Last login: Tue Feb 12 10:54:07 on ttys008 rundel@tbBook [~]$ ssh cr173@dcc-slogin.oit.duke.edu ################################################################################ # You are about to access a Duke University computer network that is intended # # for authorized users only. You should have no expectation of privacy in # # your use of this network. Use of this network constitutes consent to # # monitoring, retrieval, and disclosure of any information stored within the # # network for any purpose including criminal prosecution. # ################################################################################ cr173@dcc-slogin.oit.duke.edu's password: Last login: Mon Feb 11 16:37:49 2019 from vpn-campus-152-3-71-65.ssl.vpn.duke.edu cr173@dcc-slogin-03 ~ $ cr173@dcc-slogin-03 ~ $ cr173@dcc-slogin-03 ~ $ sinfo show partition PARTITION AVAIL TIMELIMIT NODES STATE NODELIST scavenger up 90-00:00:0 47 mix dcc-biostat-[01-03],dcc-compeb-[01-12],dcc-dailabs-[01-02,04],dcc-dhvi-[02-03],dcc-econ-[02,17,21-22],dcc-gcb-[03,62-67],dcc-jirtle-[04-06,09],dcc-khauserlab-01,dcc-kumarlab-01,dcc-lefkowitz-01,dcc-mcglynnlab-01,dcc-nicolab-01,dcc-noor-[01-02],dcc-rodrigolab-01,dcc-savageresearch-01,dcc-shawlab-01,dcc-tmolab-02,dcc-wychem-01 scavenger up 90-00:00:0 16 alloc dcc-compeb-[13-14],dcc-dhvi-01,dcc-econ-20,dcc-hashimilab-02,dcc-jirtle-[01-03],dcc-owzarteam-01,dcc-pfister-01,dcc-rausherlab-[01-02],dcc-symposium-01,dcc-tmolab-03,dcc-yoderlab-[01,03] scavenger up 90-00:00:0 59 idle dcc-aryalab-01,dcc-biodept-[01,03],dcc-bragg-[01-05],dcc-cagpm-[01-02],dcc-carin-[01-25],dcc-chg-[01-05],dcc-dailabs-[03,05],dcc-econ-[01,03,18-19,23],dcc-gcb-[01-02,04-09],dcc-jirtle-[07-08],dcc-savageresearch-02,dcc-schmidlab-01 artai-gpu up 3:00:00 3 mix dcc-dsplus-gpu-[01-02,05] artai-gpu up 3:00:00 2 alloc dcc-dsplus-gpu-[04,06] artai-gpu up 3:00:00 7 idle dcc-dsplus-gpu-[03,07-12] aryalab up 90-00:00:0 1 idle dcc-aryalab-01 biodept up 90-00:00:0 2 idle dcc-biodept-[01,03] biostat up 90-00:00:0 3 mix dcc-biostat-[01-03] brownlab-gpu up 7-00:00:00 4 idle dcc-brownlab-gpu-[01-04] cagpm up 90-00:00:0 2 idle dcc-cagpm-[01-02] carin up 90-00:00:0 25 idle dcc-carin-[01-25] carin-gpu up 7-00:00:00 6 mix dcc-carin-gpu-[01,06-08,10-11] carin-gpu up 7-00:00:00 6 idle dcc-carin-gpu-[02-05,09,12] chg up 90-00:00:0 5 idle dcc-chg-[01-05] collinslab up 90-00:00:0 4 mix dcc-collinslab-gpu-[01-04] common* up 90-00:00:0 156 mix dcc-core-[05,07-13,17-52,55-56,58-61,63-64,75,77,80,82,85-86,88-89,91,95,99,106-108,110-112,117-118,122-127,130-136,138-140,142-146,149-150,152,161,163-164,167,169-171,173-183,185-189,192-193,196-201,203-211,213-214,216-228,230-232,234,238-239] common* up 90-00:00:0 70 alloc dcc-core-[01-04,06,14-16,53-54,57,62,65,74,76,78-79,81,83-84,87,90,92-94,96-98,100,109,113-116,119-121,128-129,137,141,147-148,151,153-160,162,165-166,168,172,184,190-191,194-195,202,212,215,229,233,235-237] common-large up 90-00:00:0 1 mix dcc-core-101 compeb up 90-00:00:0 12 mix dcc-compeb-[01-12] compeb up 90-00:00:0 2 alloc dcc-compeb-[13-14] dailabs up 90-00:00:0 3 mix dcc-dailabs-[01-02,04] dailabs up 90-00:00:0 2 idle dcc-dailabs-[03,05] dbchem up 90-00:00:0 4 mix dcc-dbchem-[01-02,04,18] dbchem up 90-00:00:0 14 alloc dcc-dbchem-[03,05-17] dhvi up 90-00:00:0 2 mix dcc-dhvi-[02-03] dhvi up 90-00:00:0 1 alloc dcc-dhvi-01 dhvi-gpu up 90-00:00:0 16 alloc dcc-dhvi-gpu-[01-08,10-16,18] dhvi-gpu up 90-00:00:0 4 idle dcc-dhvi-gpu-[09,17,19-20] strucbio-cryosparc-gpu up 7-00:00:00 1 idle dcc-dhvi-strucbio-gpu-01 dhvi-strucbio-gpu up 7-00:00:00 4 idle dcc-dhvi-strucbio-gpu-[02-05] dolbowlab up 90-00:00:0 1 idle dcc-dolbowlab-01 donglab up 90-00:00:0 3 idle dcc-donglab-[01-03] dsplus-gpu up 7-00:00:00 3 mix dcc-dsplus-gpu-[01-02,05] dsplus-gpu up 7-00:00:00 2 alloc dcc-dsplus-gpu-[04,06] dsplus-gpu up 7-00:00:00 7 idle dcc-dsplus-gpu-[03,07-12] ece-gpu-high up 6:00:00 16 idle dcc-ece-gpu-[05-20] ece-gpu-low up 6:00:00 16 idle dcc-ece-gpu-[05-20] econ up 90-00:00:0 4 mix dcc-econ-[02,17,21-22] econ up 90-00:00:0 1 alloc dcc-econ-20 econ up 90-00:00:0 5 idle