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cluster:97 [2011/02/15 16:10]
hmeij
cluster:97 [2012/02/16 14:09] (current)
hmeij
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 \\ \\
 **[[cluster:0|Home]]** **[[cluster:0|Home]]**
 +
 +==== Summary ====
 +
 +The purpose of this testing is to find out how fast the storage systems respond either directly attached to compute nodes, or attached via ethernet (gigabit ethernet) or infiniband (SDR via queue imw or QDR via queue hp12).  When using infiniband interconnects we use IPoIB (IP traffic over infiniband interconnects which theoretically might be 3-4 times faster than ethernet).
 +
 +So, nothing beats directly attached storage ofcourse (scenario: fastlocal.dell.out below), the attached disk arrays on compute nodes in the ehwfd queue.  Each node is presented with 230 gb of dedicated disk space provided by seven 10K disks using Raid 0 (all drives read and write simultaneously).  IOZone suite finished in an hour.
 +
 +However, that queue may be a bottle neck (only 4 compute nodes in the ehwfd queue) or perhaps 230 GB is not enough (for 8 job slots).  So one alternative is the use of MYSANSCRATCH in your submit scripts.  MYSANSCRATCH refers to a directory made for you by the scheduler at location /sanscratch/JOBPID which is a Raid 5 filesystem of 5 TB provided by 5 disks spinning at 7.2K.  IOZone suite was done in 2 hrs 45 mins (scenario: san.hp.out).
 +
 +For an example of using MYSANSCRATCH, look at the bottom of this page.  You will have to stage your data in the directory provided and copy the results back to your home directory when finished.  The scheduler will remove the directory. 
  
 ==== IOZone ==== ==== IOZone ====
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 On cluster greentail, a separate logical volume presents /home.  This volume is comprised of 12 1TB disks at 7.2K RPM speeds.  Same as above in terms of NFS mount across infiniband.  Note that the disks involved for /home are different than those for /sanscratch.  As expected it falls slightly short of the sancratch volume performance but not by much.  However, as users exercise the /home volume this may become a larger gap. On cluster greentail, a separate logical volume presents /home.  This volume is comprised of 12 1TB disks at 7.2K RPM speeds.  Same as above in terms of NFS mount across infiniband.  Note that the disks involved for /home are different than those for /sanscratch.  As expected it falls slightly short of the sancratch volume performance but not by much.  However, as users exercise the /home volume this may become a larger gap.
 +
 + * home.dell.out ** real    (4 hours and 8 mins)**
 +
 +This was running against greentail's /home mounted via gigabit ethernet Force 10 switch on the petaltail/swallowtail cluster (runnning on node c28).  So just one hour penalty versus running locally on greentail.  Not bad at all, will seriously speed up jobs on the Dell cluster then.
  
 ==== Graphs ==== ==== Graphs ====
  
-IOZone generates lots of interesting graphs, whose interpretations elude me somewhat still.  But it is obvious in some graphs were anomalies exists, iow at sudden thresholds the performance starts to nose dive.+IOZone generates lots of interesting graphs, whose interpretations elude me somewhat still.  But it is obvious in some graphs were anomalies exists;  at sudden thresholds the performance starts to nose dive.
  
-  * [[http://greentail.wesleyan.edu:81/iozone/petaltail/report_local|report_local]] (missing)+  * [[http://greentail.wesleyan.edu:81/iozone/petaltail/report_local|report_local]]
   * [[http://greentail.wesleyan.edu:81/iozone/petaltail/report_fastlocal|report_fastlocal]]   * [[http://greentail.wesleyan.edu:81/iozone/petaltail/report_fastlocal|report_fastlocal]]
   * [[http://greentail.wesleyan.edu:81/iozone/petaltail/report_san|report_san]]   * [[http://greentail.wesleyan.edu:81/iozone/petaltail/report_san|report_san]]
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   * [[http://greentail.wesleyan.edu:81/iozone/greentail/report_home|report_home]]   * [[http://greentail.wesleyan.edu:81/iozone/greentail/report_home|report_home]]
  
 +
 +==== Sample ====
 +
 +Using MYSANSCRATCH with gaussian jobs (you can use any queue but hp12 will be the fastest):
 +
 +<code>
 +
 +#!/bin/bash
 +#BSUB -q hp12
 +#BSUB -o out 
 +#BSUB -e err 
 +#BSUB -J test
 +# job slots: change both lines, also inside gaussian.com
 +#BSUB -n 8
 +#BSUB -x
 +
 +# unique job scratch dirs
 +MYSANSCRATCH=/sanscratch/$LSB_JOBID
 +MYLOCALSCRATCH=/localscratch/$LSB_JOBID
 +export MYSANSCRATCH MYLOCALSCRATCH
 +
 +# cd to remote working dir
 +cd $MYSANSCRATCH
 +pwd
 +
 +# environment
 +export GAUSS_SCRDIR="$MYSANSCRATCH"
 +export g09root="/share/apps/gaussian/g09root"
 +. $g09root/g09/bsd/g09.profile
 +
 +# stage input data 
 +rm -rf ~/gaussian/err ~/gaussian/out*
 +cp ~/gaussian/gaussian.com .
 +
 +# run
 +time g09 < gaussian.com > gaussian.log
 +
 +# save results
 +cp gaussian.log ~/gaussian/output.$LSB_JOBID
 +
 +
 +</code>
  
 \\ \\
 **[[cluster:0|Home]]** **[[cluster:0|Home]]**
cluster/97.1297804210.txt.gz ยท Last modified: 2011/02/15 16:10 by hmeij