A Quick Review of On-Disk Layout of Some Popular Disk File Systems by Wasim Ahmad Bhat , S
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Sequence Listings Webinar Suzannah K. Sundby Carl Oppedahl
Suzannah K. Sundby Canady + Lortz LLP Sequence Listings Webinar January 9, 2018 – Updated Version Carl Oppedahl Oppedahl Patent Law Firm LLC DISCLAIMER These materials and views expressed today reflect only the personal views of the author and do not necessarily represent the views of other members and clients of the author’s organizations. These materials are public information and have been prepared solely for educational purposes to contribute to the understanding of U.S. intellectual property law. While every attempt was made to ensure that these materials are accurate, errors or omissions may be contained therein, for which any liability is disclaimed. These materials and views are not a source of legal advice and do not establish any form of attorney-client relationship with the authors and their law firms. Why are some sequence errors not identified by Checker? Is “SEQ ID NO” required before sequences in Specifications? Do you recommend using the PatentIn Software? How do you correct sequence listing errors in PCTs? What about the new WIPO ST.26 Standard? Is Checker worthwhile? How can I easily edit sequence listings generated by others? Can I use other software to generate sequence listings? How do I file sequence listings using EFS-Web and ePCT? How long does it take the USPTO to review and approve? Any risk TYFNIL of using certain sequence descriptors? Help! IT locked down my computer… what do I do? Any sequence listing tips? Why Practitioners Should Know and Do Usually lack of time to send to outside vendors Last minute changes to applications (apps) containing sequences (seqs) Particularly, changes to claims Not hostage to staff/vendors, overtime, etc. -
Copy on Write Based File Systems Performance Analysis and Implementation
Copy On Write Based File Systems Performance Analysis And Implementation Sakis Kasampalis Kongens Lyngby 2010 IMM-MSC-2010-63 Technical University of Denmark Department Of Informatics Building 321, DK-2800 Kongens Lyngby, Denmark Phone +45 45253351, Fax +45 45882673 [email protected] www.imm.dtu.dk Abstract In this work I am focusing on Copy On Write based file systems. Copy On Write is used on modern file systems for providing (1) metadata and data consistency using transactional semantics, (2) cheap and instant backups using snapshots and clones. This thesis is divided into two main parts. The first part focuses on the design and performance of Copy On Write based file systems. Recent efforts aiming at creating a Copy On Write based file system are ZFS, Btrfs, ext3cow, Hammer, and LLFS. My work focuses only on ZFS and Btrfs, since they support the most advanced features. The main goals of ZFS and Btrfs are to offer a scalable, fault tolerant, and easy to administrate file system. I evaluate the performance and scalability of ZFS and Btrfs. The evaluation includes studying their design and testing their performance and scalability against a set of recommended file system benchmarks. Most computers are already based on multi-core and multiple processor architec- tures. Because of that, the need for using concurrent programming models has increased. Transactions can be very helpful for supporting concurrent program- ming models, which ensure that system updates are consistent. Unfortunately, the majority of operating systems and file systems either do not support trans- actions at all, or they simply do not expose them to the users. -
Study of File System Evolution
Study of File System Evolution Swaminathan Sundararaman, Sriram Subramanian Department of Computer Science University of Wisconsin {swami, srirams} @cs.wisc.edu Abstract File systems have traditionally been a major area of file systems are typically developed and maintained by research and development. This is evident from the several programmer across the globe. At any point in existence of over 50 file systems of varying popularity time, for a file system, there are three to six active in the current version of the Linux kernel. They developers, ten to fifteen patch contributors but a single represent a complex subsystem of the kernel, with each maintainer. These people communicate through file system employing different strategies for tackling individual file system mailing lists [14, 16, 18] various issues. Although there are many file systems in submitting proposals for new features, enhancements, Linux, there has been no prior work (to the best of our reporting bugs, submitting and reviewing patches for knowledge) on understanding how file systems evolve. known bugs. The problems with the open source We believe that such information would be useful to the development approach is that all communication is file system community allowing developers to learn buried in the mailing list archives and aren’t easily from previous experiences. accessible to others. As a result when new file systems are developed they do not leverage past experience and This paper looks at six file systems (Ext2, Ext3, Ext4, could end up re-inventing the wheel. To make things JFS, ReiserFS, and XFS) from a historical perspective worse, people could typically end up doing the same (between kernel versions 1.0 to 2.6) to get an insight on mistakes as done in other file systems. -
