A linux tutorial for hpc sintomas de hernia discal lumbar l4 l5

#!/bin/bash # KEEP # specify the Q run in; MODIFY based causas del dolor lumbar parte baja espalda on the output of ‘q’ # so you can submit to an underused Q #$ -q free* # the qstat job name; this name -> $JOB_NAME variable # MODIFY to reflect your run #$ -N testqsub # use the real bash shell – KEEP #$ -S /bin/bash # execute the job out of the current dir and direct the error # (.e) and output (.o) to the same directory … # Generally, KEEP, unless you have good reason NOT to use it. #$ -cwd # … Except, in this case, merge the output (.o) and error (.e) into one file # If you’re submitting LOTS of jobs, this halves the filecount and also allows # you to see what error came at what point in the job. # KEEP unless there’s # good reason NOT to use it. #$ -j y #!!


NB: that the .e and .o files noted above are the STDERR and STDOUT, not necessarily #!! the programmatic output that you might be expecting. That output may well be sent to #!! other estenosis lumbar files, depending on how the app was written. # You may use the following email notifications ONLY IF you’re NOT using array jobs. # If you’re using array jobs !!ABSOLUTELY DO NOT USE email escoliosis dextroconvexa notification!! # mail me ( ${USER} will pick up YOUR user name. ) Generally, KEEP #$ -M ${USER}@uci.edu # when the job (b)egins, (e)nds, (a)borts, or (s)uspends # MODIFY, based on what you want to be notified about # BUT !!NEVER!!EVER!! USE THIS FOR AN ARRAY JOB #$ -m beas # for the 2 settings below, you should first run your application behind # ‘/usr/bin/time -v’ to determine about how much time and memory it requires. # obviously, the 1st time you won’t know what it will take. # also, see: https://hpc.oit.uci.edu/HPC_USER_HOWTO.html#SGE_script_params # for some useful SGE directives # if your program will or can use multiple cores via threading, OpenMP, # or other parallel operations, reserve the number of cores here. # make sure it can use the cores; otherwise omit. # MODIFY (see for more options dolor lumbar izquierdo) #$ -pe openmp 16 # reserve this much RAM at the start of the job # MODIFY #$ -l mem_size=2G ###### END SGE PARAMETERS ###### ###### BEGIN BASH operacion de columna lumbar recuperacion CODE ###### # no more hiding them behind ‘#$’ # KEEP to identify which server the job ended up, in case there was a problem

echo "Running on `hostname`" # NOTE1: if a bash variable can /possibly/ be misinterpreted in a string, # use the ‘braced’ version of it: ${VAR} instead of $VAR # NOTE2: DOUBLE quotes ("") allow variable substitution # SINGLE quotes (”) do not. # in the uncommented line below, "${USER}" would substituted for your username, # ‘hjm’ for example, but ‘$USER’ or even ‘${USER}’ would not – it would # be passed thru as a literal $USER or ${USER} # The line below is a an example; it really has no valid use in real life. # Also: $USER is a freebie environment variable; it is always defined as your login name. # MODIFY dolor lumbar derecho y pierna or DELETE ME = "${USER}" # set a temporary output dir on the LOCAL /scratch filesystem (so data doesn’t # cross the network). NOTE: no spaces around the ‘=’ # the diff between TMPDIR and TMPRUNDIR is that TMPDIR is where any TEMPORARY files # are written and dolor lumbar izquierdo cadera TMPRUNDIR is where the output files are left (which then # have to be copied back to ‘safe’ storage.) Generally, KEEP. TMPDIR =/scratch / ${ME} # We’ll name the job subdir the same as the jobname (set above with ‘#$ -N ..’) # Generally, KEEP TMPRUNDIR = ${TMPDIR}/${JOB_NAME} # set an input directory (where your input data is – $HOME is a universal variable) # Often, you’ll be getting your data from one of the distributed filesystems, # so $HOME may not be appropriate. MODIFY for the particular run. INDIR = ${HOME}/guppy_analysis / 2.3 . 44/broad / 2013 / 12 / 46.599 # and final dolor lumbar lado derecho results dir in one place (where your output will stay long-term) # As above, MODIFY FINALDIR = ${HOME}/guppy/r 03- 20- 2013 # this is where you keep your MD5 checksums locally, altho they’ll need to be copied # elsewhere to be safe (see below) MD5SUMDIR = ${HOME}/md5sums/guppy/r 03- 20- 2013/md5sums

