bsub and Matlab - matlab

I'm running matlab jobs on a remote server. The documentation says to run 'script.m', use the following command:
bsub -o script.out -R "rusage[matlab=1:duration=1]" matlab -nodisplay script
This doesn't seem to do much (or anything).
However,
bsub -o script.out -R "rusage[matlab=1:duration=1]" matlab -nodisplay -r "script"
works though. Any idea why the -r and quotation marks were omitted in the documentation? Was this simply a mistake, or am I misunderstanding something.

That looks just plain wrong to me, MATLAB has always needed the -r option to run a script.

Related

Can you get full command line from process ID (including command line arguments, etc)?

This question is in addition to the question asked here: https://unix.stackexchange.com/questions/163145/how-to-get-whole-command-line-from-a-process. On my system, the following command results in a PID (as expected):
CUDA_VISIBLE_DEVICES=4,5 python3 main.py 1> out.txt 2> err.txt &
Now, the methods in the stack exchange link above provide many solutions. However, when trying these solutions, I only receive the following information:
python3 main.py
Is there a way to return the entire command line "CUDA_VISIBLE_DEVICES=4,5 python3 main.py 1> out.txt 2> err.txt &", not just the portion "python3 main.py"?
No.
Assuming you're on a Linux system, you can find the individual bits, but you can't put it together.
Assume also that the process's PID is in $pid
The CUDA_VISIBLE_DEVICES=4,5 variable gets added to the environment of the python command. You can find it in /proc/$pid/environ but you can't tell which of those variables were specified on the command line: the user could have written
export CUDA_VISIBLE_DEVICES=4,5
python3 main.py 1> out.txt 2> err.txt &
The file redirections are available in /proc/$pid/fd:
/proc/$pid/fd/1 is a symbolic link to out.txt
/proc/$pid/fd/2 is a symbolic link to err.txt
I don't know how to tell if a process is running in the background.
Since you're just interested in the environment: with bash
declare -A environ
while IFS='=' read -r -d '' var value; do
environ["$var"]="$value"
done < /proc/$pid/environ
echo "process has CUDA_VISIBLE_DEVICE value ${environ[CUDA_VISIBLE_DEVICE]}"

Easy way to write cp -a in PowerShell

So since PowerShell seems to have alises to bash commands they still don't follow them 100%...
What is the easiest way to write bash's cp -a in PowerShell format?
The -r flag which stands for recursive.
cp -r

How can I get zsh to inherit the complete autocompletion?

I have an little shell script (named "run") which redirects all output of a program to /dev/null:
#!/bin/bash
$# &> /dev/null &
disown +
How can I say zsh that the whole autocompletion shall work for this?
I mean
$ run git com<TAB>
autocomplete to
$ run git commit
I was able to make that work by adding:
compdef _command run
to my .zshrc file.
I've based my answer on this bash question. It was worth giving it a try with compdef - surprisingly it worked.
As I'm still zsh/autocompletion newbie I cannot explain the inner workings and you should probably go through the documentation or other sources to find more on the topic.

Why Parameter Expansion is not working? [duplicate]

