Re: [gridengine users] Reported memory usage too high

s from overbooking a node. Thank you, Nico ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users

Re: [gridengine users] sgemaster crash

ebugging (man sge_dl). William ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users -- Alex Chekholko ch...@stanford.edu 347-401-4860 ___ users mailing list users@

Re: [gridengine users] qmaster worker error message

OK, we figured it out, the user has an orphaned tmux session which has a shell in it with the command watch qdel * On 11/30/2015 04:27 PM, Alex Chekholko wrote: Hi, My qmaster messages log is continuously printing, every 2s: 11/30/2015 16:21:28|worker|scg3-hn01|E|The job * of user(s

[gridengine users] qmaster worker error message

Hi, My qmaster messages log is continuously printing, every 2s: 11/30/2015 16:21:28|worker|scg3-hn01|E|The job * of user(s) yangili does not exist 11/30/2015 16:21:30|worker|scg3-hn01|E|The job * of user(s) yangili does not exist 11/30/2015 16:21:32|worker|scg3-hn01|E|The job * of user(s)

Re: [gridengine users] qlogin + X11 + pam_sge_authorize ?

On 06/08/2015 12:49 AM, William Hay wrote: On Fri, 5 Jun 2015 22:16:12 + Alex Chekholko ch...@stanford.edu wrote: Hi all, I have a standard grid engine cluster (sge-8.1.8 tarball from Dave Love's site) where users use qlogin to get interactive shells on compute nodes, and we use a qlogin

Re: [gridengine users] qlogin, interactive sessions, and cgroups

has released the mem_free and slots for others to use. If anyone has advice on how I can set this up to accomplish my three goals, it would be very much appreciated. I can post any configuration / logs / details required. Thanks, -Chris Tobey -- Alex Chekholko ch...@stanford.edu

[gridengine users] qlogin + X11 + pam_sge_authorize ?

://arc.liv.ac.uk/SGE/htmlman/htmlman8/pam_sge-qrsh-setup.html is for, no matter how many times I re-read those man pages. Do I need both pam_sge-qrsh-setup and pam_sge_authorize? Regards, -- Alex Chekholko ch...@stanford.edu ___ users mailing list users

Re: [gridengine users] Jenkins integration?

There is a general API called DRMAA http://en.wikipedia.org/wiki/DRMAA We have an example local app that uses it to track state of grid engine jobs: https://github.com/StanfordBioinformatics/SJM I found one result for DRMAA Jenkins in Google:

Re: [gridengine users] tcl jsv error - bash related

On 11/6/14, 12:22 AM, William Hay wrote: On Wed, 5 Nov 2014 23:08:53 + Alex Chekholko ch...@stanford.edu wrote: So I have a bash env var called BASH_FUNC_module() and when the tcl jsv tries to make a TCL variable with that name, it errors out because of the parenthesis. I think

[gridengine users] tcl jsv error - bash related

need to do to make the -V flag to qsub work again? I found a page like this, but we don't have mismatched bash versions: https://rc.fas.harvard.edu/shellshock-update-issue-temporarily-affecting-slurm-jobs-software-modules/ Regards, -- Alex Chekholko ch...@stanford.edu

Re: [gridengine users] Basic information working on cluster

@gridengine.org https://gridengine.org/mailman/listinfo/users -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users

Re: [gridengine users] Grid engine does not send no job-mails

/ --- ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org

Re: [gridengine users] Resource Reservation logging

://gridengine.org/mailman/listinfo/users -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users

Re: [gridengine users] Upgrading form SGE to OGE

Normally you would leave the old install in place while the old jobs finish. Since you used a different communications port and different path, you can have the new daemons running alongside the old daemons and they don't know about each other. Direct users to submit jobs to the new

Re: [gridengine users] modify host selection algorithm?

Hi, Right, you want: queue_sort_method load and load_formula slots. Per Reuti's link. You can easily test by submitting some test jobs on an empty cluster and see that they all get assigned to the same host, leaving other hosts empty, until the host with the most slots used if filled up.

