How do we check in a shell script if there is an update_lock when running the pipeline baseline_update.sh script? The return status is always 0.
./control/baseline_update.sh
echo "isLockHeld " $?
When we run Endeca's command to check isLockHeld the same 4 INFO lines return for both scenarios when there is a lock and when there is not a lock.
./control/runcommand.sh LockManager isLockHeld update_lock
[12.12.13 10:55:44] INFO: Checking definition from AppConfig.xml against existing EAC provisioning.
[12.12.13 10:55:45] INFO: Updating provisioning for component 'Forge'
[12.12.13 10:55:45] INFO: Updating definition for component 'Forge'
[12.12.13 10:55:46] INFO: Definition updated.
We were expecting isLockHeld to return a boolean 'True' or 'False'.
http://docs.oracle.com/cd/E35639_01/DeploymentTemplate.321/apidoc/eacToolkit/com/endeca/soleng/eac/toolkit/base/LockManager.html#isLockHeld(java.lang.String)
eaccmd.sh list-flags --app your_app_name
You can then remove them with
eaccmd.sh remove-all-flags --app your_app_name
Related
Is a multiline script block in a gitlab-ci pipeline immediately aborted if a call within these instructions returns an exit code that is not equal to zero?
[gitlab-ci.yml]
stage: test
script:
- export ENVIRONMENTS=$(cat $STAGE-environments.txt)
- |
for ENVIRONMENT in ${ENVIRONMENTS}; do
echo "create tests for stage '$STAGE' and environment '$ENVIRONMENT'"
create_test $STAGE $ENVIRONMENT
fill_test $STAGE $ENVIRONMENT
done
The two calls "create_test" and "fill_test" are two bash script functions that return an exit code not equal to zero in the event of an error. If this happens, I want the gitlab-ci stage "test" to stop immediately and mark the job as failed.
Do I have to adapt the multiline script for this?
I'm running Snakemake in a cluster environment and would like to use S3 as shared file system for writing output files.
Options --default-remote-provider, --default-remote-prefix and --no-shared-fs are set accordingly. The cluster uses UGE as scheduler, so setting --cluster is straightforward, but how do I set --cluster-status, whose use is enforced when using --no-shared-fs?
My best guess was a naive --cluster-status "qstat -j" which resulted in
subprocess.CalledProcessError: Command 'qstat Your job 2 ("snakejob.bwa_map.1.sh") has been submitted' returned non-zero exit status 1.
So I guess my question is, how do I get the actual jobid in there?
Thanks!
Andreas
EDIT 1:
I found https://groups.google.com/forum/#!topic/snakemake/7cyqAIfgeq4, so cluster-status has to be a script. So I wrote a Python script that is able to parse the above line, however snakemake still fails with:
/bin/sh: -c: line 0: syntax error near unexpected token `('
/bin/sh: -c: line 0: `/home/ec2-user/clusterstatus.py Your job 2 ("snakejob.bwa_map.1.sh") has been submitted'
...
subprocess.CalledProcessError: Command '/home/ec2-user/clusterstatus.py
Your job 2 ("snakejob.bwa_map.1.sh") has been submitted' returned non-zero exit status 1.
To answer my own question:
First, I needed the -terse option for qsub (which I had not added at first in my case and snakemake somehow remembered the wrong cluster command
Secondly, the cluster-status argument needs to point to a script being able to get the job status (job id being the only argument) and output "failed", "running" or "success".
I want to use the pidof by a process given by name in tcl. I have used [exec pidof $proc_name ], but it always returns an error: child process exited abnormally.
I read somewhere exec always treat non-zero return as error as pidof return the process id number. Does anyone know if there is a workaround? Thanks in advance!
I want to use pidof is that i want to see if that process is running if not i will restart the process.
The problem is that pidof does strange things with exit codes:
Exit Status
At least one program was found with the requested name.
No program was found with the requested name.
This interacts badly with exec which treats a non-zero exit code as indicating that it should tell the rest of Tcl that there was an error.
The simplest way of dealing with this is a little extra shell script wrapper. Let's hide it inside a procedure for convenience:
proc pidof {name} {
exec /bin/bash -c "pidof '$name'; exit \$(( \$? - 1 ))"
}
All that does is subtract 1 from the exit code before it hits back into Tcl.
