Attempting to run gzip from a command prompt to compress any file returns
gzip: /usr/bin/gzip is not a directory or a regular file - ignored
as the first line of output.
Here's what I can think of to share that may shed some light:
oslevel
7.1.0.0
echo $SHELL
/usr/bin/ksh
gzip -V
gzip 1.2.4 (18 Aug 93)
Compilation options:
DIRENT UTIME STDC_HEADERS HAVE_UNISTD_H
To produce the error, all I have to do is try to compress any file with gzip (i.e. gzip test.out). The error occurs when run from the command prompt as well as when run from cron.
Any thoughts as to why this is happening?
Additional requsted information:
gzip -h
gzip 1.2.4 (18 Aug 93)
usage: gzip [-cdfhlLnNrtvV19] [-S suffix] [file ...]
-c --stdout write on standard output, keep original files unchanged
-d --decompress decompress
-f --force force overwrite of output file and compress links
-h --help give this help
-l --list list compressed file contents
-L --license display software license
-n --no-name do not save or restore the original name and time stamp
-N --name save or restore the original name and time stamp
-q --quiet suppress all warnings
-r --recursive operate recursively on directories
-S .suf --suffix .suf use suffix .suf on compressed files
-t --test test compressed file integrity
-v --verbose verbose mode
-V --version display version number
-1 --fast compress faster
-9 --best compress better
file... files to (de)compress. If none given, use standard input.
file /usr/bin/gzip
/usr/bin/gzip: executable (RISC System/6000) or object module
gzip *.out
gzip: /usr/bin/gzip is not a directory or a regular file - ignored
gzip -d *.gz
gzip: /usr/bin/gzip is not a directory or a regular file - ignored
Found the issue:
We have an environment file where we load common environment variables. One line in the file is
export GZIP="/usr/bin/gzip"
According to the gzip documentation, the GZIP environment variable is used to specify options. So, it's probably taking that as part of the command line. And, since it's not really an option, it's interpreting the value as being a file name, which it can't gzip because it's actually a symbolic link. By unsetting the variable, the error goes away.
Related
I'm looking for a way to extract huge dataset (18 TB+ found here https://github.com/cvdfoundation/open-images-dataset#download-images-with-bounding-boxes-annotations) with this in mind I need the process to be fast (i.e. I don't want to spend twice the time for first copying and then extracting files) Also I don't want archives to take extra space not even one 20 gb+ archive.
Any thoughts on how one can achieve that?
If you can arrange to pipe the data straight into tar, it can uncompress and extract it without needing a temporary file.
Here is a example. First create a tar file to play with
$ echo abc >one
$ echo def >two
$ tar cvf test.tar
$ tar cvf test.tar one two
one
two
$ gzip test.tar
Remove the test files
$ rm one two
$ ls one two
ls: cannot access one: No such file or directory
ls: cannot access two: No such file or directory
Now extract the contents by piping the compressed tar file into the tar command.
$ cat test.tar.gz | tar xzvf -
one
two
$ ls one two
one two
The only part missing now is how to download the data and pipe it into tar. Assuming you can access the URL with wget, you can get it to send the data to stdout. So you end up with this
wget -qO- https://youtdata | tar xzvf -
Sometimes I get errors when I download files from a cloud with python-swiftclient, like this one:
Error downloading object 'uploads/1/image.png': Object GET failed: https://orbit.brightbox.com/v1/acc-12345/uploads/1/image.png 500 Internal Error b'An error occurred'
To search for the all errors and re-download failed files I would want to save output of the swift command to a file
I tried to do the following ways:
swift-cli -A https://orbit.brightbox.com/v1/acc-12345 \
-U user -K secret download uploads 2>&1 | tee uploads.log
# and
swift-cli -A https://orbit.brightbox.com/v1/acc-12345 \
-U user -K secret download uploads > uploads.log
But this didn't work. man swift describes -o option
For a single object download, you may use the -o [--output]
option to redirect the output to a specific file or if "-" then just redirect to stdout or with --no-download actually not to write anything to disk.
but when I try to download a directory with -o option if fails with
-o option only allowed for single file downloads
How can I save log to a file when I download a directory with swift CLI?
Actually redirecting output to a file works with swift-client:
swift-cli -A https://orbit.brightbox.com/v1/acc-12345 \
-U user -K secret download uploads > uploads.log
I was confused because after I started the command above, in another terminal window I did
tail -f uploads.log
But it didn't give me any output (like I was seeing when I was running the download command without redirection).
