Difference between revisions of "Using the IRIDIA Cluster"
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| + | See [[http://majorana.ulb.ac.be/wordpress/ http://majorana.ulb.ac.be/wordpress/]] |
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| − | == Cluster composition == |
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| − | Currently the IRIDIA cluster is composed by two racks. The first one contains 1 server (majorana) + 32 computational nodes (from c0-0 to c0-31), while the second contains 16 computational nodes (from c1-0 to c1-15). In total the cluster is composed of 96 CPUs (64 single-core + 32 dual-core) dedicated to computations and 2 CPUs for administrative purposes. |
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| − | Each of the units in the first rack (from c0-0 to c0-31) features 2 CPUs AMD Opteron 244 (each with 1MB L2 cache) working at 1,75GHz and 2GB of RAM. Nodes from c0-0 to c0-15 have 4 modules of 512MB 400MHz DDR ECC REG DIMM. Nodes from c0-16 to c0-31 have 8 modules of 256MB 400MHz DDR ECC REG DIMM. |
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| − | Each of the units in the second rack (from c1-0 to c1-15) features 2 Dual-Core AMD Opteron Processors 2216 HE (each with 2x1MB L2 cache) working at 2,4GHz and 4GB of RAM. |
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| − | COMPLEX_NAME: '''opteron244''' |
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| − | - 2 Single-Core AMD Opteron244 @ 1,75GHz |
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| − | nodes: c0-0, c0-1, c0-2, c0-3, c0-4, c0-5, c0-6, c0-7, c0-8, c0-9, c0-10, c0-11, c0-12, c0-13, c0-14, c0-15, c0-16, c0-17, c0-18, c0-19, c0-20, c0-21, c0-22, c0-23, c0-24, c0-25, c0-26, c0-27, c0-28, c0-29, c0-30, c0-31 |
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| − | COMPLEX_NAME: '''opteron2216''' |
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| − | - 2 Dual-Core AMD Opteron2216 HE @ 2,4GHz |
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| − | nodes: c1-0, c1-1, c1-2, c1-3, c1-4, c1-5, c1-6, c1-7, c1-8, c1-9, c1-10, c1-11, c1-12, c1-13, c1-14, c1-15 |
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| − | === Cluster status === |
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| − | {| border=1 cellspacing=0 cellpadding=2 |
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| − | ! Node !! Effect !! Date !! Note |
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| − | |- |
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| − | | c0-0 || offline || 13 Jul 07 || cpu-fan broken |
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| − | |- |
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| − | | c0-1 || || || |
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| − | |- |
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| − | | c0-2 || offline || 19 Nov 07 || during boot node is stuck at grub |
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| − | |- |
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| − | | c0-3 || || || |
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| − | |- |
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| − | | c0-4 || offline || 19 Nov 07 || during boot node is stuck at grub |
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| − | |- |
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| − | | c0-5 || || || |
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| − | |- |
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| − | | c0-6 || offline || 19 Nov 07 || during boot node is stuck at grub |
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| − | |- |
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| − | | c0-7 || || || |
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| − | |- |
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| − | | c0-8 || || || |
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| − | |- |
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| − | | c0-9 || offline || 24 Aug 07 || ethernet card not recognized |
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| − | |- |
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| − | | c0-10 || || || |
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| − | |- |
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| − | | c0-11 || || || |
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| − | |- |
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| − | | c0-12 || || || |
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| − | |- |
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| − | | c0-13 || || || |
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| − | |- |
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| − | | c0-14 || || || |
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| − | |- |
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| − | | c0-15 || || || |
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| − | |- |
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| − | | c0-16 || offline || 19 Nov 07 || during boot node is stuck at grub |
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| − | |- |
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| − | | c0-17 || || || |
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| − | |- |
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| − | | c0-18 || || || |
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| − | |- |
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| − | | c0-19 || || || |
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| − | |- |
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| − | | c0-20 || || || |
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| − | |- |
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| − | | c0-21 || || || |
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| − | |- |
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| − | | c0-22 || || || |
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| − | |- |
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| − | | c0-23 || || || |
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| − | |- |
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| − | | c0-24 || offline || 13 Jul 07 || power supply broken |
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| − | |- |
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| − | | c0-25 || || || |
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| − | |- |
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| − | | c0-26 || || || |
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| − | |- |
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| − | | c0-27 || || || |
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| − | |- |
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| − | | c0-28 || || || |
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| − | |- |
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| − | | c0-29 || || || |
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| − | |- |
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| − | | c0-30 || || || |
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| − | |- |
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| − | | c0-31 || || || |
