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  • program won't find math.h anymore

    - by 130490868091234
    After a long time, I downloaded a program I co-developed and tried to recompile it on my Ubuntu Linux 12.04, but it seems it does not find math.h anymore. This may be because something has changed recently in gcc, but I can't figure out if it's something wrong in src/Makefile.am or a missing dependency: Download from http://www.ub.edu/softevol/variscan/: tar xzf variscan-2.0.2.tar.gz cd variscan-2.0.2/ make distclean sh ./autogen.sh make I get: [...] gcc -DNDEBUG -O3 -W -Wall -ansi -pedantic -lm -o variscan variscan.o statistics.o common.o linefile.o memalloc.o dlist.o errabort.o dystring.o intExp.o kxTok.o pop.o window.o free.o output.o readphylip.o readaxt.o readmga.o readmaf.o readhapmap.o readxmfa.o readmav.o ran1.o swcolumn.o swnet.o swpoly.o swref.o statistics.o: In function `calculate_Fu_and_Li_D': statistics.c:(.text+0x497): undefined reference to `sqrt' statistics.o: In function `calculate_Fu_and_Li_F': statistics.c:(.text+0x569): undefined reference to `sqrt' statistics.o: In function `calculate_Fu_and_Li_D_star': statistics.c:(.text+0x63b): undefined reference to `sqrt' statistics.o: In function `calculate_Fu_and_Li_F_star': statistics.c:(.text+0x75c): undefined reference to `sqrt' statistics.o: In function `calculate_Tajima_D': statistics.c:(.text+0x85d): undefined reference to `sqrt' statistics.o:statistics.c:(.text+0xcb1): more undefined references to `sqrt' follow statistics.o: In function `calcRunMode21Stats': statistics.c:(.text+0xe02): undefined reference to `log' statistics.o: In function `correctedDivergence': statistics.c:(.text+0xe5a): undefined reference to `log' statistics.o: In function `calcRunMode22Stats': statistics.c:(.text+0x104a): undefined reference to `sqrt' statistics.o: In function `calculate_Fu_fs': statistics.c:(.text+0x11a8): undefined reference to `fabsl' statistics.c:(.text+0x11ca): undefined reference to `powl' statistics.c:(.text+0x11f2): undefined reference to `logl' statistics.o: In function `calculateStatistics': statistics.c:(.text+0x13f2): undefined reference to `log' collect2: ld returned 1 exit status make[1]: *** [variscan] Error 1 make[1]: Leaving directory `/home/avilella/variscan/latest/variscan-2.0.2/src' make: *** [all-recursive] Error 1 The libraries are there because this simple example works perfectly well: $ gcc test.c -o test -lm $ cat test.c #include <stdio.h> #include <math.h> int main(void) { double x = 0.5; double result = sqrt(x); printf("The hyperbolic cosine of %lf is %lf\n", x, result); return 0; } Any ideas?

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  • Is there a command like pstree for libraries?

    - by flashnode
    I need to determine whether a library named libunaSA.so is being called directly by the process or by another library called libtoki2.so. I guess what I'm looking for is a pstree for libraries. The system is running RHEL 5.3 Beta. This output shows the two libraries in the process map # grep -e toki -e una /proc/2335/maps 0043f000-004ad000 r-xp 00000000 08:02 543465 /usr/lib/libtoki2.so 004ad000-004c5000 rwxp 0006d000 08:02 543465 /usr/lib/libtoki2.so 01185000-01397000 r-xp 00000000 08:02 543503 /usr/lib/libunaSA.so 01397000-013dc000 rwxp 00211000 08:02 543503 /usr/lib/libunaSA.so This output shows that only the libtoki2.so library is in the current cache # ldconfig -p | grep -e una -e toki libtoki2.so (libc6) => /usr/lib/libtoki2.so libtoki.so.4.4.1 (libc6) => /usr/lib/libtoki.so.4.4.1 libtoki.so.2 (libc6) => /usr/lib/libtoki.so.2 I attached strace to the running process but it doesn't provide much output # strace -p 2335 Process 2335 attached - interrupt to quit futex(0xb7ef5bd8, FUTEX_WAIT, 2336, NULL Here's the output to ldd for each library # ldd /usr/lib/libtoki2.so linux-gate.so.1 => (0x00a0a000) libdl.so.2 => /lib/libdl.so.2 (0x001bd000) libstdc++-libc6.2-2.so.3 => /usr/lib/libstdc++-libc6.2-2.so.3 (0x00f3f000) libm.so.6 => /lib/libm.so.6 (0x00b27000) libc.so.6 => /lib/libc.so.6 (0x0043d000) /lib/ld-linux.so.2 (0x00742000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00110000) # ldd /usr/lib/libunaSA.so linux-gate.so.1 => (0x00244000) libpthread.so.0 => /lib/libpthread.so.0 (0x00baf000) libdl.so.2 => /lib/libdl.so.2 (0x007fa000) libstdc++-libc6.2-2.so.3 => /usr/lib/libstdc++-libc6.2-2.so.3 (0x009ce000) libm.so.6 => /lib/libm.so.6 (0x00c96000) libc.so.6 => /lib/libc.so.6 (0x004a2000) /lib/ld-linux.so.2 (0x00742000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00a9f000)

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  • does android 1.5 saves fpu regs on context switch

