- users-list - monetdb.org

[MonetDB-users] Error during making buildtools (branch MonetDB_1-18)
by Ying Zhang 06 Jun '07

06 Jun '07

Hi all, I have just checked out the release branch and try to rebuild everything from scratch (on andorea). Making buildtools gives the following error: Making install in conf make[1]: Entering directory `/export/scratch1/zhang/monet/stable/buildtools/build-debug/conf' make[1]: *** No rule to make target `buildtools-config', needed by `all-am'. Stop. make[1]: Leaving directory `/export/scratch1/zhang/monet/stable/buildtools/build-debug/conf' make: *** [install-recursive] Error 1 Does anyone have an idea about this? I believe that building environment is clean. Thanks! Jennie

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[MonetDB-users] building monetdb5 on windows
by Colin Foss 05 Jun '07

05 Jun '07

Are there any plans to create a script similar to monetdb-install.sh for Windows?

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[MonetDB-users] XRPC problem: too many parameters
by Makoto YUI 02 Jun '07

02 Jun '07

Hi, I caught an error (see attached file) at the remote method invocation of XRPC. While I'm not sure whether my query is correct or not, is there imitation of parameters in XRPC? The query and dataset used in the evaluation are put on here. http://db-www.naist.jp/~makoto-y/tmp/xrpc.tgz Thanks, Makoto YUI P.S. To: list-admin please ignore previous mail from wrong address MAPI = monetdb@localhost:50000 QUERY = import module namespace test = "xrpc-test-function" at "/usr/share/MonetDB/xrpc/export/xrpc-mod.xq"; (: local database :) declare variable $blast-gb := fn:doc("blast-gb.xml")/result; declare variable $blast-uniprot := fn:doc("blast-uniprot.xml")/result; (: remote basebase :) declare variable $remote-endpoint := "xanadu.naist.jp"; let $gb_entry := (for $e in $blast-gb/BlastOutput let $hit := $e/BlastOutput_iterations/Iteration/Iteration_hits/Hit ERROR = !WARNING: doLoopLiftedRPC: error occurred during RPC call to "xanadu.naist.jp" !ERROR: CMDhttp_post: too many parameters. !ERROR: CMDhttp_post: operation failed. MAPI = monetdb@localhost:50000 QUERY = import module namespace test = "xrpc-test-function" at "/usr/share/MonetDB/xrpc/export/xrpc-mod.xq"; (: local database :) declare variable $blast-gb := fn:doc("blast-gb.xml")/result; declare variable $blast-uniprot := fn:doc("blast-uniprot.xml")/result; (: remote basebase :) declare variable $remote-endpoint := "xanadu.naist.jp"; let $gb_entry := (for $e in $blast-gb/BlastOutput let $hit := $e/BlastOutput_iterations/Iteration/Iteration_hits/Hit ERROR = !ERROR: doLoopLiftedRPC: execution failed at all destinations mapi_query_part:1705:import module namespace test = "xrpc-test-function" at "/usr/share/MonetDB/xrpc/export/xrpc-mod.xq"; (: local database :) declare variable $blast-gb := fn:doc("blast-gb.xml")/result; declare variable $blast-uniprot := fn:doc("blast-uniprot.xml")/result; (: remote basebase :) declare variable $remote-endpoint := "xanadu.naist.jp"; let $gb_entry := (for $e in $blast-gb/BlastOutput let $hit := $e/BlastOutput_iterations/Iteration/Iteration_hits/Hit where $hit/Hit_num = 1 and $hit/Hit_hsps/Hsp/Hsp_evalue/text() <= 1.0e-8 return $e), $uniprot_entry := (for $e in $blast-uniprot/BlastOutput let $hit := $e/BlastOutput_iterations/Iteration/Iteration_hits/Hit where $hit/Hit_num = 1 and $hit/Hit_hsps/Hsp/Hsp_evalue/text() <= 1.0e-8 return $e) where $gb_entry/BlastOutput_query-def/text() = $uniprot_entry/BlastOutput_query-def/text() return <result> { let $gb-hit := $gb_entry/BlastOutput_iterations/Iteration/Iteration_hits/Hit, $gb-key := $gb-hit/Hit_gb/text() return let $genbank-remote-entries := execute at {$remote-endpoint} { test:q1($gb-key) } for $remote_entry at $pos in $genbank-remote-entries let $gb_definition := $remote_entry/INSDSeq_definition, $gb_feature := $remote_entry/INSDSeq_feature-table/INSDFeature, $blast_evalue := $gb-hit[Hit_gb/text() = $remote_entry/INSDSeq_accession-version/text()]/Hit_hsps/Hsp/Hsp_evalue return <genbank num="{ $pos }">{ $blast_evalue, $gb_definition, $gb_feature } </genbank> } </result> fetch next block: start at:2 got next block: length:269 text:XRPC_Client_Serialisation: 626 microsec !WARNING: doLoopLiftedRPC: error occurred during RPC call to "xanadu.naist.jp" !ERROR: CMDhttp_post: too many parameters. !ERROR: CMDhttp_post: operation failed. !ERROR: doLoopLiftedRPC: execution failed at all destinations got complete block: text:XRPC_Client_Serialisation: 626 microsec !WARNING: doLoopLiftedRPC: error occurred during RPC call to "xanadu.naist.jp" !ERROR: CMDhttp_post: too many parameters. !ERROR: CMDhttp_post: operation failed. !ERROR: doLoopLiftedRPC: execution failed at all destinations read_line:XRPC_Client_Serialisation: 626 microsec allocating new result set XRPC_Client_Serialisation: 626 microsec got complete block: text:!WARNING: doLoopLiftedRPC: error occurred during RPC call to "xanadu.naist.jp" !ERROR: CMDhttp_post: too many parameters. !ERROR: CMDhttp_post: operation failed. !ERROR: doLoopLiftedRPC: execution failed at all destinations read_line:!WARNING: doLoopLiftedRPC: error occurred during RPC call to "xanadu.naist.jp" allocating new result set got complete block: text:!ERROR: CMDhttp_post: too many parameters. !ERROR: CMDhttp_post: operation failed. !ERROR: doLoopLiftedRPC: execution failed at all destinations read_line:!ERROR: CMDhttp_post: too many parameters. got complete block: text:!ERROR: CMDhttp_post: operation failed. !ERROR: doLoopLiftedRPC: execution failed at all destinations read_line:!ERROR: CMDhttp_post: operation failed. got complete block: text: !ERROR: doLoopLiftedRPC: execution failed at all destinations read_line: closing result set got complete block: text:!ERROR: doLoopLiftedRPC: execution failed at all destinations read_line:!ERROR: doLoopLiftedRPC: execution failed at all destinations allocating new result set fetch next block: start at:271 got next block: length:0 text: got complete block: text: read_line: closing result set closing result set Timer 1014.527 msec

