-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 14/11/13 15:41, Reuti wrote: > Am 14.11.2013 um 10:44 schrieb William Hay: > >> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 > >> We have a user who has a program submitting jobs via DRMAA which >> is invoking our client side jsv. Unfortunately it appears that >> it spawns one client JSV per job which never terminates leading >> to it filling up the process table. IMAO the DRMAA interface >> should either reuse the JSV > > You are accessing the JSV by a native specification in DRMAA, as > it's not part of DRMAA? It would for sure be good if there would be > such a facility to attach an open JSV to an invoked session in > DRMAA. > Unfortunately I'm not accessing the JSV myself. One of the users on our cluster is using GATK (http://www.broadinstitute.org/gatk/) which is using the GATK-Queue software to submit jobs to our cluster via DRMAA. From our point of view we see a java process on the submit node that has spawned off one copy of each client side jsv per job it queues. I'm assuming that somewhere in the grid engine DRMAA library is the code that invokes these as it submits the job.
> >> or terminate it but apparently it doesn't do that (at least in >> 6.2u3) When using the perl API does one really need to return >> from jsv_on_verify or could I just terminate the jsv after > > What do you mean by "terminate" - something else than return in the > usual way? > > After sending the jsv_accept within perl just calling exit which terminates the jsv process. Unfortunately something seems to keep respawning them up to the number of submitted jobs. >> jsv_reject/jsv_accept/jsv_correct/jsv_reject_wait? > > Yes. In fact it has to return after this call: > > From `man jsv_script_interface`: > > jsv_accept() This function can only be used in jsv_on_verify(). > After it has been called, the function jsv_on_verify() has to > return immediately. > > > Depending on Perl (resp. Bash's "return") is therefore the one and > only command after the if-then-else for the various exit > conditions. > I agree that is what the API docs say but the API is just a wrapper around the protocol and AFAICT from reading the perl module the only reason to return is to permit processing of the next job. Since it appears that each invocation of the JSV proceses a single job terminating the JSV should be harmless (other than freeing resources) > -- Reuti > > >> -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) >> Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ > >> iQIcBAEBAgAGBQJShJtOAAoJEKCzH4joEjNWD7gP/117moG9X8cteFDi/zI+RuqD >> AXlsC8I6jQf9xtkuIbP/1AhFeE4SActh9MBTAMR/fasGh/yBWmPyJZtvT/+q61tb >> g0tR2QmI60B1ZAyIj1a/MjQuLZN+tl2GRjNB0XLn1h58xd1tViNMuVlepqxzvVwn >> Yl/MBr9bgDNPG4sFwotmxk5XhFpipGDT7D9f6gRhpc8LY6CLy7vTcfLnA8pJryGg >> Q7PAFH6qM0+0OAjcGyxuCjgbO6aUwRDYLd0mdmOla8CN03Bx8gutLgvVl+hqWKME >> U0JtYyzAjTzxzbz6zm0ktV/gA/JylzLH6ECUVxCBS1f9pO5wFXwkK+QpcAeSAE9h >> 8gThPCu/EMnm1a3Y9uyMokzxiEkI1qXzKzrKytbFJAJn3wPdnpjR/aOWJW4lOhFg >> yz0rXfoXyQK8IQmQaQIG6Nisky/AonO9ja+ulIVNG7YwUqupKkeU8WuqqVCVO7Cz >> W32yonUpFcCmopeyzHIPdLxvrESnXwKPOKf/YvrvokBY5UzW0zyXAVtvwhA28CIc >> 1+7Nfmf0cHlFunpgJIRcS1+baNNJOH1c7aR1cqSz4fSH6cH2jZcyhmSfpROENJ0u >> 7zk9fa22Xswm/F1aHFJHXQE2XsqJ14RiRS6AU7cQ3vGUjaAZvTgLd31397HSMJ1Z >> JoAIDdSERuTPvdQh2CuN =+QCH -----END PGP SIGNATURE----- > >> _______________________________________________ users mailing >> list [email protected] >> https://gridengine.org/mailman/listinfo/users > > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJShd4HAAoJEKCzH4joEjNWmdsP/2uKLoa3PKkTpmjerlHvfcgM 6XPKBiIFYWHIxWwhe9VNjEaRIVGEC5bVEARtECx1BV30vhd3hraRf5xQfl24GjiP G77dXulSywI7A0hQ1sJgQ+A/jF/0f+clWHOkZE/dypcxsw58jLUPN5Pt7tgNlvQZ 6isnArDxW2+AVZn8kjDFbDRTchW1i94ipK8rMZHmn1T78oWu28hnc3Py7dY9xiwo 9XHQ5a3uNIUwh9NSe7ISAipzQmBYTAMP8ptynGCBA88VaEKx8FZ8OUQyuvGjXf5o SG3anbqLfGQ3uE3WdTwy5rVJ6CobhgGLU9hfeLDtkqcigLcNP+iQEpsVRDhxmXls 5nJ2zbKe75yGQLv1zlhMbOXIjdBHAOHq9JTX4kaTjTy8VYlUC/8PvdwFj3bg+txv rD1kykQ5y3BQ8uBIqcMxY4HmYGjUsksR39XdGX1PAoVt94qEABkOwIQmMLeq0N/S B4KYm9xNvmpluL38tXh1gv7VFdOdiutknKCQOVdAjKztVMaueQs7gd3bvLh4lOFz 4RToI5BU0Dyb/zmh3Fqy6RUUW5tSz5V27r90A2D8EkS2SIky1EvXSWaXSTChDtku FtwM0LCMnzXtf9nVeyR2qlzZR6QsgHy00XapwfjuSVwa/OMpuPZ7Fl2Vp0//zlkc SHy2ES+qabUAFgdtl4f5 =rYl7 -----END PGP SIGNATURE----- _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
