[[TracNav(TOC)]] = Rasdaman FAQ = Here you can find answers to some of the most frequently asked questions about `rasdaman`. If you have a question not answered on this page, you can ask it on the mailing lists. You may want to consult these sources of information in addition: * [wiki:Download Download & installation guide] * [wiki:FormatsSupported Data formats supported] ---- [[PageOutline(2-4,Contents,inline)]] ---- == Download == === Cannot download from git repository === * Probably your provider does not allow port 9418 which git uses. See the [wiki:Download download page] for alternatives. == Installation == === Using automake I get an error message "directory should not contain /" === * Probably you have an outdated automake version installed, we have seen such problems with 1.7.9. Upgrade to at least 1.10.1. === ''./configure'' complains that some further packages are required during installation === * These are summarized on the [wiki:RequiredPackages] page. === ''./configure'' complains about missing ''curses'' === ... although ''ncurses'' is there. * You have run into a [http://bugs.gentoo.org/67481 bug in the ncurses package]; in /usr/lib, manually create symlinks ''libcurses.a -> libncurses.a'' and ''libcurses.so -> libncurses.so''. === ''./configure'' complains that some required files, like install-sh, cannot be found === * retry ''./configure'' after running {{{ $ automake --add-missing }}} === ''./configure'' complains that C++ compiler cannot create executables === * This means that either you haven't installed gcc/g++ or something got corrupted. On Debian it seems to happen when adding LIBS='-lecpg -lgdal1.7.0' to the ./configure command. === make complains about missing Makefiles === ...such as in the time/ directory, and issues error messages like "No rule to make target `../time/libtime.a', needed by `rasserver'. Stop.". * retry ''./configure'' after running {{{ $ autoreconf $ automake }}} === I get C++ compilation errors. === * Make sure you use the proper compiler version (see [wiki:RequiredPackages]). GNU folks have a relaxed view on backwards compatibility even with minor release changes, and we have experienced problems related to this in the past. === On a 64bit architecture I get linkage errors (e.g., when linking GDAL with the rasdaman driver) like "relocation R_X86_64_32 against `.bss' can not be used" === * Make sure you use the proper compiler version (see [wiki:RequiredPackages]). GNU folks have a relaxed view on backwards compatibility even with minor release changes, and we have experienced problems related to this in the past. * retry ''./configure'' with these extra flags: {{{ $ ./configure CFLAGS=-fPIC CXXFLAGS=-fPIC LDFLAGS=-fPIC ...other options... $ make install }}} === rview doesn't work in 64 bit systems === If you try to run rview and you get one of the errors: {{{ ./rview: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory }}} or {{{ ./rview: error while loading shared libraries: libXp.so.6: wrong ELF class: ELFCLASS64 }}} then you are trying to run rview with libXp.so.6 64 bit version, and rview doesn't work with it. rview is a deprecated application and, as such, one should not expect any future workaround for this problem. You can, however, run rview in 64 bits system, if you install the libXp.so.6 32 bit version. To do this: 1. add repository for 32-bit systems (optional, only necessary in more recent OS where ia32-libs is not available by default, e.g. Ubuntu 64 bits 13.10 or higher): {{{ $ sudo gedit /etc/apt/sources.list }}} add following line in the end of file: {{{ deb http://cz.archive.ubuntu.com/ubuntu raring main universe }}} 2. install `ia32-libs`: {{{ $ sudo apt-get update $ sudo apt-get install ia32-libs }}} (this will install libXp.so.6, among other 32-bit libraries) rview works, now, but if not, you can link the 32 bit library (/usr/lib32) to /usr/lib. Note: Installing lib32z1, lib32ncurses5 or lib32bz2-1.0 libs DOES NOT install libXp.so.6 === I get Java compilation errors. === * If, during '''make''', you get errors like this: {{{ javac -d bin src/org/odmg/*.java src/rasj/*.java src/rasj/global/*.java src/rasj/clientcommhttp/*.java src/rasj/odmg/*.java src/rasj/rnp/*.java Exception in thread "main" java.lang.NoSuchFieldError: