diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..b500796 --- /dev/null +++ b/.gitignore @@ -0,0 +1,12 @@ +group +*.out +*.trash +*.err +*.lock +.nfs* +current_state + +bsdmainutils/ +du.sh +disk_usage.sh +update_logs/ diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. Therefore, you have +certain responsibilities if you distribute copies of the software, or if +you modify it: responsibilities to respect the freedom of others. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must pass on to the recipients the same +freedoms that you received. You must make sure that they, too, receive +or can get the source code. And you must show them these terms so they +know their rights. + + Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License +giving you legal permission to copy, distribute and/or modify it. + + For the developers' and authors' protection, the GPL clearly explains +that there is no warranty for this free software. For both users' and +authors' sake, the GPL requires that modified versions be marked as +changed, so that their problems will not be attributed erroneously to +authors of previous versions. + + Some devices are designed to deny users access to install or run +modified versions of the software inside them, although the manufacturer +can do so. This is fundamentally incompatible with the aim of +protecting users' freedom to change the software. The systematic +pattern of such abuse occurs in the area of products for individuals to +use, which is precisely where it is most unacceptable. Therefore, we +have designed this version of the GPL to prohibit the practice for those +products. If such problems arise substantially in other domains, we +stand ready to extend this provision to those domains in future versions +of the GPL, as needed to protect the freedom of users. + + Finally, every program is threatened constantly by software patents. +States should not allow patents to restrict development and use of +software on general-purpose computers, but in those that do, we wish to +avoid the special danger that patents applied to a free program could +make it effectively proprietary. To prevent this, the GPL assures that +patents cannot be used to render the program non-free. + + The precise terms and conditions for copying, distribution and +modification follow. + + TERMS AND CONDITIONS + + 0. Definitions. + + "This License" refers to version 3 of the GNU General Public License. + + "Copyright" also means copyright-like laws that apply to other kinds of +works, such as semiconductor masks. + + "The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + + To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of an +exact copy. The resulting work is called a "modified version" of the +earlier work or a work "based on" the earlier work. + + A "covered work" means either the unmodified Program or a work based +on the Program. + + To "propagate" a work means to do anything with it that, without +permission, would make you directly or secondarily liable for +infringement under applicable copyright law, except executing it on a +computer or modifying a private copy. Propagation includes copying, +distribution (with or without modification), making available to the +public, and in some countries other activities as well. + + To "convey" a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user through +a computer network, with no transfer of a copy, is not conveying. + + An interactive user interface displays "Appropriate Legal Notices" +to the extent that it includes a convenient and prominently visible +feature that (1) displays an appropriate copyright notice, and (2) +tells the user that there is no warranty for the work (except to the +extent that warranties are provided), that licensees may convey the +work under this License, and how to view a copy of this License. If +the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + + 1. Source Code. + + The "source code" for a work means the preferred form of the work +for making modifications to it. "Object code" means any non-source +form of a work. + + A "Standard Interface" means an interface that either is an official +standard defined by a recognized standards body, or, in the case of +interfaces specified for a particular programming language, one that +is widely used among developers working in that language. + + The "System Libraries" of an executable work include anything, other +than the work as a whole, that (a) is included in the normal form of +packaging a Major Component, but which is not part of that Major +Component, and (b) serves only to enable use of the work with that +Major Component, or to implement a Standard Interface for which an +implementation is available to the public in source code form. A +"Major Component", in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system +(if any) on which the executable work runs, or a compiler used to +produce the work, or an object code interpreter used to run it. + + The "Corresponding Source" for a work in object code form means all +the source code needed to generate, install, and (for an executable +work) run the object code and to modify the work, including scripts to +control those activities. However, it does not include the work's +System Libraries, or general-purpose tools or generally available free +programs which are used unmodified in performing those activities but +which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for +the work, and the source code for shared libraries and dynamically +linked subprograms that the work is specifically designed to require, +such as by intimate data communication or control flow between those +subprograms and other parts of the work. + + The Corresponding Source need not include anything that users +can regenerate automatically from other parts of the Corresponding +Source. + + The Corresponding Source for a work in source code form is that +same work. + + 2. Basic Permissions. + + All rights granted under this License are granted for the term of +copyright on the Program, and are irrevocable provided the stated +conditions are met. This License explicitly affirms your unlimited +permission to run the unmodified Program. The output from running a +covered work is covered by this License only if the output, given its +content, constitutes a covered work. This License acknowledges your +rights of fair use or other equivalent, as provided by copyright law. + + You may make, run and propagate covered works that you do not +convey, without conditions so long as your license otherwise remains +in force. You may convey covered works to others for the sole purpose +of having them make modifications exclusively for you, or provide you +with facilities for running those works, provided