Active @ UNDELETE Users Guide | TOC | 2
Active @ UNDELETE Users Guide | TOC | 2 Contents Legal Statement..................................................................................................4 Active@ UNDELETE Overview............................................................................. 5 Getting Started with Active@ UNDELETE........................................................... 6 Active@ UNDELETE Views And Windows......................................................................................6 Recovery Explorer View.................................................................................................... 7 Logical Drive Scan Result View.......................................................................................... 7 Physical Device Scan View................................................................................................ 8 Search Results View........................................................................................................10 Application Log...............................................................................................................11 Welcome View................................................................................................................11 Using Active@ UNDELETE Overview................................................................. 13 Recover deleted Files and Folders.............................................................................................. 14 Scan a Volume (Logical Drive) for deleted files..................................................................15 -
Dealing with Document Size Limits
Dealing with Document Size Limits Introduction The Electronic Case Filing system will not accept PDF documents larger than ten megabytes (MB). If the document size is less than 10 MB, it can be filed electronically just as it is. If it is larger than 10 MB, it will need to be divided into two or more documents, with each document being less than 10 MB. Word Processing Documents Documents created with a word processing program (such as WordPerfect or Microsoft Word) and correctly converted to PDF will generally be smaller than a scanned document. Because of variances in software, usage, and content, it is difficult to estimate the number of pages that would constitute 10 MB. (Note: See “Verifying File Size” below and for larger documents, see “Splitting PDF Documents into Multiple Documents” below.) Scanned Documents Although the judges’ Filing Preferences indicate a preference for conversion of documents rather than scanning, it will be necessary to scan some documents for filing, e.g., evidentiary attachments must be scanned. Here are some things to remember: • Documents scanned to PDF are generally much larger than those converted through a word processor. • While embedded fonts may be necessary for special situations, e.g., trademark, they will increase the file size. • If graphs or color photos are included, just a few pages can easily exceed the 10 MB limit. Here are some guidelines: • The court’s standard scanner resolution is 300 dots per inch (DPI). Avoid using higher resolutions as this will create much larger file sizes. • Normally, the output should be set to black and white. -
ECE 598 – Advanced Operating Systems Lecture 19
ECE 598 { Advanced Operating Systems Lecture 19 Vince Weaver http://web.eece.maine.edu/~vweaver [email protected] 7 April 2016 Announcements • Homework #7 was due • Homework #8 will be posted 1 Why use FAT over ext2? • FAT simpler, easy to code • FAT supported on all major OSes • ext2 faster, more robust filename and permissions 2 btrfs • B-tree fs (similar to a binary tree, but with pages full of leaves) • overwrite filesystem (overwite on modify) vs CoW • Copy on write. When write to a file, old data not overwritten. Since old data not over-written, crash recovery better Eventually old data garbage collected • Data in extents 3 • Copy-on-write • Forest of trees: { sub-volumes { extent-allocation { checksum tree { chunk device { reloc • On-line defragmentation • On-line volume growth 4 • Built-in RAID • Transparent compression • Snapshots • Checksums on data and meta-data • De-duplication • Cloning { can make an exact snapshot of file, copy-on- write different than link, different inodles but same blocks 5 Embedded • Designed to be small, simple, read-only? • romfs { 32 byte header (magic, size, checksum,name) { Repeating files (pointer to next [0 if none]), info, size, checksum, file name, file data • cramfs 6 ZFS Advanced OS from Sun/Oracle. Similar in idea to btrfs indirect still, not extent based? 7 ReFS Resilient FS, Microsoft's answer to brtfs and zfs 8 Networked File Systems • Allow a centralized file server to export a filesystem to multiple clients. • Provide file level access, not just raw blocks (NBD) • Clustered filesystems also exist, where multiple servers work in conjunction. -
