PDF 4.6 - OpendTect
Contents
1. export 0 before opening a terminal xterm amp In your control panel open the System item Go in the Advanced tab select the Environment Variables option Add a new user or system variable of name RSFROOT pointing towards C cygwin usr local rsf if cygwin was installed at its default location C cygwin Accept and exit 42 OpendTect Application Management Documentation version 4 6 This variable is setup once in the settings and does not need to be specified after each boot On the next startup of OpendTect Madagascar should be available 432. 5 5 4 Start Processing Multi Machine processing feature could be used from several utilities in OpendTect like creating seismic attribute output or creating a steering cube All these utilities have a Multiple machines options which will launch the Multi machine Processing window Now on the left of this window a list box will contain all the available hosts based on the BatchHosts file select any of the machines from this list and start processing The annotated screen shot describes the fields and their purpose TA Nr inlines per job 5 77 Processing smalls 3 Available hosts Muli Machine Processing Output storage location Temporary storage locatidh F SurveysiFS3_DemoSeismics Select Data from BatchHost file Used hosts dgbindial 05 localhost 92 168 4 102 VVindows 64 development Machine 192 168 4 104 initialising 92 168 4 104 Windows 32 development Machine dgbindial 05 initialising 192 168 4 102 initialising Stop View log Nice level 0 19 ice level 0 19 The progress output o o ares individual processes Started Started Started Started Started Started Started processing processing processing processing processing processing processing processing inmrine inline inline inline inline inline inline inline 72 S54E ISZ I6 F Lue 495 497 dgbindialOs 498 500 192 168 4 102 501 503 192 168 4 104
3. Application Management Documentation version 4 6 could either be renamed or its contents copied and pasted in the newly created BatchHosts file OpendTect will use this file to communicate to the remote hosts and launch processes remotely on them Follow the example file format to add the list of remote machines and their details in the respective fields Things are done in a bit different way on Unix and Windows so some of the configuration are different on these platforms which is mentioned in details later in the chapter 5 5 2 Multi Machine Batch Processing on Windows Running Multi Machine batch processing on Windows requires few pre configurable steps like adding the list and specifications of the remote hosts to the batch hosts file sharing the survey folder and starting the remote_processing service daemon on each of these remote host machines All these steps are clarified below On Windows we assume that the survey folder DataRoot is on a central server and the user works from a workstation local host along with some other machines connected to the network which can be used as remote hosts for processing The survey folder has to be shared and mapped on each of the host machine Then install OpendTect on all the hosts and start the daemon service which comes with the installation in each of them In case of local host machine the daemon is not needed Create the BatchHosts file on the local host which contains information ab
4. In the new installer you will have the choice as seen below OpendTect Installation Manager V4 6 09 T 3 Jeg Proxy settings S Installation Manager Release OpendTect 4 6 current a Install OpendTect 4 4 previous Prepare offline installation packages Installation base directory C Program Files OpendTect The information following in this section deals with online installation or upgrade For creating offline installation packages please see Section 2 1 2 Offline Installation OpendTect Application Management Documentation version 4 6 gq EER Selection Jog What packages do you wantto select initially C GPL Typical GPL only free installation C Academic Typical academic installation Commercial Typical commercial installation C Pick want to pick each package by hand The figure above suggests to select the package type of OpendTect To read more about OpendTect packages type please refer to our web page of licensing types http www opendtect org index php download html OpendTect Application Management Documentation version 4 6 2 1 1 Package manager OpendTect Package Manager BAX utilities OpendTect 4 6 current 4 6 0 at C Program Files OpendTect S Installation Manager All bd N OpendTect Dip Steering OpendTect Neural Network Horizon Cube The programs and libraries for the OpendTect base system Common Contour Binning Sequence Stratigraphic Inter
5. Utilities Export download list 6 0 atC OD_Doc Rollback Show log file Sal a The utilities menu has the following options 1 Export download list 2 Rollback 3 Show log file Each of these options are explained below in details 2 1 1 1 1 Export download list This option allows the user to download the list of URLs of the individual packages from the download site This list is stored in a text file which can be used later to download these files directly without the help of the installer program After downloading user can run his her own unzipping scripts to install the packages manually This facility was only developed for the Linux users Windows users can use this feature provided they can prepare their own installation scripts for the installation 2 1 1 1 2 Rollback Rollback tool allows you to restore your previous version of the installation If after updating the software you feel uncomfortable with some of the new features and want to go back to your previous installation you have to use this tool As this tool will change your entire installation so you have to use it cautiously 2 1 1 1 3 Show log file The installation manager keeps track of all the action it is executing in a log file This log file can be viewed from this tool This is useful for debugging purposes If 11 OpendTect Application Management Documentation version 4 6 you face any trouble during the installation process you can send this fi
6. for example in C Licenses and the normally the debug log file 24 OpendTect Application Management Documentation version 4 6 can be placed in the same directory Now you can press the Save service button Then you can start the service in the Start Stop Reread tab If you want to run OpendTect from another computer you need to copy the license file to that computer and use the same utility Now go to the Utilities tab and enter Vendor Name dgbld and select the path to the license file Then press Override Path That should be enough to make the computer find the license manager service on the remote machine For simple node locked and demo licenses there is also a menu in OpendTect for end users 4 2 2 1 1 Installation using a license file Your main source of information is http opendtect org lic flexlm_inst_win html Very often you just need to install a new license file Then on the local machine you can use the license manager tools to specify override the license file OD is supposed to look at Once you have fired up the License Manager Tools you can see a tab Utilities That one contains a button List All Vendor Paths There you can see that there is a path Im_dgb which is the one used by OpendTect You can override this if you 1 enter Im_dgb in the vendor name field 2 click the button and select a license file 3 press the Override Path button 4 2 2 1 2 Installation using a licens