that you comply with +the terms of this License in conveying all material for which you do +not control copyright. Those thus making or running the covered works +for you must do so exclusively on your behalf, under your direction +and control, on terms that prohibit them from making any copies of +your copyrighted material outside their relationship with you. + + Conveying under any other circumstances is permitted solely under +the conditions stated below. Sublicensing is not allowed; section 10 +makes it unnecessary. + + 3. Protecting Users' Legal Rights From Anti-Circumvention Law. + + No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + + When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such circumvention +is effected by exercising rights under this License with respect to +the covered work, and you disclaim any intention to limit operation or +modification of the work as a means of enforcing, against the work's +users, your or third parties' legal rights to forbid circumvention of +technological measures. + + 4. Conveying Verbatim Copies. + + You may convey verbatim copies of the Program's source code as you +receive it, in any medium, provided that you conspicuously and +appropriately publish on each copy an appropriate copyright notice; +keep intact all notices stating that this License and any +non-permissive terms added in accord with section 7 apply to the code; +keep intact all notices of the absence of any warranty; and give all +recipients a copy of this License along with the Program. + + You may charge any price or no price for each copy that you convey, +and you may offer support or warranty protection for a fee. + + 5. Conveying Modified Source Versions. + + You may convey a work based on the Program, or the modifications to +produce it from the Program, in the form of source code under the +terms of section 4, provided that you also meet all of these conditions: + + a) The work must carry prominent notices stating that you modified + it, and giving a relevant date. + + b) The work must carry prominent notices stating that it is + released under this License and any conditions added under section + 7. This requirement modifies the requirement in section 4 to + "keep intact all notices". + + c) You must license the entire work, as a whole, under this + License to anyone who comes into possession of a copy. This + License will therefore apply, along with any applicable section 7 + additional terms, to the whole of the work, and all its parts, + regardless of how they are packaged. This License gives no + permission to license the work in any other way, but it does not + invalidate such permission if you have separately received it. + + d) If the work has interactive user interfaces, each must display + Appropriate Legal Notices; however, if the Program has interactive + interfaces that do not display Appropriate Legal Notices, your + work need not make them do so. + + A compilation of a covered work with other separate and independent +works, which are not by their nature extensions of the covered work, +and which are not combined with it such as to form a larger program, +in or on a volume of a storage or distribution medium, is called an +"aggregate" if the compilation and its resulting copyright are not +used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work +in an aggregate does not cause this License to apply to the other +parts of the aggregate. + + 6. Conveying Non-Source Forms. + + You may convey a covered work in object code form under the terms +of sections 4 and 5, provided that you also convey the +machine-readable Corresponding Source under the terms of this License, +in one of these ways: + + a) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by the + Corresponding Source fixed on a durable physical medium + customarily used for software interchange. + + b) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by a + written offer, valid for at least three years and valid for as + long as you offer spare parts or customer support for that product + model, to give anyone who possesses the object code either (1) a + copy of the Corresponding Source for all the software in the + product that is covered by this License, on a durable physical + medium customarily used for software interchange, for a price no + more than your reasonable cost of physically performing this + conveying of source, or (2) access to copy the + Corresponding Source from a network server at no charge. + + c) Convey individual copies of the object code with a copy of the + written offer to provide the Corresponding Source. This + alternative is allowed only occasionally and noncommercially, and + only if you received the object code with such an offer, in accord + with subsection 6b. + + d) Convey the object code by offering access from a designated + place (gratis or for a charge), and offer equivalent access to the + Corresponding Source in the same way through the same place at no + further charge. You need not require recipients to copy the + Corresponding Source along with the object code. If the place to + copy the object code is a network server, the Corresponding Source + may be on a different server (operated by you or a third party) + that supports equivalent copying facilities, provided you maintain + clear directions next to the object code saying where to find the + Corresponding Source. Regardless of what server hosts the + Corresponding Source, you remain obligated to ensure that it is + available for as long as needed to satisfy these requirements. + + e) Convey the object code using peer-to-peer transmission, provided + you inform other peers where the object code and Corresponding + Source of the work are being offered to the general public at no + charge under subsection 6d. + + A separable portion of the object code, whose source code is excluded +from the Corresponding Source as a System Library, need not be +included in conveying the object code work. + + A "User Product" is either (1) a "consumer product", which means any +tangible personal property which is normally used for personal, family, +or household purposes, or (2) anything designed or sold for incorporation +into a dwelling. In determining whether a product is a consumer product, +doubtful cases shall be resolved in favor of coverage. For a particular +product received by a particular user, "normally used" refers to a +typical or common use of that class of product, regardless of the status +of the particular user or of the way in which the particular user +actually uses, or expects or is expected to use, the product. A product +is a consumer product regardless of whether the product has substantial +commercial, industrial or non-consumer uses, unless such