dcc-econ-[01,03,18-19,23] gcb up 90-00:00:0 7 mix dcc-gcb-[03,62-67] gcb up 90-00:00:0 8 idle dcc-gcb-[01-02,04-09] gpu-common up 2-00:00:00 2 alloc dcc-gpu-[31-32] hashimilab up 90-00:00:0 1 alloc dcc-hashimilab-02 herringlab up 90-00:00:0 1 idle dcc-herringlab-01 herringlab-low up 90-00:00:0 1 idle dcc-herringlab-01 hpc up 90-00:00:0 1 alloc dcc-symposium-01 jirtle up 90-00:00:0 4 mix dcc-jirtle-[04-06,09] jirtle up 90-00:00:0 3 alloc dcc-jirtle-[01-03] jirtle up 90-00:00:0 2 idle dcc-jirtle-[07-08] khauserlab up 90-00:00:0 1 mix dcc-khauserlab-01 kumarlab up 90-00:00:0 1 mix dcc-kumarlab-01 lefkowitz up 90-00:00:0 1 mix dcc-lefkowitz-01 mcglynnlab up 90-00:00:0 1 mix dcc-mcglynnlab-01 nicolab up 90-00:00:0 1 mix dcc-nicolab-01 noor up 90-00:00:0 2 mix dcc-noor-[01-02] nsoe-it up 90-00:00:0 1 idle dcc-nsoe-it-01 owzarteam up 90-00:00:0 1 alloc dcc-owzarteam-01 pcharbon up 90-00:00:0 2 mix dcc-pcharbon-[18,20] pcharbon up 90-00:00:0 18 alloc dcc-pcharbon-[01-17,19] pfisterlab up 90-00:00:0 1 alloc dcc-pfister-01 psklab up 90-00:00:0 1 idle dcc-psklab-01 randleslab up 90-00:00:0 21 idle dcc-randleslab-[01-21] randleslab-gpu up 90-00:00:0 7 mix dcc-ib-a-rlab-gpu-ad29-[26,28,32,34],dcc-ib-a-rlab-gpu-ae29-[26,28,30] randleslab-gpu up 90-00:00:0 3 idle dcc-ib-a-rlab-gpu-ad29-30,dcc-ib-a-rlab-gpu-ae29-[32,34] randleslab-high up 90-00:00:0 54 mix dcc-ib-a-rlab-ad29-[01-18,20,23-25],dcc-ib-a-rlab-ae29-[01-25],dcc-ib-a-rlab-gpu-ad29-[26,28,32,34],dcc-ib-a-rlab-gpu-ae29-[26,28,30] randleslab-high up 90-00:00:0 6 idle dcc-ib-a-rlab-ad29-[19,21-22],dcc-ib-a-rlab-gpu-ad29-30,dcc-ib-a-rlab-gpu-ae29-[32,34] randleslab-ib up 90-00:00:0 54 mix dcc-ib-a-rlab-ad29-[01-18,20,23-25],dcc-ib-a-rlab-ae29-[01-25],dcc-ib-a-rlab-gpu-ad29-[26,28,32,34],dcc-ib-a-rlab-gpu-ae29-[26,28,30] randleslab-ib up 90-00:00:0 6 idle dcc-ib-a-rlab-ad29-[19,21-22],dcc-ib-a-rlab-gpu-ad29-30,dcc-ib-a-rlab-gpu-ae29-[32,34] randleslab-ib-low up 90-00:00:0 54 mix dcc-ib-a-rlab-ad29-[01-18,20,23-25],dcc-ib-a-rlab-ae29-[01-25],dcc-ib-a-rlab-gpu-ad29-[26,28,32,34],dcc-ib-a-rlab-gpu-ae29-[26,28,30] randleslab-ib-low up 90-00:00:0 6 idle dcc-ib-a-rlab-ad29-[19,21-22],dcc-ib-a-rlab-gpu-ad29-30,dcc-ib-a-rlab-gpu-ae29-[32,34] rausherlab up 90-00:00:0 2 alloc dcc-rausherlab-[01-02] rodrigolab up 90-00:00:0 1 mix dcc-rodrigolab-01 savageresearch up 90-00:00:0 1 mix dcc-savageresearch-01 savageresearch up 90-00:00:0 1 idle dcc-savageresearch-02 shawlab up 90-00:00:0 1 mix dcc-shawlab-01 schmidlab up 90-00:00:0 1 idle dcc-schmidlab-01 statdept up 90-00:00:0 1 idle dcc-statdept-01 statdept-low up 90-00:00:0 1 idle dcc-statdept-01 tcfdg up 90-00:00:0 5 idle dcc-bragg-[01-05] tmolab up 90-00:00:0 1 mix dcc-tmolab-02 tmolab up 90-00:00:0 1 alloc dcc-tmolab-03 ultrasound up 90-00:00:0 11 idle dcc-ultrasound-[01-11] ultrasound-gpu up 90-00:00:0 4 idle dcc-ultrasound-gpu-[01-04] volfovskylab up 90-00:00:0 1 idle dcc-volfovskylab-01 volfovskylab-low up 90-00:00:0 1 idle dcc-volfovskylab-01 wmglab up 90-00:00:0 1 comp dcc-peterchev-09 wmglab up 90-00:00:0 11 mix dcc-peterchev-01,dcc-wmglab-[02-03,17,24-26,29-30,36-37] wmglab up 90-00:00:0 14 alloc dcc-peterchev-[05-06],dcc-wmglab-[15-16,18-23,31-34] wmglab up 90-00:00:0 11 idle dcc-peterchev-[02-04,07-08],dcc-wmglab-[01,04-05,27-28,35] wychem up 90-00:00:0 1 mix dcc-wychem-01 yoderlab up 90-00:00:0 2 alloc dcc-yoderlab-[01,03] cr173@dcc-slogin-03 ~ $ cr173@dcc-slogin-03 ~ $ srun --partition=statdept --account=statdept --pty bash srun: job 46524561 queued and waiting for resources srun: job 46524561 has been allocated resources cr173@dcc-statdept-01 ~ $ exit exit cr173@dcc-slogin-03 ~ $ srun --partition=herringlab-low --account=statdept --pty bash srun: job 46524573 queued and waiting for resources srun: job 46524573 has been allocated resources cr173@dcc-herringlab-01 ~ $ top top - 11:56:16 up 139 days, 21:17, 0 users, load average: 0.47, 0.42, 0.41 Tasks: 623 total, 1 running, 622 sleeping, 0 stopped, 0 zombie %Cpu(s): 0.0 us, 0.0 sy, 0.0 ni,100.0 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st %Node0 : 0.0 us, 0.0 sy, 