Re: [gridengine users] h_vmem not actually restricting memory usage?

Hi Brett, I saw the issue with JOB vs YES when the jobs were requesting more than one complex. e.g. qsub -l h_vmem=10G,h_stack=10M was not hitting memory limits when JOB was set. If your jobs are only requesting one complex, the JOB setting should work as expected, and you can try both ways

Re: [gridengine users] strategy for h_vmem and multi-slot jobs?

showing negative values. So on clusters where our users request also h_stack in addition to h_vmem, we've had to set it back to 'YES' and have the users do the division by slots at job submission. Regards, -- Alex Chekholko ch...@stanford.edu ___ users

[gridengine users] h_vmem not honored at all?

only requests this one complex. Suggestions? Regards, -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users

Re: [gridengine users] Memory allocation woes. Any thoughts?

Hi Jake, You can do 'qhost -F h_vmem,mem_free,virtual_free', that might be a useful view for you. In general, I've only ever used one of the three complexes above. Which one(s) do you have defined for the execution hosts? e.g. qconf -se compute-1-7 h_vmem will map to 'ulimit -v' mem_free

Re: [gridengine users] h_vmem negative values?

linux-x64 32 12.81 63.0G8.4G9.8G 27.8M Host Resource(s): hc:h_vmem=1.000G Is there anything I can do to diagnose this issue? On 10/31/12 3:19 PM, Dave Love wrote: Alex Chekholko ch...@stanford.edu writes: Hi Reuti, Thanks for your response, here's the output

Re: [gridengine users] h_vmem negative values?

, Oct 18, 2012 at 6:53 PM, Alex Chekholko ch...@stanford.edu wrote: Hi, Running Rocks 6, so whatever GE version is included there. h_vmem is set consumable and per job, 4G default: -bash-4.1$ qconf -sc |grep h_vmem h_vmem h_vmem MEMORY =YES JOB 4G 0 each exec

Re: [gridengine users] h_vmem negative values?

wrote: Am 19.10.2012 um 20:58 schrieb Alex Chekholko: qhost values seem fine: ... scg3-0-11 lx26-amd64 32 27.15 63.0G 38.3G9.8G 393.6M scg3-0-12 lx26-amd64 32 27.36 63.0G 38.7G9.8G 33.6M scg3-0-13 lx26-amd64 32 22.61 63.0G

Re: [gridengine users] h_vmem negative values?

after the job already started? -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users

Re: [gridengine users] qlogin sets TERM var to dumb?

On 10/18/12 3:14 AM, Reuti wrote: Am 28.09.2012 um 21:15 schrieb Alex Chekholko: Hi, I have a fresh install of Open Grid Scheduler on a new cluster and I see that when I do a qlogin session, the environment variable TERM gets set to dumb. On my other clusters I see it gets set to linux

[gridengine users] h_vmem negative values?

to be cycled for the setting to take effect? I can try that next. Regards, -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users

Re: [gridengine users] qmaster: hard descriptor limit and soft descriptor limit?

limits.conf? I bet if you restart the process, it'll get the settings from your current root shell, and all will be well. Regards, -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo

Re: [gridengine users] KRB5 support

it for that. I don't see why this would require a reinstall. You probably need to shut it all down and modify the bootstrap file, but that should be it. IIRC it depends on whether their GE binaries were compiled with Kerberos support or not. -- Alex Chekholko ch...@stanford.edu

Re: [gridengine users] Limit jobs in a queue to those requesting a resource

testq=1 will go in that queue. relevant thread: http://gridengine.org/pipermail/users/2012-March/002972.html On 10/05/2012 03:36 PM, Orion Poplawski wrote: I'd like to create a queue that only allows jobs that have requested a specific resource requirement. Is that possible? -- Alex

Re: [gridengine users] SGE with KRB5

On 10/05/2012 04:09 AM, Dave Love wrote: Alex Chekholko ch...@stanford.edu writes: Hi Christoph, We do have it working with AUKS, which is mostly outside GE. Is that better than DESY's arcx system, or are they roughly equivalent? I can't remember why arcx seemed a better bet on a quick look

Re: [gridengine users] SGE with KRB5

, Christoph Gesendet von meinem Windows Phone ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users -- Alex Chekholko ch...@stanford.edu ___ users mailing list users

[gridengine users] qlogin sets TERM var to dumb?