uses represent +the only significant mode of use of the product. + + "Installation Information" for a User Product means any methods, +procedures, authorization keys, or other information required to install +and execute modified versions of a covered work in that User Product from +a modified version of its Corresponding Source. The information must +suffice to ensure that the continued functioning of the modified object +code is in no case prevented or interfered with solely because +modification has been made. + + If you convey an object code work under this section in, or with, or +specifically for use in, a User Product, and the conveying occurs as +part of a transaction in which the right of possession and use of the +User Product is transferred to the recipient in perpetuity or for a +fixed term (regardless of how the transaction is characterized), the +Corresponding Source conveyed under this section must be accompanied +by the Installation Information. But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + + The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or updates +for a work that has been modified or installed by the recipient, or for +the User Product in which it has been modified or installed. Access to a +network may be denied when the modification itself materially and +adversely affects the operation of the network or violates the rules and +protocols for communication across the network. + + Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + + 7. Additional Terms. + + "Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + + When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + + Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders of +that material) supplement the terms of this License with terms: + + a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or + + b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or + + c) Prohibiting misrepresentation of the origin of that material, or + requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or + + d) Limiting the use for publicity purposes of names of licensors or + authors of the material; or + + e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or + + f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions of + it) with contractual assumptions of liability to the recipient, for + any liability that these contractual assumptions directly impose on + those licensors and authors. + + All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + + If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + + Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; +the above requirements apply either way. + + 8. Termination. + + You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + + However, if you cease all violation of this License, then your +license from a particular copyright holder is reinstated (a) +provisionally, unless and until the copyright holder explicitly and +finally terminates your license, and (b) permanently, if the copyright +holder fails to notify you of the violation by some reasonable means +prior to 60 days after the cessation. + + Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + + Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + + 9. Acceptance Not Required for Having Copies. + + You are not required to accept this License in order to receive or +run a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + + 10. Automatic Licensing of Downstream Recipients. + + Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + + An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + + You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + + 11. Patents. + + A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + + A contributor's "essential patent claims" are all patent claims +owned or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + + Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + + In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + + If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + + If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + + A patent license is "discriminatory" if it does not include within +the scope of its coverage, prohibits the exercise of, or is +conditioned on the non-exercise of one or more of the rights that are +specifically granted under this License. You may not convey a covered +work if you are a party to an arrangement with a third party that is +in the business of distributing software, under which you make payment +to the third party based on the extent of your activity of conveying +the work, and under which the third party grants, to any of the +parties who would receive the covered work from you, a discriminatory +patent license (a) in connection with copies of the covered work +conveyed by you (or copies made from those copies), or (b) primarily +for and in connection with specific products or compilations that +contain the covered work, unless you entered into that arrangement, +or that patent license was granted, prior to 28 March 2007. + + Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + + 12. No Surrender of Others' Freedom. + + If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you may +not convey it at all. For example, if you agree to terms that obligate you +to collect a royalty for further conveying from those to whom you convey +the Program, the only way you could satisfy both those terms and this +License would be to refrain entirely from conveying the Program. + + 13. Use with the GNU Affero General Public License. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md new file mode 100644 index 0000000..d7e82d9 --- /dev/null +++ b/README.md @@ -0,0 +1,204 @@ +# Introduction + +Utilities that help to find duplicate directories or files +on large filesystems using slurm if present. All files +will be hashed with sha256 in the process and results +are stored in text files to enable easy access and prevent +code injection. + +## Files + +We calculate hashes for all files with `sha256sum` and sort the result. +The output is in the form `size,sha256,file-path`. +Duplicate entries will be collected next to each other and +large files will be at the bottom. + +## Directories + +In order to identify duplicate directories, we concatenate the sorted +size, sha256 and name of all contained files and directories and apply sha256 o +the resulting string. That leaves us with a hash sum per directory. The result +will be sorted and filtered for duplicated hashes which identify +potentially duplicate directories and exclude all pairs of directories that +are not exactly identical. + +# Instruction + +Run `./update_file_hashes ...