(You could also fix this using the techniques described in the exec manual but I think it's simpler to fix on the bash side this time.)
I ran into this and ended up causing some issues with the old linux environment I run in (no bash and exit code handling was a bit different with busybox).
My solution that should work anywhere would be similar to what a few suggested:
proc pidof {name} {
catch {exec -ignorestderr -- pidof $name} pid
if {[string is entier -strict $pid]} {
return $pid
}
}
What is the meaning of return value 127 from $? in UNIX.
Value 127 is returned by /bin/sh when the given command is not found within your PATH system variable and it is not a built-in shell command. In other words, the system doesn't understand your command, because it doesn't know where to find the binary you're trying to call.
Generally it means:
127 - command not found
but it can also mean that the command is found,
but a library that is required by the command is NOT found.
127 - command not found
example: $caat
The error message will
bash:
caat: command not found
now you check using echo $?
A shell convention is that a successful executable should exit with the value 0. Anything else can be interpreted as a failure of some sort, on part of bash or the executable you that just ran. See also $PIPESTATUS and the EXIT STATUS section of the bash man page:
For the shell’s purposes, a command which exits with a zero exit status has succeeded. An exit status
of zero indicates success. A non-zero exit status indicates failure. When a command terminates on a
fatal signal N, bash uses the value of 128+N as the exit status.
If a command is not found, the child process created to execute it returns a status of 127. If a com-
mand is found but is not executable, the return status is 126.
If a command fails because of an error during expansion or redirection, the exit status is greater than
zero.
Shell builtin commands return a status of 0 (true) if successful, and non-zero (false) if an error
occurs while they execute. All builtins return an exit status of 2 to indicate incorrect usage.
Bash itself returns the exit status of the last command executed, unless a syntax error occurs, in
which case it exits with a non-zero value. See also the exit builtin command below.
It has no special meaning, other than that the last process to exit did so with an exit status of 127.
However, it is also used by bash (assuming you're using bash as a shell) to tell you that the command you tried to execute couldn't be executed (i.e. it couldn't be found). It's unfortunately not immediately deducible though, if the process exited with status 127, or if it couldn't found.
EDIT:
Not immediately deducible, except for the output on the console, but this is stack overflow, so I assume you're doing this in a script.
If you're trying to run a program using a scripting language, you may need to include the full path of the scripting language and the file to execute. For example:
exec('/usr/local/bin/node /usr/local/lib/node_modules/uglifycss/uglifycss in.css > out.css');
This error is also at times deceiving. It says file is not found even though the files is indeed present. It could be because of invalid unreadable special characters present in the files that could be caused by the editor you are using. This link might help you in such cases.
-bash: ./my_script: /bin/bash^M: bad interpreter: No such file or directory
The best way to find out if it is this issue is to simple place an echo statement in the entire file and verify if the same error is thrown.
If the IBM mainframe JCL has some extra characters or numbers at the end of the name of unix script being called then it can throw such error.
In addition to the given answers, note that running a script file with incorrect end-of-line characters could also result in 127 exit code if you use /bin/sh as your shell.
As an example, if you run a shell script with CRLF end-of-line characters in a UNIX-based system and in the /bin/sh shell, it is possible to encounter some errors like the following I've got after running my script named my_test.sh :
$ ./my_test.sh
sh: 2: ./my_test.sh: not found
$ echo $?
127
As a note, using /bin/bash, I got 126 exit code, which is in accordance with gnu.org documentation about the bash :
If a command is not found, the child process created to execute it returns a status of 127. If a command is found but is not executable, the return status is 126.
Finally, here is the result of running my script in /bin/bash :
arman#Debian-1100:~$ ./my_test.sh
-bash: ./my_test.sh: /bin/bash^M: bad interpreter: No such file or directory
arman#Debian-1100:~$ echo $?
126
go to C:\Program Files\Git\etc
open gitconfig with notepad
change
[core]
autocrlf = true
To
[core]
autocrlf = false
I'm betting that someone has already solved this and maybe I'm using the wrong search terms for google to tell me the answer, but here is my situation.