module load guppy / 2.3 . 44 # and execute this command. Note: this is an FAKE COMMAND and FAKE OPTIONS; your app will # have different names for these directories or you may have to specify them in a dotfile. # it’s useful to break radiografia de columna lumbar normal the execution line into readable chunks by ending a section # with a continuation char (\) which MUST be the LAST character on the line # (no following spaces) # also note that the command is prefixed by ‘/usr/bin/time -v’. # This records the actual runtime and memory usage of the command which is useful to # figure out what Qs and servers to use. You should do this with all your significant commands # (but not utilities like ‘ls’)

# get a datestamp, useful for tagging the filenames created. KEEP. DATESTAMP =`date +%Y- %m- %d :%H :%M :%S` # no spaces in case we need that format # generate md5 checksums of all output data to be able to # check for corruption if anything happens to the filesystem, god forbid. # KEEP MD5FILE = ${MD5SUMDIR}/${JOB_NAME} .md5

#!/bin/bash escoliosis lumbar leve # specify the Q run in; MODIFY based on the output of ‘q’ # so you can submit to an underused Q #$ -q free* # the qstat job name; this name -> $JOB_NAME variable # MODIFY to reflect your run #$ -N task-array # use the real bash shell – KEEP #$ -S /bin/bash # execute the dolor lumbar cie 10 job out of the current dir and direct the error # (.e) and output (.o) to the same directory … # Generally, KEEP, unless you have good reason NOT to use it. #$ -cwd # … Except, in this case, merge the output (.o) and error (.e) into one file # If you’re submitting LOTS of jobs, this halves the filecount and also allows # you to see what error came at what point in the job. # KEEP unless there’s # good reason NOT escoliosis lumbar derecha to use it. #$ -j y #!! NB: that the .e and .o files noted above are the STDERR and STDOUT, not necessarily #!! the programmatic output that you might be expecting. That output may well be sent to #!! other files, depending on how the app was written. # !! ABSOLUTELY DO NOT USE email notificationa for TASK ARRAYS !! # !! THIS IS A TASK ARRAY !! # and here we define the range of the TASK ARRAY index, from 1 to 40 # Remember the variable that carries this variables is called ‘$SGE_TASK_ID’. #$ -t 1-40 ###### END SGE PARAMETERS ###### ###### BEGIN BASH CODE ###### # no more hiding them behind ‘#$’ # uncomment the following line for dolor lumbar embarazo testing in a bash shell prior to submitting it to SGE # then RE-comment it when you qsub it. # SGE_TASK_ID=33 # let’s define an output dir & create it. OUTDIR = $HOME/test_task_dir

# format the $SGE_TASK_ID to the format required (5 digits, with leading zeros) # in the format string "%05d", the ‘0’ means to pad with zeros, the ‘5’ means 5 digits, # the ‘d’ means to format as an integer (no decimal point). If for some reason you wanted to # to format as a floating point number, "%09.4f" would print ’66’ as ‘0066.0000’ # (9 characters, 4 decimal points escoliosis dorsolumbar izquierda, leading zeros to pad it out) nbr = $( printf "%05d" $SGE_TASK_ID ) # now an integer like ‘5’ is represented as ‘00005’ FILENAME = "humhep7_${nbr}.fq" # so $FILENAME would be ~ ‘humhep7_00005.fq’ # now do a test to see if the filenames are generated correctly. # note that 40 jobs are all going to try to write to that file at approx the same time.