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[MonetDB-users] Data Load Issue
by Venks 01 Jun '07

01 Jun '07

Hi, I am trying to load a 12.8 Million row table using COPY command. The table has about 256 columns. After 4 or 5 hours of running, the server terminated abruptly. I am running this on a AMD 64 Bit running Redhat Linux with 3GB of memory and lots of swap space. Any help in identifying the issue would be appreciated. Thanks, - Venks

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Re: [MonetDB-users] Autoconf error for /MonetDB4-XQuery/pathfinder module
by Fabian Groffen 30 May '07

30 May '07

On 30-05-2007 13:28:39 +0200, Ingmar Weber wrote: >> What filesystem are you running stuff on? Do you build in your sources? >> Is your clock set correctly? Do you use NFS by chance? > > Yes, I'm building things on an NFS filesystem. I'm building everything from > the tarball that's downloadable. I get the same error message independent > of running the monetdb-install.sh (or something like this) or by running > configure/make/make install by hand. > > The system clock seems to be working fine as far as I can tell. At least > I've never had problems with it (or when using SVN or CVS). > > Is NFS a known source of trouble? Then I could try installing it again on a > local hard drive. If the clock of the NFS server is out of sync with your local clock, make can get confused. Try building on local (/var/tmp?) disk space to avoid this. I hope that solves it. Also, if you copy the sources, make sure you preserve the mtimes of the original, e.g. by using cp -pPR or rsync -a.

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Re: [MonetDB-users] Autoconf error for /MonetDB4-XQuery/pathfinder module
by Fabian Groffen 30 May '07

30 May '07

On 30-05-2007 12:07:26 +0200, Ingmar Weber wrote: > > This looks very much like a problem with perl on your machine. > > Quite possibly. Any detailed suggestions? I'm just not quite sure, what > exactly is wrong and how I could fix it. (e.g. by somehow telling MonetDB > to look for Perl related things there rather than there etc.) I'm not familiar with Debian and Perl, but I think something is just looking at a wrong architecture or in another place than it reports. > The output is this: > /amd64/usr/lib/perl/5.8/auto/Data/Dumper/Dumper.so: ELF 64-bit LSB shared > object, AMD x86-64, version 1 (SYSV), stripped Looks normal to me. > > Apart from this issue, it appears strange to me that autoconf/automake > are being used. > > Well, strictly speaking the error is caused by this line in the (generated) > Makefile: > cd . && /bin/sh > /local/var/tmp/MonetDB-1180453562/MonetDB4-XQuery/pathfinder/conf/missing > --run autoconf It shouldn't do this, IMO. Running autoconf should only be done if configure has to be regenerated, which it does not have to. > But this script (.../conf/missing --run autoconf) behaves exactly like > autoconf. The error message is the same, independent of whether I run the > Makefile or type autconf by hand. What filesystem are you running stuff on? Do you build in your sources? Is your clock set correctly? Do you use NFS by chance?

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[MonetDB-users] Autoconf error for /MonetDB4-XQuery/pathfinder module
by Ingmar Weber 30 May '07