0.0 ni,100.0 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st KiB Mem : 75938112+total, 74440166+free, 5180136 used, 9799324 buff/cache KiB Swap: 2097148 total, 2097148 free, 0 used. 75066035+avail Mem PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 79175 cr173 20 0 172836 2868 1624 R 0.8 0.0 0:00.05 top 1 root 20 0 54644 6860 4008 S 0.0 0.0 47:41.66 systemd 2 root 20 0 0 0 0 S 0.0 0.0 0:02.94 kthreadd 3 root 20 0 0 0 0 S 0.0 0.0 0:00.10 ksoftirqd/0 5 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0H 7 root rt 0 0 0 0 S 0.0 0.0 0:00.28 migration/0 8 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcu_bh 9 root 20 0 0 0 0 S 0.0 0.0 60:23.47 rcu_sched 10 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 lru-add-drain 11 root rt 0 0 0 0 S 0.0 0.0 0:23.72 watchdog/0 12 root rt 0 0 0 0 S 0.0 0.0 0:22.24 watchdog/1 13 root rt 0 0 0 0 S 0.0 0.0 0:00.27 migration/1 14 root 20 0 0 0 0 S 0.0 0.0 0:00.08 ksoftirqd/1 16 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/1:0H 17 root rt 0 0 0 0 S 0.0 0.0 0:21.64 watchdog/2 18 root rt 0 0 0 0 S 0.0 0.0 0:00.26 migration/2 19 root 20 0 0 0 0 S 0.0 0.0 0:00.07 ksoftirqd/2 21 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/2:0H 22 root rt 0 0 0 0 S 0.0 0.0 0:21.43 watchdog/3 23 root rt 0 0 0 0 S 0.0 0.0 0:00.27 migration/3 24 root 20 0 0 0 0 S 0.0 0.0 0:00.09 ksoftirqd/3 26 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/3:0H 27 root rt 0 0 0 0 S 0.0 0.0 0:22.23 watchdog/4 28 root rt 0 0 0 0 S 0.0 0.0 0:00.29 migration/4 29 root 20 0 0 0 0 S 0.0 0.0 0:00.08 ksoftirqd/4 31 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/4:0H 32 root rt 0 0 0 0 S 0.0 0.0 0:21.93 watchdog/5 33 root rt 0 0 0 0 S 0.0 0.0 0:00.28 migration/5 cr173@dcc-herringlab-01 ~ $ exit exit cr173@dcc-slogin-03 ~ $ srun --partition=herringlab-low --account=statdept --pty bash ▽ #!/usr/bin/bash cr173@dcc-slogin-03 ~ $ srun --partition=statdept --account=statdept -c60 --pty bash srun: job 46524593 queued and waiting for resources srun: job 46524593 has been allocated resources cr173@dcc-statdept-01 ~ $ exit exit cr173@dcc-slogin-03 ~ $ vim multi_part.sh cr173@dcc-slogin-03 ~ $ ls cov_mat.R example_pm25 ex_pm25.simg multi_part.sh rocker_bayes.simg tidyverse.simg cov.rds example_sbatch gerrymandering-xsede parttest r-ver.simg cr173@dcc-slogin-03 ~ $ mkdir tmp cr173@dcc-slogin-03 ~ $ mv multi_part.sh tmp/ cr173@dcc-slogin-03 ~ $ l;s -bash: l: command not found -bash: s: command not found cr173@dcc-slogin-03 ~ $ cd tmp/ cr173@dcc-slogin-03 ~/tmp $ ls multi_part.sh cr173@dcc-slogin-03 ~/tmp $ sbatch multi_part.sh Submitted batch job 46525215 cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[3-10] statdept- multi_pa cr173 PD 0:00 1 (None) 46525215_1 herringla multi_pa cr173 R 0:02 1 dcc-herringlab-01 46525215_2 herringla multi_pa cr173 R 0:02 1 dcc-herringlab-01 cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[3-10] statdept- multi_pa cr173 PD 0:00 1 (None) 46525215_1 herringla multi_pa cr173 R 0:05 1 dcc-herringlab-01 46525215_2 herringla multi_pa cr173 R 0:05 1 dcc-herringlab-01 cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[3-10] statdept- multi_pa cr173 PD 0:00 1 (None) cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[3-10] statdept- multi_pa cr173 PD 0:00 1 (None) cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[3-10] statdept- multi_pa cr173 PD 0:00 1 (None) cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[5-10] statdept- multi_pa cr173 PD 0:00 1 (None) 46525215_3 herringla multi_pa cr173 R 0:02 1 dcc-herringlab-01 46525215_4 herringla multi_pa cr173 R 0:02 1 dcc-herringlab-01 cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[5-10] statdept- multi_pa cr173 PD 0:00 1 (None) cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[5-10] statdept- multi_pa cr173 PD 0:00 1 (None) ▽ #!