#!/bin/bash
jobname="job_201312161447_0003"
jobname_pre=${jobname:0:16}
jobname_post=${jobname:17}
This bash script gives me Bad substitution error on ubuntu. Any help will be highly appreciated.
The default shell (/bin/sh) under Ubuntu points to dash, not bash.
me#pc:~$ readlink -f $(which sh)
/bin/dash
So if you chmod +x your_script_file.sh and then run it with ./your_script_file.sh, or if you run it with bash your_script_file.sh, it should work fine.
Running it with sh your_script_file.sh will not work because the hashbang line will be ignored and the script will be interpreted by dash, which does not support that string substitution syntax.
I had the same problem. Make sure your script didnt have
#!/bin/sh
at the top of your script. Instead, you should add
#!/bin/bash
For others that arrive here, this exact message will also appear when using the env variable syntax for commands, for example ${which sh} instead of the correct $(which sh)
Your script syntax is valid bash and good.
Possible causes for the failure:
Your bash is not really bash but ksh or some other shell which doesn't understand bash's parameter substitution. Because your script looks fine and works with bash.
Do ls -l /bin/bash and check it's really bash and not sym-linked to some other shell.
If you do have bash on your system, then you may be executing your script the wrong way like: ksh script.sh or sh script.sh (and your default shell is not bash). Since you have proper shebang, if you have bash ./script.sh or bash ./script.sh should be fine.
Try running the script explicitly using bash command rather than just executing it as executable.
Also, make sure you don't have an empty string for the first line of your script.
i.e. make sure #!/bin/bash is the very first line of your script.
Not relevant to your example, but you can also get the Bad substitution error in Bash for any substitution syntax that Bash does not recognize. This could be:
Stray whitespace. E.g. bash -c '${x }'
A typo. E.g. bash -c '${x;-}'
A feature that was added in a later Bash version. E.g. bash -c '${x#Q}' before Bash 4.4.
If you have multiple substitutions in the same expression, Bash may not be very helpful in pinpointing the problematic expression. E.g.:
$ bash -c '"${x } multiline string
$y"'
bash: line 1: ${x } multiline string
$y: bad substitution
Both - bash or dash - work, but the syntax needs to be:
FILENAME=/my/complex/path/name.ext
NEWNAME=${FILENAME%ext}new
I was adding a dollar sign twice in an expression with curly braces in bash:
cp -r $PROJECT_NAME ${$PROJECT_NAME}2
instead of
cp -r $PROJECT_NAME ${PROJECT_NAME}2
I have found that this issue is either caused by the marked answer or you have a line or space before the bash declaration
Looks like "+x" causes problems:
root#raspi1:~# cat > /tmp/btest
#!/bin/bash
jobname="job_201312161447_0003"
jobname_pre=${jobname:0:16}
jobname_post=${jobname:17}
root#raspi1:~# chmod +x /tmp/btest
root#raspi1:~# /tmp/btest
root#raspi1:~# sh -x /tmp/btest
+ jobname=job_201312161447_0003
/tmp/btest: 4: /tmp/btest: Bad substitution
in my case (under ubuntu 18.04), I have mixed $( ${} ) that works fine:
BACKUPED_NB=$(ls ${HOST_BACKUP_DIR}*${CONTAINER_NAME}.backup.sql.gz | wc --lines)
full example here.
I used #!bin/bash as well tried all approaches like no line before or after #!bin/bash.
Then also tried using +x but still didn't work.
Finally i tried running the script ./script.sh it worked fine.
#!/bin/bash
jobname="job_201312161447_0003"
jobname_post=${jobname:17}
root#ip-10-2-250-36:/home/bitnami/python-module/workflow_scripts# sh jaru.sh
jaru.sh: 3: jaru.sh: Bad substitution
root#ip-10-2-250-36:/home/bitnami/python-module/workflow_scripts# ./jaru.sh
root#ip-10-2-250-36:/home/bitnami/python-module/workflow_scripts#

how to retrive a perl file using wget and execute it using a one-liner?

I'm looking to use wget to retrieve a perl file and execute it in one line. Does anyone know if this is possible/how I would go about doing this?
In order to use wget for this purpose, you would use the -O flag and give it the '-' character as an argument. From the manpage:
-O file
--output-document=file
Giving '-' as the "file" option to -O tells it to send it's output to stdout, which can then be piped into the Perl command.
You can provide the -q flag as well to turn off wget's own warning and message output:
-q
--quiet
Turn off Wget's output.
This will make things look cleaner in the shell.
So you would end up with something like:
wget -qO - http://127.0.0.1/myscript.pl | perl -
For more information on I/O redirection take a look at this:
http://www.tldp.org/LDP/abs/html/io-redirection.html
Just download and pipe to perl
curl -L http://your_location.pl | perl -
You'll sometimes see code like for install modules like cpanm.