30 May '07

Hey, When I try to install monetdb (either using the monetdb-install.sh script or the configure/make/make install mechanism in each directory) I get the following error for the MonetDB4-XQuery module: ----- this error occurs at the beginning of the 'make', caused by automake ---- Can't load '/amd64/usr/lib/perl/5.8/auto/Data/Dumper/Dumper.so' for module Data::Dumper: /amd64/usr/lib/perl/5.8/auto/Data/Dumper/Dumper.so: cannot open shared object file: No such file or directory at /amd64/usr/lib/perl/5.8/XSLoader.pm line 68. at /amd64/usr/lib/perl/5.8/Data/Dumper.pm line 27 Compilation failed in require at /usr/share/autoconf/Autom4te/C4che.pm line 35. BEGIN failed--compilation aborted at /usr/share/autoconf/Autom4te/C4che.pm line 35. Compilation failed in require at /usr/bin/autom4te line 39. BEGIN failed--compilation aborted at /usr/bin/autom4te line 39. ---------------- Note that the /amd64/usr/lib/perl/5.8/* files all exist in the places named above! Still, it generates the "No such file or directory". --------------------------------- Line 68 (and surroundings) of XSLoader.pm reads as: # Many dynamic extension loading problems will appear to come from # this section of code: XYZ failed at line 123 of DynaLoader.pm. # Often these errors are actually occurring in the initialisation # C code of the extension XS file. Perl reports the error as being # in this perl code simply because this was the last perl code # it executed. my $libref = dl_load_file($file, 0) or do { require Carp; Carp::croak("Can't load '$file' for module $module: " . dl_error()); }; push(@dl_librefs,$libref); # record loaded object --------------------------------- --------------------------------- Line 27 of Dumper.pm reads as: XSLoader::load 'Data::Dumper'; --------------------------------- The error above I also get when I simply type "automake". I currently suspect some 32 bit vs. 64 bit problem, as the machine I'm compiling things on (2x Dual-Core AMD Opteron Processor 2220 SE) can run in either 32 or 64 bit mode. uname outputs: "2.6.16.29.2.amd64-smp" Any (other) ideas? Should I post some other debug information? The output of "configure" is posted below. The other packages of (Monet DB Common etc.) run through smoothly. THANKS! Ingmar ------------- output of "configure" for MonetDB4-XQuery/pathfinder ----- iweber@dork:/scratch/KM/ir-scratch/ingmar/MonetDB-SuperBall/MonetDB-Venus-SuperBall-SR1/MonetDB4-XQuery/pathfinder [10083] ./configure --prefix='/scratch/KM/ir-scratch/ingmar/MonetDB-SuperBall/installation/' --enable-optimize --disable-debug --with-libxml2=/amd64/usr checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking target system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /amd64/usr/bin//install -c checking whether build environment is sane... yes checking for gawk... /usr/bin/gawk checking whether make sets $(MAKE)... yes checking for monetdb-config... /scratch/KM/ir-scratch/ingmar/MonetDB-SuperBall/installation/bin/monetdb-config checking whether MonetDB Common version 1.16.2 or newer is installed... yes: found version 1.16.2 checking for style of include used by make... GNU checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking dependency style of gcc... none checking for egrep... grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking how to run the C preprocessor... gcc -E checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ANSI C... (cached) none needed checking dependency style of gcc... (cached) none checking for long... yes checking size of long... 8 checking whether byte ordering is bigendian... no checking which Linux distribution we're using... Debian3.1 checking if your compiler is C99 compliant... yes checking for ant... no checking for java... no checking for javac... no checking for jar... no checking for javadoc... no checking for monetdb4-config... /scratch/KM/ir-scratch/ingmar/MonetDB-SuperBall/installation/bin/monetdb4-config checking whether MonetDB4 version 4.16.2 or newer is installed... yes: found version 4.16.2 checking for monetdb-clients-config... /scratch/KM/ir-scratch/ingmar/MonetDB-SuperBall/installation/bin/monetdb-clients-config checking whether MonetDB Clients version 1.16.2 or newer is installed... yes: found version 1.16.2 checking for a sed that does not truncate output... /amd64/bin//sed checking for option to reload object files... -r checking for BSD-compatible nm... /amd64/usr/bin//nm -B checking whether ln -s works... yes checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for g77... no checking for f77... no checking for xlf... no checking for frt... no checking for pgf77... no checking for fort77... no checking for fl32... no checking for af77... no checking for f90... no checking for xlf90... no checking for pgf90... no checking for epcf90... no checking for f95... no checking for fort... no checking for xlf95... no checking for ifc... no checking for efc... no checking for pgf95... no checking for lf95... no checking for gfortran... no checking whether we are using the GNU Fortran 77 compiler... no checking whether accepts -g... no checking for flex... no checking for lex... no checking for yywrap in -lfl... no checking for yywrap in -ll... no checking for a BSD-compatible install... /amd64/usr/bin//install -c checking for ld used by gcc... ld -IPA -m elf_x86_64 checking if the linker (ld -IPA -m elf_x86_64) is GNU ld... yes checking the maximum length of command line arguments... 32768 checking command to parse /amd64/usr/bin//nm -B output from gcc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if gcc static flag works... yes checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC checking if gcc PIC flag -fPIC works... yes checking if gcc supports -c -o file.o... yes checking whether the gcc linker (ld -IPA -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no configure: creating libtool appending configuration tag "CXX" to libtool checking for ld used by g++... ld -IPA -m elf_x86_64 checking if the linker (ld -IPA -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (ld -IPA -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC checking if g++ PIC flag -fPIC works... yes checking if g++ supports -c -o file.o... yes checking whether the g++ linker (ld -IPA -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes appending configuration tag "F77" to libtool checking for ANSI C header files... (cached) no checking whether time.h and sys/time.h may both be included... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking alloca.h usability... yes checking alloca.h presence... yes checking for alloca.h... yes checking getopt.h usability... yes checking getopt.h presence... yes checking for getopt.h... yes checking netdb.h usability... yes checking netdb.h presence... yes checking for netdb.h... yes checking for sys/types.h... (cached) yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGE_FILES value needed for large files... no checking for an ANSI C-conforming const... yes checking for size_t... yes checking return type of signal handlers... void checking for ptrdiff_t... yes checking for ssize_t... yes checking for __int64... no checking for long long... yes checking for char... yes checking size of char... 1 checking for short... yes checking size of short... 2 checking for int... yes checking size of int... 4 checking for long... (cached) yes checking size of long... (cached) 8 checking for void *... yes checking size of void *... 