/usr/bin/bash cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[7-10] statdept- multi_pa cr173 PD 0:00 1 (None) cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[7-10] statdept- multi_pa cr173 PD 0:00 1 (None) cr173@dcc-slogin-03 ~/tmp $ ls multi_part.sh slurm-46525215_1.out slurm-46525215_2.out slurm-46525215_3.out slurm-46525215_4.out slurm-46525215_5.out slurm-46525215_6.out cr173@dcc-slogin-03 ~/tmp $ grep "" *.out slurm-46525215_1.out:dcc-herringlab-01 slurm-46525215_2.out:dcc-herringlab-01 slurm-46525215_3.out:dcc-herringlab-01 slurm-46525215_4.out:dcc-herringlab-01 slurm-46525215_5.out:dcc-herringlab-01 slurm-46525215_6.out:dcc-herringlab-01 cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[9-10] statdept- multi_pa cr173 PD 0:00 1 (Resources) cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[9-10] statdept- multi_pa cr173 PD 0:00 1 (Resources) cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[9-10] statdept- multi_pa cr173 PD 0:00 1 (Resources) cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[9-10] statdept- multi_pa cr173 PD 0:00 1 (Resources) cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[9-10] statdept- multi_pa cr173 PD 0:00 1 (Resources) cr173@dcc-slogin-03 ~/tmp $ ls multi_part.sh slurm-46525215_2.out slurm-46525215_4.out slurm-46525215_6.out slurm-46525215_8.out slurm-46525215_1.out slurm-46525215_3.out slurm-46525215_5.out slurm-46525215_7.out cr173@dcc-slogin-03 ~/tmp $ cp multi_part.sh small_multi_part.sh cr173@dcc-slogin-03 ~/tmp $ vim small_multi_part.sh cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525215_[9-10] statdept- multi_pa cr173 PD 0:00 1 (Resources) cr173@dcc-slogin-03 ~/tmp $ sbatch small_multi_part.sh Submitted batch job 46525236 cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525236_[1-200] statdept- small_mu cr173 PD 0:00 1 (Resources) cr173@dcc-slogin-03 ~/tmp $ grep "" *.out slurm-46525215_1.out:dcc-herringlab-01 slurm-46525215_2.out:dcc-herringlab-01 slurm-46525215_3.out:dcc-herringlab-01 slurm-46525215_4.out:dcc-herringlab-01 slurm-46525215_5.out:dcc-herringlab-01 slurm-46525215_6.out:dcc-herringlab-01 slurm-46525215_7.out:dcc-volfovskylab-01 slurm-46525215_8.out:dcc-volfovskylab-01 cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525236_[25-200] statdept- small_mu cr173 PD 0:00 1 (Resources) cr173@dcc-slogin-03 ~/tmp $ ls multi_part.sh slurm-46525215_2.out slurm-46525215_4.out slurm-46525215_6.out slurm-46525215_8.out slurm-46525215_1.out slurm-46525215_3.out slurm-46525215_5.out slurm-46525215_7.out small_multi_part.sh cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525236_29 herringla small_mu cr173 CG 0:04 1 dcc-herringlab-01 46525236_[49-200] statdept- small_mu cr173 PD 0:00 1 (Resources) 46525236_43 herringla small_mu cr173 R 0:03 1 dcc-herringlab-01 46525236_44 herringla small_mu cr173 R 0:03 1 dcc-herringlab-01 46525236_45 herringla small_mu cr173 R 0:03 1 dcc-herringlab-01 46525236_46 herringla small_mu cr173 R 0:03 1 dcc-herringlab-01 46525236_47 herringla small_mu cr173 R 0:03 1 dcc-herringlab-01 46525236_48 herringla small_mu cr173 R 0:03 1 dcc-herringlab-01 46525236_28 herringla small_mu cr173 R 0:04 1 dcc-herringlab-01 46525236_30 herringla small_mu cr173 R 0:04 1 dcc-herringlab-01 46525236_33 herringla small_mu cr173 R 0:04 1 dcc-herringlab-01 46525236_34 herringla small_mu cr173 R 0:04 1 dcc-herringlab-01 46525236_35 herringla small_mu cr173 R 0:04 1 dcc-herringlab-01 46525236_36 herringla small_mu cr173 R 0:04 1 dcc-herringlab-01 46525236_37 herringla small_mu cr173 R 0:04 1 dcc-herringlab-01 46525236_38 herringla small_mu cr173 R 0:04 1 dcc-herringlab-01 46525236_39 herringla small_mu cr173 R 0:04 1 dcc-herringlab-01 46525236_40 herringla small_mu cr173 R 0:04 1 dcc-herringlab-01 46525236_41 herringla small_mu cr173 R 0:04 1 dcc-herringlab-01 46525236_42 herringla small_mu cr173 R 0:04 1 dcc-herringlab-01 cr173@dcc-slogin-03 ~/tmp $ squeue -u cr173 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 46525236_[73-200] statdept- small_mu cr173 PD 0:00 1 (Resources) cr173@dcc-slogin-03 ~/tmp $ ls multi_part.sh slurm-46525236_13.out slurm-46525236_26.out slurm-46525236_39.out slurm-46525236_51.out slurm-46525236_64.out slurm-46525215_10.out slurm-46525236_14.out slurm-46525236_27.out slurm-46525236_3.out slurm-46525236_52.out