7. to the OpendTect user through the user interface This file defines which ones are available what parameters must be passed and provides info on the programs Also here the file format is straightforward for details about what the entries mean exactly please contact OpendTect support 4 2 5 6 Default mouse button bindings MouseControls A list of standard mouse button bindings have been compiled in the MouseControls file The user can select one of these setups in OpendTect If more setups are needed add those to this file Even the new user default can be set The Default Default is the OpenInventor default which is also adopted by Landmark 4 2 5 7 Default Attribute Sets Attribs The attribute sets in this directory are available to users as initial sets In principle any set created by any user can be placed in this directory to make it available for all OpendTect users This requires one extra step however addition to the Object Management File omf The omf file needs to be edited with at text editor an entry similar to the existing ones should be added but with another ID on the first line of the entry Alternatively you can copy the entry as it appears in the omf in the user s project s Attribs subdirectory s omf Plugins can put their own default attribute set in xxAttrib subdirectories OpendTect will scan for such directories automatically 4 2 5 8 The Initial survey BasicSurvey 30 OpendTect Applic
8. txt In INSTALL txt the installation procedure is described On Windows you need to download one or more self extracting executables On UNIX type systems you may have to download a script install od or inst_pkgs od All scripts take no arguments and should be easy to complete Please read INSTALL txt carefully Regarding the selection of installation directory you should choose a directory that is accessible on all machines that will run OpendTect or one of its batch programs This is especially important for multi machine processing which is indispensable for surveys of considerable size Every machine that needs to be used for this multi machine processing needs to be able to access OpendTect under the same directory name 4 2 2 Licensing Many commercial plugins for OpendTect use FlexLM licensing The FlexLM end user manual can be found at http opendtect org lic endusermanual The main source of information from opendtect org is http opendtect org lic doc flexlm_installation_guide html Some hints There are two types of licenses node locked and floating A node locked license is locked to a certain machine Node locked licenses have only got lines like this FEATURE dTectNN lm_dgb 4 400 1 jan 2013 uncounted C42442D673EF HOSTID 000039eb8bda FEATURE dTectDS lm_dgb 4 400 1 jan 2013 uncounted 766915A97FB6 HOSTID 000039eb8bda Also demo licenses these have HOSTID DEMO but look the sam
9. 504 506 dgbindialOs 507 509 192 168 4 102 510 512 dgbindial0s 513 515 192 168 4 104 40 OpendTect Application Management Documentation version 4 6 5 6 UNIX The environment The environment for the programs is set in the following sequence see bin init_dtect e General initialisation e g DTECT_APPL and possibly DTECT_DATA are set e LD_LIBRARY_PATH and PATH are extended with one directory In some installations this has been a problem because Landmark adds an incredible amount of directories to the PATH We think it is not unreasonable to require the ability of adding one single directory to the executable path Therefore we leave it to the system administrators to shorten the PATH to allow at least the OpendTect binary directory to be added to the path e The initialisation scripts for the plugin packages are automatically sourced by init_dtect 5 7 Madagascar processing The Madagascar connection plugin implements a link to an existing Madagascar installation Thus the installation of Madagascar is out of the scope of this manual Additional setup may be required see part of the user environment On Windows you can only use Madagascar in combination with Cygwin Getting this to work with a native Windows program like OpendTect is not always easy Here s how we succeeded e Download the latest Cygwin installator http www cygwin com mirrors html and Madagascar sources 41 OpendTect Applicati
10. OpendTect Application Management Documentation version 4 6 Bert Bril Copyright 2002 2013 by dGB Beheer B V All rights reserved No part of this publication may be reproduced and or published by print photo print microfilm or any other means without the written consent of dGB Beheer B V Under the terms and conditions of either of the license holders are permitted to make hardcopies for internal use GNU GPL Commercial agreement Academic agreement Table of Contents 1 Data storage 1 1 Data management 1 2 DTECT_DATA the data access point 2 Installation 2 1 Installation Manager 2 1 1 Package manager 2 1 1 1 Utilities menu 2 1 1 1 1 Export download list 2 1 1 1 2 Rollback 2 1 1 1 3 Show log file 2 1 2 Offline installation 2 1 2 1 Package Verification 2 2 Auto update policy 2 3 Connection Settings 3 User environment 3 1 General 3 2 Finding OpendTect 3 3 Project sharing 3 4 Madagascar processing 3 5 The GMT link 4 Application 4 1 Organization 4 2 Content 4 2 1 Installation scripts and INSTALL txt 4 2 2 Licensing 4 2 2 1 Windows 4 2 2 1 1 Installation using a license file 4 2 2 1 2 Installation using a license server 4 2 2 2 Unix 4 2 2 3 FlexLM host IDs OpendTect Application Management Documentation version 4 6 4 2 2 4 Vendor Daemons 4 2 3 UNIX User startup scripts 4 2 4 bin Executables 4 2 4 1 Program scripts 4 2 4 2 Platform specific lux32 lux64 mac win32 win64 subdirect
