Dear All, I have a perl script that works initially by fetching hundreds of files from a server. I know that gnu parallel is really suited for getting files from an ftp site using wget command in parallel. I would like to use the advantage of this awesome Gnu prallel tool by calling inside my perl script. Is that possible, if so an example would be very much appreciated. ? Regards Yacob
--- On Sun, 20/1/13, Nanditha Rao <[email protected]> wrote: From: Nanditha Rao <[email protected]> Subject: Re: Multiple jobs on a multicore machine or cluster To: [email protected] Date: Sunday, 20 January, 2013, 9:45 Never mind. I figured out that I had to transfer the files using --transfer before running them. And that it gets copied to the home directory of the destination machine by default. On Sat, Jan 19, 2013 at 12:58 AM, Nanditha Rao <[email protected]> wrote: 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 directorydecoder_node_1_line0_sim_3.sp: No such file or directorydecoder_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
