Last login: Mon Dec 2 11:48:45 on ttys000 administrators-iMac:~ hoyen$ ssh -p 222 hoyen@login.rci.sc.edu Warning: Permanently added the ECDSA host key for IP address '[129.252.167.229]:222' to the list of known hosts. hoyen@login.rci.sc.edu's password: /etc/profile.d/lang.sh: line 19: warning: setlocale: LC_CTYPE: cannot change locale (UTF-8): No such file or directory Duo two-factor login for hoyen Enter a passcode or select one of the following options: 1. Duo Push to XXX-XXX-3068 2. Phone call to XXX-XXX-3068 3. SMS passcodes to XXX-XXX-3068 Passcode or option (1-3): 1 Pushed a login request to your device... Success. Logging you in... [hoyen@login001 ~]$ [hoyen@login001 ~]$ [hoyen@login001 ~]$ [hoyen@login001 ~]$ module avail ---------------------------------------- /cm/local/modulefiles ----------------------------------------- cluster-tools/7.3 interactive/int openldap cmd ipmitool/1.8.17 openmpi/mlnx/gcc/64/1.10.5a1 dot module-git shared freeipmi/1.5.2 module-info singularity/2.0 gcc/6.1.0 null singularity/2.3.1 ---------------------------------------- /cm/shared/modulefiles ---------------------------------------- abaqus/V6R2016x intel/mpi/32/2017/6.256 abaqus/V6R2017x intel/mpi/64/2017/1.132 abaqus/V6R2017x-mcnairpy intel/mpi/64/2017/6.256 abawaca/gcc/1.07 intel/mpi/64/5.1.3/2016.4.258 abinit/8.10.2 intel/mpi/mic/2017/1.132 abyss/gcc/2.1.0 intel/mpi/mic/2017/6.256 abyss/gcc/2.1.5 intel/mpi/mic/5.1.3/2016.4.258 acml/gcc/64/5.3.1 intel/suite/64/16.0.4 acml/gcc/fma4/5.3.1 intel/suite/64/2017 acml/gcc/mp/64/5.3.1 intel/tbb/32/2017/1.132 acml/gcc/mp/fma4/5.3.1 intel/tbb/32/2017/6.256 acml/gcc-int64/64/5.3.1 intel/tbb/32/4.4.6/2016.4.258 acml/gcc-int64/fma4/5.3.1 intel/tbb/64/2017/1.132 acml/gcc-int64/mp/64/5.3.1 intel/tbb/64/2017/6.256 acml/gcc-int64/mp/fma4/5.3.1 intel/tbb/64/4.4.6/2016.4.258 acml/intel/64/5.3.1 intel/tbb/mic/2017/1.132 acml/intel/fma4/5.3.1 intel/tbb/mic/2017/6.256 acml/intel/mp/64/5.3.1 intel/tbb/mic/4.4.6/2016.4.258 acml/intel/mp/fma4/5.3.1 intel-cluster-runtime/ia32/3.8 acml/intel-int64/64/5.3.1 intel-cluster-runtime/intel64/3.8 acml/intel-int64/fma4/5.3.1 intel-cluster-runtime/mic/3.8 acml/intel-int64/mp/64/5.3.1 intel-tbb-oss/ia32/2017_20161128oss acml/intel-int64/mp/fma4/5.3.1 intel-tbb-oss/ia32/2017_20170807oss acml/open64/64/5.3.1 intel-tbb-oss/intel64/2017_20161128oss acml/open64/fma4/5.3.1 intel-tbb-oss/intel64/2017_20170807oss acml/open64/mp/64/5.3.1 iozone/3_434 acml/open64/mp/fma4/5.3.1 JAGS/gcc/4.3.0 acml/open64-int64/64/5.3.1 java/1.8.0_151 acml/open64-int64/fma4/5.3.1 java/1.8.0_162 acml/open64-int64/mp/64/5.3.1 kallisto/gcc/0.44.0 acml/open64-int64/mp/fma4/5.3.1 lammps/gcc/openmpi-gpu/mar2017 afni/17.2.16 lammps/intel/aug72019-mpi amber/gcc/gpu/16 lammps/intel/aug72019-mpi-reaxc