8 checking for size_t... (cached) yes checking size of size_t... 8 checking for ssize_t... (cached) yes checking size of ssize_t... 8 checking for ptrdiff_t... (cached) yes checking size of ptrdiff_t... 8 checking for long long... (cached) yes checking size of long long... 8 checking for __int64... (cached) no checking size of __int64... 0 checking for ftruncate... yes checking for gettimeofday... yes checking for opendir... yes checking whether ln -s works... yes checking for rm... rm -f checking for mv... mv -f checking for lockfile... echo checking for bash... /bin/sh checking for rpmbuild... no checking for rpm... no checking for an ANSI C-conforming const... (cached) yes checking for inline... inline checking for python... no checking for perl... /amd64/usr/bin//perl checking for objc... no checking pthread.h usability... yes checking pthread.h presence... yes checking for pthread.h... yes checking semaphore.h usability... yes checking semaphore.h presence... yes checking for semaphore.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sem_init in -lpthreadGC2... no checking for sem_init in -lpthreadGC1... no checking for sem_init in -lpthreadGC... no checking for sem_init in -lpthread... yes checking for pthread_sigmask in -lpthread... yes checking for pthread_kill_other_threads_np in -lpthread... no checking readline/readline.h usability... yes checking readline/readline.h presence... yes checking for readline/readline.h... yes checking for readline in -lreadline... yes checking for rl_completion_matches in -lreadline... yes checking for SSL_read in -lssl... no checking for ERR_get_error in -lcrypto... no checking for dlopen in -ldl... yes checking for malloc in -lmalloc... no checking for mallopt... yes checking for mallinfo... yes checking for gethostbyname_r... yes checking for setsockopt... yes checking for SOCKET... no checking for socklen_t... yes checking for libz... auto checking for libbz2... auto checking for getopt_long... yes checking libperfctr.h usability... no checking libperfctr.h presence... no checking for libperfctr.h... no checking libpperf.h usability... no checking libpperf.h presence... no checking for libpperf.h... no checking pcl.h usability... no checking pcl.h presence... no checking for pcl.h... no checking for pcre-config... no pcre-config not found; please use --with-pcre=<path> checking for pcre >= 4.5... no (without pcre-config to query the pcre version, we assume it's < 4.5) checking regex.h usability... yes checking regex.h presence... yes checking for regex.h... yes checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking langinfo.h usability... yes checking langinfo.h presence... yes checking for langinfo.h... yes checking for nl_langinfo... yes checking for setlocale... yes checking iconv.h usability... yes checking iconv.h presence... yes checking for iconv.h... yes checking for iconv_t... yes checking for iconv in -liconv... no checking for libiconv in -liconv... no checking for iconv... yes checking for texi2html... no checking for latex2html... no checking for latex... no checking for pdflatex... no checking for dvips... no checking for fig2dev... no checking postscript option... eps checking /amd64/usr/bin//install -c --backup option... --backup=nil checking for php-config... no Cannot find php-config. Please use --with-php-config=PATH no checking for monetdb5-config... no checking whether gcc and cc understand -c and -o together... yes checking for unistd.h... (cached) yes checking for getopt.h... (cached) yes checking for getopt_long... (cached) yes checking stdbool.h usability... yes checking stdbool.h presence... yes checking for stdbool.h... yes checking for bool... no checking for stdint.h... (cached) yes checking for socklen_t... (cached) yes checking libgen.h usability... yes checking libgen.h presence... yes checking for libgen.h... yes checking for basename... yes checking for int... (cached) yes checking size of int... (cached) 4 checking for void *... (cached) yes checking size of void *... (cached) 8 checking if your compiler understands `__attribute__'... yes checking signal.h usability... yes checking signal.h presence... yes checking for signal.h... yes checking return type of signal handlers... (cached) void checking for strings.h... (cached) yes checking for strcasecmp... yes checking for xml2-config.64... no checking for xml2-64-config... no checking for xml2-config... /amd64/usr/bin/xml2-config checking for libxml/parser.h... yes checking for xmlParseDocument in -lxml2... yes checking libxml/SAX2.h usability... yes checking libxml/SAX2.h presence... yes checking for libxml/SAX2.h... yes configure: The following compiler options will be used to integrate the libxml2 XML parsing library: To find the libxml2 include files: -I/usr/include/libxml2 To find the libxml2 library: -L/amd64/usr/lib64 -L/usr/lib -lxml2 -lz -lpthread -lm SAX2 support: HAVE_SAX2=1 checking for string.h... (cached) yes checking for strdup... yes checking for strtok_r... yes checking time.h usability... yes checking time.h presence... yes checking for time.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking utime.h usability... yes checking utime.h presence... yes checking for utime.h... yes checking sys/utime.h usability... no checking sys/utime.h presence... no checking for sys/utime.h... no checking sys/times.h usability... yes checking sys/times.h presence... yes checking for sys/times.h... yes checking whether time.h and sys/time.h may both be included... (cached) yes checking whether struct tm is in sys/time.h or time.h... time.h checking for struct tm.tm_zone... no checking for tzname... yes checking whether utime accepts a null argument... yes checking for ftime... yes checking for times... yes checking for ctime_r... yes checking for localtime_r... yes checking ctime_r3... no configure: creating ./config.status config.status: creating Makefile config.status: creating MonetDB-XQuery.spec config.status: creating RunMapprove config.status: creating RunMapprove.bat config.status: creating RunMtest config.status: creating RunMtest.bat config.status: creating extra.mk config.status: creating rpm.mk config.status: creating compiler/Makefile config.status: creating conf/Makefile config.status: creating modules/Makefile config.status: creating runtime/Makefile config.status: creating runtime5/Makefile config.status: creating src/Makefile config.status: creating compiler/algebra/Makefile config.status: creating compiler/core/Makefile config.status: creating compiler/debug/Makefile config.status: creating compiler/include/Makefile config.status: creating compiler/mem/Makefile config.status: creating compiler/mil/Makefile config.status: creating compiler/parser/Makefile config.status: creating compiler/schema/Makefile config.status: creating compiler/semantics/Makefile config.status: creating compiler/sql/Makefile config.status: creating modules/pftijah/Makefile config.status: creating runtime/xrpc/Makefile config.status: creating src/tools/Makefile config.status: creating compiler/algebra/map/Makefile config.status: creating compiler/algebra/opt/Makefile config.status: creating compiler/algebra/prop/Makefile config.status: creating runtime/xrpc/admin/Makefile config.status: creating runtime/xrpc/export/Makefile config.status: creating pf_config.h config.status: pf_config.h is unchanged config.status: executing depfiles commands