slurm-46525236_65.out slurm-46525215_1.out slurm-46525236_15.out slurm-46525236_28.out slurm-46525236_40.out slurm-46525236_53.out slurm-46525236_66.out slurm-46525215_2.out slurm-46525236_16.out slurm-46525236_29.out slurm-46525236_41.out slurm-46525236_54.out slurm-46525236_67.out slurm-46525215_3.out slurm-46525236_17.out slurm-46525236_2.out slurm-46525236_42.out slurm-46525236_55.out slurm-46525236_68.out slurm-46525215_4.out slurm-46525236_18.out slurm-46525236_30.out slurm-46525236_43.out slurm-46525236_56.out slurm-46525236_69.out slurm-46525215_5.out slurm-46525236_19.out slurm-46525236_31.out slurm-46525236_44.out slurm-46525236_57.out slurm-46525236_6.out slurm-46525215_6.out slurm-46525236_1.out slurm-46525236_32.out slurm-46525236_45.out slurm-46525236_58.out slurm-46525236_70.out slurm-46525215_7.out slurm-46525236_20.out slurm-46525236_33.out slurm-46525236_46.out slurm-46525236_59.out slurm-46525236_71.out slurm-46525215_8.out slurm-46525236_21.out slurm-46525236_34.out slurm-46525236_47.out slurm-46525236_5.out slurm-46525236_72.out slurm-46525215_9.out slurm-46525236_22.out slurm-46525236_35.out slurm-46525236_48.out slurm-46525236_60.out slurm-46525236_7.out slurm-46525236_10.out slurm-46525236_23.out slurm-46525236_36.out slurm-46525236_49.out slurm-46525236_61.out slurm-46525236_8.out slurm-46525236_11.out slurm-46525236_24.out slurm-46525236_37.out slurm-46525236_4.out slurm-46525236_62.out slurm-46525236_9.out slurm-46525236_12.out slurm-46525236_25.out slurm-46525236_38.out slurm-46525236_50.out slurm-46525236_63.out small_multi_part.sh cr173@dcc-slogin-03 ~/tmp $ grep "" *.out slurm-46525215_10.out:dcc-statdept-01 slurm-46525215_1.out:dcc-herringlab-01 slurm-46525215_2.out:dcc-herringlab-01 slurm-46525215_3.out:dcc-herringlab-01 slurm-46525215_4.out:dcc-herringlab-01 slurm-46525215_5.out:dcc-herringlab-01 slurm-46525215_6.out:dcc-herringlab-01 slurm-46525215_7.out:dcc-volfovskylab-01 slurm-46525215_8.out:dcc-volfovskylab-01 slurm-46525215_9.out:dcc-statdept-01 slurm-46525236_10.out:dcc-herringlab-01 slurm-46525236_11.out:dcc-herringlab-01 slurm-46525236_12.out:dcc-herringlab-01 slurm-46525236_13.out:dcc-herringlab-01 slurm-46525236_14.out:dcc-herringlab-01 slurm-46525236_15.out:dcc-herringlab-01 slurm-46525236_16.out:dcc-herringlab-01 slurm-46525236_17.out:dcc-herringlab-01 slurm-46525236_18.out:dcc-herringlab-01 slurm-46525236_19.out:dcc-herringlab-01 slurm-46525236_1.out:dcc-herringlab-01 slurm-46525236_20.out:dcc-herringlab-01 slurm-46525236_21.out:dcc-herringlab-01 slurm-46525236_22.out:dcc-herringlab-01 slurm-46525236_23.out:dcc-herringlab-01 slurm-46525236_24.out:dcc-herringlab-01 slurm-46525236_25.out:dcc-herringlab-01 slurm-46525236_26.out:dcc-herringlab-01 slurm-46525236_27.out:dcc-herringlab-01 slurm-46525236_28.out:dcc-herringlab-01 slurm-46525236_29.out:dcc-herringlab-01 slurm-46525236_2.out:dcc-herringlab-01 slurm-46525236_30.out:dcc-herringlab-01 slurm-46525236_31.out:dcc-herringlab-01 slurm-46525236_32.out:dcc-herringlab-01 slurm-46525236_33.out:dcc-herringlab-01 slurm-46525236_34.out:dcc-herringlab-01 slurm-46525236_35.out:dcc-herringlab-01 slurm-46525236_36.out:dcc-herringlab-01 slurm-46525236_37.out:dcc-herringlab-01 slurm-46525236_38.out:dcc-herringlab-01 slurm-46525236_39.out:dcc-herringlab-01 slurm-46525236_3.out:dcc-herringlab-01 slurm-46525236_40.out:dcc-herringlab-01 slurm-46525236_41.out:dcc-herringlab-01 slurm-46525236_42.out:dcc-herringlab-01 slurm-46525236_43.out:dcc-herringlab-01 slurm-46525236_44.out:dcc-herringlab-01 slurm-46525236_45.out:dcc-herringlab-01 slurm-46525236_46.out:dcc-herringlab-01 slurm-46525236_47.out:dcc-herringlab-01 slurm-46525236_48.out:dcc-herringlab-01 slurm-46525236_49.out:dcc-herringlab-01 slurm-46525236_4.out:dcc-herringlab-01 slurm-46525236_50.out:dcc-herringlab-01 slurm-46525236_51.out:dcc-herringlab-01 slurm-46525236_52.out:dcc-herringlab-01 slurm-46525236_53.out:dcc-herringlab-01 slurm-46525236_54.out:dcc-herringlab-01 slurm-46525236_55.out:dcc-herringlab-01 slurm-46525236_56.out:dcc-herringlab-01 slurm-46525236_57.out:dcc-herringlab-01 