` to make or update the file hash +tables. This can be run by all users of the group (s. Group Usage) from +anywhere on the server. If you run the script without arguments, it reports the +state of any currently running hash update. + +In order to use the tables to find duplicate +files or directories you can run `./update_dupes`. +This utility should only be run by the maintainer. + +The scripts queue a slurm job if slurm is available that +that will wait for other jobs of the same repo. +You can run jobs locally with the option `--local` or `-l`. + +Directories listed in `blacklist` are not included. + +The result tables are explained below. + +## Group Usage + +If you want all members of a given group to be able to update the hash table +with `update_file_hashes`, write the group name to a file `group` in the +same directory as `update_file_hashes` and protect it from manipulation. + +## Freeable space + +After finding the duplicates estimate for the total amount of disc space that +could be saved by removing all duplicate files can be calculated with +`./sum_duplicate_size`. + +## Missing Duplicates + +By default, all sub-directories of directories, that have a duplicate, are +removed in `dupes.out` because they are duplicates +as well anyway. E.g., if `A` is a duplicate of `B` then all sub-dirs +, e.g., `A/a` and `B/a` are duplicates of one another and +will not be listed seperately. + +However, sometimes there is an independent duplicate +of the sub-directory, e.g., `C/a` is a duplicate of `A/a` and `B/a` +but `C` is **not** a duplicate of `A`. Then only `C/a` will be listed +with no visible duplicate in `dubes.out`. + +Worse, if `C` has another duplicate `D` the independent duplications +`A/a`=`B/a`=`C/a`=`D/a` will not be listed at all. But +the duplication of the super-directories `A`=`B` and `C`=`D` will be +listed. We consider this scenario to be a very rare case. + +If you want to make sure a directory or file has no more duplicates you +are not aware of use `dupes_with_subs.out`! + +## Disk Usage Utility + +When all files are hashed one can us `du` to +quickly calculate the byte size of any directory or file +among the searched once with: +```{bash} +./du /* ... +``` +If `./update_dupes` was run recently you can use it with the +option `-q` or `--quick`. This works faster for large directories. + +## Removing Directories + +If you want to remove selected directories from the tables you can also +use the partial update scripts by setting the environment variable +`PURGE`. This will reomve the entries for ` ...`: +```{bash} +PURGE=yes ./update_file_hashes ... +``` + +## Difference + +Sometimes it is surprising that two very similar directories do not show up in +`dupes.out` and also have different hashes in `dir_hashes.out`. For such +cases, you can use `diff` to find out why they differ. The utility gives you +all files that are unique in a set of directories. To get all files that +occure only once either in `` or `` use +```{bash} +./diff +``` +If two files with the same name are listed they probably differ in +the sub-directory possition, size or hash sum. + +## Show Duplicates + +One way is to browse the `human_dupes.out` result table where the largest +duplicates are listed first. If you want to list all duplicates of a given path +you can use the `./dupes` utility. It returns the duplicate files in the format +`,,`. + - `./dupes ...` returns one line per duplicate file and the + input path as a descriptive title to each set of duplicates. The returned + duplicates do not include the given paths themselves. + - `./dupes ...` returns all files with the given tag of the + format `,` and the tag as a descriptive title. This is much + faster than using paths. + - `./dupes , , ...` returns all duplicates of the + given files. That does not include the given paths themselves and is as fast + as using tags. + - `./dupes -r ...` returns all files inside the given + directories that have a hashed duplicate somewhere in the file system. + +The listed formats of the arguments can also be mixed. + +Instead of given arguments, you can also pipe them in. One use case is to +look for all duplicates **to** the non unique files in the given directories with +```{bash} +./dupes -r ... | ./dupes +``` +and if you want to list all the duplicates including those inside the given +directories you can pass only the tags with +```{bash} +./dupes -r ... | cut -d , -f 1,2 | ./dupes +``` + +## Emulate sha256deep + +The utility `./hashdeep ` uses the table of hashed files to quickly emulate +the output of [sha256deep](http://md5deep.sourceforge.net/start-md5deep.html) +`sha256deep `. + +## Logs + +All calls of `update_file_hashes` and `update_dupes` are logged in `./update_logs/`. + +# Result Tables + +The results are used in some of the utilities above. Featured tables are: + - `file_hashes.out` All hashed files in the format `,,`. + - `sorted_file_hashes.out` Hashed files sorted by path in the format `,,`. + - `dir_hashes.out` All directory hashes (available only after `update_dupes`). + - `dupes.out` Duplicates without entries inside of duplicated directories. + Sorted from large to small. + - `human_dupes.out` As above with human readable sizes. + - `dupes_with_subs.out` As `dupes.out` with **all** duplicate files and directiries + and sorted with `LC_COLLATE=C` for fast lookup with the `./look` utility. + + +# Dependencies + +All dependencies come with most linux distributions but the shipped version of +`look` from [bsdmainutils](https://packages.debian.org/de/sid/bsdmainutils) +often comes with a bug that does not allow to work with files larger than 2GB. +This repo comes with a patched version that was compiled on Ubuntu 18.04 x86_64. +If you have issues running it please compile your own patched +[bsdmainutils-look](https://github.com/stuartraetaylor/bsdmainutils-look) +and replace the file `./look` with your binary or a link to it. + +Other dependencies and their version we teted with are + - bash 4.4.20 + - bc 1.07.1 + - GNU Awk 4.1.4 + - GNU coreutils 8.28 + - GNU parallel 20161222 + - GNU sed 4.4 + - util-linux 2.31.1 + +If available we also support + - slurm-wlm 17.11.2 + +# Note + +We use GNU parallel: +*O. Tange (2018): GNU Parallel 2018, March 2018, https://doi.org/10.5281/zenodo.1146014.* + +# Code Maintainer + +The maintainer must be aware that filenames in Linux can contain any character +except the null `\x00` and the forward slash `/`. This can complicate the +processing of the hash tables and breaks many common text processing solutions +in rare cases. Since there are many users with many files on the system those +cases tend to exist. + +Another curiosity is the output of `sha256` for wired filenames. You can test +this with `touch "a\b"; sha256 "a\b"`. The backslash in the filename is escaped +and strangely, the hash sum starts with a backslash which is not part of the +correct sum for files with size 0. This behavior is explained +[here](https://unix.stackexchange.com/questions/313733/various-checksums-utilities-precede-hash-with-backslash). + diff --git a/cronjob b/cronjob new file mode 100755 index 0000000..8e3e1b8 --- /dev/null +++ b/cronjob @@ -0,0 +1,20 @@ +#! /bin/bash - + +dir="$(dirname $(readlink -f ${BASH_SOURCE[0]}))" +cd "$dir" +source utilities.sh + +last=$(find update_logs | sort -t. -k2 -n | tail -n1 | \ + sed 's|.