11. ation Management Documentation version 4 6 This directory is copied in its entirety when a user creates a new survey i e a new project Like all OpendTect surveys the directory can be copied on the UNIX or Windows level note make sure hidden files are copied too Therefore companies can customize and extend initial survey contents by changing adding to this survey 4 2 5 9 OpendTect documentation doc The OpendTect documentation if installed can be reached from inside OpendTect via the Help menu From outside OpendTect index html in the directory doc User base can be opened For printing PDF files may be available on the opendtect org web site Documentation for plugin packages may also be present in the doc User directory The name of such a directory should be package_name and a mnuinfo file is mandatory This file contains the menu name start url and optional a shortcut Open the file about html for version and contributors to the OpendTect project 31 OpendTect Application Management Documentation version 4 6 Chapter 5 Running OpendTect Table of Contents 5 1 First Start Up 5 2 General 5 3 OpenGL 5 4 UNIX OpenWorks GeoFrame and Petrel 5 5 Remote Batch Processing 5 6 UNIX The environment 5 7 Madagascar processing gt OpendTect 5 1 First Start Up There are a couple of considerations on first start up The Data Access Point This will be SDTECT_DATA Installati
12. ations Pick sets Polygons Madagascar Data related to the Madagascar Tool Models Modeling descriptions Misc a o Sessions NLAs Non Linear Analysis models OpendTect Application Management Documentation version 4 6 usually Neural networks Proc Processing files Seismics Seismic data Imported attribute Wavelets Surfaces Horizons Faults WelliInfo Well data OpendTect Application Management Documentation version 4 6 Chapter 2 Installation Table of Contents 2 1 Installation Manager 2 2 Auto update policy 2 3 Connection Settings OpendTect Utilities SSIS Help Settings gt Tools gt i EA Plugins Installation Installation Manager Show log file Auto uptrate policy Translate Connection Settings License utilities gt 2 1 Installation Manager OpendTect Application Management Documentation version 4 6 OpendTect Installation Manager V4 6 00 S 3 oeg Proxy settings S Installation Manager Release OpendTect 4 6 current Install Update Online Prepare offline installation packages Installation base directory C Program Files OpendTect Connected to http fdownload opendtect org relman internal The installation manager is a wizard to install upgrade the existing OpendTect Current Previous releases The release type field is used to select the release that is needed to be installed upgraded
13. ble is seen as a series of colors RGB optional transparency on a fictive measure of 0 to 1 Every color table needs a definition of the values 0 and 1 but more colors can be defined in between For example the well known Red white black color scale is defined as Name Red White Black Value Color 0 255 0 0 Value Color 0 25 255 200 0 Value Color 0 5 255 255 255 Value Color 4 1 0 0 0 0 1 ali 0 E Ww D H Transparency 0 0 0 Transparency 1 1 0 Undef color 50 200 150 Marker color 240 0 NONMNMNNNMNN DN LN On six lines you see the definition of colors format Red Green Blue separated by back quotes On the Value Color lines these are preceded by the position in the color table here 0 0 25 0 5 and 1 In the above example there is no transparency a simple full transparency in the middle example would be 2 Transparency 0 0 0 2 Transparency 1 0 5 1 29 OpendTect Application Management Documentation version 4 6 2 Transparency 2 1 0 4 2 5 4 Default user settings odSettings The default user settings are copied to the user s home directory when the user starts OpendTect for the very first time The file format is straightforward for details about what the entries mean exactly please contact OpendTect support 4 2 5 5 Default available batch programs BatchPrograms A selection of system utilities and OpendTect batch programs will be available
14. date the drivers at least every half year also on Linux This is essential not doing it can and will cause all sorts of problems for the users from small details to all out crashes 34 OpendTect Application Management Documentation version 4 6 5 4 UNIX OpenWorks GeoFrame and Petrel ARK CLS maintain a series of plugins accessing the mainstream platforms commonly used in the industry The ARKCLS WorkStation Access WSA plugin is commonly used for import and export SeisWorks or GeoFrame data directly There is also a Petrel OceanView access plugin The WSA servers support OpenWorks R2003 and R5000 and GeoFrame 4 0 4 4 To use these plugins OpendTect needs to be started from a properly prepared environment Essentially OpenWorks GeoFrame or Petrel must also be runnable in that environment The startup script will check for this For OpenWorks the OWHOME variable is checked for GeoFrame GF_PATH The full initialization and checking sequence can be found if the plugin is installed in odinit arkcls Starting OpendTect from a GeoFrame or OpenWorks xterm is recommended You will need one or more licenses for the WSA and POA connections 5 5 Remote Batch Processing OpendTect users need a lot of processing power Therefore chances are that they want lots of processing access to other machines The OpendTect multi machine batch utility provides this It relies on remote shell execution and NFS mounting or Windows share
15. e are handled like this Another kind of license files require a machine designated as license server On this machine a daemon UNIX or service Windows will keep track of the licenses available These are typically used when OpendTect can run on multiple computers These license files look like this 23 OpendTect Application Management Documentation version 4 6 SERVER ourserv 000c6e00bbb8 DAEMON lm dgb full_path_to 1lm_dgb FEATURE dTectDS lm_dgb 4 400 1 jan 2013 4 B47BBC613640 DUP_GROUP D FEATURE dTectNN lm_dgb 4 400 1 jan 2013 4 3FC4443E7619 DUP_GROUP D The file is read like this FlexLM needs to start a server on machine ourserv with FlexLM host ID 000c6e00bbb8 To start this server use a program Im_dgb exe Until 1 Jan 2013 you can use dTectDS and dTectNN with 4 concurrent users version 4 4 and lower 4 2 2 1 Windows The normal way to specify a FlexLM license file on Windows is to simply start OpendTect If you did not specify a license file yet OpendTect will ask for one Simply follow the instructions on the screen Sometimes this doesn t work for example if you want to use another license file Then you can use the FlexLM utility program available in the Windows start menu for OpendTect License Manager Tools LMTOOLS exe Everything should be manageable from this program although things can be a little confusing If you need to install on a Wind
