On Fri, Jan 18, 2013 at 12:53 AM, Ole Tange <[email protected]> wrote: > On Thu, Jan 17, 2013 at 12:58 PM, Nanditha Rao <[email protected]> > wrote: > > > 1. I need to run multiple jobs on a multicore (and multithreaded) > machine. I > > am using the GNU Parallel utility to distribute jobs across the cores to > > speed up the task. The commands to be executed are available in a file > > called 'commands'. I use the following command to run the GNU Parallel. > > > > cat commands | parallel -j +0 > > > > As per the guidance at this location- gnu parallel, this command is > supposed > > to use all the cores to run this task. My machine has 2 cores and 2 > threads > > per core. > > I take it that you have a CPU with hyperthreading. > [Nanditha: I guess so. I am using an Intel core i3 laptop to test this tool out..]
> > > The system monitor however shows 4 CPUs (CPU1 and CPU2 belong to > > core1, CPU3 and CPU4 belong to core2). Each job (simulation) takes about > 20 > > seconds to run on a single core. I ran 2 jobs in parallel using this GNU > > parallel utility with the command above. I observe in the system monitor > > What system monitor are you using? > [Nanditha: gnome-system-monitor on ubuntu] > > > that, if the 2 jobs are assigned to cpu1 and cpu2 (that is the same > core), > > there is obviously no speed-up. > > Why obviously? Normally I measure a speedup of 30-70% when using > hyperthreading. > [Nanditha: I somehow dont see a speedup. Running a single job on single thread on single core versus two threads on the same core is taking the same time- about 20seconds] > > > They take about 40seconds to finish, which > > is about the time they would take if run sequentially. However, sometimes > > the tool distributes the 2 jobs to CPU1 and CPU3 or CPU4 (which means, 2 > > jobs are assigned to 2 different cores). In this case, both jobs finish > > parallely in 20 seconds. > > GNU Parallel does not do the distributing; it simply spawns jobs. The > distribution is done by your operating system. > > > Now, I want to know if there is a way in which I can force the tool to > run > > on different "cores" and not on different "threads" on the same core, so > > that there is appreciable speed-up. Any help is appreciated. Thanks! > > If you are using GNU/Linux you can use taskset which can set a mask on > which cores a task can be scheduled on. If you want every other: > 1010(bin) = 0xA. For a 128 core machine you could run: > > cat commands | taskset 0xaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa parallel -j +0 > [Nanditha: Tried this, thanks. But seems like it doesnt help speedup the jobs as assumed by me earlier] > > > 2. Also, I want to know if there is a way to run this utility over a > cluster > > of machines.. say, there are four 12-core machines in a cluster (making > it a > > 48-core cluster). > > cat commands | parallel -j +0 -S server1,server2,server3,server4 > [Nanditha: I tried this option. cat commands|parallel -j +0 --sshlogin username@ip_address However, I get an error that the files listed the 'commands' file are not to be found. Basically I am running a simulation and invoking the commands through the file called 'commands'. Is there some path I need to specify as to where they should get copied in the destination server? Or by default where does it get copied to and where do I go to see my results file. This is the error I get (where each file is part of the command that I specify in 'commands':) decoder_node_1_line0_sim_4.sp: No such file or directory decoder_node_1_line0_sim_3.sp: No such file or directory decoder_node_1_line0_sim_1.sp: No such file or directory decoder_node_1_line0_sim_2.sp: No such file or directory My commands file contains: ngspice decoder_node_1_line0_sim_1.sp ngspice decoder_node_1_line0_sim_2.sp ngspice decoder_node_1_line0_sim_3.sp ngspice decoder_node_1_line0_sim_4.sp and the tool parallel is being invoked from the directory in which these files are present. So, I expect that the tool should pick these files up from the current directory and distribute it to the server and run them. It runs locally on my machine, but the -S option gives me the above error. Can you pls suggest? Thanks! > Please read > http://www.gnu.org/software/parallel/man.html#example__using_remote_computers > or watch the intro videos: > https://www.youtube.com/playlist?list=PL284C9FF2488BC6D1 > > > /Ole >