amber/gcc/openmpi/16 lammps/intel/mar2017-mpi amber/gcc/openmpi-gpu/16 lapack/gcc/64/3.6.0 amber/intel/mpi/16 lapack/open64/64/3.6.0 ants/gcc/2.2 matlab/R2017b bamtools/gcc/2.4.1 matlab/R2019a bbmap/gcc/37.93 matlab/R2019b bbmap/gcc/38.16 maxbin/gcc/2.2.4 bcftools/gcc/1.5 megahit/gcc/1.1.3 bcl2fastq2/gcc/2.2.0 megahit/gcc/1.2.7 beast/1.10+beaglegpu metabat/gcc/2.12.1 bedtools/gcc/2.27.1 meta-marc/0 blacs/openmpi/gcc/64/1.1patch03 miRA/1.2.0 blacs/openmpi/intel/64/1.1patch03 miRExpress/2.1.4 blacs/openmpi/open64/64/1.1patch03 miRge/2018 blas/gcc/64/3.6.0 MISA/2019 blas/intel/64/3.6.0 mmc-mcx/2017 blas/open64/64/3.6.0 mpich/ge/gcc/64/3.2rc2 blast/gcc/2.6.0 mpich/ge/open64/64/3.2rc2 blat/35 mpich/ge/pgi/64/3.2rc2 bonnie++/1.97.1 mpiexec/0.84_432 bowtie/intel/1.2.1.1 MUMmer/3.23 bowtie2/intel/2.3.2 mvapich2/gcc/64/2.2rc1 bwa/3.16 mvapich2/open64/64/2.2rc1 caffe/1.0 netcdf/gcc/64/4.4.0 caffe/dependencies/ref netcdf/intel/4.6.2-c-fortran caffe2/deps netcdf/open64/64/4.4.0 cellranger/3.0.2 netperf/2.7.0 cellranger/3.1.0 nwchem/gcc-omp/6.8 checkm/gcc/1.0.9 oases/gcc/0.2.09 cloudy/gcc/c17 open64/4.5.2.1 cloudy/openmpi/c17 openblas/dynamic/0.2.18 cmake/3.12 opencv/gcc/64/3.3.0 cmdstan/2.17 opencv3/3.1.0 cmgui/7.3 opencv4/4.0.1 CONCOCT/0.4.0 opencv4/4.0.1-gnu6.4 converge/2.4.27 openmpi/gcc/64/1.10.1 critic2/gcc/stable openmpi/gcc/64/4.0.1 cuda/10.0 openmpi/gcc/64/4.0.1-ucx cuda/10.1 openmpi/intel/64/1.10.1 cuda/7.5 openmpi/open64/64/1.10.1 cuda/8.0 openmpi/pgi/64/1.10.1 cuda/9.0 pear/0.9.11 cuda/9.1 pgi/64/17.3 cuda/9.2 picard/2017 cudaica/2019 picard/2018 cufflinks/gcc/2.2.1 plink/gcc/6.2 DAS_Tool/1.1 pplacer/gcc/1.1 deeparg/0.7.9.58 prodigal/gcc/2.6.3 default-environment pycharm/2017.2.3 DFTB/18.2 python2.7/anaconda/4.4.0 diamond/0.9.24 python2.7/anaconda/5.0.0 dos2unix/7.4 python2.7/anaconda/base emboss/6.6.0 python3/anaconda/2019.03 epacts/3.2.6 python3/anaconda/2019.07 evigene/may2018 python3/anaconda/5.0.1 fastp/0.20.0 python3/anaconda/5.1.0-base fastqc/0.11.5 python3/anaconda/5.2.0 fastx/0.0.13 python3/anaconda/ai-lab fftw2/openmpi/gcc/64/double/2.1.5 qe/gcc/6.2.0 fftw2/openmpi/gcc/64/float/2.1.5 qe/gcc/6.3-developer fftw2/openmpi/open64/64/double/2.1.5 qe/intel/6.4.1 fftw2/openmpi/open64/64/float/2.1.5 qt/4.8.7 fftw3/openmpi/gcc/64/3.3.4 R/gcc/3.1.0 fftw3/openmpi/intel/64/3.3.4 R/gcc/3.4.1 fftw3/openmpi/open64/64/3.3.4 R/gcc/3.5.0 fftw3/openmpi/pgi/64/3.3.4 R/gcc/3.5.1 firefly/intel/mpi/8.2.0 R/gcc/3.6.0 freesurfer/2017 R/intel/3.4.1 fsl/5.0.10 ROMS/gcc/env fsl/6.0.0 rsem/1.3.0 fsl/6.0.1 samtools/gcc/1.5 gamess/gcc/sockets/apr2017 SAPT/gcc/2016.1 GATK/3.8.0 sbt/gcc/1.0.1 GATK/4.0.5.1 scalapack/openmpi/gcc/64/2.0.2 GATK/4.1.3.0 scalapack/openmpi/intel/64/2.0.2 gcc/4.9.1 sge/2011.11p1 gcc/6.4.0 