16. e Started On 07 05 2013 At 14 10 32 M Missoula Software amp FileZilla FTP Client gt o Yuze vim 7 3 gt A VideoLan gt x Microsoft Excel 2010 P Microsoft PowerPoin zl License Manager To Fia Remote Processing fm 440 gt License Manager Tools Remote Processing Service E Uninstall OpendTect 4 4 0 amp VLC media player ski Sa OpendTect m WinRAR gt Citrix Log Off g Turn Off Computer All Programs Remote Processing service Show Window Start Stop 14 19 dinsdag 7 5 2013 System tray notification 5 5 3 Multi Machine Batch Processing on Linux On Linux the process is quite simple only modifying the BatchHosts file with relevant information about the remote host machines is enough As the communication is performed using remote shell commands so there is no need for running the daemon here The process is described below 5 5 3 1 Configuring BatchHosts file on Linux On Linux the multi machine communication is done using remote shell commands like rsh or ssh In the BatchHoats file the default is already set to rsh The user can also change this to ssh if needed The list of computers to be used has to be entered in the following format IP Addresss Name in user display platform Shared data location e g 39 OpendTect Application Management Documentation version 4 6 192 168 4 10 32 bit Linux Machine lux32 dsk d2 Surveys
17. e server Again your primary source of information is http opendtect org lic flexlm_inst_win html If you want to share a common site license amongst multiple users and or hosts you can install the Flexlm license manager as a Windows service the equivalent of Unix daemons However this does not work for demo licenses These have to be installed on the local host Note 1 One not so obvious thing is that in the Config services tab the Service name combobox is editable Note 2 If OD complains it might be that the console window contains some info about what is wrong 25 OpendTect Application Management Documentation version 4 6 4 2 2 2 Unix Your main source of information is http opendtect org lic flexlm_inst_unix html Some remarks Make sure you work under the same user that installed OpendTect The start vendor_name lmgrd scripts can be used when you have no company policy on start stop of FlexLM daemons The script takes one optional argument if this argument is stop then the daemon s will be stopped rather than started If the start mode is used the output of the daemons is redirected to license package_name log For every commercial plugin package you should find a UNIX script install package_name license in the installation directory that reads obtained license files and writes those to the correct position in the OpendTect tree If you have your own FlexLM management procedures e g FlexAd
18. easy to see how to use this file as an example of a BatchHosts file If you do not place such a BatchHosts file in a location specified in the data locations section OpendTect will ask the Operating System for remote host names via the g sethostent type functions This can result in a lot of choices for the user or none 28 OpendTect Application Management Documentation version 4 6 See also the section on remote batch processing Make sure remote machines need to have a well synchronized system time About the First port entry the multi machine processing processing needs a free TCP port to do its work It starts at a port number which is used if it s free If not the program will try one higher and so forth The starting port is by default set to 19636 If this clashes with any application that means if that other application is not flexible in its port allocation overrule it The name of the BatchHosts file can be overridden using the environment variable DTECT_BATCH_HOSTS_FILENAME You can also specify a filename full path using the DTECT_BATCH_HOSTS_FILEPATH environment variable 4 2 5 3 Default Color tables ColTabs The ColTabs file in the data directory contains the default color tables that every new user will get The user can never remove these tables but s he can change the definition only in their own environment The format of the file is quite simple The only thing to explain is the concept A color ta
19. f the DTECT_USER environment variable is set see project sharing 17 OpendTect Application Management Documentation version 4 6 3 2 Finding OpendTect For installations not on windows users will have to be able to find OpendTect There is no procedure initiated by the OpendTect installation to put the startup scripts in the user s path Whether you want to put start_dtect in their path at login or set an alias for it create a desktop link or even other solutions is simply not something we take care of Note that this is one of the reasons why OpendTect need not be and should preferably not be installed by root 3 3 Project sharing OpendTect projects can be shared by many users The only real obstacle in practice would be the access permissions There are two main strategies to get this right e Make sure the users belong to a common work group and on UNIX set their umask so that files are created with group write permission by default e Create a special user id s for OpendTect projects The different users can then work under the same Operating system user ID For this strategy to work an additional environment variable needs to be set DTECT_USER OpendTect will automatically use other settings and allow different projects for the same userID depending on the setting of DTECT_USER The latter strategy has been used at dGB for years At login under our cases user the user is prompted to
20. gpg or pgp must be used an encryption program These programs are normally installed in most linux installations and can be found at http www gnupg org dGB s public key has to be downloaded to your keyring This is only necessary for the initial verification To obtain the key use gpg itself gpg keyserver pgp mit edu search keys support dgbes com You may chose any keyserver you want as they all share data Once you have located our key import it to your keyring Secondly to avoid warning messages edit the key and tell gpg that you trust it gpg edit key support dgbes com and then type trust as command Once you have our key installed you are ready to verify the packages This is done 14 OpendTect Application Management Documentation version 4 6 by gpg bash gt gpg verify demosurvey zip sig This will check that demosurvey zip has not changed since the file demosurvey zip sig was generated in our office A positive output may look like this gpg Signature made Thu Oct 4 08 46 01 2012 CEST using DSA key ID AO2F407E gpg checking the trustdb gpg 3 marginal s needed 1 complete s needed PGP trust model gpg depth 0 valid 1 signed trust 0 Oq On Om Of lu gpg next trustdb check due at 2022 03 13 gpg Good signature from dGB Earth Sciences B V Software package signing key 2 2 Auto update policy The auto update policy can be defined and changed by a user B
