I'm trying to collect some data at every second to different file(preferably timed name file). I'm trying to use watch command but it's not behaving as per expectation.
watch -p -n 1 "curl -s http://127.0.0.1:9273/metrics > `date +'%H-%M-%S'`.txt"
Only 1 file is created and data is being directed to it. I was expecting it to write to different files. I'm not looking to alternative methods. Can it be modified to achieve said task?
quote it with single quote
or wrap the command line passed to watch , with bash -c
pay attention to the quotes i used, they can not be swapped
both following command works for one second per file
watch -p -n 1 'curl -s http://127.0.0.1:9273/metrics > `date +'%H-%M-%S'`.txt'
watch -p -n 1 'bash -c "curl -s http://127.0.0.1:9273/metrics > `date +'%H-%M-%S'`.txt"'
I am relatively new to informatics, and have just discovered the virtues of the parallel command. However, I am having trouble using this in conjunction with piping and output.
I am using this command:
parallel -j 2 echo ./hisat2 --dta -p 32 -x path/to/index -U {} | ./samtools view -b - > /path/to/storage/folder/{/.}.bam :::: fs1 > executable.sh
fs1 contains a list of all the files I want to run. executable.sh is the executable command list. I wish for each file listed in fs1 to be individually processed by a program (called hisat2) and the ouput sam file to be converted into bam format with samtools. However, it does not seem to like the piping - it complains with the following:
bash: /path/to/storage/folder/{/.}.bam: No such file or directory
parallel: Warning: Input is read from the terminal. Only experts do this on purpose. Press CTRL-D to exit.
How can I overcome this? Is the only way around this to first process all files to sam, and then parallel bam convert?
You need to quote the pipe and redirection:
parallel -j 2 "./hisat2 --dta -p 32 -x path/to/index -U {} | ./samtools view -b - > /path/to/storage/folder/{/.}.bam" :::: fs1
Use --dry-run to see what would be run:
parallel --dry-run -j 2 "./hisat2 --dta -p 32 -x path/to/index -U {} | ./samtools view -b - > /path/to/storage/folder/{/.}.bam" :::: fs1
(Are you sure samtools is in current dir? Usually that is installed for a wider audience.)
May I suggest you spend an hour walking through man parallel_tutorial? Your command line will love you for it.
I am trying to run a script (1.sh)
spin -a /home/files/1/1.pml;
gcc -O2 -DXUSAFE -DSAFETY -DNOCLAIM -w -o pan pan.c >log1.txt;
./pan -m100000 >log2.txt;
spin -p -s -r -X -v -n123 -l -g -k /home/files/1/1.pml.trail \
-u10000 /home/files/1/1.pml >log3.txt;
The command spin -a ...; generates temporary files (pan.c, pan.h) which is used by the next gcc -O2.. command. If I run the script in terminal it creates the temporary files in the same location.
I want to run multiple scripts parallelly. I tried two things, first to write a script to run then in a loop in background (parallel.sh)
for((i=1;i<1800;i++))
do
/home/files/$i/$i.sh &
done
and secondly use parallel gnu parallel -j0 sh /home/files/{}/{}.sh ::: {1..1800}.
Both method created temp file in the location from where they were called from instead of the script location.
For example if I run the script 'parallel.sh' from home/files the temp file are created in "home/files" instead of the location "home/files/1","home/files/2", etc.
Please suggest a method so that the temporary file generated by the script 1.sh,2.sh,.. are created in the directory /home/file/1/, /home/files/2/,.. respectively while I run the parallel script parallel.sh or parallel GNU in terminal from location /home.
The trick is to change the working directory for each command.
When your computer can really run up to 1800 such processes at the same time without heating up the climate:
for i in {1..1800}; do (cd $i && ./$i.sh) & done
When running in parallel, and your processes are cpu-bound, it usually does not gain throughput when running more than the number of processors:
seq 1 1800 | xargs -n1 -P8 -I% sh -c 'cd % && ./%.sh'
Try:
parallel 'cd /home/files/{}; sh {}.sh' ::: {1..1800}
It will run one process per core, and may be faster than '-j0' (only testing can tell with certainty).