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[MonetDB-users] MonetDB Release Preparation
by Martin Kersten 29 May '07

29 May '07

Dear fellow MonetDB developers/users, we plan to have a new release of the MonetDB software family within the next two weeks, i.e., Feature Freeze: Friday Jun 01 2007 Release: Monday Jun 11 2007 This release cycle is used to reduce the component dependencies, such that we are better prepared to release individual components more frequently. A synopsis of what to expect: MonetDB 5 beta status is dropped and it becomes the sole back-end for the SQL front-end. SQL now supports Persistent Stored Modules. XQuery Update Facility has undergone a large series of stress tests to improve correctness, performance and robustness against concurrent updates. Many bug-fixes based on highly appreciated feedback from our user community. The priorities set for post-release actions as agreed upon by the development team are: shortterm:(summer) SQL GIS geometry model testing and release SQL/XML support development and release PF/SQL exploration (research focus) Skyserver demo website (target 2.7TB online demo) midterm: (fall) Remote SQL execution in a cluster setting SQL adaptive partitioning of large databases XQuery Algebra -> MIL compiler Date/time support in XQuery MonetDB Private BATs policy (kernel modification) lngterm: (fall/spring) XQuery Algebra -> MAL compiler public release of StreetTivo for collaborative media analysis Of course, as always, progress in each of these areas depend on availability of resources and their contribution to our research agenda. We are looking forward to messages from projects based on/exploitation of the MonetDB platform. We plan to add a section in the website to make this work more broadly visible. regards, Martin

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Re: [MonetDB-users] Compile problems (CVS, Ubuntu 7.04) (Java Client JDBC Version)
by Ramon Nogueira 27 May '07