21. how to launch the installation package Information OpendTect offline installation packages created successfully under C J DOCUME 1 demoiLOCALS 1 Tempiod_offline_win32 Please use od_setup exe to install the packqe Windows offline pop up info Information x OpendTect offline installation packages created successfully under SLA itmpiod_offline_lux64 To install the downloaded packages please run the unix_install csh script Linux offline pop up info Please note The Platform option refers to the intended installation platform and not the platform of the machine currently being used to download the packages if different For information on how to verify packages installed offline please look here Offline Package Verification Procedure 13 OpendTect Application Management Documentation version 4 6 2 1 2 1 Package Verification We generate signature files for all packages Normally a package is a zip file downloadable from our website For OpendTect version 4 4 0 please visit http www opendtect org relman 4 4 0 For OpendTect version 4 6 0 please visit http www opendtect org relman 4 6 0 For each zip file there is a zip sig file containing a digital certificate that can be used to verify that the package has not been tampered with during transit To verify a package download the corresponding zip sig file and place it in the same directory as the package file
22. icenses are handled by running processes There is one process for each vendor who has a FLEX Im licensed product on the network This process is called the vendor daemon The vendor daemon keeps track of how many licenses are checked out and who has them If the vendor daemon terminates for any reason all users lose their licenses Client programs communicate with the vendor daemon through TCP IP or UDP IP sockets The client where the application runs and the daemon processes the license server can run on separate nodes on your network Also the traffic between the client and the license manager daemon is machine independent allowing for heterogeneous networks For a more complete explanation please read this The necessary Vendor Daemons for OpendTect can be found in the Vendor sub directory here For dGB http www opendtect org lic Vendors dGB latest For ArkCLS http www opendtect org lic Vendors ArkCls For SitFal htto www opendtect org lic Vendors Geolnfo Please select the relevant plug in and download the package corresponding to the architecture of the licence server 4 2 3 UNIX User startup scripts The main script the user will need to run is start_dtect in the installation root Some power users will also want to run the exec_prog script to start specific command line or batch utilities Essentially start_dtect takes no arguments but arguments given will be passed to the od_main executable which
23. in 5 minutes the program considers the machine dead It will remove the machine from the used machines list and allocates the job to the next machine that is selected or becomes free Note the 5 minutes timeout can be overridden using the environment variable DTECT_MM_CL_FAIL_TO which can be used to set the desired timeout in seconds This leads us to the thing that needs to be checked on Unix based systems NFS has an option to cache file attributes This can cause NFS to report that a file is not there when it in fact does exist We recommend this attribute caching is turned off which is in fact the default on Solaris systems On Linux the default caching time can be as high as 30 seconds For mounting we therefore recommend noac Not available on Linux and actimeo 0 as extra mount options for remote disks In terms of licensing we encourage to tie any licensing to actual users working with it Although we have no control on plugin builders we advocate to never license per cpu per machine and so forth No extra licenses should be needed for processing on remote hosts The licensing should be per actual user and therefore on the GUI level 5 5 1 Setting up BatchHosts file The BatchHosts file should actually be a text file containing the list of remote machines and some relevant details about these machines A BatchHosts_example file already comes with the installation inside the OpendTect data folder this file 36 OpendTect
24. is a standard X 27 OpendTect Application Management Documentation version 4 6 Windows and Qt application The exec_prog script will always have a first argument which is the program to be executed The rest of the arguments will be passed to the program If you have the GNU debugger installed gdb then users will be able to send crash reports to opendtect org for feedback This can be highly useful to solve problems for users 4 2 4 bin Executables 4 2 4 1 Program scripts The program scripts are called from within OpendTect or the OpendTect startup scripts Remote execution is always done through od_exec_rmt UNIX only local execution through od_exec 4 2 4 2 Platform specific lux32 lux64 mac win32 win64 subdirectories The OpendTect executables are dynamically linked against the shared libraries in the so subdirectory Bug fixes or special purpose updates usually consist of a replacement in this directory 4 2 5 Program data 4 2 5 1 Location of Program data files Data files for the OpendTect programs are located in the data subdirectory If you want to overrule certain defaults like a custom default empty survey or standard color bars then you can make changes in this directory Note that you have to make these changes in every update or re install 4 2 5 2 Batch Processing Hosts BatchHosts In the data sub directory in the installation directory you will find a file BatchHosts_example It is
25. le to OpendTect support if needed 2 1 2 Offline installation You may also choose to create packages for offline installation These packages are created in such a way as to function cross platform For example you may download the Linux 64bit package onto a Windows machine and then transfer and install it onto the Linux system or vice versa OpendTect Installation Manager V4 6 00 wal Woe m Proxy settings Installation Manager S Release OpendTect 4 6 current A Install Update Online Prepare offline installation packages Download directory Wemp od_offline_win32 Platform Windows 32 bits v You will need to select the OpendTect version and toggle to Prepare offline installation packages You may either choose your download directory or leave the default You will first be prompted to select the package type of OpendTect To read more about OpendTect packages type please refer to our web page describing licensing types http www opendtect org index php download html 12 OpendTect Application Management Documentation version 4 6 gy EER Selection Jog What packages do you wantto select initially C GPL Typical GPL only free installation C Academic Typical academic installation Commercial Typical commercial installation C Pick want to pick each package by hand On completion of the download you will be reminded of the location in a pop up window and informed of
