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Brock Palen brockpalen

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#delete all my jobs,
# only do this if you have fewer than a few hundred jobs.
qdel $(qselect -u $USER)
#delete all my queued jobs
qdel $(qselect -u $USER -s Q)
#delete all my jobs submiting with the wrong account
qdel $(qselect -u $USER -A wrongaccount)
brockpalen /
Last active Aug 29, 2015
#build hydra with PBS support
tar -xzf hydra-3.1.tar.gz
cd hydra-3.1
#configure with needed path to
#<toque install prefix>/lib/
./configure \
--prefix=<install prefix> \
--with-toque=<torque install prefix> \
brockpalen /
Last active Aug 29, 2015
Running VNC on the Flux Cluster
#create an ssh tunnel vis flux-xfer to the machine with our VNC Display.
#this example works for Mac, Linux, and Cygwin
#find your vnchost and display number:
ls -rt ~/.vnc/
# eg:
# eg: <== host running vnc
# eg: 1 <== display number
brockpalen / hfss2014
Last active Aug 29, 2015
hfss/2014.0.0 shared memory parallel example PBS script
View hfss2014
#PBS -N jobname
#PBS -A account_flux
#PBS -l qos=flux
#PBS -l walltime=1:00:00,nodes=1:ppn=12,pmem=3800mb
#PBS -q flux
brockpalen / globus-connect-server.conf
Last active Aug 29, 2015
Globus Connect Server config file, for creating a GridFTP Globus endpoint using University of Michigan CiLogin for OAuth.
View globus-connect-server.conf
; Globus User Configuration
; These settings configure how to contact Globus when
; creating or modifying an endpoint.
; Globus user name. If not set, or left at its default, then the
; value of GLOBUS_USER environment variable is used, falling back to
; prompting if it is not present.
brockpalen / matlab-gpu-ex2.m
Last active Aug 29, 2015
Example of using Matlab with GPUS and doing all computation on the GPU
View matlab-gpu-ex2.m
%Brock Palen 1/2014
%To compare against a single core run:
% hwloc-bind core:0 matlab -r gen\(1e4\) #first core
% hwloc-bind socket:0 matlab -r gen\(1e4\) #first socket all cores
function gen(dim)
if ischar(dim)
brockpalen / matlab-gpu-ex1.m
Last active Jan 4, 2016
This example shows simple use of gpuArray() to use built in GPU functions on MATLAB
View matlab-gpu-ex1.m
%Brock Palen 1/2014
%To compare against a single core run:
% hwloc-bind core:0 matlab -r caenfft\(1e7\)
function caenfft(dim)
if ischar(dim)
View theano-gpu
#Example for Theano 0.6 on CAEN-HPC FluxG
#load modules
module load python/2.7.5 cuda/5.5 theano/0.6
#use device=gpu to let our system autoselect the GPU to use
#use device=cpu to run your code on another system
THEANO_FLAGS='floatX=float32,device=gpu' python