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[Jgi-users] JGI-NERSC weekly newsletter

Author: Tony Wildish <>
Date: 2017-09-13 15:38:25

Training Opportunities * A SLURM Hands-On Workshopwill be held Thursday, Sept 28 from 12-2pm in 149B. Hopefully by now everyone knows that Genepool is moving to SLURM, and we received lots of great feedback about what you need at last month’s training sessions. We’re planning this workshop as an opportunity for you to learn about the Denovo test system, to convert YOUR submission scripts from UGE to SLURM, practice submitting and monitoring your jobs, and best practices to minimize job charges. If you’re interested in attending it is critical that you sign upat THIS LINK <>. Space is limited! * Cori/SLURM/Denovo Training slidesare available at the Genepool training and tutorials page: o A recording will be made available soon, for those who missed it. Upcoming Outages * Quarterly Maintenance will be a multiple day outage. In early October, both Cori and Edison will be unavailable for up to 5 days while our Emergency Power Off system is upgraded and an additional pump is installed in support of water-cooling the large HPC systems. The expected start date is Friday, October 6. General Information * Denovo is available for testing. It’s not production-ready yet, nonetheless, we encourage you to try it out and let us know what’s missing. Please file tickets, via mail to, for any problems you find. o The timeline for migrating Genepool nodes to Denovo and retiring UGE is still uncertain, though we expect the move to be fast once Denovo is production-ready. This is likely to be a hot topic for the next few months, so we request all groups who are currently active on Genepool to please send representatives to the regular Sysops meetings(see below) where these matters are discussed. o Note that we expect users on Denovo to use containers for bioinformatics software as far as possible, and to make an effort at portability to Cori. o There is a list of currently installed software modules and known issues <>which will be updated until the system is stable. If your favorite package isn’t working, please check there for news before filing a ticket. * There is a regular JGI-NERSC SysOpsmeeting on Thursday afternoon, 3pm-4pm in room 101, where general computing issues are discussed among a wider audience. The meeting is held weekly except for the last Thursday of each month. If you’re interested, or would like to know more, send us an email or come along to Office Hours for a chat. * NERSC Data Day/NUG Data Competition Info Now OnlineMore details about the Data Competition, which will be held the morning of Wednesday, September 20 as part of NERSC's joint Data Day and NUG annual meeting, are now available at Why not give it a go! * NERSC Office Hours.Regular office hours are in Room 413 at the JGI. o Wednesdays 10am-12pm o Thursdays 10am-12pm - Tony. * Procmon weekly report* Top Ten Projects By CPUhour Place Project Processes CPU hours 1 fungal-annotation.p 1623086 25776.13 2 plant-assembly.p 57474 23447.87 3 prok-scell.p 1664990 16826.53 4 gentech-rqc.p 84997 12020.81 5 plant-annotation.p 297919 8653.64 6 fungal-assembly.p 20775 7045.54 7 gentech-rnd.p 546129 5123.94 8 prok-assembly.p 27686 4763.50 9 plant-diversity.p 39627 3050.58 10 prok-annotation.p 63032 2642.33 Top Ten Users By CPUhour Place User Processes CPU hours 1 asafl 1675 16143.68 2 bredeson 20221 15462.82 3 annotrub 964674 13275.06 4 frankk 651967 12453.46 5 qc_user 118412 10865.91 6 sqshu 294338 8424.13 7 nolan 542 7774.70 8 eugeneg 5434 3012.08 9 amudd 652 3009.45 10 annau 11841 2919.61 Top Ten Executables By CPUhour Place Executable Processes CPU hours 1 blastp 310533 18772.95 2 lastal 1527 16784.69 3 spades 413709 10724.51 4 cross_match 46400 8126.45 5 overlapInCore 2655 7567.33 6 blasr 1156 7387.35 7 bwa 1025 7167.54 8 pindel 100 4883.62 9 blastall 88044 4442.67 10 blastn 4857 4283.24 _______________________________________________ Jgi-users mailing list

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