If your scripts only vary by the number, consider rewriting it as a general script or bash function that takes the number as an argument:
spinit() {
num=$1
spin -a /home/files/$num/$num.pml;
gcc -O2 -DXUSAFE -DSAFETY -DNOCLAIM -w -o pan pan.c >log1.txt;
./pan -m100000 >log2.txt;
spin -p -s -r -X -v -n123 -l -g -k /home/files/$num/$num.pml.trail \
-u10000 /home/files/$num/$num.pml >log3.txt;
}
export -f spinit
parallel 'cd /home/files/{}; spinit {}' ::: {1..1800}
I want to download some pages from a website and I did it successfully using curl but I was wondering if somehow curl downloads multiple pages at a time just like most of the download managers do, it will speed up things a little bit. Is it possible to do it in curl command line utility?
The current command I am using is
curl 'http://www...../?page=[1-10]' 2>&1 > 1.html
Here I am downloading pages from 1 to 10 and storing them in a file named 1.html.
Also, is it possible for curl to write output of each URL to separate file say URL.html, where URL is the actual URL of the page under process.
My answer is a bit late, but I believe all of the existing answers fall just a little short. The way I do things like this is with xargs, which is capable of running a specified number of commands in subprocesses.
The one-liner I would use is, simply:
$ seq 1 10 | xargs -n1 -P2 bash -c 'i=$0; url="http://example.com/?page${i}.html"; curl -O -s $url'
This warrants some explanation. The use of -n 1 instructs xargs to process a single input argument at a time. In this example, the numbers 1 ... 10 are each processed separately. And -P 2 tells xargs to keep 2 subprocesses running all the time, each one handling a single argument, until all of the input arguments have been processed.
You can think of this as MapReduce in the shell. Or perhaps just the Map phase. Regardless, it's an effective way to get a lot of work done while ensuring that you don't fork bomb your machine. It's possible to do something similar in a for loop in a shell, but end up doing process management, which starts to seem pretty pointless once you realize how insanely great this use of xargs is.
Update: I suspect that my example with xargs could be improved (at least on Mac OS X and BSD with the -J flag). With GNU Parallel, the command is a bit less unwieldy as well:
parallel --jobs 2 curl -O -s http://example.com/?page{}.html ::: {1..10}
Well, curl is just a simple UNIX process. You can have as many of these curl processes running in parallel and sending their outputs to different files.
curl can use the filename part of the URL to generate the local file. Just use the -O option (man curl for details).
You could use something like the following
urls="http://example.com/?page1.html http://example.com?page2.html" # add more URLs here
for url in $urls; do
# run the curl job in the background so we can start another job
# and disable the progress bar (-s)
echo "fetching $url"
curl $url -O -s &
done
wait #wait for all background jobs to terminate
As of 7.66.0, the curl utility finally has built-in support for parallel downloads of multiple URLs within a single non-blocking process, which should be much faster and more resource-efficient compared to xargs and background spawning, in most cases:
curl -Z 'http://httpbin.org/anything/[1-9].{txt,html}' -o '#1.#2'
This will download 18 links in parallel and write them out to 18 different files, also in parallel. The official announcement of this feature from Daniel Stenberg is here: https://daniel.haxx.se/blog/2019/07/22/curl-goez-parallel/
For launching of parallel commands, why not use the venerable make command line utility.. It supports parallell execution and dependency tracking and whatnot.
How? In the directory where you are downloading the files, create a new file called Makefile with the following contents:
# which page numbers to fetch
numbers := $(shell seq 1 10)
# default target which depends on files 1.html .. 10.html
# (patsubst replaces % with %.html for each number)
all: $(patsubst %,%.html,$(numbers))
# the rule which tells how to generate a %.html dependency
# $# is the target filename e.g. 1.html
%.html:
curl -C - 'http://www...../?page='$(patsubst %.html,%,$#) -o $#.tmp
mv $#.tmp $#
NOTE The last two lines should start with a TAB character (instead of 8 spaces) or make will not accept the file.
Now you just run:
make -k -j 5
The curl command I used will store the output in 1.html.tmp and only if the curl command succeeds then it will be renamed to 1.html (by the mv command on the next line). Thus if some download should fail, you can just re-run the same make command and it will resume/retry downloading the files that failed to download during the first time. Once all files have been successfully downloaded, make will report that there is nothing more to be done, so there is no harm in running it one extra time to be "safe".
