Hi i have set up passwordless ssh set up and have perl call ssh -o "BatchMode yes" user#host "runMe.pl arg1 arg2"
runMe.pl calls matlab and the function run_online with the given args.
nohup matlab -nojvm -nodisplay -r "run_online('$imgfolder/$folder/', '$ARGV[0]$folder', '/homes/rbise/results/mitosis/$ARGV[0]/$folder/')" > out.txt < /dev/null &
for some reason matlab never starts running. why is this?
thanks
This is substantially a duplicate of the [perl] question that was asked immediately previously to this one -- at least, the answer is the same. You have no controlling terminal when you connect with ssh. Try ssh -o "BatchMode yes" user#host "bash -c runMe.pl arg1 arg2".
Related
I have the need to start a java rest server with concourse that lives on an Ubuntu 18.04 machine. The version of concourse my company uses is 5.5.11. The server code is written in Java, so a simple java -jar <uber.jar> suffices from the command line (see below). In production, I will not have this simple luxury, hence my question.
I have an scp command working that copies the .jar from concourse to the target Ubuntu machine:
scp -i /tmp/key.p8 -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null ./${NEW_DIR}/${ARTIFACT_NAME}.${ARTIFACT_FILE_TYPE} ${SRV_ACCOUNT_USER}#${JAVA_VM_HOST}:/var/www
Note that my private key is passed with -i and I can confirm that is working.
I followed this other SO Q&A that seemed to be promising: Getting ssh to execute a command in the background on target machine
, but after trying a few permutations of the suggested solution and other answers, I still don't have my rest service kicked off.
I've tried a few permutations of this line in my concourse script:
ssh -f -i /tmp/pvt_key1.p8 -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null ${SRV_ACCOUNT_USER}#${JAVA_VM_HOST} "bash -c 'nohup java -jar /var/www/${ARTIFACT_NAME}.${ARTIFACT_FILE_TYPE} -c \"/opt/testcerts/clientkeystore\" -w \"password\" > /dev/null 2>&1 &'"
I've tried with and without the -f and -t switches in ssh, with and without the file stream redirection, with and without nohup and the Linux background ('&') command and various ways to escape the quotes.
At the bash prompt, this line successfully starts my server. The two switches are needed to point to the certificate and provide the password:
java -jar rest-service.jar -c "/opt/certificates/clientkeystore" -w "password"
I really think this is possible to do in Concourse, but I'm stuck at this point.
After a lot of trial an error, it seems I needed to do this:
ssh -f -i /tmp/pvt_key1.p8 -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null ${SRV_ACCOUNT_USER}#${JAVA_VM_HOST} "bash -c 'sudo java -jar /var/www/${ARTIFACT_NAME}.${ARTIFACT_FILE_TYPE} -c \"/path/to/my/certificate\" -w \"password\" > /var/www/log.txt 2>&1 &'"
The key was I was missing the 'sudo' portion of the command. Using nohup as opposed to putting in a Linux bash background indicator ('&') seems to give me an error in the pipeline. This works for me, but others are welcome to post responses with better answers or methods that might be a better practice.
I need to expand variables before running the SCP command as a result I can't use single quote. If I run the script using double quotes in Powershell ISE it works fine.
But doesn't work if I run the script through command prompt.
I'm using zabbix to run the script which calls the script as [cmd /C "powershell -NoProfile -ExecutionPolicy Bypass -File .\myscript.ps1"]
Here is the code that needs to run SCP using Cygwin bash.
if ((test-path "$zipFile"))
{
C:\cygwin\bin\bash.exe -l "set -x; scp /cygdrive/e/logs/$foldername/dir1/$foldername.zip root#10.10.10.10:~/"
}
Output:
/usr/bin/bash: set -x; /cygdrive/e/logs/myfolder/dir1/server.zip root#10.10.10.10:~/: No such file or directory
If I run the same command above in Cygwin manually it works.
I even tried to use bash -l -c but then the SSH session is stuck maybe because the root#10.10.10.10 becomes $1 according to the documentation.
Documentation link
-c If the -c option is present, then commands are read from
the first non-option argument command_string. If there are
arguments after the command_string, the first argument is
assigned to $0 and any remaining arguments are assigned to
the positional parameters. The assignment to $0 sets the
name of the shell, which is used in warning and error
messages.
Figured it out. It was halting when using bash -c was due to StrictHostKeyChecking, the known hosts thing (where you get a prompt to type yes/no). I set the -v switch to SCP and it showed me the Debug logs where it was halting.
Had to set scp -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null options.