26. mel SDTECT_DATA Name2 will result in a fully functional new project in directory Name2 immediately Note that the user recognizes a survey by the directory name 1 2 DTECT_DATA the data access point Installation of OpendTect usually means making available a base directory from which the project data can be reached The location of this directory can be set in the user s environment as DTECT_DATA although especially on Windows this will usually be done behind the scenes through a user setting Default DATA directory Anyway the DTECT_DATA directory must be e reachable from every machine that needs to access the data e accessible for the users for read write When users create a new project known as Survey in OpendTect they can choose to locate the project directory on another disk than the SDTECT_DATA directory In that case OpendTect will locate the directory on the specified location and put a link in the SDTECT_DATA directory Therefore this directory does not necessarily have to have a lot of disk storage available The directory structure is as follows Table 2 1 Directory structure SDTECT_DATA omf project_dir user defined name OpendTect Application Management Documentation version 4 6 omf Survey defs 2DGeom Coordinates for 2D seismic lines Attribs Attribute sets Features Point related data Cross plot NN training GMT Data related to the General Mapping Tool Loc
27. min you still have to make sure that a file license package_name dat is present in the application directory containing the necessary license information The FlexLM end user manual can be found at http opendtect org lic endusermanual The two things needed by your plugin vendor to issue a license are the hostname obtainable on UNIX with the hostname command Windows Start Settings Control panel System tab Network identification and the host identification That identification can be obtained by running the FlexLM utility Imhostid After installing OpendTect the Imhostid command can be run from the Utilities BatchPrograms menu 4 2 2 3 FlexLM host IDs It is in general possible to obtain the FlexLM hostid before installing OpendTect Table 1 2 FlexLM IDs Solaris hostid sbin ifconfig look for HWAddr i e the MAC address of the main Linux network card sbin ifconfig look for ether the MAC address of the main network Mac OS X Said 26 OpendTect Application Management Documentation version 4 6 MS Run ipconfig all in a DOS command prompt window and look for Windows each Physical address entry choose the main network MAC address For license files additionally the host name will be required although host names can be changed at any time On UNIX this is simply the output of hostname on Windows the Host Name from the ipconfig all is required 4 2 2 4 Vendor Daemons In FLEX Im l
28. on Management Documentation version 4 6 http rsf sourceforge net Download in a temporary folder C temp for instance Extract the Madagascar sources to a folder that you rename from madagacar to rsf Install Cygwin accept the default settings but select at least the following packages per section o Devel gcc libnetpbm devel make mingw runtime subversion swig o Editors vim o Graphics jpeg o Interpreters python o Python Numeric numpy if available o X11 xorg X11 base libXaw 3d devel Open a Cygwin session Edit the bashrc file to add some madagascar environment variables Madagascar initialization export RSFROOT usr local rsf if n SPYTHONPATH then export PYTHONPATH S PYTHONPATH RSFROOT lib else export PYTHONPATH SRSFROOT 1lib fi export PATH PATH RSFROOT bin export DATAPATH var tmp Enter the command source bashrc Copy the source to your emulated linux filesystem cp cygdrive c temp rsf usr local go to this folder cd usr local rsf Compile madagascar using the following successive commands 1 configure If Checking for SCons returns no the script configure will need to be launched a second time 2 make 3 make install 4 make clean Now you can close your Cygwin terminal or test the Madagascar installation The testing and use of Madagascar without OpendTect will require to start the X server xwin amp and set the display
29. on of OpendTect usually means making available a base directory from which the project data can be reached The location of this directory can be set in the user s environment as DTECT_DATA although especially on Windows this will usually be done behind the scenes through a user setting Default DATA directory Anyway the DTECT_DATA directory must be reachable from every machine that needs to access the data accessible for the users for read write See Section 1 2 DTECT_DATA 32 OpendTect Application Management Documentation version 4 6 Licenses On first start up for example following re installation you will be prompted to install license s It is vital to ensure that they are correctly installed and findable There are other ways to achieve this same result 1 Soft link Place the license in the root of the installation directory or make a link there to where the license is located 2 Set up an environment variable LM_LICENSE_FILE port host for multiple entries use port host1 port host2 port hostetc 3 In Windows you see a pop up on start up for dGB and on usage for the ArkCLS and SITFAL plugins asking you to specify the license server system this needs to be done as Administrator to set this for all users In the License file you may change the host name and add a port number or port host to the right hand side of the Mac address though you may not change the Mac address For example SERVER m
30. ories 4 2 5 Program data 4 2 5 1 Location of Program data files 4 2 5 2 Batch Processing Hosts BatchHosts 4 2 5 3 Default Color tables ColTabs 4 2 5 4 Default user settings odSettings 4 2 5 5 Default available batch programs BatchPrograms 4 2 5 6 Default mouse button bindings MouseControls 4 2 5 7 Default Attribute Sets Attribs 4 2 5 8 The Initial survey BasicSurvey 4 2 5 9 OpendTect documentation doc 5 Running OpendTect 5 1 First Start Up 5 2 General 5 3 OpenGL 5 4 UNIX OpenWorks GeoFrame and Petrel 5 5 Remote Batch Processing 5 5 1 Setting up BatchHosts file 5 5 2 Multi Machine Batch Processing on Windows 5 5 2 1 Configuring BatchHosts file on Windows 5 5 2 2 Mapping Survey folder 5 5 2 3 Start the daemon on remote machines 5 5 3 Multi Machine Batch Processing on Linux 5 5 3 1 Configuring BatchHosts file on Linux 5 5 4 Start Processing 5 6 UNIX The environment 5 7 Madagascar processing OpendTect Application Management Documentation version 4 6 Chapter 1 Data storage Table of Contents 1 1 Data management 1 2 DTECT_DATA the data access point OpendTect 1 1 Data management OpendTect was not designed for extensive data management Although it may be used for this purpose we realize that in many cases OpendTect maintains project storage for data further maintained in company data stores like OpenWorks or GeoFrame Users can choose to put projects on any storage area