I have a script that I want to run, but I want it to run only when scheduled and only one at a time. (can't run the script simultaneously)
Now the sticky part is that say I have a table called "myhappyschedule" which has the data I need and the scheduled time. This table can have multiple scheduled times even at the same time, each one would run this script. So essentially I need a queue of each time the script fires and they all need to wait for each one before it to finish. (sometimes this can take just a minute for the script to execute sometimes its many many minutes)
What I'm thinking about doing is making a script that checks myhappyschedule every 5 min and gathers up those that are scheduled, puts them into a queue where another script can execute each 'job' or occurrence in the queue in order. Which all of this sounds messy.
To make this longer - I should say that I'm allowing users to schedule things in myhappyschedule and not edit crontab.
What can be done about this? File locks and scripts calling scripts?
add a column exec_status to myhappytable (maybe also time_started and time_finished, see pseudocode)
run the following cron script every x minutes
pseudocode of cron script:
[create/check pid lock (optional, but see "A potential pitfall" below)]
get number of rows from myhappytable where (exec_status == executing_now)
if it is > 0, exit
begin loop
get one row from myhappytable
where (exec_status == not_yet_run) and (scheduled_time <= now)
order by scheduled_time asc
if no such row, exit
set row exec_status to executing_now (maybe set time_started to now)
execute whatever command the row contains
set row exec_status to completed
(maybe also store the command output/return as well, set time_finished to now)
end loop
[delete pid lock file (complementary to the starting pid lock check)]
This way, the script first checks if none of the commands is running, then runs first not-yet run command, until there are no more commands to be run at the given moment. Also, you can see what command is executing by querying the database.
A potential pitfall: if the cron script is killed, a scheduled task will remain in "executing_now" state. That's what the pid lock at beginning and end is for: to see if the cron script terminated properly. pseudocode of create/check pidlock:
if exists pidlockfile then
check if process id given in file exists
if not exists then
update myhappytable set exec_status = error_cronscript_died_while_executing_this
where exec_status == executing_now
delete pidlockfile
else (previous instance still running)
exit
endif
endif
create pidlockfile containing cron script process id
You can use the at(1) command inside your script to schedule its next run. Before it exits, it can check myhappyschedule for the next run time. You don't need cron at all, really.
I came across this question while researching for a solution to the queuing problem. For the benefit of anyone else searching here is my solution.
Combine this with a cron that starts jobs as they are scheduled (even if they are scheduled to run at the same time) and that solves the problem you described as well.
Problem
At most one instance of the script should be running.
We want to cue up requests to process them as fast as possible.
ie. We need a pipeline to the script.
Solution:
Create a pipeline to any script. Done using a small bash script (further down).
The script can be called as
./pipeline "<any command and arguments go here>"
Example:
./pipeline sleep 10 &
./pipeline shabugabu &
./pipeline single_instance_script some arguments &
./pipeline single_instance_script some other_argumnts &
./pipeline "single_instance_script some yet_other_arguments > output.txt" &
..etc
The script creates a new named pipe for each command. So the above will create named pipes: sleep, shabugabu, and single_instance_script
In this case the initial call will start a reader and run single_instance_script with some arguments as arguments. Once the call completes, the reader will grab the next request off the pipe and execute with some other_arguments, complete, grab the next etc...
This script will block requesting processes so call it as a background job (& at the end) or as a detached process with at (at now <<< "./pipeline some_script")
#!/bin/bash -Eue
# Using command name as the pipeline name
pipeline=$(basename $(expr "$1" : '\(^[^[:space:]]*\)')).pipe
is_reader=false
function _pipeline_cleanup {
if $is_reader; then
rm -f $pipeline
fi
rm -f $pipeline.lock
exit
}
trap _pipeline_cleanup INT TERM EXIT
# Dispatch/initialization section, critical
lockfile $pipeline.lock
if [[ -p $pipeline ]]
then
echo "$*" > $pipeline
exit
fi
is_reader=true
mkfifo $pipeline
echo "$*" > $pipeline &
rm -f $pipeline.lock
# Reader section
while read command < $pipeline
do
echo "$(date) - Executing $command"
($command) &> /dev/null
done