slurm-46525236_58.out:dcc-herringlab-01 slurm-46525236_59.out:dcc-herringlab-01 slurm-46525236_5.out:dcc-herringlab-01 slurm-46525236_60.out:dcc-herringlab-01 slurm-46525236_61.out:dcc-herringlab-01 slurm-46525236_62.out:dcc-herringlab-01 slurm-46525236_63.out:dcc-herringlab-01 slurm-46525236_64.out:dcc-herringlab-01 slurm-46525236_65.out:dcc-herringlab-01 slurm-46525236_66.out:dcc-herringlab-01 slurm-46525236_67.out:dcc-herringlab-01 slurm-46525236_68.out:dcc-herringlab-01 slurm-46525236_69.out:dcc-herringlab-01 slurm-46525236_6.out:dcc-herringlab-01 slurm-46525236_70.out:dcc-herringlab-01 slurm-46525236_71.out:dcc-herringlab-01 slurm-46525236_72.out:dcc-herringlab-01 slurm-46525236_7.out:dcc-herringlab-01 slurm-46525236_8.out:dcc-herringlab-01 slurm-46525236_9.out:dcc-herringlab-01 cr173@dcc-slogin-03 ~/tmp $ cr173@dcc-slogin-03 ~/tmp $ cd /opt/apps/ cr173@dcc-slogin-03 /opt/apps $ ls admin cloog-0.18.1 images matlabR2015a openmm R-3.0.3 slurm amber11 cuda-5.5 include matlabR2016a openmm5.2 rhel6 staging amber12 cufflinks-2.1.1 intel mcl pb_mpi1.5a rhel7 stata anaconda3 dev intelcsl modulefiles perl-5.16.2 rldev stata13 bayenv2 doc isl mpc-0.9 perl-5.20.1 sas th224 beagle drv6 jellyfish mpfr-3.0.0 Python-2.7.1 sbgrid tophat BEASTv1.7.5 EMBOSS-6.6.0 lib NAMD_2.10_Source Python-2.7.10 sbgrid-linux64 tophat-2.0.10 BEASTv1.8.0 etc lib64 novocraft Python-2.7.3 sbin tophat-bowtie bedtools2-2.19.1 gcc libexec nwchem Python-2.7.5 sdg trinityrnaseq-2.1.1 bin GenomeAnalysisTK-2.3-9 log4cpp nwchem-6.3r2 Python-3.3.2 sge_data boost_1_55_0 gmp-4.3.2 mathematica8 nwchem-6.3.revision2-src.2013-10-17 Python-3.3.3 share bwa-0.7.9a icm-3.8-0 MATLAB nwchem-src-2013-02-06 Queue-2.3-9 signalp-4.1 chem ima2 matlabR2014a nwchem-trunk R-2.15.2 sing cr173@dcc-slogin-03 /opt/apps $ module list No Modulefiles Currently Loaded. cr173@dcc-slogin-03 /opt/apps $ module show cr173@dcc-slogin-03 /opt/apps $ cd ~/example_pm25/ cr173@dcc-slogin-03 ~/example_pm25 $ git pull remote: Enumerating objects: 5, done. remote: Counting objects: 100% (5/5), done. remote: Compressing objects: 100% (1/1), done. remote: Total 3 (delta 2), reused 3 (delta 2), pack-reused 0 Unpacking objects: 100% (3/3), done. From https://github.com/Sta790-Sp19/example_pm25 af5771b..ac0acd6 parallel -> origin/parallel Updating af5771b..ac0acd6 Fast-forward 1_matrix_mult.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) cr173@dcc-slogin-03 ~/example_pm25 $ cr173@dcc-slogin-03 ~/example_pm25 $ ls 1_matrix_mult.R 2_matrix_chol.R 3_spbayes.R data gp_pm25.Rproj cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -c4 singularity exec ../r-ver.simg Rscript 1_matrix_mult.R 1 1 srun: job 46528435 queued and waiting for resources srun: job 46528435 has been allocated resources [[1]] user system elapsed 55.444 8.162 16.057 Run time: 16.09171s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -c4 singularity exec ../r-ver.simg Rscript 1_matrix_mult.R 1 1 srun: job 46528443 queued and waiting for resources srun: job 46528443 has been allocated resources [[1]] user system elapsed 54.122 6.936 15.416 Run time: 15.45001s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -n2 -c4 singularity exec ../r-ver.simg Rscript 1_matrix_mult.R 1 1 srun: job 46528444 queued and waiting for resources srun: job 46528444 has been allocated resources [[1]] user system elapsed 61.399 40.480 23.674 Run time: 23.71334s [[1]] user system elapsed 59.794 28.852 23.955 Run time: 23.99171s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -n4 -c4 singularity exec ../r-ver.simg Rscript 1_matrix_mult.R 1 1 srun: job 46528913 queued and waiting for resources srun: job 46528913 has been allocated resources [[1]] user system elapsed 70.205 36.423 25.881 Run time: 25.92368s [[1]] user system elapsed 66.367 30.787 25.973 Run time: 26.01245s [[1]] user system elapsed 69.295 32.250 25.964 Run time: 26.00382s [[1]] user system elapsed 72.462 36.299 26.090 Run time: 26.1311s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -n1 -c4 singularity exec ../r-ver.simg Rscript 1_matrix_mult.R 1 1 srun: job 