR)/$(WIN_PRG_DIR)/VC/VS2010/*
#$(PACK_TOOL) $(PACK_OPTION) "$#" --ignore-failed-read /c/$(WIN_PRG_DIR)/VC/VS2010
As you can see, the tar package is stored in ~/MS_bak_MSYS/tools/VC/VC_2010.tar.bz2. I run the script in ~/qqaa. ~/MS_bak_MSYS is excluded from tar command. So, the tar file I am creating is not inside a directory I am trying to put into tar file. This is why I felt it strange that the warning came up.
I also encounter the tar messages "changed as we read it". For me these message occurred when I was making tar file of Linux file system in bitbake build environment. This error was sporadic.
For me this was not due to creating tar file from the same directory. I am assuming there is actually some file overwritten or changed during tar file creation.
The message is a warning and it still creates the tar file. We can still suppress these warning message by setting option
--warning=no-file-changed
(http://www.gnu.org/software/tar/manual/html_section/warnings.html
)
Still the exit code return by the tar is "1" in warning message case:
http://www.gnu.org/software/tar/manual/html_section/Synopsis.html
So if we are calling the tar file from some function in scripts, we can handle the exit code something like this:
set +e
tar -czf sample.tar.gz dir1 dir2
exitcode=$?
if [ "$exitcode" != "1" ] && [ "$exitcode" != "0" ]; then
exit $exitcode
fi
set -e
Although its very late but I recently had the same issue.
Issue is because dir . is changing as xyz.tar.gz is created after running the command. There are two solutions:
Solution 1:
tar will not mind if the archive is created in any directory inside .. There can be reasons why can't create the archive outside the work space. Worked around it by creating a temporary directory for putting the archive as:
mkdir artefacts
tar -zcvf artefacts/archive.tar.gz --exclude=./artefacts .
echo $?
0
Solution 2:
This one I like. create the archive file before running tar:
touch archive.tar.gz
tar --exclude=archive.tar.gz -zcvf archive.tar.gz .
echo $?
0
If you want help debugging a problem like this you need to provide the make rule or at least the tar command you invoked. How can we see what's wrong with the command if there's no command to see?
However, 99% of the time an error like this means that you're creating the tar file inside a directory that you're trying to put into the tar file. So, when tar tries to read the directory it finds the tar file as a member of the directory, starts to read it and write it out to the tar file, and so between the time it starts to read the tar file and when it finishes reading the tar file, the tar file has changed.
So for example something like:
tar cf ./foo.tar .
There's no way to "stop" this, because it's not wrong. Just put your tar file somewhere else when you create it, or find another way (using --exclude or whatever) to omit the tar file.
Here is a one-liner for ignoring the tar exit status if it is 1. There is no need to set +e as in sandeep's script. If the tar exit status is 0 or 1, this one-liner will return with exit status 0. Otherwise it will return with exit status 1. This is different from sandeep's script where the original exit status value is preserved if it is different from 1.
tar -czf sample.tar.gz dir1 dir2 || [[ $? -eq 1 ]]
To enhance Fabian's one-liner; let us say that we want to ignore only exit status 1 but to preserve the exit status if it is anything else:
tar -czf sample.tar.gz dir1 dir2 || ( export ret=$?; [[ $ret -eq 1 ]] || exit "$ret" )
This does everything sandeep's script does, on one line.
Simply using an outer directory for the output, solved the problem for me.
sudo tar czf ./../31OCT18.tar.gz ./
Exit codes for tar are restricted, so you don't get to much information.
You can assume that ec=1 is safe to ignore, but it might trip - i.e. the gzip-example in other posts (exit code from external programs).
The reason for the file changed as we read it error/warning can be varying.
A log file inside the directory.
Writing to a tar file in the same directory you are trying to back up.
etc.
Possible workarounds can involve:
exclude known files (log files, tar-files, etc)
ensure log files are written to other directories
This can be quite involved, so you might want to still just run the tar command and preferably safely ignore some errors / warnings.
To do this you will have to:
Save the tar output.
Save the exit code
Check the output against known warnings and errors, not unlike tar's own ignore.
Conditionally pass another exit code to the next program in the pipe.
In OP's case this would have to be wrapped in a script and run as PACK_TOOL.
# List of errors and warnings from "tar" which we will safely ignore.
# Adapt to your findings and needs
IGNORE_ERROR="^tar:.*(Removing leading|socket ignored|file changed as we read it)"
# Save stderr from "tar"
RET=$(tar zcf $BACKUP --exclude Cache --exclude output.log --exclude "*cron*sysout*" $DIR 2>&1)
EC=$? # Save "tar's" exit code
echo "$RET"
if [ $EC -ne 0 ]
then
# Check the RET output, remove (grep -v) any errors / warning you wish to ignore
REAL_ERRORS=$(echo "$RET" | grep "^tar: " | grep -Ev "${IGNORE_ERROR:?}")
# If there is any output left you actually got an error to check
if [ -n "$REAL_ERRORS" ]
then
echo "ERROR during backup of ${DIR:?} to ${BACKUP:?}"
else
echo "OK backup of (warnings ignored) ${DIR:?}"
EC=0
fi
else
echo "OK backup of ${DIR:?}"
fi
It worked for me by adding a simple sleep timeout of 20 sec.
This might happen if your source directory is still writing. Hence put a sleep so that the backup would finish and then tar should work fine. This also helped me in getting the right exit status.
sleep 20
tar -czf ${DB}.${DATE}.tgz ./${DB}.${DATE}
I am not sure does it suit you but I noticed that tar does not fail on changed/deleted files in pipe mode. See what I mean.
Test script:
#!/usr/bin/env bash
set -ex
tar cpf - ./files | aws s3 cp - s3://my-bucket/files.tar
echo $?
Deleting random files manually...
Output:
+ aws s3 cp - s3://my-bucket/files.tar
+ tar cpf - ./files
tar: ./files/default_images: File removed before we read it
tar: ./files: file changed as we read it
+ echo 0
0
Answer should be very simple: Don't save your tar file while "Taring" it in the same directory.
Just do: tar -cvzf resources/docker/php/php.tar.gz .
Eventually,
it will tar the current directory and save it to another directory.
That's easy peasy, lemon squeezy fellas