The complete line now looks like the following:
c:\$cygwin_folder\bin\bash.exe -c ("/usr/bin/scp -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -v -i /cygdrive/c/cygwin/home/myuser/.ssh/id_rsa /cygdrive/e/logs/$foldername/dir1/$foldername.zip root#10.10.10.10:~/")
On RHEL, the below command works:
psql -h hostname -U username -p port_no -d database -f /tmp/myfile.sql &> logfile01.txt
On FreeBSD, this throws error:
"Invalid null command"
Please suggest.
If you use this only on the command line then there is no need to change the shell.
To redirect stdout and stderr to a file in C-Shell synthax simply use ">& filename".
Different story is, if you want to write shell scripts. Bourne Shell and it's clones (like i.e. Bash) are better suited for writing script. See this Unix FAQ "Csh Programming Considered Harmful": http://www.faqs.org/faqs/unix-faq/shell/csh-whynot/
This redirection works in bash
&> logfile01.txt
, but it does not work in csh which is the default shell in FreeBSD.
# set | grep shell
shell /bin/csh
# ls -la &> logfile01.txt
Invalid null command.
Bash is not installed by default. You can install it
pkg install bash
and configure it as the default shell.
I am using plink.exe from cmd in Windows 10, to ssh to Ubuntu 16.04. In there, I am running MATLAB, to run the following command:
try, someFunction('path/to/files', 'algorithm'), exit(); catch ME, warning(ME.message), exit(); end
For this, I generate the following command to handle ssh, executing matlab and run the above command:
C:\plink.exe user#server -pw ****** "matlab -nodesktop -nosplash -noawt -r 'try, someFunction('path/to/files', 'algorithm'), exit(); catch ME, warning(ME.message), exit(); end'
Running the above command, I get the following error in MATLAB:
Warning: Undefined function or variable 'path/to/files'.
As it turns out, in matlab, the command is constructed like following:
someFunction(path/to/files, algorithm)
which is without "single quotes": thank you, plink :( .
Can you please help to generate the correct command? or if there is already a question asked with similar problem, I would be thankful to direct me to it.
Thanks,
It's not Plink fault. It's how Windows command-line interpreter works.
Adding cmd and batch-file tags, so that you may get answers from experts on the field.
Anyway, I can see two solutions:
Put your command to a file like:
matlab -nodesktop -nosplash -noawt -r "try, someFunction('path/to/files', 'algorithm'), exit(); catch ME, warning(ME.message), exit(); end"
And use the file (command.txt) with Plink like:
C:\plink.exe user#server -pw ****** -m command.txt
If you do not want to use a separate file for the command, this should work too:
echo matlab -nodesktop -nosplash -noawt -r "try, someFunction('path/to/files', 'algorithm'), exit(); catch ME, warning(ME.message), exit(); end" | C:\plink.exe user#server -pw ****** -T
(Note the -T switch).
So in my script I need to make to calls to unix, and I do it via the system command like so:
system "bash -i -c 'addmothernode'";
...
perl code ...
...
system "bash -i -c 'addnode -ip=$_'";
However, whenever I run both of these commands in the same script, for some reason my process is stopped like this:
[1]+ Stopped perl boot.pl
And the script can only be finished when I run fg %1. When I only have one of these system calls in, the perl script finishes successfully. But I need both commands because they depend on each other. Anyone have any ideas about what's going on? Thanks!
UPDATE:
A lot of answers below are saying I don't need to use bash -i to run a system command, and I know typically this is true but I need to use aliases that I have created and if I do not use this the aliases won't be recognized. So I do need bash -i.
This problem is unrelated to perl. You can easily reproduce the situation if you start two bashes in the interactive mode (-i) one after another:
$ cat 1.sh
bash -i -c 'sleep 1'
bash -i -c 'sleep 1'
$ bash 1.sh
[1]+ Stopped bash 1.sh
Of course it would be better to run bash in the non-interactive mode (without -i) or run the program directly, without bash, but if you need for some reason bash -i you can protect its run with setsid:
$ cat 1.sh
setsid bash -i -c 'sleep 1'
setsid bash -i -c 'sleep 1'
echo done
$ bash 1.sh
done
The bash -i means run an interactive shell; so you have two shells both reading from the terminal.
Try removing the -i options.
system "addmothernode";
should work.
To execute a command, bash is not needed. The Perl system function is like the system C function, it calls by default sh.
man system
exec
The standard to which the caller conforms determines which shell is used. See standards(5).
Standard Shell Used
______________________________________________________________
1989 ANSI C, 1990 ISO C, 1999 ISO C, /usr/xpg4/bin/sh
POSIX.1 (1990-2001), SUS, SUSv2, SUSv3,
XPG4
POSIX.1 (1988), SVID3, XPG3, no standard /usr/bin/sh
specified