*/\([^.]*\)\..*|\1|') 2> /dev/null +running=$(get_running --name="finding duplicates") + +if [[ "$last" == "update_dupes" ]]; then + >&2 printf 'There are no logs after the last run of update_dupes.\n' + >&2 printf 'The cronjob will be skipped.\n' +elif [[ ! -z "$running" ]]; then + >&2 printf 'An instance of update_dupes with slurm id ' + >&2 printf '%s is already runnign.\n' "$running" + >&2 printf 'The cronjob will be skipped.\n' +else + ./update_dupes +fi diff --git a/diff b/diff new file mode 100755 index 0000000..3c618c1 --- /dev/null +++ b/diff @@ -0,0 +1,52 @@ +#! /bin/bash - + +# Returns the files that are unique among the dirs +if [[ "$1" == "-h" ]] || [[ "$1" == "--help" ]]; then + >&2 printf "Usage: $0 ...\n" + exit 0 +fi + +dir="$(dirname $(readlink -f ${BASH_SOURCE[0]}))" +export LC_ALL=C # byte-wise sorting +export GREP_COLOR='32' +export look="$dir/look" +export sorted_filehashes="$dir/sorted_file_hashes.out" + +tempHashes=$(mktemp -p /dev/shm) +tempOut=$(mktemp -p /dev/shm) +trap "rm $tempHashes $tempOut" EXIT + +getFileHashes()( + path="$(readlink -f "$1")" + path="${path//\\/\\\\}" + path="${path//$'\n'/\\n}" + escaped=$(printf '%s' "$path" | \ + sed -r 's/([\$\.\*\/\[\\^])/\\\1/g' | \ + sed 's/[]]/\[]]/g') + replace=$(printf '%s' "$path" | \ + sed -r 's/(["&\/\\])/\\\1/g') + modLine(){ sed "s|^$escaped|$replace/|g"; } + tempFile=$(mktemp -p /dev/shm) + trap "rm $tempFile" RETURN + "$look" "$path/" "$sorted_filehashes" | \ + modLine > $tempFile + if [[ $? -ne 0 || ! -s $tempFile ]]; then + # fallback since look can not deal with special chars + text='\e[33mWarning:\e[0m No matches -> using slower grep for %s\n' + >&2 printf "$text" "$path" + grep -aF "$path" "$sorted_filehashes" | \ + modLine > $tempFile + fi + if [[ ! -s $tempFile ]]; then + >&2 printf '\e[33mWarning:\e[0m No entries found for %s\n' "$path" + fi + cat $tempFile +) +export -f getFileHashes + +printf '%s\0' "$@" | parallel --will-cite -0 -k getFileHashes | tee $tempOut | \ + sed 's|^.*//||g' | sort | uniq -u > $tempHashes +ColorEsc=$(printf '\e[0m') +grep -aFf $tempHashes --color=always $tempOut | \ + sed "s|//|/|g; s/,[^,]*,[^,]*$/$ColorEsc/g" + diff --git a/du b/du new file mode 100755 index 0000000..f7bb6fb --- /dev/null +++ b/du @@ -0,0 +1,73 @@ +#! /bin/bash - + +# This script uses the sorted_file_hases.out to +# quickly estimate file and directory sizes of +# all passed paths. It also exepts globbings. +# Usage: ./du ... + +export LC_ALL=C # byte-wise sorting +export OPTERR=0 # silent getopts +dir="$(dirname $(readlink -f ${BASH_SOURCE[0]}))" +export look="$dir/look" +export sorted_filehashes="$dir/sorted_file_hashes.out" +export dirhashes="$dir/dir_hashes.out" + +read -d '' help_message << EOF +Usage $0 [-q, --quick] ... + +-q, --quick : Quick mode (requires dir_hashes e.g. by update_dupes). +EOF + +disp_help(){ + printf '%s\n' "$help_message" +} + +get_func="slow_getsize" +while getopts "h?q-:" opt; do + case "$opt" in + -) case "${OPTARG}" in + quick) QUICK=TRUE;; + help) disp_help + exit 0;; + *) disp_help + exit 1;; + esac ;; + q) get_func="quick_getsize";; + h) disp_help + exit 0;; + *) disp_help + exit 1;; + esac +done + +slow_getsize(){ + f="$(realpath "$*")" + path="${f//\\/\\\\}" + path="${path//$'\n'/\\n}" + size=$(cat <("$look" "$path" "$sorted_filehashes") <(printf "0,0,0") | \ + parallel --will-cite --pipe \ + "sed -e 's/.*,\([0-9]*\),[^,]*$/\1/g' -e '/[^0-9]/d'" | paste -sd+ | bc) + size=$(numfmt --to=iec $size) + printf '%s\t%s\n' "$size" "$*" +} +quick_getsize(){ + f="$(realpath "$*")" + path="${f//\\/\\\\}" + path="${path//$'\n'/\\n}" + if [[ -d "$f" ]]; then + SIZE="$(grep -F ",$path/" "$dirhashes" | cut -d, -f1 | \ + awk 'BEGIN{a=0}{if ($1>0+a) a=$1} END{print a}')" + elif [[ -f "$f" ]]; then + SIZE=$("$look" "$path," "$sorted_filehashes" | head -n1 | \ + sed -n 's/^.*,\([0-9]*\),[^,]*$/\1/p') + else + m="Error: Type of %s cannot be determined since it does not exist.\\n" + >&2 printf "$m" "$*" + return + fi + [[ -z "$SIZE" ]] && SIZE="0" || SIZE="$(numfmt --to=iec "$SIZE")" + printf '%s\t%s\n' "$SIZE" "$*" +} +export -f slow_getsize quick_getsize + +printf '%s\0' "${@:$OPTIND}" | parallel --will-cite -k -0 "$get_func" diff --git a/dupes b/dupes new file mode 100755 index 0000000..9e24914 --- /dev/null +++ b/dupes @@ -0,0 +1,97 @@ +#! /bin/bash - + +# Usage: ./dupes [-r, --recursive] ... +# Finds all duplicates of the passed paths and when +# the -r obtion is passed, all duplicate files within. + +export dir="$(dirname $(readlink -f ${BASH_SOURCE[0]}))" +source "$dir/utilities.sh" + +if [[ "$1" == "-r" ]] || [[ "$1" == "--recursive" ]]; then + REC=TRUE +elif [[ "$1" == "-h" ]] || [[ "$1" == "--help" ]]; then + >&2 printf "Usage: $0 [-r, --recursive] ...\n" + exit 0 +else + REC=FALSE +fi + +export LC_ALL=C # byte-wise sorting +export GREP_COLOR='32' + +export dirhashs="$dir/dir_hashes.out" +export sorted_filehashes="$dir/sorted_file_hashes.out" +export sorted_dupes="$dir/dupes_with_subs.out" + +(readlink $(type -p mup) | grep "update_file_hashes$") &> /dev/null && \ + export SMUP="mup" || export SMUP="update_file_hashes" + +search_recursive(){ + arg="$1" + [ $TITLE == TRUE ] && printf '\e[33mDuplicates in %s:\e[0m\n' "$arg" + fl="$(realpath "$arg")" + path="${fl//\\/\\\\\\\\}" + path="${path//$'\n'/\\\\n}" + path="${path//\"/\\\"}" + dupes=$(parallel --will-cite --pipepart -a "$sorted_dupes" \ + "grep -aF \",$path\"" | sub_remove) + if [[ -z "$dupes" ]]; then + >&2 printf 'No duplicates found in %s.\n' "$arg" + exit 0 + fi + printf '%s\n' "$dupes" +} + +list_dupes(){ + arg="$1" + fl="$(readlink -f "$arg")" + path="${fl//\\/\\\\}" + path="${path//$'\n'/\\n}" + unset tag + if [[ -d "$fl" ]]; then + tag=$(grep -aF ",$path/" "$dirhashs" | sub_remove | cut -d, -f1,2) + if [[ -z $tag ]]; then + >&2 printf 'The directory %s has not been hashed yet.\n' "$arg" + >&2 printf 'Run `%s %s` and `update_dupes` first!\n' "$SMUP" "$arg" + exit 1 + fi + elif [[ -f "$fl" ]]; then + tag=$("$dir/look" "$path," "$sorted_filehashes" | \ + sed -n 's/.*,\([0-9]*,[^,]*\)$/\1/p') + if [[ -z $tag ]]; then + >&2 printf 'The filte %s has not been hashed yet.\n' "$arg" + >&2 printf 'Run `update_dupes` first!\n' + exit 1 + fi + elif [[ "$arg" =~ ^[0-9]+,[^,]+,?