46528966 queued and waiting for resources srun: job 46528966 has been allocated resources [[1]] user system elapsed 60.335 12.179 18.281 Run time: 18.31571s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -n1 -c8 singularity exec ../r-ver.simg Rscript 1_matrix_mult.R 2 2 srun: job 46529019 queued and waiting for resources srun: job 46529019 has been allocated resources [[1]] user system elapsed 57.202 22.536 22.792 [[2]] user system elapsed 60.254 41.032 22.767 Run time: 22.85356s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -n1 -c8 singularity exec ../r-ver.simg Rscript 1_matrix_mult.R 2 2 srun: job 46529055 queued and waiting for resources srun: job 46529055 has been allocated resources [[1]] user system elapsed 57.397 20.834 18.305 [[2]] user system elapsed 55.666 11.224 16.636 Run time: 18.37081s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -n2 -c4 singularity exec ../r-ver.simg Rscript 1_matrix_mult.R 1 1 srun: job 46529076 queued and waiting for resources srun: job 46529076 has been allocated resources [[1]] user system elapsed 58.253 25.514 19.650 Run time: 19.69007s [[1]] user system elapsed 57.277 19.418 20.191 Run time: 20.22706s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -N2 -c4 singularity exec ../r-ver.simg Rscript 1_matrix_mult.R 1 1 srun: Requested partition configuration not available now srun: job 46529081 queued and waiting for resources ^Csrun: Job allocation 46529081 has been revoked cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=common -N2 -c4 singularity exec ../r-ver.simg Rscript 1_matrix_mult.R 1 1 srun: job 46529133 queued and waiting for resources srun: job 46529133 has been allocated resources [[1]] user system elapsed 57.790 16.816 18.818 Run time: 18.94174s [[1]] user system elapsed 273.878 159.388 108.800 Run time: 109.2411s cr173@dcc-slogin-03 ~/example_pm25 $ cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=common -n1 -c4 singularity exec ../r-ver.simg Rscript 2_matrix_chol.R 1 1 srun: job 46531056 queued and waiting for resources ^Csrun: Job allocation 46531056 has been revoked srun: Force Terminated job 46531056 cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -n1 -c4 singularity exec ../r-ver.simg Rscript 2_matrix_chol.R 1 1 srun: job 46531094 queued and waiting for resources srun: job 46531094 has been allocated resources Error in parallel::mclapply(seq_len(niter), function(x) { : object 'niter' not found Calls: print -> Execution halted srun: error: dcc-statdept-01: task 0: Exited with exit code 1 cr173@dcc-slogin-03 ~/example_pm25 $ git pull remote: Enumerating objects: 5, done. remote: Counting objects: 100% (5/5), done. remote: Compressing objects: 100% (1/1), done. remote: Total 3 (delta 2), reused 3 (delta 2), pack-reused 0 Unpacking objects: 100% (3/3), done. From https://github.com/Sta790-Sp19/example_pm25 ac0acd6..b3ed741 parallel -> origin/parallel Updating ac0acd6..b3ed741 Fast-forward 2_matrix_chol.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -n1 -c4 singularity exec ../r-ver.simg Rscript 2_matrix_chol.R 1 1 srun: job 46531223 queued and waiting for resources ^Lsrun: job 46531223 has been allocated resources [[1]] user system elapsed 11.651 13.285 6.481 Run time: 6.520751s cr173@dcc-slogin-03 ~/example_pm25 $ cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -n1 -c4 singularity exec ../r-ver.simg Rscript 2_matrix_chol.R 1 1 srun: job 46531280 queued and waiting for resources srun: job 46531280 has been allocated resources [[1]] user system elapsed 11.452 12.522 6.237 Run time: 6.275233s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -n2 -c4 singularity exec ../r-ver.simg Rscript 2_matrix_chol.R 1 1 srun: job 46531404 queued and waiting for resources srun: job 46531404 has been allocated resources [[1]] user system elapsed 11.247 11.364 5.492 Run time: 5.534253s [[1]] user system elapsed 12.098 15.184 6.504 Run time: 6.544704s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -n1 -c4 singularity exec ../r-ver.simg Rscript 2_matrix_chol.R 1 1 srun: job 46531547 queued and waiting for resources srun: job 