. Regards, -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users

Re: [gridengine users] 10GbE TOR's and performance tuning.

blade/node infrastructure. Thanks! --JC -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users

Re: [gridengine users] 10GbE TOR's and performance tuning.

I found a reference Some Cisco switches are even permanently configured this way -- they can receive pause frames but never emit them. http://virtualthreads.blogspot.com/2006/02/beware-ethernet-flow-control.html On 09/13/2012 11:17 AM, Alex Chekholko wrote: 3. What of hardware flow control

[gridengine users] AMD 62xx performance was:Re: How to Restrict forking?

when you get a chance? -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users

Re: [gridengine users] debugging commlib errors?

Hi, For a low-level gridengine test, you can use the 'qping' command between various grid engine daemons. I would guess that during the time that you see the commlib error, your qping also wouldn't work. E.g. from an exec host: qping -info QMASTER_NAME 6444 qmaster 1 See the qping man

[gridengine users] queues not erroring out when jobs error out

specific to the queue. per http://arc.liv.ac.uk/SGE/howto/troubleshooting.html We also have a load sensor that checks for the presence of this filesystem, but the load sensor only updates every few minutes, while the filesystem tends to disappear for only about 60s. Regards, -- Alex Chekholko

Re: [gridengine users] load_formula and PE jobs

, for PE jobs, it seems as if GE does not abide by the load_formula. Does the scheduler use a different load formula for single core jobs verses parallel jobs suing the PE environment setup? Joseph -- Alex Chekholko ch...@stanford.edu ___ users mailing

Re: [gridengine users] qalter not successful

ECS, VUW, NZ ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users -- Alex Chekholko ch...@stanford.edu 347-401-4860 ___ users mailing list users@gridengine.org https

Re: [gridengine users] Over-subscription of hosts -- the role of slots and queues

that they don't overlap. The fact that the problem doesn't come up with multiple parallel jobs may be because of load thresholds. What do you think of my solution? If it's nonsense, can anyone suggest what the problem may be? -- Alex Chekholko ch...@stanford.edu

Re: [gridengine users] Requesting h_vmem or memfree

', the latter is mem_free in 'qconf -se'. Regards, -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users

Re: [gridengine users] Dynamic Resources?

a sensor instead. e.g. http://gridscheduler.sourceforge.net/howto/loadsensor.html Regards, -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users

Re: [gridengine users] MATLAB + SGE experts?

/ Regards, -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users

Re: [gridengine users] qacct in xml?

with finished jobs. thanks in advance for help gerard ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users -- Alex Chekholko ch...@stanford.edu 347-401-4860

Re: [gridengine users] SC11 anyone?

! -- Daniel Boone ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users -- Alex Chekholko ch...@stanford.edu 347-401-4860 ___ users mailing list users

Re: [gridengine users] current status of Kerberos support (and maybe AFS)?

you might have. Good Luck, Mark Mark Suhovecky HPC System Administrator Center for Research Computing University of Notre Dame suhove...@nd.edu From: users-boun...@gridengine.org [users-boun...@gridengine.org] On Behalf Of Alex Chekholko [ch

[gridengine users] current status of Kerberos support (and maybe AFS)?

will work with modern GE 6.2u5+? Regards, -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users

Re: [gridengine users] Queue and Parallell Environments

where you specify which parallel environments your queue definition has. -- Alex Chekholko ch...@stanford.edu ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users

Re: [gridengine users] Maximum memory for running process?

Yes, think of it as a high water mark over the duration of the process. 6.2u5 has a bug in accounting that particular metric, but previous and later versions do not. - Original Message - From: William Deegan b...@baddogconsulting.com To: Gridengine Users Group users@gridengine.org