ShengBTE/intel/mpi/1.1.1 gcc/singularity/2.3.1 simka/1.5.1 gdb/7.11 singularity/2.6.0 gem5/X86 slurm/16.05.8 gflow/gcc/1.7 SNANA/gcc/10_60d globalarrays/openmpi/gcc/64/5.4 snpEff/12_2017 globalarrays/openmpi/open64/64/5.4 SNPiR/12_2017 gmp/6.1.2 SOAPdenovo/gcc/r240 gsl/2.4 sortmerna/2.1b gwyddion/gcc/2.50 spades/gcc/3.11 hdf5/1.6.10 spades/gcc/3.12 hdf5_18/1.8.17 stan/gcc/2.17 hisat2/2.1.0 star/2.5 hmmer/gcc/3.1 star/2.7.2b hmmer/gcc/3.2.1 star/star-fusion hpl/2.2 stata/gcc/14 htslib/gcc/1.5 stringtie/1.3.3 hwloc/1.11.3 subread/1.5.3 intel/compiler/32/2017/17.0.6 tensorflow/1.3 intel/compiler/64/16.0.4/2016.4.258 tophat/gcc/2.1.1 intel/compiler/64/2017/17.0.6 torque/6.0.2 intel/daal/64/2017/1.132 transabyss/gcc/2.0.1 intel/gdb/64/2017/1.132 transrate/1.0.3 intel/gdb/64/7.8.0/2016.4.258 trimmomatic/0.36 intel/ipp/64/2017/1.132 trinity/gcc/2.6.6 intel/ipp/64/9.0.4/2016.4.258 trinity/gcc/2.8.4 intel/itac/2017/1.024 TSN/2017 intel/mkl/64/11.3.4/2016.4.258 valgrind/3.14 intel/mkl/64/2017/1.132 vasp/intel/5.4.4-mpi(default) intel/mkl/64/2017/6.256 vasp/intel/5.4.4-mpi-nmax256 intel/mkl/mic/11.3.4/2016.4.258 vcf2maf/2017 intel/mkl/mic/2017/1.132 wannier/gcc/2.1.0 intel/mkl/mic/2017/6.256 wrf/3.9.1-deprecated intel/mpi/32/2017/1.132 wrf/3.9.1-mpich [hoyen@login001 ~]$ [hoyen@login001 ~]$ ls Ingo751 Rlibs SimulationsM2-0.Rdata bin hyperion3.sh submit.sh MetaLA Rplots.pdf Varout-HCauchy.RData data qiime2-2018.4-py35-linux-conda.yml [hoyen@login001 ~]$ more submit.sh #!/bin/sh #SBATCH --job-name=test #SBATCH -n 1 #SBATCH -N 1 #SBATCH --output job%j.out #SBATCH --error job%j.err #SBATCH -p defq,hoy-lab module load python2.7/anaconda/base export TMPDIR=/local source activate qiime #source activate qiime2-2018.4 ###script commands below this line hostname print_qiime_config.py [hoyen@login001 ~]$ [hoyen@login001 ~]$ ls Ingo751 Rlibs SimulationsM2-0.Rdata bin hyperion3.sh submit.sh MetaLA Rplots.pdf Varout-HCauchy.RData data qiime2-2018.4-py35-linux-conda.yml [hoyen@login001 ~]$ ls Ingo751 Rplots.pdf bin mtest.R submit.sh MetaLA SimulationsM2-0.Rdata data mtest.sh test.R Rlibs Varout-HCauchy.RData hyperion3.sh qiime2-2018.4-py35-linux-conda.yml test.sh [hoyen@login001 ~]$ sbatch test.sh Submitted batch job 4691563 [hoyen@login001 ~]$ squeue -u hoyen JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 4691563_[1] defq test hoyen PD 0:00 1 (None) [hoyen@login001 ~]$ ls Ingo751 Rplots.pdf bin mtest.R submit.sh MetaLA SimulationsM2-0.Rdata data mtest.sh test.R Rlibs Varout-HCauchy.RData hyperion3.sh qiime2-2018.4-py35-linux-conda.yml test.sh [hoyen@login001 ~]$ mkdir test [hoyen@login001 ~]$ ls Ingo751 Rplots.pdf bin mtest.R submit.sh test.sh MetaLA SimulationsM2-0.Rdata data mtest.sh test Rlibs Varout-HCauchy.RData hyperion3.sh