27 May '07

OK, actually going to use CVS, since that's probably easier. Just a point about compiling the Java client (which as far as I can tell, is required for install MonetDB4-server): it doesn't compile with the version of JDBC shipped in Sun JDK 6. Basically, the JDBC interfaces have been extended and so we get errors about 'class is not abstract and does not override method ...'. I fixed this the first time by adding stubs that just threw OperationNotSupportedException. Then it compiled. R. On 5/27/07, Ramon Nogueira <ramon.nogueira(a)gmail.com> wrote: > Hehe, ok I can't resist. Gonna try again with the install script and > the tricks to prevent downloading again and again. I have clean all > traces of MonetDB from my machine. If you can't provide a .deb, what > about a precompiled set of binaries for generic Linux, statically > linked with all dependencies. Its not pretty, but it would be easy for > the users. The problem with the rpms on my Ubuntu system is basically > that Debian uses a different versioning scheme for the shared > libraries (the ones I had problems with were libssl and libcrypto). > Couldn't you just statically link these in and then provide a simple > install script? Many, many people use Debian-based systems and it > would greatly improve coverage for MonetDB. I will do what I can to > help if this compile goes well. > > R. > > On 5/26/07, Stefan Manegold <Stefan.Manegold(a)cwi.nl> wrote: > > Ramon, > > > > once you have time and bandwidth, could you please first remove any remains > > of MonetDB (sources, builddirs, anything installed in you chosen prefix of > > buildtools, MonetDB, clinerts, MonetDB4, pathfinder, etc.), > > and then try from scratch, again, the way you prefer to install MonetDB. > > Stop as soon as the first problem occurs (if any ;-)) and report it here. > > > > Unfortunaltely, we do not have (access to) any Debian and/or Ubuntu > > (anymore), hence, we cannot provide any .deb packages. > > > > Kind regards, > > > > Stefan > > > > > > On Sat, May 26, 2007 at 10:24:55AM +0200, Ramon Nogueira wrote: > > > Yup, first I tried installing from the "Super Source Tarball"; then > > > from `alien'ed rpm; then individual tarballs; the install script; then > > > CVS! The problem with the install script is that it downloads things > > > afresh each time and I really can't afford that (I am in South Africa > > > where unfortunately, we still need to think about bandwidth). Here is > > > the (different) error I get when I try to compile the pathfinder > > > source tarball from sourceforge (against CVS components): > > > > > > gcc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I/usr/local/include/MonetDB > > > -I/usr/local/include/MonetDB/common -I/usr/local/include/MonetDB/gdk > > > -I/usr/local/include/MonetDB4 -I/usr/local/include/MonetDB4/monet > > > -I/usr/local/include/MonetDB4/plain > > > -I/usr/local/include/MonetDB4/contrib > > > -I/usr/local/include/MonetDB4/mapi > > > -I/usr/local/include/MonetDB4/calibrator -I/usr/include/libxml2 > > > -I../compiler/include -I./../compiler/include -DLIBPATHFINDER -O2 > > > -std=c99 -O6 -fomit-frame-pointer -finline-functions -falign-loops=4 > > > -falign-jumps=4 -falign-functions=4 -fexpensive-optimizations > > > -funroll-loops -frerun-cse-after-loop -frerun-loop-opt > > > -Wno-declaration-after-statement -DEMBEDDED -DMT -DNO_CGI -DNO_AUTH > > > -DIO_MAX=10240 -c pathfinder.c -fPIC -DPIC -o > > > .libs/lib_pathfinder_la-pathfinder.o > > > /export/scratch0/monet/monet.GNU.64.64.d.14791/pathfinder/runtime/pathfinder.mx: > > > In function 'xquery_function_call': > > > /export/scratch0/monet/monet.GNU.64.64.d.14791/pathfinder/runtime/pathfinder.mx:3980: > > > error: expected ')' before 'LLFMT' > > > /export/scratch0/monet/monet.GNU.64.64.d.14791/pathfinder/runtime/pathfinder.mx:5417:34: > > > error: macro "MT_init_lock" requires 2 arguments, but only 1 given > > > /export/scratch0/monet/monet.GNU.64.64.d.14791/pathfinder/runtime/pathfinder.mx: > > > In function 'xquery_prelude': > > > /export/scratch0/monet/monet.GNU.64.64.d.14791/pathfinder/runtime/pathfinder.mx:5417: > > > error: 'MT_init_lock' undeclared (first use in this function) > > > /export/scratch0/monet/monet.GNU.64.64.d.14791/pathfinder/runtime/pathfinder.mx:5417: > > > error: (Each undeclared identifier is reported only once > > > /export/scratch0/monet/monet.GNU.64.64.d.14791/pathfinder/runtime/pathfinder.mx:5417: > > > error: for each function it appears in.) > > > /export/scratch0/monet/monet.GNU.64.64.d.14791/pathfinder/runtime/pathfinder.mx:5418:32: > > > error: macro "MT_init_lock" requires 2 arguments, but only 1 given > > > /export/scratch0/monet/monet.GNU.64.64.d.14791/pathfinder/runtime/pathfinder.mx:5419:31: > > > error: macro "MT_init_lock" requires 2 arguments, but only 1 given > > > make[4]: *** [lib_pathfinder_la-pathfinder.lo] Error 1 > > > make[4]: Leaving directory > > > `/home/ramon/software/monetdb/pathfinder-0.16.2/runtime' > > > make[3]: *** [all-recursive] Error 1 > > > make[3]: Leaving directory > > > `/home/ramon/software/monetdb/pathfinder-0.16.2/runtime' > > > make[2]: *** [all] Error 2 > > > make[2]: Leaving directory > > > `/home/ramon/software/monetdb/pathfinder-0.16.2/runtime' > > > make[1]: *** [all-recursive] Error 1 > > > make[1]: Leaving directory `/home/ramon/software/monetdb/pathfinder-0.16.2' > > > make: *** [all] Error 2 > > > > > > > > > On 5/26/07, Stefan Manegold <Stefan.Manegold(a)cwi.nl> wrote: > > > > Hi Ramon, > > > > > > > > On Sat, May 26, 2007 at 08:37:26AM +0200, Ramon Nogueira wrote: > > > > > Thanks for such a rapid response! > > > > > > > > welcome --- you were just "lucky" ;-) > > > > > > > > > I checked out the source from CVS (including buildtools, I forgot to > > > > > mention that) with the following command: > > > > > cvs -d:pserver:anonymous@monetdb.cvs.sourceforge.net:/cvsroot/monetdb > > > > > checkout (buildtools|MonetDB|MonetDB4|pathfinder}. > > > > > > > > looks good (well, I'm sure you also included clients, as you mentioned in > > > > your first email). > > > > > > > > > I'm not too savvy wrt CVS, so not sure if this represents the latest code. > > > > > > > > It is --- well, provided SourceForge does not run the anonymous pserver > > > > access on backup server that run behind (again), but even then the > > > > conpilation should work fine ... > > > > > > > > > For calling configure, I did not specify any other command line > > > > > parameters (just ./configure). I created separate build directories > > > > > build/MonetDB, build/pathfinder... and issued the ./configure and make > > > > > commands in those directories after doing ./bootstrap in the source > > > > > directories. I also tries following the instructions in the file > > > > > pathfinder/INSTALL which instructed me to do the configure/make in the > > > > > same directory as the source with the same error. > > > > > > > > sounds just right --- hence, I'm puzzled; I have no idea, yet(?), what > > > > causes this problem (i.e., where the bogus path > > > > /export/scratch1/monet/monet.GNU.32.32.d.14791/MonetDB/.GNU.32.32.d-Fedora6/ > > > > come from... > > > > > > > > Do you by any chance have a previous source (CVS or tarball) or binary (RPM) > > > > installation of MonetDB on your machine? Possibly even the remains of an > > > > uncomplete/aborted/failed RPM installation? > > > > > > > > Stefan > > > > > > > > > > > > > On 5/26/07, Stefan Manegold <Stefan.Manegold(a)cwi.nl> wrote: > > > > > > Hi Ramon, > > > > > > > > > > > > thank you very much for using MonetDB, and sorry for the inconvenience with > > > > > > compiling pathfinder. > > > > > > > > > > > > The error looks indeed strange. Actually