31. out remote host s IP address host names and the mapped survey folder corresponding to each of the machines All these sections are explained below in details 5 5 2 1 Configuring BatchHosts file on Windows As mentioned earlier the BatchHosts file has to be created and configured so that OpendTect can communicate with the remote hosts A BatchHosts_example file comes with OpendTect installation and could be found in the data folder The file consists of a header section followed by information about the remote host machines The header section contains details about the remote shell nice level and the port number for Windows the port number is only used but nice level and remote shell are Unix specific The structure of the remote host section is like this IP Address Description Platform Survey folder 37 OpendTect Application Management Documentation version 4 6 Each of fields are described below IP Address The IP address of the machine or the name of the machine in the network Description more informative description which users see in the list of available hosts in Multi Machine processing window Platform The platform on which the local host is running i e win if the remote host is a Windows machine Survey folder The full path of the survey folder along with the mapped drive Here is used in place of for drives as is already used as the field separator Please note that the local host is automa
32. ows server you should really take a look athttp opendtect org lic doc flexlm_installation_guide html in particular http opendtect org lic doc flexlm_inst_win html The main choice you have is whether you need to install using services or with a license file Which of the two depends on the license file you have got and the machine you are on If you have a node locked license you always have to choose to set up using a license file Also demo licenses where HOSTID DEMO and machines that are not designated to be SERVER of a floating license In the start tab select Configuration using License file You can then select the file to use but that often doesn t work Then go to the Utilities tab and enter Vendor Name dgbld and select the path to the license file Then press Override Path If you have a floating license you must start the service on the machine mentioned in the header of the license file On that machine start the License manager Tools In the start tab select Configuration using services Then click the Config Services tab which has now appeared Enter a name for the service for example OD dGB lic man Confusing here is that the combo box is an editable field You have to find the path to the Imgrd exe This may be vendor specific for example dGB has all license related files in a directory C Program Files OpendTect bin winlm dgb The path to the license file is something you have chosen yourself
33. pretation System More info Vell Correlation Panel SynthRock Beta Seismic Coloured Inversion Seismic Spectral Blueing Seismic Feature Enhancement Seismic Net Pay MPSI UltraFast Stochastic Inversion Field 2D Petrel Connector Velocity Model Building um PDF3D Computer Log Analysis Software CLAS Madagascar Link Creator OpendTect Web GMT Link GPR plugin User Documentation Installed version 4 6 0 4d Action needed Documentation for the dGB Plugins Developers package Available version 4 6 0 4d None Developers Documentation OOO PSSOOR OOOO C Re Install OpendTect The last window of the wizard is the OpendTect Package Manager see above figure Multiple items can be selected from the list by checking in or out Optionally the relevant package combination could also be selected from the top list box The installation manager will automatically recognize the previously installed version at the selected path and will prompt it in the nstalled version field To read more about a particular item in the list select the item by clicking on it and read the description on to the right panel 2 1 1 1 Utilities menu 10 OpendTect Application Management Documentation version 4 6 On the top left corner of the package selection window there is a Utilities menu which offers some useful functions for the installation manager a 9 OpendTect Package Manager
34. s to do its work Therefore Unix i e Linux and Mac users should have a valid sHomz rhosts file writeable by the user only i e file permissions must be rw r r The Unix systems that need to be available for processing need to have rsh or ssh enabled NFS or Windows network shares are needed to make the application directory and the data directory available on all hosts that are used for processing On Unix in case rsh access is not possible you can use ssh which must then be set up with 35 OpendTect Application Management Documentation version 4 6 public key authentication without passwords If on Unix machines no BatchHosts file is present OpendTect calls the system utilities of the hostent sethostent gethostent etc type to get a table of hosts for the user to select from How the Operating System builds the lists is dependent on the particular system setup most likely etc hosts and or the NIS tables are consulted The hostent functions are old and not very good up to the task We recommend to always create a BatchHosts file The program will try to use the machines that are selected when necessary So when a job is finished on a machine it will see which machine from the used machines list is free most likely the same machine and start the next job on that machine Sometimes the machine selected has problems is down or the network is overloaded In any case if the machine does not react with
35. they like In addition large data objects like seismic cubes can be relocated to other directories using for example the Manage Seismics dialog This relocation is possible because selection of cubes is not done on basis of file name Rather the user specifies a name for each cube and the system translates this automatically into a default file name Later location and file name may be changed whilst retaining the same object ID and name Seismic cubes can have a class like Imported Steering and Attribute cubes This difference is maintained in the Object Manager but is not apparent on the Operating System level In the Object Management File Seismics omf the type can be seen as in Type Steering Currently all Seismic cubes are stored in the CBVS file format which is an platform specific binary format Although the storage is platform dependent all CBVS files can be read by OpendTect fully transparently across platform boundaries CBVS cubes can be stored in multiple files where the first file usually contains most of the header info Subsequent files belonging to the same cube can be recognised by the 01 02 etc in the filename For 2D seismics this system is also used now for the different lines in a line set OpendTect Application Management Documentation version 4 6 OpendTect projects can be copied on the Operating System level at the DTECT_DATA level Therefore a command like cp a SDTECT_DATA Na