qiime2-2018.4-py35-linux-conda.yml test.R [hoyen@login001 ~]$ cd test [hoyen@login001 test]$ ls [hoyen@login001 test]$ cd .. [hoyen@login001 ~]$ mv *test* ~/test/. mv: cannot move 'test' to a subdirectory of itself, '/home/hoyen/test/./test' [hoyen@login001 ~]$ mv *test.R ~/test/. mv: cannot stat '*test.R': No such file or directory [hoyen@login001 ~]$ mv test.R ~/test/. mv: cannot stat 'test.R': No such file or directory [hoyen@login001 ~]$ ls Ingo751 Rlibs SimulationsM2-0.Rdata bin hyperion3.sh submit.sh MetaLA Rplots.pdf Varout-HCauchy.RData data qiime2-2018.4-py35-linux-conda.yml test [hoyen@login001 ~]$ cd test [hoyen@login001 test]$ ls mtest.R mtest.sh test.R test.sh [hoyen@login001 test]$ [hoyen@login001 test]$ [hoyen@login001 test]$ module avail R ---------------------------------------- /cm/shared/modulefiles ---------------------------------------- R/gcc/3.1.0 R/gcc/3.4.1 R/gcc/3.5.0 R/gcc/3.5.1 R/gcc/3.6.0 R/intel/3.4.1 ROMS/gcc/env [hoyen@login001 test]$ module load R/gcc/3.6.0 [hoyen@login001 test]$ R R version 3.6.0 (2019-04-26) -- "Planting of a Tree" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. During startup - Warning message: Setting LC_CTYPE failed, using "C" > > .libPaths("~/Rlibs") > > library("rjags") Error in library("rjags") : 'rjags' is not a valid installed package > > > x<-runif(100) > x [1] 0.23813154 0.36127001 0.89840282 0.50370282 0.69619252 0.58224795 [7] 0.43226841 0.74590927 0.79696949 0.67495931 0.50622670 0.74039117 [13] 0.95434950 0.27979882 0.43298368 0.75464542 0.21378875 0.30196006 [19] 0.80381244 0.55257374 0.47125969 0.27808482 0.77681308 0.64230207 [25] 0.25621641 0.93287847 0.60484313 0.67152233 0.21171195 0.01026539 [31] 0.31004585 0.60751359 0.83164890 0.56349064 0.53152416 0.02081168 [37] 0.32485519 0.18843173 0.69094266 0.65564778 0.09390335 0.27171371 [43] 0.16918936 0.83689412 0.21744289 0.96126494 0.94232192 0.26255890 [49] 0.95685246 0.28235922 0.43367172 0.32075380 0.98303513 0.66766856 [55] 0.60370666 0.96710288 0.06684942 0.85642785 0.13591505 0.47064718 [61] 0.05908168 0.20125377 0.11952111 0.36138349 0.02168199 0.91265491 [67] 0.62075573 0.36807624 0.47029454 0.95570198 0.54461515 0.64667719 [73] 0.69222584 0.93377991 0.44478869 0.33321966 0.65731627 0.17198149 [79] 0.51551399 0.44509515 0.23436662 0.37443357 0.13659702 0.56823736 [85] 0.13993352 0.44220427 0.16669624 0.41446329 0.36386222 0.57062202 [91] 0.47378230 0.49625364 0.28452414 0.48471778 0.48283825 0.87399424 [97] 0.63131649 0.82670862 0.62675397 0.65039537 > > q() Save workspace image? [y/n/c]: n [hoyen@login001 test]$ ls mtest.R mtest.sh test.R test.sh [hoyen@login001 test]$ ls mtest.R mtest.sh test.R test.sh [hoyen@login001 test]$ [hoyen@login001 test]$ [hoyen@login001 test]$