46531547 has been allocated resources [[1]] user system elapsed 10.662 8.744 5.076 Run time: 5.114331s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -n1 -c4 singularity exec ../r-ver.simg Rscript 2_matrix_chol.R 1 1 srun: job 46531588 queued and waiting for resources srun: job 46531588 has been allocated resources [[1]] user system elapsed 12.330 17.458 7.675 Run time: 7.713274s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -n1 -c8 singularity exec ../r-ver.simg Rscript 2_matrix_chol.R 2 2 srun: job 46531632 queued and waiting for resources srun: job 46531632 has been allocated resources [[1]] user system elapsed 11.292 11.221 5.662 [[2]] user system elapsed 11.036 10.398 5.737 Run time: 5.802528s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -n1 -c16 singularity exec ../r-ver.simg Rscript 2_matrix_chol.R 4 4 srun: job 46531709 queued and waiting for resources srun: job 46531709 has been allocated resources [[1]] user system elapsed 11.845 14.806 6.611 [[2]] user system elapsed 11.736 13.967 6.770 [[3]] user system elapsed 11.754 14.032 6.720 [[4]] user system elapsed 11.877 14.378 6.750 Run time: 6.844206s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -n4 -c4 singularity exec ../r-ver.simg Rscript 2_matrix_chol.R 1 1 srun: job 46531880 queued and waiting for resources srun: job 46531880 has been allocated resources [[1]] user system elapsed 14.180 21.611 5.807 Run time: 5.850246s [[1]] user system elapsed 16.722 24.541 5.894 Run time: 5.936519s [[1]] user system elapsed 15.978 24.564 7.211 Run time: 7.487923s [[1]] user system elapsed 14.829 24.813 6.594 Run time: 6.882702s cr173@dcc-slogin-03 ~/example_pm25 $ cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -c16 1_matrix_mult.R 2_matrix_chol.R 3_spbayes.R data/ .git/ .gitignore gp_pm25.Rproj cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -c16 singularity exec ../ .bash_history cov_mat.R ex_pm25.simg parttest/ .singularity/ .viminfo .bash_logout cov.rds gerrymandering-xsede/ .pki/ .ssh/ .zshrc .bash_profile example_pm25/ .gitignore rocker_bayes.simg tidyverse.simg .bashrc example_sbatch/ .kshrc r-ver.simg tmp/ cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -c16 singularity exec ../ex example_pm25/ example_sbatch/ ex_pm25.simg cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=statdept --account=statdept -c16 singularity exec ../ex_pm25.simg Rscript 3_spbayes.R 1 1 srun: job 46532562 queued and waiting for resources srun: job 46532562 has been allocated resources Start iter 1 End iter 1 Run time: 150.9296s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=volfovskylab-low --account=volfovskylab-low -c32 singularity exec ../ex_pm25.simg Rscript 3_spbayes.R 1 1 srun: error: Unable to allocate resources: Invalid account or account/partition combination specified cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=volfovsky-low --account=volfovsky-low -c32 singularity exec ../ex_pm25.simg Rscript 3_spbayes.R 1 1 srun: error: invalid partition specified: volfovsky-low srun: error: Unable to allocate resources: Invalid partition name specified cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=volfovskylab-low --account=statdept -c32 singularity exec ../ex_pm25.simg Rscript 3_spbayes.R 1 1 srun: job 46533829 queued and waiting for resources srun: job 46533829 has been allocated resources Start iter 1 End iter 1 Run time: 54.98369s cr173@dcc-slogin-03 ~/example_pm25 $ srun --partition=common -N4 -c4 singularity exec ../ex_pm25.simg Rscript 3_spbayes.R 1 1 srun: job 46534517 queued and waiting for resources srun: job 46534517 has been allocated resources Start iter 1 Start iter 1 Start iter 1 Start iter 1 End iter 1 Run time: 84.15221s End iter 1 Run time: 87.11683s End iter 1 Run time: 88.24731s ^Csrun: interrupt (one more within 1 sec to abort) srun: step:46534517.0 task 3: running srun: step:46534517.0 tasks 0-2: exited srun: Force Terminated job 46534517 srun: Job step aborted: Waiting up to 32 seconds for job step to finish. srun: error: dcc-core-52: task 3: Terminated cr173@dcc-slogin-03 ~/example_pm25 $