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Class Note for COSC 6374 with Professor Gabriel at UH


Class Note for COSC 6374 with Professor Gabriel at UH

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This 14 page Class Notes was uploaded by an elite notetaker on Friday February 6, 2015. The Class Notes belongs to a course at University of Houston taught by a professor in Fall. Since its upload, it has received 13 views.

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Date Created: 02/06/15
2 31 P TL COSC 6374 Parallel Computation Parallel O I O basics Edgar Gabriel Spring 2009 I Concept of a clugters local Cl K Compute node message passing network administrative network cost 74 Parallel compulauon Edgar Gabriel PSTL I O Problem I Every node has its own local disk Most applications require data and executable to be locally available eg an MPI application using multiple nodes requires executable to be available on all nodes in the same directory using the same name Multiple processes need to access the same file potentially different portions efficiency coscu Parallelcomputauon r r EdgarGabnel 3 PSTL I Basic characteristics of storage devices Capacity amount of data a device can store o Transfer rate or bandwidth amount of data at which a device can readwrite in a certain amount of time o Access time or latency delay before the first byte is moved Prefix Abbreviation Base ten Base two kilo kibi K Ki 10quot3 2quot101024 Mega mebi M Mi 10quot6 2quot20 Giga gibi G Gi 10quot9 2quot30 Tera tebi T Ti 10quot12 2quot40 Peta pebi P Pi 10quot15 2quot50 cost 74 Parallel Computation Edgar Gabriel PSTL I UNIX File Access Model o A File is a sequence of bytes o When a program opens a file the file system establishes a file pointer The file pointer is an integer indicating the position in the file where the next byte will be written read o Disk drives read and write data in fixedsized units disk sectors o File systems allocate space in blocks which is a fixed number of contiguous disk sectors o In UNIX based file systems the blocks that hold data are listed in an inode An inode contains the information needed to find all the blocks that belong to a file o If a file is too large and an inode can not hold the whole list of blocks intermediate nodes indirect blocks are introduced coscu Parallelcompulauon r r EdgarGabnel 211 p PSTL I Write operations Write the le systems copies bytes from the user buffer into system buffer If buffer lled up system sends data to disk System buffering allows file systems to collect full blocks of data before sending to disk File system can send several blocks at once to the disk delayed write or write behind Data not really saved in the case of a system crash For very large write operations the additional copy from user to system buffer couldshould be avoided cost 74 Parallel Computatlon Edgar Gabriel PSTL I Read operations Read File system determines which blocks contain requested data Read blocks from disk into system buffer Copy data from system buffer into user memory System buffering file system always reads a full block file caching If application reads data sequentially prefetching read ahead can improve performance Prefetching harmful to the performance if application has a random access pattern coscu Parallelcomputauon r r EdgarGabnel 3 PSTL I Dealing with disk latency Caching and buffering Avoids repeated access to the same block Allows a file system to smooth out IO behavior Helps to hide the latency of the hard drives Lowers the performance of IO operations for irregular access Nonblocking 0 gives users control over prefetching and delayed writing Initiate readwrite operations as soon as possible Wait for the finishing of the readwrite operations just when absolutely necessary cost 74 Parallel Computatlon Edgar Gabriel 2111 PSTL I Improving Disk Bandwidth disk striping Utilize multiple hard drives Split a file into constant chunks and distribute them across all disks Three relevant parameters Stripe factor number of disks Stripe depth size of each block Which disk contains the first block of the file Block 1 Block 2 Block 3 Block n Disk 1 Disk 3 Disk 4 cosc74 Farallelcomputztlon r N EdgarGabnel p PVSTL I Disk striping Ideal assumption bN P P bN 1 with N number of bytes to be written b bandwidth p number of disks Realistically bNP lt P bN 1 since N is often not large enough to fully utilize p hard drives networking overhead cost 74 Parauelcompumuon f quot7 EdgarGabnel i r PSTL I Two levels of disk striping I Using a RAID controller Hardware typically a single box number of disks 3n cuscscmezxaiei common 7 Eager Esme 2 I n RSTL Redundant arrays of independent disks I RAID Goals improve reliability and performance of an ID system improve performance of an IID system Several RAID levels defined RAID 0 disk striping widwout redundant storage JBOD just a bunch of disks No fault tolerance Good for high transfer rates ie readwrite bandwid w of a single large file Good for high request rates ie access time to many small files RAID 1 mirroring All data is replicated on two or more disks Does notimprove write performance and just moderately the read performance cps scm 7 mm commie