Seems like that swift-client writes to a file in batches and I needed to wait about a minute until tail -f dumps into the console a hundred of lines like this
uploads/documents/1/image.png [auth 0.000s, headers 0.390s, total 14.361s, 0.034 MB/s]
Httpd processes use a non-default configuration file if they are run with the -f flag.
For example
/home/myuser/apache/httpd-2.4.8/bin/httpd -f /confFiles/apache/2.4.8/apache.conf -k start
will use this configuration file: /confFiles/apache/2.4.8/apache.conf
I need to get this location and would rather not have to check for possible -f flags used to start httpd.
The answer here says to run /path/to/httpd -V and concatenate
-D SERVER_CONFIG_FILE="conf/httpd.conf"
with
-D HTTPD_ROOT="/etc/httpd"
to get the final path to the config file.
However, this path will not be the correct one if the -f flag is used to start the httpd process.
Is there a command that can get the config file that is actually being used by the process?
The answer you refer to mentions the paths httpd was compiled with, but as you say those can be manually changed with parameters.
The simple way to check is the command line, if process is called "httpd" (standard name), a simple ps will reveal the config file being used:
ps auxw | grep httpd
Or querying the server if server has mod_info loaded, in command line or with your favourite browser:
curl "http://yourserver.example.com/server-info?server" | grep -i "config file"
Note: mod_info should not be publicaly available for everyone to see.
I normally compress using tar zcvf and decompress using tar zxvf (using gzip due to habit).
I've recently gotten a quad core CPU with hyperthreading, so I have 8 logical cores, and I notice that many of the cores are unused during compression/decompression.
Is there any way I can utilize the unused cores to make it faster?
You can also use the tar flag "--use-compress-program=" to tell tar what compression program to use.
For example use:
tar -c --use-compress-program=pigz -f tar.file dir_to_zip
You can use pigz instead of gzip, which does gzip compression on multiple cores. Instead of using the -z option, you would pipe it through pigz:
tar cf - paths-to-archive | pigz > archive.tar.gz
By default, pigz uses the number of available cores, or eight if it could not query that. You can ask for more with -p n, e.g. -p 32. pigz has the same options as gzip, so you can request better compression with -9. E.g.
tar cf - paths-to-archive | pigz -9 -p 32 > archive.tar.gz
Common approach
There is option for tar program:
-I, --use-compress-program PROG
filter through PROG (must accept -d)
You can use multithread version of archiver or compressor utility.
Most popular multithread archivers are pigz (instead of gzip) and pbzip2 (instead of bzip2). For instance:
$ tar -I pbzip2 -cf OUTPUT_FILE.tar.bz2 paths_to_archive
$ tar --use-compress-program=pigz -cf OUTPUT_FILE.tar.gz paths_to_archive
Archiver must accept -d. If your replacement utility hasn't this parameter and/or you need specify additional parameters, then use pipes (add parameters if necessary):
$ tar cf - paths_to_archive | pbzip2 > OUTPUT_FILE.tar.gz
$ tar cf - paths_to_archive | pigz > OUTPUT_FILE.tar.gz
Input and output of singlethread and multithread are compatible. You can compress using multithread version and decompress using singlethread version and vice versa.
p7zip
For p7zip for compression you need a small shell script like the following:
#!/bin/sh
case $1 in
-d) 7za -txz -si -so e;;
*) 7za -txz -si -so a .;;
esac 2>/dev/null
Save it as 7zhelper.sh. Here the example of usage:
$ tar -I 7zhelper.sh -cf OUTPUT_FILE.tar.7z paths_to_archive
$ tar -I 7zhelper.sh -xf OUTPUT_FILE.tar.7z
xz
Regarding multithreaded XZ support. If you are running version 5.2.0 or above of XZ Utils, you can utilize multiple cores for compression by setting -T or --threads to an appropriate value via the environmental variable XZ_DEFAULTS (e.g. XZ_DEFAULTS="-T 0").
This is a fragment of man for 5.1.0alpha version:
Multithreaded compression and decompression are not implemented yet, so this
option has no effect for now.