it make me wonder whether you > > > > > > indeed (try to) compile the CVS code base (and if so which one, the latest > > > > > > HEAD or some release branch?) or whether you are using the source tarballs? > > > > > > Of course, `bootstrap` is only required for the CVS version, but you do not > > > > > > mention buildtools, which is also required (only) for the CVS version. > > > > > > The requested but not found path > > > > > > (/export/scratch1/monet/monet.GNU.32.32.d.14791/MonetDB/.GNU.32.32.d-Fedora6/lib/libbat.la) > > > > > > is (as far as I can see) not contained in our CVS source base (except from > > > > > > some testing stable output), but *might* be in the source tarballs (though > > > > > > it should be ignored there. > > > > > > > > > > > > To analyse the problem further could you please send us the complete > > > > > > commandlines of you `configure` call for buildtools, MonetDB, clients, > > > > > > MonetDB4 & pathfinder? > > > > > > > > > > > > Kind regards > > > > > > > > > > > > Stefan > > > > > > > > > > > > > > > > > > On Sat, May 26, 2007 at 07:58:05AM +0200, Ramon Nogueira wrote: > > > > > > > Hi, > > > > > > > > > > > > > > Trying to install MonetDB4 and pathfinder from CVS. I succeeded in > > > > > > > compiling and installing (into /usr/local) MonetDB, client and > > > > > > > MonetDB4 modules. `bootstrap' and `configure' both succeed from > > > > > > > pathfinder, but `make' produces the following error. Also, on another > > > > > > > note, I think it should be made clearer that installation of `client' > > > > > > > is a prerequisite for MonetDB4 server since this is quite a > > > > > > > counterintuitive order of dependency (server on client). I am on Linux > > > > > > > 2.6.20-15-generic i686 GNU/Linux. > > > > > > > > > > > > > > Output from `make': > > > > > > > --------------------------------------------------------------------------- > > > > > > > (cd .libs && rm -f libpf.la && ln -s ../libpf.la libpf.la) > > > > > > > /bin/bash ../libtool --tag=CC --mode=link gcc -DLIBPF_SUPPORT -g > > > > > > > -O2 -Wall -Wextra -std=c99 -Werror-implicit-function-declaration > > > > > > > -Werror -Wpointer-arith -Wdeclaration-after-statement > > > > > > > -Wno-declaration-after-statement -DEMBEDDED -DMT -DNO_CGI -DNO_AUTH > > > > > > > -DIO_MAX=10240 -o lib_pf_support.la -rpath > > > > > > > /usr/local/lib/MonetDB4/lib lib_pf_support_la-pf_support.glue.lo > > > > > > > lib_pf_support_la-pf_support.lo lib_pf_support_la-staircasejoin.lo > > > > > > > lib_pf_support_la-prec_foll.lo lib_pf_support_la-shredder.lo > > > > > > > libserialize.la libpf.la -lxml2 -L/usr/lib -lxml2 -ldl > > > > > > > -L/usr/local/lib -lbat -lstream -L/usr/local/lib -lmonet -lpthread > > > > > > > -L/usr/local/lib/MonetDB4/lib -l_lock -l_monettime -l_streams > > > > > > > -l_builtin -l_ascii_io -l_algebra -l_constant > > > > > > > gcc -shared .libs/lib_pf_support_la-pf_support.glue.o > > > > > > > .libs/lib_pf_support_la-pf_support.o > > > > > > > .libs/lib_pf_support_la-staircasejoin.o > > > > > > > .libs/lib_pf_support_la-prec_foll.o .libs/lib_pf_support_la-shredder.o > > > > > > > -Wl,--whole-archive ./.libs/libserialize.a ./.libs/libpf.a > > > > > > > -Wl,--no-whole-archive -Wl,--rpath -Wl,/usr/local/lib/MonetDB4/lib > > > > > > > -Wl,--rpath -Wl,/usr/local/lib/MonetDB4/lib -L/usr/lib > > > > > > > /usr/lib/libxml2.so -ldl -L/usr/local/lib /usr/lib/libbat.so > > > > > > > /usr/lib/libstream.so /usr/lib/libmonet.so -lpthread > > > > > > > -L/usr/local/lib/MonetDB4/lib /usr/local/lib/MonetDB4/lib/lib_lock.so > > > > > > > /usr/local/lib/MonetDB4/lib/lib_monettime.so > > > > > > > /usr/local/lib/MonetDB4/lib/lib_streams.so > > > > > > > /usr/local/lib/MonetDB4/lib/lib_builtin.so > > > > > > > /usr/local/lib/MonetDB4/lib/lib_ascii_io.so > > > > > > > /usr/local/lib/MonetDB4/lib/lib_algebra.so > > > > > > > /usr/local/lib/MonetDB4/lib/lib_constant.so -Wl,-soname > > > > > > > -Wl,lib_pf_support.so.0 -o .libs/lib_pf_support.so.0.0.0 > > > > > > > (cd .libs && rm -f lib_pf_support.so.0 && ln -s > > > > > > > lib_pf_support.so.0.0.0 lib_pf_support.so.0) > > > > > > > (cd .libs && rm -f lib_pf_support.so && ln -s lib_pf_support.so.0.0.0 > > > > > > > lib_pf_support.so) > > > > > > > creating lib_pf_support.la > > > > > > > /bin/sed: can't read > > > > > > > /export/scratch1/monet/monet.GNU.32.32.d.14791/MonetDB/.GNU.32.32.d-Fedora6/lib/libbat.la: > > > > > > > No such file or directory > > > > > > > libtool: link: `/export/scratch1/monet/monet.GNU.32.32.d.14791/MonetDB/.GNU.32.32.d-Fedora6/lib/libbat.la' > > > > > > > is not a valid libtool archive > > > > > > > make[2]: *** [lib_pf_support.la] Error 1 > > > > > > > make[2]: *** Deleting file `lib_pf_support.la' > > > > > > > make[2]: Leaving directory `/home/ramon/software/monetdb/cvs/pathfinder/runtime' > > > > > > > make[1]: *** [all-recursive] Error 1 > > > > > > > make[1]: Leaving directory `/home/ramon/software/monetdb/cvs/pathfinder' > > > > > > > make: *** [all] Error 2 > > > > > > > > > > > > > > ----------------------------------------------------------------------------- > > > > > > > > > > > > > > Your help is greatly appreciated. > > > > > > > > > > > > > > Ramon Nogueira > > > > > > > > > > > > > > ------------------------------------------------------------------------- > > > > > > > This SF.net email is sponsored by DB2 Express > > > > > > > Download DB2 Express C - the FREE version of DB2 express and take > > > > > > > control of your XML. No limits. Just data. Click to get it now. > > > > > > > http://sourceforge.net/powerbar/db2/ > > > > > > > _______________________________________________ > > > > > > > MonetDB-users mailing list > > > > > > > MonetDB-users(a)lists.sourceforge.net > > > > > > > https://lists.sourceforge.net/lists/listinfo/monetdb-users > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > | Dr. Stefan Manegold | mailto:Stefan.Manegold@cwi.nl | > > > > > > | CWI, P.O.Box 94079 | http://www.cwi.nl/~manegold/ | > > > > > > | 1090 GB Amsterdam | Tel.: +31 (20) 592-4212 | > > > > > > | The Netherlands | Fax : +31 (20) 592-4312 | > > > > > > > > > > > > > > > > ------------------------------------------------------------------------- > > > > > This SF.net email is sponsored by DB2 Express > > > > > Download DB2 Express C - the FREE version of DB2 express and take > > > > > control of your XML. No limits. Just data. Click to get it now. > > > > > http://sourceforge.net/powerbar/db2/ > > > > > _______________________________________________ > > > > > MonetDB-users mailing list > > > > > MonetDB-users(a)lists.sourceforge.net > > > > > https://lists.sourceforge.net/lists/listinfo/monetdb-users > > > > > > > > > > > > > > > > > > -- > > > > | Dr. Stefan Manegold | mailto:Stefan.Manegold@cwi.nl | > > > > | CWI, P.O.Box 94079 | http://www.cwi.nl/~manegold/ | > > > > | 1090 GB Amsterdam | Tel.: +31 (20) 592-4212 | > > > > | The Netherlands | Fax : +31 (20) 592-4312 | > > > > > > > > > > ------------------------------------------------------------------------- > > > This SF.net email is sponsored by DB2 Express > > > Download DB2 Express C - the FREE version of DB2 express and take > > > control of your XML. No limits. Just data. Click to get it now. > > > http://sourceforge.net/powerbar/db2/ > > > _______________________________________________ > > > MonetDB-users mailing list > > > MonetDB-users(a)lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/monetdb-users > > > > > > > -- > > | Dr. Stefan Manegold | mailto:Stefan.Manegold@cwi.nl | > > | CWI, P.O.Box 94079 | http://www.cwi.nl/~manegold/ | > > | 1090 GB Amsterdam | Tel.: +31 (20) 592-4212 | > > | The Netherlands | Fax : +31 (20) 592-4312 | > > >