$ ]]; then + tag="$arg" + elif [[ "$arg" =~ ^[0-9]+,[^,]+ ]]; then + path="${arg#*,*,}" + tag="${arg%"$path"}" + arg="$path" + fi + if [[ -z "$tag" ]]; then + >&2 printf 'Using slow pattern search for %s.\n' "$arg" + >&2 printf 'Pass "," or "" for faster results.\n' + dupes=$(grep --color=always -aF "$arg" "$sorted_dupes") + else + tag="${tag%,}," + dupes=$("$dir/look" $tag "$sorted_dupes" | grep -vF "$tag$path") + fi + if [[ -z "$dupes" ]]; then + >&2 printf '\e[33mNo duplicate found for %s.\e[0m\n' "$arg" + exit 0 + fi + ndupes=$(printf "%s" "$dupes" | grep -c "^") + (( $ndupes > 1 )) && s="s" || s="" + printf '\e[33m%d duplicate%s of %s:\e[0m\n' "$ndupes" "$s" "$arg" + printf '%s\n' "$dupes" +} +export -f search_recursive list_dupes sub_remove + +if [ $REC == TRUE ]; then + (($#!=2)) && [ -t 1 ] && export TITLE=TRUE || export TITLE=FALSE + parallel --will-cite -k -n1 search_recursive ::: "${@:2}" +else + parallel --will-cite -k -n1 list_dupes ::: "$@" +fi diff --git a/get_dupes b/get_dupes new file mode 100755 index 0000000..d22d6b6 --- /dev/null +++ b/get_dupes @@ -0,0 +1,81 @@ +#! /bin/bash - + +inFiles="dir_hashes.out file_hashes.out" +outFile="dupes.out" +nthreads=$(nproc) + +export LC_ALL=C # byte-wise sorting +export OPTERR=0 # silent getopts +[[ -z "$TMPDIR" ]] && export TMPDIR=/dev/shm # in memory + +read -d '' help_message << EOF +Usage $0 [-s, --skip] [-j number] [-i input] [-i input2] ... [-o output] + +-s, --skip : Skip removal of subdirectories of duplicates. +-j number : Maximum number of threads. (Default $nthreads) +-i input : Input file. Can be used multipe times. (Defaults $inFiles) +-w output : Output file with subdirectories. +-o output : Output file without subdirectories. (Default $outFile) +EOF + +disp_help(){ + printf '%s\n' "$help_message" +} +trap exit ERR + +unset woutFile +while getopts "h?sj:i:o:w:-:" opt; do + case "$opt" in + -) case "${OPTARG}" in + skip) SKIPSUB=1;; + help) disp_help + exit 0;; + *) disp_help + exit 1;; + esac ;; + s) SKIPSUB="TRUE";; + i) oinFiles+=("$OPTARG");; + o) outFile="$OPTARG";; + w) woutFile="$OPTARG";; + j) nthreads="$OPTARG";; + h) disp_help + exit 0;; + *) disp_help + exit 1;; + esac +done +[[ -z $oinFiles ]] || inFiles="${oinFiles[@]}" +[[ "$nthreads" =~ ^[0-9]+$ ]] || { disp_help; exit 1; } +[[ -z "$woutFile" ]] && woutFile="${outFile%.out}_with_subs.out" + +tempHashes=$(mktemp) +tempPatterns=$(mktemp) +tempOut=$(mktemp) +trap exit INT TERM ERR HUP +trapF(){ + rm -r $tempHashes $tempPatterns $tempOut \ + $tempOut2 2> /dev/null + exit +} +trap trapF EXIT +sortThreads=$(($nthreads<8?$nthreads:8)) + +printf 'Sorting by size and hash...\n' +cat $inFiles | grep -va "^#\|^%\|^0," | \ + sort --parallel=$sortThreads -S 50% \ + -t / -k 1 -o $tempHashes + +printf 'Collecting duplicate hashes...\n' +cut -d / -f 1 $tempHashes | uniq -d > $tempPatterns + +printf 'Filtering none duplicates...\n' +join -t / -j 1 $tempPatterns $tempHashes > $tempOut + +printf 'Sorting results...\n' +sort -u -o "$woutFile" $tempOut + +[[ "$SKIPSUB" == "TRUE" ]] && exit 0 + +printf 'Removing sub-directories of duplicates...\n' +source utilities.sh +sub_remove $tempOut $nthreads --delete | sizeHashSort > "$outFile" diff --git a/hashdeep b/hashdeep new file mode 100755 index 0000000..70c3b93 --- /dev/null +++ b/hashdeep @@ -0,0 +1,32 @@ +#! /bin/bash - + +# Emulates the output of sha256deep for the given directories +# from the previously hashed table file_hashes.out +if [[ "$1" == "-h" ]] || [[ "$1" == "--help" ]]; then + >&2 printf "Usage: $0 \n" + exit 0 +fi + +dir="$(dirname $(readlink -f ${BASH_SOURCE[0]}))" + +path="$(readlink -f "$1")" +path="${path//\\/\\\\}" +path="${path//$'\n'/\\n}" +escaped=$(printf '%s' "$path" | \ + sed -r 's/([\$\.\*\/\[\\^])/\\\1/g' | \ + sed 's/[]]/\[]]/g') +replace=$(printf '%s' "$1" | \ + sed -r 's/(["&\/\\])/\\\1/g') + +printf -v pattern '^[0-9]*,[^,]*,%s' "$escaped" +printf -v rep 's/\(^[0-9]*,[^,]*,\)%s/\\1%s/' "$escaped" "$replace" +export pattern rep +export LC_ALL=C # byte-wise sorting + +printf '%%%% hashdeep imitate by ' +printf 'https://github.com/fraunhofer-izi/duplicates\n' +printf '%%%% size,sha256,filename\n' +printf '## Invoked from: %s\n' "$(pwd -P)" + +parallel --will-cite -k --pipepart -a "$dir/file_hashes.out" \ + --block 100M 'grep -e "$pattern" | sed -e "$rep"' diff --git a/human_sizes b/human_sizes new file mode 100755 index 0000000..914cae8 --- /dev/null +++ b/human_sizes @@ -0,0 +1,18 @@ +#! /bin/bash - + +# This scripts appends a human readable file size to the +# beginning of each line for files with the line format +# , +# and prints the result stdout. +# Usage: ./human_sizes + +if [[ -z "$*" ]] +then + inFile="dupes.out" +else + inFile="$*" +fi + +export LC_ALL=C # so sed works with wired chars + +paste <(cut -d, -f1 "$inFile" | numfmt --to=iec) "$inFile" diff --git a/look b/look new file mode 100755 index 0000000..ac26042 Binary files /dev/null and b/look differ diff --git a/look_license b/look_license new file mode 100644 index 0000000..43ca176 --- /dev/null +++ b/look_license @@ -0,0 +1,26 @@ +Copyright (C) 1980 -1998 The Regents of the University of California. +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions +are met: +1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. +2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. +4. Neither the name of the University nor the names of its contributors + may be used to endorse or promote products derived from this software + without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS + OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) +HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF +SUCH DAMAGE. diff --git a/make_dir_hashes b/make_dir_hashes new file mode 100755 index 0000000..5afea75 --- /dev/null +++ b/make_dir_hashes @@ -0,0 +1,112 @@ +#! /bin/bash - +#SBATCH --job-name="directory hashes" +#SBATCH --ntasks=1 +#SBATCH --cpus-per-task=16 +#SBATCH --mem=140G +#SBATCH --time=10-00:00:00 +#SBATCH --mail-type=ALL +#SBATCH --out=make_dir_hashes.out + +inFile="sorted_file_hashes.out" +outFile="dir_hashes.out" +processOut=".dir_hashes.process.out" + +if [[ -z $SLURM_CPUS_PER_TASK ]]; then + nCPU=$(nproc) +else + nCPU=$SLURM_CPUS_PER_TASK +fi + +export procID=$$ +export LC_ALL=C # byte-wise sorting +[[ -z "$TMPDIR" ]] && export TMPDIR=/dev/shm # in memory +export tdir=$(mktemp -d) +export token_f=$(mktemp) +progress=$(mktemp) +ln -s "$(readlink -f "$inFile")" $tdir.out +trap '>&2 printf "\rInterrupted (Ctrl+C)...\n"; exit 130' INT +trap '>&2 printf "Terminated (kill)...\n"; exit 143' TERM +trap '>&2 printf "Connection to user lost...\n"; exit 129' HUP +trap '>&2 printf "Broken pipe...\n"; exit 141' PIPE +trapF(){ + ec=$? + exec 2> /dev/null + trap '' INT && kill -INT -- -"$BASHPID" + rm -r $tdir $progress $tdir.out $token_f $processOut + exit $ec +} +trap "trapF" EXIT + +printf '%d' "$((nCPU-1))" > $token_f +takeTokens(){ + ( + flock -x -w .01 200 || exit 1 + tokens=$(<$token_f) + spend=$(($tokens>$1?