However this will not work for decompression of files that haven't also
been compressed with threading enabled. From man for version 5.2.2:
Threaded decompression hasn't been implemented yet. It will only work
on files that contain multiple blocks with size information in
block headers. All files compressed in multi-threaded mode meet this
condition, but files compressed in single-threaded mode don't even if
--block-size=size is used.
Recompiling with replacement
If you build tar from sources, then you can recompile with parameters
--with-gzip=pigz
--with-bzip2=lbzip2
--with-lzip=plzip
After recompiling tar with these options you can check the output of tar's help:
$ tar --help | grep "lbzip2\|plzip\|pigz"
-j, --bzip2 filter the archive through lbzip2
--lzip filter the archive through plzip
-z, --gzip, --gunzip, --ungzip filter the archive through pigz
You can use the shortcut -I for tar's --use-compress-program switch, and invoke pbzip2 for bzip2 compression on multiple cores:
tar -I pbzip2 -cf OUTPUT_FILE.tar.bz2 DIRECTORY_TO_COMPRESS/
If you want to have more flexibility with filenames and compression options, you can use:
find /my/path/ -type f -name "*.sql" -o -name "*.log" -exec \
tar -P --transform='s#/my/path/##g' -cf - {} + | \
pigz -9 -p 4 > myarchive.tar.gz
Step 1: find
find /my/path/ -type f -name "*.sql" -o -name "*.log" -exec
This command will look for the files you want to archive, in this case /my/path/*.sql and /my/path/*.log. Add as many -o -name "pattern" as you want.
-exec will execute the next command using the results of find: tar
Step 2: tar
tar -P --transform='s#/my/path/##g' -cf - {} +
--transform is a simple string replacement parameter. It will strip the path of the files from the archive so the tarball's root becomes the current directory when extracting. Note that you can't use -C option to change directory as you'll lose benefits of find: all files of the directory would be included.
-P tells tar to use absolute paths, so it doesn't trigger the warning "Removing leading `/' from member names". Leading '/' with be removed by --transform anyway.
-cf - tells tar to use the tarball name we'll specify later
{} + uses everyfiles that find found previously
Step 3: pigz
pigz -9 -p 4
Use as many parameters as you want.
In this case -9 is the compression level and -p 4 is the number of cores dedicated to compression.
If you run this on a heavy loaded webserver, you probably don't want to use all available cores.
Step 4: archive name
> myarchive.tar.gz
Finally.
A relatively newer (de)compression tool you might want to consider is zstandard. It does an excellent job of utilizing spare cores, and it has made some great trade-offs when it comes to compression ratio vs. (de)compression time. It is also highly tweak-able depending on your compression ratio needs.
Here is an example for tar with modern zstd compressor, as finding out good examples on this one was difficult:
apt poem to install zstd and pv utilities for Ubuntu
Compress multiple files and folders (zstd command alone can only do single files)
Display progress using pv - shows the total bytes compressed and compression speed GB/sec real-time
Use all physical cores with -T0
Set compression level higher than the default with -8
Display the resulting wall clock and CPU time used after the operation is finished using time
apt install zstd pv
DATA_DIR=/path/to/my/folder/to/compress
TARGET=/path/to/my/arcive.tar.zst
time (cd $DATA_DIR && tar -cf - * | pv | zstd -T0 -8 -o $TARGET)
I'd like to compare a few files from the bazaar branch lp:ubuntu/nvidia-graphics-drivers. I'm mainly interested in the debian subdirectory inside that branch, but due to the binary blob in http://bazaar.launchpad.net/~ubuntu-branches/ubuntu/oneiric/nvidia-graphics-drivers/oneiric/files, it takes ages to get just the text files. I've already downloaded 555MB and it's still counting.
Is it possible to retrieve a bazaar branch, including or excluding certain files by one of the following properties:
file size
file extension
file name (include only debian/ for example)
I do not need to push back any changes, nor do I need to view the history of a file. I just want to compare two files in the debian/ directory, files with the .in extension and files without.
As far as I'm aware, no. You're downloading the branch history, not just the individual files. And each file is an integral part of the branch's history.
On the bright side, you only have to check it out once. Unless those binary files change, they'll be skipped the next time you pull from Launchpad.
Depending on the branch's history, you may be able to cut down on the download size if you use a lightweight checkout (bzr checkout --lightweight). But of course, that may come back and bite you later, as it means you won't get a local copy of the branch, only the checked-out files. So it'll work much like SVN, where every operation has to go through the server. And as long as you don't need to look at the branch history, or commit your changes, that should serve you just fine, I believe.
