[slurm-users] run bash script in spank plugin

[Tueur Volvo]

I would like to run a bash script or binary executable as root (even if the
user who started the job doesn't have root rights) at the end of a job if I
put an option in my spank plugin

2018-06-04 16:36 GMT+02:00 John Hearns <hearnsj at googlemail.com>:

> That kinnddd....  of...  defeats...  the.... purpose....  of a job
> scheduler.
> I am very sure that you know why you need this and you have a good reason
> for doing it.  Over to others on the list, sorry.
>
> On 4 June 2018 at 16:15, Tueur Volvo <huitre39 at gmail.com> wrote:
>
>> no I don't have dependency treated.
>>
>> during the job, I would like to run a program on the machine running the
>> job
>> but I'd like the program to keep running even after the job ends.
>>
>> 2018-06-04 15:30 GMT+02:00 John Hearns <hearnsj at googlemail.com>:
>>
>>> Tueur what are you trying to achieve here?  The example you give is
>>> touch /tmp/newfile.txt'
>>> I think you are trying to send a signal to another process. Could this
>>> be 'Hey - the job has finished and there is a new file for you to process'
>>> If that is so, there may be better ways to do this. If you have a
>>> post-processing step, then you can submit a job whihc depends on the main
>>> job.
>>> https://hpc.nih.gov/docs/job_dependencies.html
>>>
>>> On 4 June 2018 at 15:20, Tueur Volvo <huitre39 at gmail.com> wrote:
>>>
>>>> thanks for your answer, i try some solution but it's not work
>>>>
>>>> i try to add setsid and setpgrp for isolate my new process but slurm
>>>> job sleep 6secondes and reboot my machine (i test with reboot command, but
>>>> we can make other bash command, it's just example)
>>>>
>>>>         pid_t cpid; //process id's and process groups
>>>>
>>>>         cpid = fork();
>>>>
>>>>         if( cpid == 0 ){
>>>>             setsid();
>>>>             setpgrp();
>>>>             execl("/bin/sh", "sh", "-c", "sleep 10; reboot1&", NULL);
>>>>
>>>>         }
>>>>         wait(NULL);
>>>>
>>>>
>>>> maybe i have a error in my code ?
>>>>
>>>> 2018-05-31 9:37 GMT+02:00 Yair Yarom <irush at cs.huji.ac.il>:
>>>>
>>>>> Hi,
>>>>>
>>>>> I'm not sure how slurm/spank handles child processes but this might be
>>>>> intentional. So there might be some issues if this were to work.
>>>>>
>>>>> You can try instead of calling system(), to use fork() + exec(). If
>>>>> that still doesn't work, try calling setsid() before the exec(). I can
>>>>> think of situations where your process might still get killed, e.g. if
>>>>> slurm (or even systemd) kills all subprocesses of the "job", by
>>>>> looking at the cgroup. If that's the case, you'll need to move it to
>>>>> another cgroup in addition/instead of setsid().
>>>>>
>>>>>     Yair.
>>>>>
>>>>>
>>>>>
>>>>> On Wed, May 30, 2018 at 5:16 PM, Tueur Volvo <huitre39 at gmail.com>
>>>>> wrote:
>>>>> > Hello i have question, how run in background bash script in spank
>>>>> plugin ?
>>>>> >
>>>>> > in my spank plugin in function : slurm_spank_task_init_privileged
>>>>> >
>>>>> > i want to run this script :
>>>>> >
>>>>> > system("nohup bash -c 'sleep 10 ; touch /tmp/newfile.txt' &");
>>>>> >
>>>>> > i want to run in independant process this bash script, i don't want
>>>>> wait 10
>>>>> > seconde in my slurm plugin
>>>>> >
>>>>> > i have this code :
>>>>> > int slurm_spank_task_init_privileged (spank_t sp, int ac, char
>>>>> **av) {
>>>>> >
>>>>> > system("nohup bash -c 'sleep 10 ; touch /tmp/newfile.txt' &");
>>>>> >
>>>>> > return 0;
>>>>> >
>>>>> > }
>>>>> >
>>>>> > actualy it's not work, when slurm ending to run my job, he kill my
>>>>> nohup
>>>>> > command
>>>>> >
>>>>> > if i  had in my c code sleep 12, my bash script work
>>>>> >
>>>>> >
>>>>> > int slurm_spank_task_init_privileged (spank_t sp, int ac, char
>>>>> **av) {
>>>>> >
>>>>> > system("nohup bash -c 'sleep 10 ; touch /tmp/newfile.txt' &");
>>>>> >
>>>>> > sleep(12);
>>>>> >
>>>>> > return 0;
>>>>> >
>>>>> > }
>>>>> >
>>>>> > but i don't want to wait, i want to run my bash script in independant
>>>>> > process
>>>>> >
>>>>> > thanks for advance for your help
>>>>> >
>>>>> >
>>>>> >
>>>>> >
>>>>>
>>>>>
>>>>
>>>
>>
>
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