$1:$tokens)) + printf '%d' $(($tokens-$spend)) > $token_f + printf '%d' $spend + ) 200<> $token_f +} +releaseToken(){ + ( + flock -x 200 + tokens=$(<$token_f) + printf '%d' $(($tokens+1)) > $token_f + ) 200<> $token_f +} +makeHashes()( + hashtab="$1" + nthread_parent=$2 + file_token="../$3" + outDir="${hashtab%.out}" + DPATH="${outDir#$tdir}/" + mkdir -p "$outDir" + cd "$outDir" + exec 10<> <(:) + SIZE=$(cut -d / -f 1 --complement "$hashtab" | \ + tee >(sha256sum >&10) | \ + awk -F/ '{if (NF>1) print>$1".out"; else print}' | \ + sed 's/^.*,\([0-9]*\),[^,]*$/\1/g' | \ + tee >(xargs -n1 -I{} printf '1' >&4) | paste -sd+ | bc) + read -u 10 HASH dash + rm "$hashtab" + next=() + while IFS= read -r -d $'\0'; do + next+=("$REPLY") + done < <(find "$outDir" -type f -print0) + if ((${#next[@]}>0)); then + new_file_token=$(mktemp -p .) + printf '%d' ${#next[@]} > $new_file_token + nthread=$(($(takeTokens $((${#next[@]}-1)))+1)) || nthread=1 + size=$(printf '%s\0' "${next[@]}" | sed -z -e "s/'/'\"'\"'/g" | \ + xargs -0 -n 1 -P $nthread -I{} \ + bash -c "makeHashes '{}' $nthread $new_file_token" | \ + paste -sd+ | bc) + SIZE=$(($SIZE+$size)) + fi + printf '%01d\n' "$SIZE" + >&3 printf '%01d,%s,%s\n' "$SIZE" "$HASH" "$DPATH" + rm -r "$outDir" + (($nthread_parent>1)) && ( + flock -x 200 + tokens=$(<$file_token) + (($tokens<$nthread_parent)) && releaseToken && return + printf '%d' $(($tokens-1)) > $file_token + ) 200<> $file_token +) +export -f makeHashes takeTokens releaseToken + +trap 'exit 0' SIGUSR1 +./watch_dir_hashing $progress "$inFile" & +statusPID=$! + +printf '## Format: size,sha256,path\n' > "$processOut" +export thread_id=0 +size=$(makeHashes "$tdir.out" 1 3>> "$processOut" 4> $progress) +size=$(numfmt --to=iec $size) +kill -SIGUSR1 -- "$statusPID" +mv "$processOut" "$outFile" +wait $statusPID +printf 'Files with a total size of\e[34m %s\e[0m ' "$size" +printf 'have been hashed into directories.\n' + diff --git a/sum_duplicate_size b/sum_duplicate_size new file mode 100755 index 0000000..8d85440 --- /dev/null +++ b/sum_duplicate_size @@ -0,0 +1,4 @@ +#! /bin/bash - + +uniques=$(cut -d/ -f1 file_dupes.out | uniq | cut -d, -f1 | paste -sd+ | bc) +numfmt --to=iec $(( $(cut -d, -f1 file_dupes.out | paste -sd+ | bc)-$uniques )) diff --git a/update_dupes b/update_dupes new file mode 100755 index 0000000..0be562d --- /dev/null +++ b/update_dupes @@ -0,0 +1,80 @@ +#! /bin/bash - +#SBATCH --job-name="finding duplicates" +#SBATCH --ntasks=1 +#SBATCH --exclusive +#SBATCH --mem=240G +#SBATCH --time=10-00:00:00 +#SBATCH --mail-type=ALL + +[[ -z "$SLURM_JOB_ID" ]] && cd "$(dirname $(readlink -f ${BASH_SOURCE[0]}))" +source utilities.sh + +if [[ "$1" == "-h" ]] || [[ "$1" == "--help" ]]; then + >&2 printf "Usage: $0 [-l, --local]\n" + exit 0 +elif [[ "$1" != "-l" ]] && [[ "$1" != "--local" ]] \ + && [[ "$1" != "--prepared" ]] && (hash sbatch &> /dev/null); then + slurm_submit "$0" "finding duplicates" + exit 0 +fi + +export TMPDIR=/dev/shm +if [[ -z "$SLURM_JOB_ID" ]]; then + epoch=$(date +%s) + logFile="update_logs/update_dupes.$epoch" + mkdir -p "$(dirname "$logFile")" + exec &> >(trap '' INT TERM; tee -a "$logFile") +elif [[ "$1" != "--prepared" ]]; then + cmd="$(squeue -j $SLURM_JOB_ID -h -o '%o')" + >&2 printf 'Error: manual sbatch execution\n' + >&2 printf 'Usage: %s--slurm %s\n' "$cmd" + exit 1 +else + logFile="$slurmLog" +fi +lockFile="update_file_hashes.lock" +read -d '' lock_file_text << EOF +=== Finding Duplicates === +Host: $(hostname) +PID: $$ +Slurm Job ID: $SLURM_JOB_ID +User: $USER +Started: $(date) +Log: $logFile +Progress: $logFile +Lockfile: $(readlink -f "$lockFile") +EOF +read -d '' error_text 2> /dev/null << EOF +A process already seems to be runnig: +$(update_status) +Delete the lockfile if this is not correct. +EOF +if ! ( set -o noclobber; printf '%s\n' "$lock_file_text" > "$lockFile" ) \ + 2> /dev/null; then + >&2 printf '%s\n' "$error_text" + exit 1 +fi +trap '>&2 printf "\rInterrupted (Ctrl+C)...\n"; exit 130' INT +trap '>&2 printf "Terminated (kill)...\n"; exit 143' TERM +trap 'ec=$?; >&2 printf "Error encountered...\n"; exit $ec' ERR +trap '>&2 printf "Connection to user lost...\n"; exit 129' HUP +trap '>&2 printf "Broken pipe...\n"; exit 141' PIPE +trap "rm \"$lockFile\"; trap '' INT; kill -INT -- -\"$BASHPID\"; exit 0" EXIT + +printf 'Finding duplicate files...\n' +./get_dupes -s -i file_hashes.out -w file_dupes.out +printf 'A list of duplicate files can be found' +printf ' in\e[33m file_dupes.out\e[0m.\n' +printf 'Calculating duplicate file size ...\n' +printf 'You could safe\e[34m %s\e[0m' "$(./sum_duplicate_size)" +printf ' by removing all duplicate files.\n' + +printf 'Making directory hashes...\n' +./make_dir_hashes + +printf 'Finding all duplicates...\n' +./get_dupes +./human_sizes > human_dupes.out +printf 'A list of duplicates can be found' +printf ' in\e[33m dupes.out\e[0m and with human' +printf ' frienly file sizes in\e[33m human_dupes.out\e[0m.\n' diff --git a/update_file_hashes b/update_file_hashes new file mode 100755 index 0000000..ca5694e --- /dev/null +++ b/update_file_hashes @@ -0,0 +1,244 @@ +#! /bin/bash - +#SBATCH --job-name="file hash update" +#SBATCH --ntasks=1 +#SBATCH --exclusive +#SBATCH --mem=140G +#SBATCH --time=10-00:00:00 +#SBATCH --mail-type=ALL + +# This script updates/includes the file hashes for +# any given directories. +# Usage: ./update_file_hashes [-l, --local] ... + +if [[ "$1" == "-l" ]] || [[ "$1" == "--local" ]]; then + send_slurm=FALSE + ARGS=("${@:2}") +elif [[ "$1" == "-h" ]] || [[ "$1" == "--help" ]]; then + >&2 printf "Usage: $0 [-l, --local] ...\n" + exit 0 +elif (hash sbatch &> /dev/null); then + send_slurm=TRUE + ARGS=("$@") +else + send_slurm=FALSE + ARGS=("$@") +fi + +if [[ -z "$SLURM_SUBMIT_DIR" ]]; then + onSlurm=FALSE + export SortBuffer=100G + unset argDir +elif [[ "$1" != "--prepared" ]]; then + >&2 printf 'Error: manual sbatch execution\n' + exit 1 +else + onSlurm=TRUE + send_slurm=FALSE + argDir="$SLURM_SUBMIT_DIR/" + ARGS=("${@:2}") +fi + +epoch=$(date +%s) +logPart="update_logs/update_file_hashes.$epoch" +if [ $onSlurm == FALSE ]; then + export dir="$(dirname $(readlink -f ${BASH_SOURCE[0]}))" + logFile="$dir/$logPart.log" +else + export dir="$(pwd -P)" + if [[ -z "$slurmLog" ]]; then + slurmLog="$dir/$logPart.slurm" + else + epoch="${slurmLog%.*}" + epoch="${epoch##*.}" + fi + logFile="${slurmLog%.*}.log" +fi +recoveryTries=5 +outFile="$dir/file_hashes.out" +backupDir="$dir/backups" +backup="$backupDir/file_hashes.backup.$epoch.out" +sortedOutFile="$dir/sorted_file_hashes.out" +sortedProcessOut="$dir/.sorted_file_hashes.inProcess.out" +stateLog="${logFile%.