java/util/zip/Inflater.strm ...many more lines... }}} then make sure you use the [http://www.oracle.com/technetwork/java/javase/overview/index-jsp-136246.html SUN Java 6 SDK] and not the IBM one (which seems to come preinstalled on some distributions, and is buggy). === After installing I cannot find the documentation in the install directory === To include PDF and HTML documentation in the build process, which takes some time to build, you have to specify explicitly `--with-docs` when invoking `./configure` == PostgreSQL == === I get a link error, function ECPGget_connection cannot be found === * What appears to have happened is that in PostgreSQL 8.3.0 they removed ECPGget_connection and they have reintroduced it by 8.3.7. So PostgreSQL versions 8.3.0 up to (but excluding) 8.3.7 cannot be used. === I want to use a different version of PostgreSQL. Is that possible? === * You need to include a different JDBC postgresql driver (as a JAR) in the libraries folder and update the Makefile as needed. Then you can try out another PostgreSQL version, it may or may not work. Let us know your experiences to update this information! === When running the script "create_db.sh", I get !''AdminIf'' related error === ...more specifically, ''Creating base RASBASE...Warning/error in AdminIf Connect: SQLSTATE: 08001 SQLCODE: -402'' There are several possible reasons: 1. '''Execution permissions.''' Run the script as the user owning the postgresql processes. Use '''only''' that user for further work with rasdaman (see Installation Guide). If you use Ubuntu and installed postgres with apt-get, then logging in as user '''postgres''' is an option; I personally like to have a separate user ''rasdaman'' for this purpose where I also can set paths etc. to the executables once and for all. (The postgres db does not allow full access to rasdaman tools, because they do not run under the administrative user that launched the db server process.) Alternatively, make sure that the operating system user under which you run `create_db.sh` can be authenticated via the '''ident''' method, which can be set in `pg_hba.conf`. E.g. if user is "rasdaman", then in `pg_hba.conf` you should have at least: {{{ # TYPE DATABASE USER CIDR-ADDRESS METHOD local all rasdaman ident }}} 2. '''Blocked incoming connections.''' Another cause of the problem might be that postgres does not allow incoming connections. If you have Postgres v8 or more recent, modify file "postgresl.conf" and set (uncomment) the option {{{ listen_addresses = 'localhost' }}} 3. '''TCP-IP connection.''' If you have Postgres v7, set (uncomment) the following option: {{{ tcpip_socket = true }}} === I get "wrong connect string" error when first running ''rasdl'' === When I first try to run rasdl (or the rasdaman server, for that matter) against PostgreSQL after installation, the log says "server ok" but "wrong connect string" * There are several possible reasons: 1. '''Port:''' Running a database cluster on a separate port requires proper setting of environment variable PGPORT to allow for communication between rasdaman and PostgreSQL. (thanks to Mario Uhlig!) 2. '''Socket directory:''' using '/var/lock/postgresql' as socket directory makes rasdl fail for a reason still to be found. Switching back to the default socket dir '/var/run/postgresql' resolves the issue. (thanks to Alexander Herzig!) === Undefined reference to 'ECPGconnect' ... === In Ubuntu you may get this error: {{{ adminif.cc:(.text+0x4b): undefined reference to `ECPGconnect' adminif.cc:(.text+0x71): undefined reference to `ECPGtrans' adminif.cc:(.text+0x80): undefined reference to `ECPGdisconnect' ../reladminif/libreladminif.a(databaseif.o): In function `DatabaseIf::disconnect()': mdddomaintype.cc:(.text+0x720): undefined reference to `ECPGdo' collect2: ld returned 1 exit status make[2]: *** [rasserver] Error 1 make[2]: Leaving directory `/home/rasdaman/rasdaman/server' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/rasdaman/rasdaman/server' make: *** [install-recursive] Error 1 }}} To fix it, set the libs explicitly at configure, e.g. {{{ ./configure --prefix=/home/rasdaman/install LIBS='-lecpg -lgdal1.7.0' }}} === Deleting big collection imported rasimport results in 'Serializable database error...' === Check