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Old 18th April 2012, 07:00 PM
mkass Offline
Registered User
Join Date: Apr 2012
Location: Denver, CO
Posts: 2
New Cluster

Hey all

I'm trying to do a simple operation on a new cluster we have, but this is my first attempt and I'm having trouble. I have five nodes, each with 12 threads. Right now, I'm the only one using this cluster.

I have a serial program that I basically want to run multiple instances across all the threads available. I need to run this serial program on 1000 datasets, each of which is independent. I wrote a serial bash script which simply runs the program 1000 times and iterates through the datasets. I would like to be able to run 60 concurrent instances (or whatever number of threads are available), with each moving on to the next available dataset as it finishes. Since it's only 5 nodes, I have no problem manually parsing the data into five chunks and running them on each, but if it's simple to automate from the master node that would be preferable.

My serial test script runs just fine using qsub, but is only using one single thread.

I apologize for such a pedestrian question, but I don't even have a concept of the architecture required. Thanks so much.

---------- Post added at 08:20 AM ---------- Previous post was at 08:06 AM ----------

More information:

Here is my serial test scripts

Simple test program
#include <iostream>
#include <time.h>
using namespace std;

int main() {

    clock_t launch=clock();
    time_t curr=time(0);
    cout << endl;
    cout << "  Start time: " << ctime(&curr) << endl;
    sleep(5); //just to make sure they're not all running at once
    time_t curre=time(0);
    cout << "  End time: " << ctime(&curre) << endl;
    return 0;
and the script:

while [ $COUNTER -lt 500]; do
    echo "  "$COUNTER 

---------- Post added at 11:00 AM ---------- Previous post was at 08:20 AM ----------

Two partial solutions from these sites:

using pbsdsh and

using mpiexec.
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Old 23rd April 2012, 05:49 PM
mkass Offline
Registered User
Join Date: Apr 2012
Location: Denver, CO
Posts: 2
Re: New Cluster

OK, I have a set of scripts that work for me now. They're clunky and it's certainly not optimal, but they work.

Using qsub, I run a master script:
#PBS -N pbsdsh
#PBS -l nodes=5:ppn=12

cd /data/home/mkass/Jobs/aniak
octave parsejobs.m

pbsdsh -v sh $PBS_O_WORKDIR/thrrun.sh
I have an octave script, parsejobs, that creates a script for each node (I think this is how Skynet starts).
It's a little extra complicated because my 'line numbers' are not sequential, and (for reasons evident in the next script) I need sequential, numeric values for each directory.
It's in this script that the jobs are parsed out and sent to each processor.
fid = fopen('linelist.txt','rt');
nNodes = 5;
nThr = 12;

ii = 0;
while ~feof(fid)
	temp = fscanf(fid,'%s',1);
nSounds = ii;

fid = fopen('linelist.txt','rt');
lines = cell(nSounds,1);
for ii = 1:nSounds

b = floor(nSounds/nNodes);
ro = mod(nSounds,nNodes);

opspnode = zeros(nNodes,1);
opspnode(1:nNodes) = b;
for ii = 1:ro
	opspnode(ii) = opspnode(ii)+1;

opspthread = zeros(nNodes,nThr);

for ii = 1:nNodes
	b = floor(opspnode(ii)/nThr);
	ro = mod(opspnode(ii),nThr);
	opspthread(ii,:) = b;
	for jj = 1:ro
		opspthread(ii,jj) = opspthread(ii,jj) + 1;

save 'parsejobs.mat' opspthread;
save 'lines.mat' lines;

opsthrcat = reshape(opspthread,nNodes*nThr,1);
%% Make 60 scripts
for ii = 1:(nNodes*nThr)
%	fid = fopen(strcat('thrrun.',num2str(ii),'.temp.m'),'wt');
	fid = fopen(strcat('thrrun.',num2str(ii-1),'.temp.sh'),'wt');
	%each script handles 
	%fprintf(fid,'%s\n','cd $PBS_O_WORKDIR');
	fprintf(fid,'%s\n','cd /data/home/mkass/Jobs/aniak');
	t = strcat('COUNTER=',num2str(sum(opsthrcat(1:ii))-(opsthrcat(ii))+1));
	%t = strcat('while [ $COUNTER -lt ',num2str(sum(opsthrcat(1:ii))+1));
	t = ['while [ $COUNTER -lt ',num2str(sum(opsthrcat(1:ii))+1)];
	t2 = strcat(t,' ]; do');
	fprintf(fid,'%s\n','mkdir $COUNTER');
	fprintf(fid,'%s\n','cp data/$COUNTER.txt $COUNTER/');
	fprintf(fid,'%s\n','cp makeEM1DFMobs.m $COUNTER/');
	fprintf(fid,'%s\n','cp writeEM1DFMobsV3.m $COUNTER/');
	fprintf(fid,'%s\n','cp em1dfmgen.m $COUNTER/');
	fprintf(fid,'%s\n','cp start.mod $COUNTER/');
	fprintf(fid,'%s\n','cp ref.mod $COUNTER/');
	fprintf(fid,'%s\n','cp em1dfm/* $COUNTER/');
	fprintf(fid,'%s\n','cd $COUNTER/');
	fprintf(fid,'%s\n','octave makeEM1DFMobs.m');
	fprintf(fid,'%s\n','octave em1dfmgen.m');
	fprintf(fid,'%s\n','wine em1dfm.exe');
	fprintf(fid,'%s\n','rm *.exe');
	fprintf(fid,'%s\n','cd ../');
	fprintf(fid,'%s\n','let COUNTER=COUNTER+1');
%	fclose(fid);
And finally, this script executes each script written out above.
cd /data/home/mkass/Jobs/aniak
sh thrrun.$PBS_VNODENUM.temp.sh
So there you have it. An operation that would have taken 13 days was done in 5 hours. There's plenty of room for improvement, but this works for me. Cheers!

Last edited by mkass; 23rd April 2012 at 05:50 PM. Reason: Typo in the last script
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