*}.progress" +logDir="$(dirname $logFile)" +lockFile="$dir/update_file_hashes.lock" +if [ -f "$dir/group" ]; then + export HASH_GROUP=$(head -n1 "$dir/group") +fi +if ! getent group "$HASH_GROUP" &> /dev/null; then + >&2 printf 'The group "%s" does not exists and is ignored.' "$HASH_GROUP" + unset HASH_GROUP +fi + +source "$dir/utilities.sh" + +(($#==0)) && update_status && exit 0 + +searchDirs=() +for arg in "${ARGS[@]}"; do + if [[ "$arg" = /* ]]; then + absolut="$(readlink -f "$arg")" + else + absolut="$(readlink -f "${argDir}$arg")" + fi + if [[ ! -r "$absolut" ]] && [[ -z "$PURGE" ]]; then + >&2 printf 'The given file\e[33m %s\e[0m does not' "$arg" + >&2 printf ' exist or you have no read permissions. Exiting...\n' + exit 1 + fi + searchDirs+=("$absolut") +done +searchDirsString=$(printf "'%s' " "${searchDirs[@]}") +searchDirsString=${searchDirsString% } + +if [ $send_slurm == TRUE ]; then + printf 'Submitting slurm job for\e[34m %s\e[0m...\n' "$searchDirsString" + slurm_submit "$0" "${ARGS[@]}" + exit 0 +fi + + +read -d '' lock_file_text << EOF +=== File Hash Update === +Host: $(hostname) +PID: $$ +Slurm Job ID: $SLURM_JOB_ID +User: $USER +Started: $(date) +Directiories: $searchDirsString +Backup: $backup +Log: $logFile +Progress: $stateLog +Lockfile: $lockFile +EOF +read -d '' error_text 2> /dev/null << EOF +A process already seems to be runnig: +$(update_status) +Delete the lockfile if this is not correct. +EOF +if [ $onSlurm == TRUE ] && [[ -f "$lockFile" ]]; then + info="If not cancelled the job will wait until the lockfile is removed." + printf '%s\n%s\n' "$error_text" "$info" + while [[ -f "$lockFile" ]]; do sleep 10; done +fi +if ! ( set -o noclobber; printf '%s\n' "$lock_file_text" > "$lockFile" ) \ + 2> /dev/null; then + >&2 printf '%s\n' "$error_text" + exit 1 +fi + +[ $onSlurm == TRUE ] && printf 'Running on\e[34m %s\e[0m.\n' "$(hostname)" +printf 'Updating directorie(s)\e[34m %s\e[0m...\n' "$searchDirsString" +printf 'Logging into\e[33m %s\e[0m...\n' "$logFile" +mkdir -p "$logDir" +sed "s/^/# /g" "$lockFile" > "$logFile" +exec 2> >(trap '' INT TERM; tee -a "$logFile") +tempOut=$(mktemp -p /dev/shm) +mkdir -p "$backupDir" + +if [[ -z "$PURGE" ]]; then + printf 'Progress logged in\e[33m %s\e[0m...\n' "$stateLog" + (trap 'exit 0' SIGUSR1 TERM INT + exec > >(tee "$stateLog") + exec "$dir/watch_status" $tempOut "${searchDirs[@]}") & + statusPID=$! + if [[ ! -z "$HASH_GROUP" ]]; then + chown ":$HASH_GROUP" "$stateLog" + chmod g+rw "$stateLog" + fi +else + unset statusPID +fi +if [[ ! -z "$HASH_GROUP" ]]; then + chown ":$HASH_GROUP" "$logDir" "$backupDir" 2> /dev/null + chmod g+rw "$logDir" "$backupDir" 2> /dev/null + chown ":$HASH_GROUP" $tempOut "$logFile" "$lockFile" "$slurmLog" + chmod g+r $tempOut "$lockFile" + chmod g+rw "$logFile" "$slurmLog" +fi + +printf 'Creating backup\e[33m %s\e[0m and recovery trap...\n' "$backup" +if [[ -f "$outFile" ]]; then + mv "$outFile" "$backup" +else + touch "$backup" + if [[ ! -z "$HASH_GROUP" ]]; then + chown ":$HASH_GROUP" "$backup" + chmod g+rw "$backup" + fi + >&2 printf 'No results found. Initialized empty backup.\n' +fi +read -d '' note << EOF +To revert to the backup manually run: +mv '$backup' '$outFile' +EOF +trapF(){ + excode=$? + printf '\r\e[31mStopping and attempting recovery...\e[0m\n' + trap '' INT && kill -INT -- -"$BASHPID" + wait $filterPID 2> /dev/null + [[ -f "$outFile" ]] && mv "$outFile" "$outFile.trash" + while ! (mv "$backup" "$outFile"); do + ((--recoveryTries)) + if (($recoveryTries==0)); then + >&2 printf "\e[31m-----> Unable to recover backup. <-----\e[0m\n" + >&2 printf '%s\n' "$note" + break + fi + >&2 printf '\e[31mRecovery failed, %d tries left.\e[0m\n' \ + "$recoveryTries" + sleep 5 + done + rm "$sortedProcessOut" $tempOut "$lockFile" "$outFile.trash" 2> /dev/null + (($recoveryTries>0)) && >&2 printf 'Backup recovered.\n' + exit $excode +} +trap '>&2 printf "\rInterrupted (Ctrl+C)...\n"; exit 130' INT +trap '>&2 printf "Terminated (kill)...\n"; exit 143' TERM +trap 'ec=$?; >&2 printf "Error encountered...\n"; exit $ec' ERR +trap '>&2 printf "Connection to user lost...\n"; exit 129' HUP +trap '>&2 printf "Broken pipe...\n"; exit 141' PIPE +trap trapF EXIT + +printf 'Start writing new\e[33m %s\e[0m without old entries...\n' "$outFile" +grepC="grep -vaF" +for path in "${searchDirs[@]}"; do + path="${path//\\/\\\\}" + path="${path//$'\n'/\\n}" + path="${path//\'/\'\"\'\"\'}" + printf -v grepC "%s -e ',%s/'" "$grepC" "$path" +done +printf -v grepC '%s "%s"' "$grepC" "$backup" +(trap "exit 0" TERM; eval "$grepC" > "$outFile" || :) & +filterPID=$! +if [[ -z "$PURGE" ]]; then + >&2 printf 'Start hashing files into\e[33m %s\e[0m...\n' "$tempOut" + (trap "exit 0" TERM; hashThat "${searchDirs[@]}" > $tempOut) & + hashPID=$! +else + >&2 printf 'Purging directorie(s)\e[31m %s\e[0m...\n' "$searchDirsString" + unset hashPID +fi + +printf 'Waiting for processes and combining results...\n' +if [[ -z "$PURGE" ]]; then + wait $hashPID + kill -SIGUSR1 -- $statusPID +fi +wait $filterPID +cat $tempOut >> "$outFile" +rm $tempOut +wait $statusPID 2> /dev/null || : + +>&2 printf 'Sorting new results...\n' +sortByPath "$outFile" > "$sortedProcessOut" +mv "$sortedProcessOut" "$sortedOutFile" +if [[ ! -z "$HASH_GROUP" ]]; then + chown ":$HASH_GROUP" "$outFile" "$sortedOutFile" + chmod g+rw "$outFile" "$sortedOutFile" +fi +trap - EXIT INT TERM ERR HUP +rm "$lockFile" + +>&2 printf '\e[32mFinished successfully\e[0m on %s.\n' "$(date)" +printf '%s\n' "$note" diff --git a/utilities.sh b/utilities.sh new file mode 100644 index 0000000..406749c --- /dev/null +++ b/utilities.sh @@ -0,0 +1,174 @@ +#! /bin/bash - + +update_status(){ + # This script reports the state of a current + # file hash update. + dir="$(dirname $(readlink -f ${BASH_SOURCE[0]}))" + lockFile="$dir/update_file_hashes.lock" + printf -v esc '\e' + if [[ ! -f "$lockFile" ]]; then + printf "Currently there is no update running.\n" + return + fi + sed "s/^[^:]*:/${esc}[34m&${esc}[0m/g" "$lockFile" + slurmID=$(sed -n 's/Slurm Job ID: \(.*\)$/\1/p' "$lockFile") + if [[ ! -z $slurmID ]]; then + filter="JobName: \|RunTime: \|TimeLimit: \|SubmitTime: \|StartTime: " + scontrol -o show job $slurmID | \ + sed "s/\([^ ,]*\)=/\x0${esc}[34m\1: ${esc}[0m/g" | \ + grep -z "$filter" | tr '\0' '\n' + fi + progFile=$(sed -n 's/Progress: \(.*\)$/\1/p' "$lockFile") + if [[ ! -f "$progFile" ]]; then + printf "There is no progress file\e[33m %s\e[0m\n" "$progFile" + return + fi + tail -n1 "$progFile" | sed "s/.*/${esc}[32m&${esc}[0m/g" +} + +get_running(){ + # Returns running slurm jobs for the current directory. + dir="$(dirname $(readlink -f ${BASH_SOURCE[0]}))" + squeue -h -o "%i/%Z//" "$@" | grep -F "/$dir//" | \ + cut -d/ -f1 | tr '\n' ':' | head -c-1 +} + +slurm_submit(){ + # Usage: slurm_submit