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| − | |- |
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| − | | c1-0 || || || |
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| − | |- |
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| − | | c1-1 || || || |
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| − | |- |
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| − | | c1-2 || || || |
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| − | |- |
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| − | | c1-3 || || || |
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| − | |- |
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| − | | c1-4 || || || |
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| − | |- |
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| − | | c1-5 || || || |
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| − | |- |
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| − | | c1-6 || || || |
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| − | |- |
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| − | | c1-7 || || || |
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| − | |- |
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| − | | c1-8 || || || |
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| − | |- |
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| − | | c1-9 || || || |
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| − | |- |
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| − | | c1-10 || || || |
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| − | |- |
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| − | | c1-11 || || || |
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| − | |- |
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| − | | c1-12 || || || |
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| − | |- |
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| − | | c1-13 || || || |
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| − | |- |
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| − | | c1-14 || || || |
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| − | |- |
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| − | | c1-15 || || || |
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| − | |- |
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| − | |} |
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| − | == Queues == |
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| − | Each computational node has the following queues; each queue has as many slot as the number of cores in that node: |
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| − | *'''<node>.short''': jobs run in this queue at nice-level 2 for '''maximum 24h of CPU time''' (real execution of the program, without counting the time needed by the system for multitasking, etc). If a job still runs after the 24th hour, it will receive a signal SIGUSR1 and after some more time a SIGKILL that will terminate it. |
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| − | *'''<node>.medium''': jobs run in this queue at nice-level 3 (lower priority than the short ones) for '''maximum 72h of CPU time''' (real execution of the program, without counting the time needed by the system for multitasking, etc). If a job still runs after the 72nd hour, it will receive a signal SIGUSR1 and after some more time a SIGKILL that will terminate it. |
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| − | *'''<node>.long''': jobs run in this queue at nice-level 3 (lower priority than the short ones) for '''maximum 168h of CPU time''' (real execution of the program, without counting the time needed by the system for multitasking, etc). If a job still runs after the 168th hour, it will receive a signal SIGUSR1 and after some more time a SIGKILL that will terminate it. |
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| − | Summarizing: on a node up to 6 jobs (Opteron 244 nodes) or 12 jobs (Opteron 2216 nodes) can run concurrently with an average space in RAM of 341MB per job. |
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| − | '''YOU HAVE TO DESIGN YOUR COMPUTATIONS IN SUCH A WAY THAT EACH SINGLE JOB DOESN'T RUN FOR MORE THAN 7 DAYS (of CPU time)'''. |
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| − | == How to submit a job == |
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| − | To submit a job you have to create a script (that we indicate with SCRIPT_NAME.sh) with the commands you want to execute. Once you have the script, from majorana execute the command qsub SCRIPT_NAME.sh |
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| − | The script should begin like this: |
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| − | #!/bin/bash |
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| − | #$ -N NAME_OF_JOB |
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| − | #$ -cwd |
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| − | In this case the job will be scheduled for execution in one node chosen from any node, and in one queue chosen from any queue of that node. |
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| − | If you want, you can impose some restrictions on the kind of node or queue to choose from. |
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| − | To select a node with Opteron 244 CPUs, you must add to your script the line '''#$ -l opteron244''', while to select a node with Opteron 2216 CPUs, you must add to your script the line '''#$ -l opteron2216'''. |
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| − | To select only among the short queues, you must add to your script the line '''#$ -l short'''; to select only among the medium queues, you must add the line '''#$ -l medium'''; to select only among the long queues, you must add to your script the line '''#$ -l long'''. |
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| − | '''THE SCHEDULER ADDS TO THE QUEUEING SYSTEM A JOB ONLY IF THERE ARE LESS THAN 10000 JOBS IN THE QUEUE; A SAME USER CAN ADD A JOB TO THE QUEUEING SYSYEM ONLY IF HE HAS LESS THAN 1500 JOBS IN THE QUEUE'''. |
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| − | '''IF THERE IS AN EXECUTION SLOT AVAILABLE, THE SCHEDULER ASSIGN IT TO A USER JOB ONLY IF THAT USER HAS LESS THAN 64 JOBS ALREADY RUNNING'''. |
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| − | == Programming tips for the cluster == |
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| − | If the jobs needs to read/write quite much and often, in the submission script it is better to copy the input files to the /tmp directory (which is in the local harddrive of the node) and to write the output files also there, moving them in the /home/user_name directory only when the computation is over. In this way your job does not have to use NFS for each read/write operation relieving majorana of some weight (the /home partition is exported from there to all the nodes), making it more fast. |
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| − | '''REMEMBER TO REMOVE YOUR FILES FROM THE /TMP DIRECTORY ONCE THE COMPUTATION IS OVER''' |
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