CS 5600 Computer Systems
CS 5600 Computer Systems Lecture 10: File Systems What are We Doing Today? • Last week we talked extensively about hard drives and SSDs – How they work – Performance characterisEcs • This week is all about managing storage – Disks/SSDs offer a blank slate of empty blocks – How do we store files on these devices, and keep track of them? – How do we maintain high performance? – How do we maintain consistency in the face of random crashes? 2 • ParEEons and MounEng • Basics (FAT) • inodes and Blocks (ext) • Block Groups (ext2) • Journaling (ext3) • Extents and B-Trees (ext4) • Log-based File Systems 3 Building the Root File System • One of the first tasks of an OS during bootup is to build the root file system 1. Locate all bootable media – Internal and external hard disks – SSDs – Floppy disks, CDs, DVDs, USB scks 2. Locate all the parEEons on each media – Read MBR(s), extended parEEon tables, etc. 3. Mount one or more parEEons – Makes the file system(s) available for access 4 The Master Boot Record Address Size Descripon Hex Dec. (Bytes) Includes the starEng 0x000 0 Bootstrap code area 446 LBA and length of 0x1BE 446 ParEEon Entry #1 16 the parEEon 0x1CE 462 ParEEon Entry #2 16 0x1DE 478 ParEEon Entry #3 16 0x1EE 494 ParEEon Entry #4 16 0x1FE 510 Magic Number 2 Total: 512 ParEEon 1 ParEEon 2 ParEEon 3 ParEEon 4 MBR (ext3) (swap) (NTFS) (FAT32) Disk 1 ParEEon 1 MBR (NTFS) 5 Disk 2 Extended ParEEons • In some cases, you may want >4 parEEons • Modern OSes support extended parEEons Logical Logical ParEEon 1 ParEEon 2 Ext. -
Ext4 File System and Crash Consistency
1 Ext4 file system and crash consistency Changwoo Min 2 Summary of last lectures • Tools: building, exploring, and debugging Linux kernel • Core kernel infrastructure • Process management & scheduling • Interrupt & interrupt handler • Kernel synchronization • Memory management • Virtual file system • Page cache and page fault 3 Today: ext4 file system and crash consistency • File system in Linux kernel • Design considerations of a file system • History of file system • On-disk structure of Ext4 • File operations • Crash consistency 4 File system in Linux kernel User space application (ex: cp) User-space Syscalls: open, read, write, etc. Kernel-space VFS: Virtual File System Filesystems ext4 FAT32 JFFS2 Block layer Hardware Embedded Hard disk USB drive flash 5 What is a file system fundamentally? int main(int argc, char *argv[]) { int fd; char buffer[4096]; struct stat_buf; DIR *dir; struct dirent *entry; /* 1. Path name -> inode mapping */ fd = open("/home/lkp/hello.c" , O_RDONLY); /* 2. File offset -> disk block address mapping */ pread(fd, buffer, sizeof(buffer), 0); /* 3. File meta data operation */ fstat(fd, &stat_buf); printf("file size = %d\n", stat_buf.st_size); /* 4. Directory operation */ dir = opendir("/home"); entry = readdir(dir); printf("dir = %s\n", entry->d_name); return 0; } 6 Why do we care EXT4 file system? • Most widely-deployed file system • Default file system of major Linux distributions • File system used in Google data center • Default file system of Android kernel • Follows the traditional file system design 7 History of file system design 8 UFS (Unix File System) • The original UNIX file system • Design by Dennis Ritche and Ken Thompson (1974) • The first Linux file system (ext) and Minix FS has a similar layout 9 UFS (Unix File System) • Performance problem of UFS (and the first Linux file system) • Especially, long seek time between an inode and data block 10 FFS (Fast File System) • The file system of BSD UNIX • Designed by Marshall Kirk McKusick, et al. -
W4118: Linux File Systems
W4118: Linux file systems Instructor: Junfeng Yang References: Modern Operating Systems (3rd edition), Operating Systems Concepts (8th edition), previous W4118, and OS at MIT, Stanford, and UWisc File systems in Linux Linux Second Extended File System (Ext2) . What is the EXT2 on-disk layout? . What is the EXT2 directory structure? Linux Third Extended File System (Ext3) . What is the file system consistency problem? . How to solve the consistency problem using journaling? Virtual File System (VFS) . What is VFS? . What are the key data structures of Linux VFS? 1 Ext2 “Standard” Linux File System . Was the most commonly used before ext3 came out Uses FFS like layout . Each FS is composed of identical block groups . Allocation is designed to improve locality inodes contain pointers (32 bits) to blocks . Direct, Indirect, Double Indirect, Triple Indirect . Maximum file size: 4.1TB (4K Blocks) . Maximum file system size: 16TB (4K Blocks) On-disk structures defined in include/linux/ext2_fs.h 2 Ext2 Disk Layout Files in the same directory are stored in the same block group Files in different directories are spread among the block groups Picture from Tanenbaum, Modern Operating Systems 3 e, (c) 2008 Prentice-Hall, Inc. All rights reserved. 0-13-6006639 3 Block Addressing in Ext2 Twelve “direct” blocks Data Data BlockData Inode Block Block BLKSIZE/4 Indirect Data Data Blocks BlockData Block Data (BLKSIZE/4)2 Indirect Block Data BlockData Blocks Block Double Block Indirect Indirect Blocks Data Data Data (BLKSIZE/4)3 BlockData Data Indirect Block BlockData Block Block Triple Double Blocks Block Indirect Indirect Data Indirect Data BlockData Blocks Block Block Picture from Tanenbaum, Modern Operating Systems 3 e, (c) 2008 Prentice-Hall, Inc. -