Eager Esme 2 31 P TL I RAID level 2 o RAID 2 Hamming codes Each group of data bits has several check bits appended to it forming Hamming code words Each bit of a Hamming code word is stored on a separate disk Very high additional costs eg up to 50 additional capacity required o Hardly used today since parity based codes faster and easier coscu Parallelcomputauon r V EdgarGabnel a PVSTL I RAID level 3 o Parity based protection Based on exclusive OR XOR Reversible Example 01101010 data byte 1 XOR 11001001 data byte 2 10100011 parity byte Recovery 11001001 data byte 2 XOR 10100011 parity byte 01101010 recovered data byte 1 cost 74 Parallel Computatlon Edgar Gabriel PSTL RAID level 3 cont Data divided evenly into N subblocks N number of disks typically 4 or 5 Computing parity bytes generates an additional subblock Subblocks written in parallel on N1 disks For best performance data should be of size N sector size Problems with RAID level 3 All disks are always participating in every operation gt contention for applications with high access rates If data size is less than Nsector size system has to read old subblocks to calculate the parity bytes RAID level 3 good for high transfer rates coscu Parallelcomputauon r r EdgarGabnel RAID level 4 HQTL o Parity bytes for N disks calculated and stored o Parity bytes are stored on a separate disk o Files are not necessarily distributed over N disks o For read operations Determine disks for the requested blocks Read data from these disks o For write operations Retrieve the old data from the sector being overwritten Retrieve parity block from the parity disk Extract old data from the parity block using XOR operations Add the new data to the parity block using XOR Store new data Store new parity block o Bottleneck parity disk is involved in every operation cost 74 Parallel Computatlon Edgar Gabriel 1 PSTL I RAID level 5 Same as RAID 4 but parity blocks are distributed on different disks IBlock 1 lBlock 2 IBlock 3 Block 4 g l I l I I i i cosc74 Farallelcomputztlon r r EdgarGabnel p PVSTL I RAID level 6 o Tolerates the loss of more than one disk o Collection of several techniques o Eg PQ parity store parity bytes using two different algorithms and store the two parity blocks on different disks o Eg Two dimensional parity Parity disks IIIID IIIID IIIID INDIE cosc 74 Parauelcompumuon rv min 7 Edgar Gabriel I III RAID level 10 5 RAID leve 1 RAID level 0 mm 1 mirroring PSTL RAID 0 striping o Also available RAID 53 RAID 0 RAID 3 cost 74 Parallel computation EdgarGabnel PSTL Com paring RAID levels RAID Protection Space usage Good at Poor at level 0 None N Performance Data protect I Mirroring 2N Data protect Space effic 2 Hamming codes 15N Transfer rate Request rate 3 Parity N1 Transfer rate Request rate 4 Parity N1 Read req rate Write perf 5 Parity N1 Request rate Transfer rate 6 PQ or 2D N2 or Data protect Write perf MNMN 10 Mirroring 2N Performance Space effic 53 parity Nstriping Performance Space effic factor m L grarallel Compum on m 10 PSTL I Two levels of disk striping II Uslng a parallel le system 7 expuses tne lndlvldual unlts capable ufhandllng data uflen called stenage servers we nudes 2m 7 eaen smnage server mlgvl use multlple hard drlves underneath tne huud te lncrease lts neadwne bandwldm r Netadataserverwmchkaepstrackufwhlchpamufaflle are un Wmen sturage server 7 lngle dlskfallura less ufa prublem lfeach server uses underneath tne hand a RAlD 5 stenage system www J STL I Parallel File Systems Conceptual overview tempute nudes Metasdam server an smeeeeemeyu ll r STL File access on a parallel file system Cam puts nude Meladata Sew a APDlVCiuan all u m l I as maue ma Velaam m Mae 10v mlwmapmm MD a My enm ange mix 0115 Us Send din a ange a m r A l a PSTL Disk striping Requvrements a varave Derfarmance af llo averatmns usmg my mama a Nuluvle Dhysmal am 7 Have a balance netwarkhandwvdth and we handwvdth Prahlem afsvmvle dvskstrwmg a far a ma le an the numberafdvsks whvch can he used m Parallel lsllmaa Pmmmenlparallel le sysLEms a wrsz a Lustre a cvrs a NFSvA 2 lnew standard currently hemgratv edl 12 v F STL I Distributed vs Parallel File Systems Dvsmhuted Fvle Systems 7 0112159923 m a tulleman M me an vemate macmne e waeeuyeueneeewey neeaewmem e Yvanwaven mtheuxev NF 7 The Nelvmrk Fvle System V Pmtacal ma Femeee me ewe e me eeeemev v31 7 Cammumcatmn taxed an RFC lRemate Pmceduve cm 7 NF wee man mam 7 change m an wen me we mmaHy my me m the Dmcess matmadmed the me e FNe memem pen B NF Dmtacal M but men avavlahle thmugh a evavam wer maeman 7 Cheer cammgnat pen M the NF mam2m lv l39 vmvlemematmn dependent hehavmv In wmm m z PSTL I Network File System NFS Campute nude e NF chem NF Few mm AP VCiuan all new as week din a NsF NFs dieman New din NFSdaeman all mu in wwwem 13 1 PSTL I Parallel vs Distributed File Systems Concurrent access to the same file from several processes is considered to be an unlikely event Distributed file systems assume different numbers of processors than parallel file systems Distributed file systems have different security requirements than parallel file systems cosc74 Farallelcomputztlon r 7 EdgarGabnel 14


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