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[MonetDB-users] Compile problems (CVS, Ubuntu 7.04)
by Ramon Nogueira 27 May '07

27 May '07

Hi, Trying to install MonetDB4 and pathfinder from CVS. I succeeded in compiling and installing (into /usr/local) MonetDB, client and MonetDB4 modules. `bootstrap' and `configure' both succeed from pathfinder, but `make' produces the following error. Also, on another note, I think it should be made clearer that installation of `client' is a prerequisite for MonetDB4 server since this is quite a counterintuitive order of dependency (server on client). I am on Linux 2.6.20-15-generic i686 GNU/Linux. Output from `make': --------------------------------------------------------------------------- (cd .libs && rm -f libpf.la && ln -s ../libpf.la libpf.la) /bin/bash ../libtool --tag=CC --mode=link gcc -DLIBPF_SUPPORT -g -O2 -Wall -Wextra -std=c99 -Werror-implicit-function-declaration -Werror -Wpointer-arith -Wdeclaration-after-statement -Wno-declaration-after-statement -DEMBEDDED -DMT -DNO_CGI -DNO_AUTH -DIO_MAX=10240 -o lib_pf_support.la -rpath /usr/local/lib/MonetDB4/lib lib_pf_support_la-pf_support.glue.lo lib_pf_support_la-pf_support.lo lib_pf_support_la-staircasejoin.lo lib_pf_support_la-prec_foll.lo lib_pf_support_la-shredder.lo libserialize.la libpf.la -lxml2 -L/usr/lib -lxml2 -ldl -L/usr/local/lib -lbat -lstream -L/usr/local/lib -lmonet -lpthread -L/usr/local/lib/MonetDB4/lib -l_lock -l_monettime -l_streams -l_builtin -l_ascii_io -l_algebra -l_constant gcc -shared .libs/lib_pf_support_la-pf_support.glue.o .libs/lib_pf_support_la-pf_support.o .libs/lib_pf_support_la-staircasejoin.o .libs/lib_pf_support_la-prec_foll.o .libs/lib_pf_support_la-shredder.o -Wl,--whole-archive ./.libs/libserialize.a ./.libs/libpf.a -Wl,--no-whole-archive -Wl,--rpath -Wl,/usr/local/lib/MonetDB4/lib -Wl,--rpath -Wl,/usr/local/lib/MonetDB4/lib -L/usr/lib /usr/lib/libxml2.so -ldl -L/usr/local/lib /usr/lib/libbat.so /usr/lib/libstream.so /usr/lib/libmonet.so -lpthread -L/usr/local/lib/MonetDB4/lib /usr/local/lib/MonetDB4/lib/lib_lock.so /usr/local/lib/MonetDB4/lib/lib_monettime.so /usr/local/lib/MonetDB4/lib/lib_streams.so /usr/local/lib/MonetDB4/lib/lib_builtin.so /usr/local/lib/MonetDB4/lib/lib_ascii_io.so /usr/local/lib/MonetDB4/lib/lib_algebra.so /usr/local/lib/MonetDB4/lib/lib_constant.so -Wl,-soname -Wl,lib_pf_support.so.0 -o .libs/lib_pf_support.so.0.0.0 (cd .libs && rm -f lib_pf_support.so.0 && ln -s lib_pf_support.so.0.0.0 lib_pf_support.so.0) (cd .libs && rm -f lib_pf_support.so && ln -s lib_pf_support.so.0.0.0 lib_pf_support.so) creating lib_pf_support.la /bin/sed: can't read /export/scratch1/monet/monet.GNU.32.32.d.14791/MonetDB/.GNU.32.32.d-Fedora6/lib/libbat.la: No such file or directory libtool: link: `/export/scratch1/monet/monet.GNU.32.32.d.14791/MonetDB/.GNU.32.32.d-Fedora6/lib/libbat.la' is not a valid libtool archive make[2]: *** [lib_pf_support.la] Error 1 make[2]: *** Deleting file `lib_pf_support.la' make[2]: Leaving directory `/home/ramon/software/monetdb/cvs/pathfinder/runtime' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/ramon/software/monetdb/cvs/pathfinder' make: *** [all] Error 2 ----------------------------------------------------------------------------- Your help is greatly appreciated. Ramon Nogueira

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