the PostgreSQL log, usually it indicates that some parameters in the postgresql.conf need to be increased, along with SHMALL/SHMMAX parameters in the kernel. == Rasql queries == === I get syntax error ''unexpected name'' when using a floating point number === * Floating point numbers must have a leading zero, for example; "0.9" instead of ".9". === My query which uses ''log'' doesn't work === {{{ for c in (rgb) return encode(log(c.0), "jpeg") }}} * The '''log''' function needs positive numbers as arguments, and will return -Infinity if the argument is 0. You need to make sure that the input does not contain any zeros. You can check that using the query {{{ for c in (rgb) return count(c.0 = 0) }}} '''''Solution''''' (depending on your overall formula): Add 1 to the input: {{{ for c in (rgb) return encode(log(c.0+1), "jpeg") }}} === My insert query produces error 821 (cell type mismatch) === ... although I provide a TIFF file with correct pixel type: {{{ insert into FloatCollection values inv_tiff( $1 ) }}} * You need to provide an explicit cast (see section 9.8 in the Rasql Guide); a correct phrasing of this query is: {{{ insert into FloatCollection values (float) inv_tiff( $1 ) }}} === How do I position a replacement array when updating a collection? === * In an update statement, the slice coordinates are specified with the set operator, however the 2D position of the replacement array is defined by the spatial domain of the array, which by default is [0:width,0:height], and can be modified with the shift operator or the --mdddomain option of rasql. For example a query to update the 3D collection C with a 2D image of size 255x210 that should replace the region at interval [10, 100:355, 100:310]: {{{ update C set [10, *:*, *:*] assign shift(inv_tiff($1), [100, 100]) }}} See wiki:PartialUpdates for more details. Note that the shift vector applies to the second and third dimension (slice defined in the first dimension). === How does the Storage Layout Language work? === * Check the [attachment:sstdm2010.pdf Storage Layout Language paper] for more details, while the manual is not yet updated. === "Error: 100 Exception: Internal error: DL parse error." === What does this error returned by rasql mean? * You have likely inserted types to the database which names start with a rasdl reserved word. This is a known issue, see #121 for a workaround. === How can I import large images that don't fit into main memory? === * Check this short guide on [wiki:PartialUpdates partial updates] in addition to the documentation of the update statement in the [source:manuals_and_examples/manuals/doc-guides/ql-guide.pdf Query Language Guide for rasql]. === How to use the encode() function to export data === * Check [wiki:RasqlEncodeFunction this] short unofficial documentation until the Query Language Guide is updated. == rasdaview == === rasdaview returns an error "no suitable servers started", although I have servers available === * For historical reasons, rasdaview needs an RPC type rasserver running. See the Installation Guide for what this means and how such a server can be started. == Rasj and Java == === Overflow when unsigned bytes are retrieved with rasj === If I send the query ''select max_cells(c.0) from rgb as c'' via command line (rasql utility), then the result is 255 as expected; if I send this query via RasJ, then the result is -1. * Java does not have an 8-bit unsigned data type. Byte is a signed 8 bit and hence 255 is represented as -1. What you can do is to transform bytes to char by adding 2^8^ if the 2^7^ bit is set. Tested, works. Alternatively, cast to a larger data type on server side: {{{ select (long) max_cells(c.0) from rgb as c }}} === I get class version incompatibility error messages === I get weird error messages from the Java runtime system which seems to hint at class version incompatibilities, such as "Class version error" or "Class not found". * There might be a conflict with the locally provided libraries, to be found at directory $PETASCOPE/lib. Check them, and if you find a mismatch then remove them and use the resp. libraries of your local installation instead. Alternatively, consider upgrading your Java SDK to version 1.6. * Check that the versions `javac -version` and `java -version` match, otherwise you may get an error `Exception in thread "main" java.lang.UnsupportedClassVersionError: ..: Unsupported major.minor version 51.0` == WCPS / petascope == === Mixing trimming and slicing in WCPS fails === * A workaround until [ticket:64 this ticket] is fixed is to separate the two operations, e.g. instead of {{{ c[t(5),x(0:20),y(0:20)] }}} use {{{ (c[x(0:20),y(0:20)])[t(5)] }}} == Data formats == === HDF4 is said to be supported, but rasdaman reports an error === ...when trying to use ''hdf()'' or ''inv_hdf()'' - what can I do? * HDF4 needs to be compiled in explicitly. Re-generate rasdaman saying {{{ $ make clean $ autoreconf $ ./configure --with-hdf4 ...other options... $ make $ make install }}} === NetCDF is said to be supported, but rasdaman reports an error === ...when trying to use ''netcdf()'' or ''inv_netcdf()'' - what can I do? * NetCDF needs to be compiled in explicitly. Re-generate rasdaman saying {{{ $ make clean $ autoreconf $ ./configure --with-netcdf ...other options... $ make $ make install }}} Supported NetCDF library version is 4.0+. It provides netcdf4 (including HDF, classic, and 64) and netcdf3 (as the API is backwards compatible). Limitations: only atomic cell types, but no struct types are supported at this moment; and metadata are not preserved (they have to be stored separately in PostgreSQL tables) === The NetCDF generated by rasdaman is not recognized by NetCDF tools === * THe issue probably has to do with the pixel type. The 'char' type in rasdaman corresponds with the 'byte' type in netcdf. In netcdf, the 'char' type is used for the 8-bit characters intended for representing text. Therefore, the netcdf(char) result is in binary instead of ASCII. However, the netcdf(char) result is [http://cf-pcmdi.llnl.gov/conformance/compliance-checker/ validated against the compliance checker]. Note: netcdf(float) works fine. == Helping == === I want to submit a patch, how do I do this? === 1. Set your credentials (ie, your name, YOUR_FULL_NAME, and email address, EMAIL): {{{ $ git config user.name "YOUR_FULL_NAME" $ git config user.email EMAIL }}} 1. rasdaman must be configured and compiled with `--enable-strict` to make sure that your patch doesn't introduce new warnings. 1. When you commit your changes to your local copy put a meaningful message: {{{ $ git commit file1 file2 ... -m "ticket:NUMBER - commit message" }}} The subject of the patch '''must''' start with "!ticket:NUMBER - ", where NUMBER is a valid ticket number on this trac. For example this is a valid subject: "ticket:231 - subject message...". To manually fix the subject after you have created the patch, edit the patch manually and adapt the ''Subject:'' line, e.g. from {{{ Subject: [PATCH] invalid subject }}} to the below (make sure to not remove the [PATCH] part!) {{{ Subject: [PATCH] ticket:NUMBER - commit message }}} It's best to '''always''' specify exactly the files that you want to commit, instead of committing everything with the `-a` option, so that you avoid submitting unnecessary changes in your patch. 1. Then you can make the patch, e.g: {{{ $ git format-patch HEAD~1 }}} 1. Finally you can submit the generated patch to the [http://rasdaman.org/trac/rasdaman/patchmanager/ rasdaman patchmanager] '''Important:''' avoid submitting generated files like ''configure, Makefile.in'', etc. in your patch, unless the corresponding source (configure.ac, Makefile.am, ...) has been really modified. === How to report a bug/problem === It's best if you report bugs by filling a [http://rasdaman.org/trac/rasdaman/newticket new ticket]. It's always good to include as much as possible information of the setup in which the bug occurred, so we can reproduce it. In general you should include: * gcc --version * OS and architecture * how was rasdaman configured/compiled * versions of PostgreSQL's or any other libraries that may be relevant * relevant parts of the server log files To open a new ticket, you need an account in the trac system: please request one via one of our [MailingLists mailing lists]. === Why do I have to accept the [wiki:ContributorAgreement Rasdaman Contribution Agreement] when providing a patch? === Because [wiki:License for legal reasons] the project must have a trackable code provenance.