(The -k switch tells make to keep downloading the rest of the files even if one single download should fail.)
Curl can also accelerate a download of a file by splitting it into parts:
$ man curl |grep -A2 '\--range'
-r/--range <range>
(HTTP/FTP/SFTP/FILE) Retrieve a byte range (i.e a partial docu-
ment) from a HTTP/1.1, FTP or SFTP server or a local FILE.
Here is a script that will automatically launch curl with the desired number of concurrent processes: https://github.com/axelabs/splitcurl
Starting from 7.68.0 curl can fetch several urls in parallel. This example will fetch urls from urls.txt file with 3 parallel connections:
curl --parallel --parallel-immediate --parallel-max 3 --config urls.txt
urls.txt:
url = "example1.com"
output = "example1.html"
url = "example2.com"
output = "example2.html"
url = "example3.com"
output = "example3.html"
url = "example4.com"
output = "example4.html"
url = "example5.com"
output = "example5.html"
curl and wget cannot download a single file in parallel chunks, but there are alternatives:
aria2 (written in C++, available in Deb and Cygwin repo's)
aria2c -x 5 <url>
axel (written in C, available in Deb repo)
axel -n 5 <url>
wget2 (written in C, available in Deb repo)
wget2 --max-threads=5 <url>
lftp (written in C++, available in Deb repo)
lftp -n 5 <url>
hget (written in Go)
hget -n 5 <url>
pget (written in Go)
pget -p 5 <url>
Run a limited number of process is easy if your system have commands like pidof or pgrep which, given a process name, return the pids (the count of the pids tell how many are running).
Something like this:
#!/bin/sh
max=4
running_curl() {
set -- $(pidof curl)
echo $#
}
while [ $# -gt 0 ]; do
while [ $(running_curl) -ge $max ] ; do
sleep 1
done
curl "$1" --create-dirs -o "${1##*://}" &
shift
done
to call like this:
script.sh $(for i in `seq 1 10`; do printf "http://example/%s.html " "$i"; done)
The curl line of the script is untested.
I came up with a solution based on fmt and xargs. The idea is to specify multiple URLs inside braces http://example.com/page{1,2,3}.html and run them in parallel with xargs. Following would start downloading in 3 process:
seq 1 50 | fmt -w40 | tr ' ' ',' \
| awk -v url="http://example.com/" '{print url "page{" $1 "}.html"}' \
| xargs -P3 -n1 curl -o
so 4 downloadable lines of URLs are generated and sent to xargs
curl -o http://example.com/page{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16}.html
curl -o http://example.com/page{17,18,19,20,21,22,23,24,25,26,27,28,29}.html
curl -o http://example.com/page{30,31,32,33,34,35,36,37,38,39,40,41,42}.html
curl -o http://example.com/page{43,44,45,46,47,48,49,50}.html
Bash 3 or above lets you populate an array with multiple values as it expands sequence expressions:
$ urls=( "" http://example.com?page={1..4} )
$ unset urls[0]
Note the [0] value, which was provided as shorthand to make the indices line up with page numbers, since bash arrays autonumber starting at zero. This strategy obviously might not always work. Anyway, you can unset it in this example.
Now you have a an array, and you can verify the contents with declare -p:
$ declare -p urls
declare -a urls=([1]="http://example.com?Page=1" [2]="http://example.com?Page=2" [3]="http://example.com?Page=3" [4]="http://example.com?Page=4")
Now that you have a list of URLs in an array, expand the array into a curl command line:
$ curl $(for i in ${!urls[#]}; do echo "-o $i.html ${urls[$i]}"; done)
The curl command can take multiple URLs and fetch all of them, recycling the existing connection (HTTP/1.1) to a common server, but it needs the -o option before each one in order to download and save each target. Note that characters within some URLs may need to be escaped to avoid interacting with your shell.
I am not sure about curl, but you can do that using wget.
wget \
--recursive \
--no-clobber \
--page-requisites \
--html-extension \
--convert-links \
--restrict-file-names=windows \
--domains website.org \
--no-parent \
www.website.org/tutorials/html/