I ended up doing some dirty grep-ing on the HTTP response since bzr info "$branch" and bzr ls -d "$branch" "$directory" did not provide enough information to me.
The below Bash script relies on the working of Launchpads front-end Loggerhead. It recursively downloads from a given URL. Currently, it ignores *.run files. Save it as bzrdl in a directory available from $PATH and run it with bzrdl http://launchpad.net/~ubuntu-branches/ubuntu/oneiric/nvidia-graphics-drivers/oneiric/files/head:/debian/. All files will be saved in the current directory, be sure that it's empty to avoid conflicts.
#!/bin/bash
max_retries=5
rooturl="$1"
if ! [[ $rooturl =~ /$ ]]; then
echo "Usage: ${0##*/} URL"
echo "URL must end with a slash. Example URL:"
echo "http://bazaar.launchpad.net/~ubuntu-branches/ubuntu/oneiric/nvidia-graphics-drivers/oneiric/files/head:/"
exit 1
fi
tmpdir="$(mktemp -d)"
target="$(pwd)"
# used for holding HTTP response before extracting data
tmp="$(mktemp)"
# url_filter reads download URLs from stdin (piped)
url_filter() {
grep -v '\.run$'
}
get_files_from_dir() {
local slash=/
local dir="$1"
# to avoid name collision: a/b/c/ -> a.d/b.d/c.d/
local storedir="${dir//$slash/.d${slash}}"
mkdir -p "$tmpdir/$storedir" "$target/$dir"
local i subdir
for ((i=0; i<$max_retries; i++ )); do
if wget -O "$tmp" "$rooturl$dir"; then
# store file list
grep -F -B 1 '<img src="/static/images/ico_file_download.gif" alt="Download File" />' "$tmp" |\
grep '^<a' | cut -d '"' -f 2 | url_filter \
> "$tmpdir/$storedir/files"
IFS=$'\n'
for subdir in $(grep -F -B 1 '<img src="/static/images/ico_folder.gif" ' "$tmp" | \
grep -F '<a ' | rev | cut -d / -f 2 | rev); do
IFS=$' \t\n'
get_files_from_dir "$dir$subdir/"
done
return
fi
done
echo "Failed to download directory listing of: $dir" >> "$tmpdir/errors"
}
download_files() {
local slash=/
local dir="$1"
# to avoid name collision: a/b/c/ -> a.d/b.d/c.d/
local storedir="${dir//$slash/.d${slash}}"
local done=false
local subdir
cd "$tmpdir/$storedir"
for ((i=0; i<$max_retries; i++)); do
if wget -B "$rooturl$dir" -nc -i files -P "$target/$dir"; then
done=true
break
fi
done
$done || echo "Failed to download all files from $dir" >> "$tmpdir/errors"
for subdir in *.d; do
download_files "$dir${subdir%%.d}/"
done
}
get_files_from_dir ''
# make *.d expand to nothing if no directories are found
shopt -s nullglob
download_files ''
echo "TMP dir: $tmpdir"
echo "Errors : $(wc -l "$tmpdir/errors" 2>/dev/null | cut -d ' ' -f 2 || echo 0)"
The temporary directory and file is not removed afterwards, that must be done manually. Any errors (failures to download) will be written to $tmpdir/errors
It's confirmed to work with:
bzrdl http://bazaar.launchpad.net/~ubuntu-branches/ubuntu/oneiric/nvidia-settings/oneiric/files/head:/debian/
Feel free to correct any mistakes or add improvements.
There is no way to selectively check out a specific directory from a Bazaar branch at the moment, although we do have plans to add such support in the future.
There is definitely too much traffic for the clone you are doing, considering the size of the branch. It's probably a bug in the client implementation.
Here on bzr 2.4 it is still quite slow but not too bad (60s):
localhost:/tmp% bzr branch http://bazaar.launchpad.net/~ubuntu-branches/ubuntu/oneiric/nvidia-settings/oneiric
Most recent Ubuntu Oneiric version: 275.09.07-0ubuntu1
Packaging branch status: CURRENT
Branched 37 revision(s).
From the log:
[11866] 2011-07-31 00:56:57.007 INFO: Branched 37 revision(s).
56.786 Transferred: 5335kB (95.8kB/s r:5314kB w:21kB)