[Bioclusters] Tool to benchmark disk IO?

[Dan Bolser]

Thanks all again for the advice. Now I just have to persuade our IT people
to go with XFS... We have the perfect opportunity to switch over just now.

Anyway, these stats look a bit more normal (I think) with bonnie++

Test machine memory:	1548036k
NFS server memory: 	1029764k


NFS
      ------Sequential Output------ --Sequential Input- --Random-
      -Per Chr- --Block-- -Rewrite- -Per Chr- --Block-- --Seeks--
 Size K/sec %CP K/sec %CP K/sec %CP K/sec %CP K/sec %CP  /sec %CP
   8G  5291  29  6375   3  4563   2 11364  66 11250   3 267.3   1
      ------Sequential Create------ --------Random Create--------
      -Create-- --Read--- -Delete-- -Create-- --Read--- -Delete--
files  /sec %CP  /sec %CP  /sec %CP  /sec %CP  /sec %CP  /sec %CP
   16   223   0  2322   4   339   0   229   0  2460   3   323   0


IDE
      ------Sequential Output------ --Sequential Input- --Random-
      -Per Chr- --Block-- -Rewrite- -Per Chr- --Block-- --Seeks--
 Size K/sec %CP K/sec %CP K/sec %CP K/sec %CP K/sec %CP  /sec %CP
   7G 17383  95 39662  24 18243   9 17345  89 51922  14  91.1   0
      ------Sequential Create------ --------Random Create--------
      -Create-- --Read--- -Delete-- -Create-- --Read--- -Delete--
files  /sec %CP  /sec %CP  /sec %CP  /sec %CP  /sec %CP  /sec %CP
   16  1431  98 +++++ +++ +++++ +++  1392  99 +++++ +++  4225  99


SCSI
      ------Sequential Output------ --Sequential Input- --Random-
      -Per Chr- --Block-- -Rewrite- -Per Chr- --Block-- --Seeks--
 Size K/sec %CP K/sec %CP K/sec %CP K/sec %CP K/sec %CP  /sec %CP
   7G 16634  95 32241  22 13841   6 13413  69 37512  10 168.7   0
      ------Sequential Create------ --------Random Create--------
      -Create-- --Read--- -Delete-- -Create-- --Read--- -Delete--
files  /sec %CP  /sec %CP  /sec %CP  /sec %CP  /sec %CP  /sec %CP
   16  1383  97 +++++ +++ +++++ +++  1257  95 +++++ +++  3566  95


Test machine memory:	4124716k

NFS
      ------Sequential Output------ --Sequential Input- --Random-
      -Per Chr- --Block-- -Rewrite- -Per Chr- --Block-- --Seeks--
 Size K/sec %CP K/sec %CP K/sec %CP K/sec %CP K/sec %CP  /sec %CP
   8G  4826  68 10614   7  7645   6  7297  99 37843  10 348.7   1
      ------Sequential Create------ --------Random Create--------
      -Create-- --Read--- -Delete-- -Create-- --Read--- -Delete--
files  /sec %CP  /sec %CP  /sec %CP  /sec %CP  /sec %CP  /sec %CP
   16   240   0  2961   5   366   1   246   0  2938   1   351   0


Underlying NFS export is ext3 raid system (RAID5 I think) with 8 disks.

One 'issue' IT had with XFS was its performance under NFS, from what you
have said I guess that isn't an issue? i.e. NFS exported XFS is the same
as local XFS except for the network connection for all the IO? They were
worried that NFS would hide any benifits of the underlying FS.

Thanks,

Dan.




On Sat, 25 Sep 2004, Joe Landman wrote:

>Hi Guy:
>
>  With version 3 of NFS, you might try
>   
>    rsize=32768,wsize=32768,tcp,intr,hard,nfsvers=3
>
>Version 3 lets you do 32k rsize/wsize.  TCP can be (but isn't always) a 
>win. You might experiment with the noatime, and some of the other 
>switches.  There are some other "tricks" as well to tuning NFS.  It 
>isn't too difficult to hit wire speed over 100 base T, it is a bit 
>harder to hit it over gigabit.  Lots more to tune (including disk).  I 
>would recommend XFS or JFS as the underlying exported file system.  Ext3 
>still has some non-optimized serializing code paths in its journaling 
>system that make it hard to get very good performance out of it.
>
>Joe
>
>Guy Coates wrote:
>
>>One thing which makes a big difference in IO speed is tweaking the various
>>mount options:
>>
>>For your NFS mounts, the following is a good start (maybe proto=tcp if
>>your server supports it):
>>
>>rsize=8192,wsize=8192,hard,intr,vers=3,proto=udp
>>
>>
>>For ext3, mount  with "data=writeback"[1], and for reiserfs mount  with
>>"notail" options.  If you've got it compiled into your kernel, XFS is
>>worth trying too. It is quite speedy.
>>
>>Guy
>>
>>
>>[1] Check the man page for what this does; if you machine goes down in the
>>middle of a file write you stand an increase chance of that file getting
>>mangled; the filesystem itself should be OK.
>>
>> --
>>Dr. Guy Coates,  Informatics System Group
>>The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
>>Tel: +44 (0)1223 834244 ex 7199
>>
>>
>>
>>
>>
>>
>>_______________________________________________
>>Bioclusters maillist  -  Bioclusters@bioinformatics.org
>>https://bioinformatics.org/mailman/listinfo/bioclusters
>>  
>>
>
>