36. tically added to the list so there is no need to add the IP address of the local host here 5 5 2 2 Mapping Survey folder It is assumed that the survey folder is in a server which has to be shared and mapped on all host machines to be used for multi machine processing So if the survey folder is on the C drive on the server e g C Surveys then map the C drive from this machine to other host machines by choosing an available drive letter like C D S etc So the survey folder now becomes S Surveys or F Surveys on each of the machines depending on drive letter that is used 5 5 2 3 Start the daemon on remote machines Start the daemon on every remote machine by selecting Start menu gt programs gt OpendTect 4 6 0 gt Remote Processing Service This tool will add a notification icon to the system tray Once the service starts the remote machines are ready to be used as multi machine processing nodes The screen shots below shows the user interface of the Remote Processing Service and its notification icon in the system tray The service can be controlled by right clicking on the tray icon and selecting appropriate menu item like start stop or exit 38 OpendTect Application Management Documentation version 4 6 zJ wordrad Picasa 3 gt si W Microsoft Word 201 a Fa OpendTect Remote Service Manager sia ig Adobe Reader XI Google Drive gt obe Reader M Greenshot gt Event Log W Pant Servic
37. type his her name which is then used to set the DTECT_USER environment variable 18 OpendTect Application Management Documentation version 4 6 3 4 Madagascar processing To enable Madagascar processing the variable RSFROOT should be set in the user s environment pointing to an existing Madagascar installation To get the full benefit of the plugin you should also make sure there is text documentation in the Madagascar installation This should be present in SRSFROOT doc txt If there is no directory SRSFROOT doc txt or if it s empty you can run RSFROOT bin sfdoc t RSFROOT doc txt 3 5 The GMT link To activate the GMT link GMT needs to be installed The download site is http gmt soest hawaii edu After installation make sure the GMT binary directory bin is in the user s PATH For many purposes the user will want a PostScript viewer to be installed too Make sure you have a good association for postscript files in place 19 OpendTect Application Management Documentation version 4 6 Chapter 4 Application Table of Contents 4 1 Organization 4 2 Content i OpendTect 4 1 Organization In the OpendTect startup and initialisation scripts the DTECT_APPL environment variable represents the root of the installation OpendTect is installed by the OpendTect Installation Manager You can install and manage multiple release types Stable Development The base directory is a directory
38. y default the option is set to Inform when the updates are available This can be changed to Never check for updates if you prefer Please specify gog Select policy for auto update N Inform vhen new updates are present show this in OpendTect s title bar C None Never check for updates 15 OpendTect Application Management Documentation version 4 6 2 3 Connection Settings To enter the proxy information the right proxy server information must be added in the Connection Settings before running the installation This is done in the following dialog This dialog is also available directly through the Installation Manager on clicking the Proxy Settings button Connection Settings BAX Use proy Yes No HTTP Proxy Port 1 lt a x C Use uthentication User name Password 16 OpendTect Application Management Documentation version 4 6 Chapter 3 User environment Table of Contents 3 1 General 3 2 Finding OpendTect 3 3 Project sharing 3 4 Madagascar processing 3 5 The GMT link OpendTect 3 1 General Users need to be aware of only a few things to be able to use OpendTect Things become slightly more complicated when multiple users carry out shared projects The specific user settings and current survey are stored in the od hidden directory in the user s home directory The file names are settings and survey Or settings DTECT_USER and survey SDTECT_USER i
39. yodtserver 00145ebc6210 3456 host Note that this needs to be done for both the server s and the client s license file s Using this last option set port host is very useful when circumventing Firewall issues 33 OpendTect Application Management Documentation version 4 6 5 2 General There are a number of requirements to be able to run OpendTect First of all OpendTect will not start without a proper OpenGL installation which foremost and above all means good recent drivers Furthermore some minimal reasonable preconditions must be met see environment Lastly some plugins have their own requirements For example a proper SeisWorks or GeoFrame installation is required for the ArkCls WorkStation Access plugin 5 3 OpenGL The OpendTect 3D graphical engine is based upon the OpenInventor clone COIN made by SIM http www sim no http coin3d org This package in turn relies on a proper installation of OpenGL to do its work Some features of OpendTect like stereo viewing are only available if the OpenGL implementation supports it The OpenGL version is 1 2 or higher on all platforms All mainstream graphical cards are nowadays delivered with OpenGL drivers for windows High end ATI Radeon and nVidia based cards are very well up to the task Those cards work nicely under Linux too Unfortunately most Intel chipsets will not be usable For more information consult the system requirements IMPORTANT Make sure you up
40. you choose yoursef say apps OpendTect or C Program FilesOpendTect Within that directory you will have active and inactive installations The active installation trees simply have the version as directory name for example 4 4 0 Those directories contain an entire OpendTect installation The combination of the base directory and the version directory will be set in the various scripts as SDTECT_APPL In the above examples DTECT_APPL would be apps OpendTect 4 4 0 or C Program Files OpendTect 4 4 0 An OpendTect application tree is organized on both Windows and UNIX schematically like Table 1 1 Organization SDTECT_APP 20 OpendTect Application Management Documentation version 4 6 relinfo information for the installation manager Installation scripts and INSTALL txt User startup scripts lib bin Program scripts 1ux32 lux64 win32 win64 and or mac Executable S so Shared libraries plugins lux32 lux64 win32 win64 and or mac libs data Default color tables Default mouse button bindings Default user settings 21 OpendTect Application Management Documentation version 4 6 doc Default available batch programs icons Default BatchHosts created by sysadm if any Attribs BasicSurvey User SysAdm Programmer Releaselnfo 22 OpendTect Application Management Documentation version 4 6 4 2 Content 4 2 1 Installation scripts and INSTALL
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