Cygwin User's Guide
Cygwin User’s Guide Cygwin User’s Guide ii Copyright © Cygwin authors Permission is granted to make and distribute verbatim copies of this documentation provided the copyright notice and this per- mission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this documentation under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this documentation into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the Free Software Foundation. Cygwin User’s Guide iii Contents 1 Cygwin Overview 1 1.1 What is it? . .1 1.2 Quick Start Guide for those more experienced with Windows . .1 1.3 Quick Start Guide for those more experienced with UNIX . .1 1.4 Are the Cygwin tools free software? . .2 1.5 A brief history of the Cygwin project . .2 1.6 Highlights of Cygwin Functionality . .3 1.6.1 Introduction . .3 1.6.2 Permissions and Security . .3 1.6.3 File Access . .3 1.6.4 Text Mode vs. Binary Mode . .4 1.6.5 ANSI C Library . .4 1.6.6 Process Creation . .5 1.6.6.1 Problems with process creation . .5 1.6.7 Signals . .6 1.6.8 Sockets . .6 1.6.9 Select . .7 1.7 What’s new and what changed in Cygwin . .7 1.7.1 What’s new and what changed in 3.2 . -
11.7 the Windows 2000 File System
830 CASE STUDY 2: WINDOWS 2000 CHAP. 11 11.7 THE WINDOWS 2000 FILE SYSTEM Windows 2000 supports several file systems, the most important of which are FAT-16, FAT-32, and NTFS (NT File System). FAT-16 is the old MS-DOS file system. It uses 16-bit disk addresses, which limits it to disk partitions no larger than 2 GB. FAT-32 uses 32-bit disk addresses and supports disk partitions up to 2 TB. NTFS is a new file system developed specifically for Windows NT and car- ried over to Windows 2000. It uses 64-bit disk addresses and can (theoretically) support disk partitions up to 264 bytes, although other considerations limit it to smaller sizes. Windows 2000 also supports read-only file systems for CD-ROMs and DVDs. It is possible (even common) to have the same running system have access to multiple file system types available at the same time. In this chapter we will treat the NTFS file system because it is a modern file system unencumbered by the need to be fully compatible with the MS-DOS file system, which was based on the CP/M file system designed for 8-inch floppy disks more than 20 years ago. Times have changed and 8-inch floppy disks are not quite state of the art any more. Neither are their file systems. Also, NTFS differs both in user interface and implementation in a number of ways from the UNIX file system, which makes it a good second example to study. NTFS is a large and complex system and space limitations prevent us from covering all of its features, but the material presented below should give a reasonable impression of it. -
Ext3 = Ext2 + Journaling
FS Sistem datoteka-skup metoda i struktura podataka koje operativni sistem koristi za čuvanje podataka Struktura sistema datoteka: - 1. zaglavlje→neophodni podaci za funkcionisanje sistema datoteka - 2. strukture za organizaciju podataka na medijumu→meta podaci - 3. podaci→datoteke i direktorijumi Strukture podataka neophodne za realizaciju sistema datoteka: - PCB(Partition Control Block) - BCB(Boot control Block) - Kontrolne strukture za alokaciju datoteka(i-node tabela kod Linux-a) - Direktorijumske strukture koje sadrže kontrolne blokove datoteka - FCB(File Control Block) ext3 Slide 1 of 51 VIRTUELNI SISTEM DATOTEKA(VFS) Linux podržava rad sa velikim brojem sistema datoteka(ext2,ext3, XFS,FAT, NTFS...) VFS-objektno orjentisani način realizacije sistema datoteka koji omogućava korisniku da na isti način pristupa svim sistemima datoteka Način obraćanja korisnika sistemu datoteka - korisnik->API - VFS->sistem datoteka ext3 Slide 2 of 51 Linux FS Linux posmatra svaki sistem datoteka kao nezavisnu hijerarhijsku strukturu objekata(datoteka i direktorijuma) na čijem se vrhu nalazi root(/) direktorijum Objekti Linux sistema datoteka: Super block - zaglavlje(superblock) - i-node tabela I-Node Table - blokovi sa podacima - direktorijumski blokovi - blokovi indirektnih pokazivača Data Area i-node-opisuje objekte, oko 128B na disku Kompromis između veličine i-node tabele i brzine rada sistema datoteka - prvih 10-12 pokazivača na blokove sa podacima - za alokaciju većih datoteka koristi se single indirection block - za još veće datoteke