    - by fazo
    i'm asking 1.5 and up or is it dependant on what's in ".config" when compiled for my phone? (and yes, i know that android has to support processors with soft-float, but several libm on different phones do have hard-float libm) (please provide -if possible- any link to/file name of context switching function for msm 7200A/7201A)

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  • Library order is important

    - by Darryl Gove
    I've written quite extensively about link ordering issues, but I've not discussed the interaction between archive libraries and shared libraries. So let's take a simple program that calls a maths library function: #include <math.h int main() { for (int i=0; i<10000000; i++) { sin(i); } } We compile and run it to get the following performance: bash-3.2$ cc -g -O fp.c -lm bash-3.2$ timex ./a.out real 6.06 user 6.04 sys 0.01 Now most people will have heard of the optimised maths library which is added by the flag -xlibmopt. This contains optimised versions of key mathematical functions, in this instance, using the library doubles performance: bash-3.2$ cc -g -O -xlibmopt fp.c -lm bash-3.2$ timex ./a.out real 2.70 user 2.69 sys 0.00 The optimised maths library is provided as an archive library (libmopt.a), and the driver adds it to the link line just before the maths library - this causes the linker to pick the definitions provided by the static library in preference to those provided by libm. We can see the processing by asking the compiler to print out the link line: bash-3.2$ cc -### -g -O -xlibmopt fp.c -lm /usr/ccs/bin/ld ... fp.o -lmopt -lm -o a.out... The flag to the linker is -lmopt, and this is placed before the -lm flag. So what happens when the -lm flag is in the wrong place on the command line: bash-3.2$ cc -g -O -xlibmopt -lm fp.c bash-3.2$ timex ./a.out real 6.02 user 6.01 sys 0.01 If the -lm flag is before the source file (or object file for that matter), we get the slower performance from the system maths library. Why's that? If we look at the link line we can see the following ordering: /usr/ccs/bin/ld ... -lmopt -lm fp.o -o a.out So the optimised maths library is still placed before the system maths library, but the object file is placed afterwards. This would be ok if the optimised maths library were a shared library, but it is not - instead it's an archive library, and archive library processing is different - as described in the linker and library guide: "The link-editor searches an archive only to resolve undefined or tentative external references that have previously been encountered." An archive library can only be used resolve symbols that are outstanding at that point in the link processing. When fp.o is placed before the libmopt.a archive library, then the linker has an unresolved symbol defined in fp.o, and it will search the archive library to resolve that symbol. If the archive library is placed before fp.o then there are no unresolved symbols at that point, and so the linker doesn't need to use the archive library. This is why libmopt needs to be placed after the object files on the link line. On the other hand if the linker has observed any shared libraries, then at any point these are checked for any unresolved symbols. The consequence of this is that once the linker "sees" libm it will resolve any symbols it can to that library, and it will not check the archive library to resolve them. This is why libmopt needs to be placed before libm on the link line. This leads to the following order for placing files on the link line: Object files Archive libraries Shared libraries If you use this order, then things will consistently get resolved to the archive libraries rather than to the shared libaries.

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  • I get this error: "glibc detected"

    - by AKGMA
    Hi I just wrote a piece of CPP code and I compiled it using G++ in ubuntu. When I run my code everything is fine, the code runs well and gives output but doesn't exit and it gives this error: *** glibc detected *** ./a.out: free(): invalid next size (fast): 0x09f931f0 *** ======= Backtrace: ========= /lib/libc.so.6(+0x6c501)[0x3de501] /lib/libc.so.6(+0x6dd70)[0x3dfd70] /lib/libc.so.6(cfree+0x6d)[0x3e2e5d] /usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0x6e2441] ./a.out[0x8049ce6] /lib/libc.so.6(+0x2f69e)[0x3a169e] /lib/libc.so.6(+0x2f70f)[0x3a170f] /lib/libc.so.6(__libc_start_main+0xef)[0x388cef] ./a.out[0x8048a61] ======= Memory map: ======== 00219000-0021a000 r-xp 00000000 00:00 0 [vdso] 00354000-00370000 r-xp 00000000 08:01 8781845 /lib/ld-2.12.1.so 00370000-00371000 r--p 0001b000 08:01 8781845 /lib/ld-2.12.1.so 00371000-00372000 rw-p 0001c000 08:01 8781845 /lib/ld-2.12.1.so 00372000-004c9000 r-xp 00000000 08:01 8781869 /lib/libc-2.12.1.so 004c9000-004ca000 ---p 00157000 08:01 8781869 /lib/libc-2.12.1.so 004ca000-004cc000 r--p 00157000 08:01 8781869 /lib/libc-2.12.1.so 004cc000-004cd000 rw-p 00159000 08:01 8781869 /lib/libc-2.12.1.so 004cd000-004d0000 rw-p 00000000 00:00 0 00638000-00717000 r-xp 00000000 08:01 3935829 /usr/lib/libstdc++.so.6.0.14 00717000-0071b000 r--p 000de000 08:01 3935829 /usr/lib/libstdc++.so.6.0.14 0071b000-0071c000 rw-p 000e2000 08:01 3935829 /usr/lib/libstdc++.so.6.0.14 0071c000-00723000 rw-p 00000000 00:00 0 00909000-0092d000 r-xp 00000000 08:01 8781918 /lib/libm-2.12.1.so 0092d000-0092e000 r--p 00023000 08:01 8781918 /lib/libm-2.12.1.so 0092e000-0092f000 rw-p 00024000 08:01 8781918 /lib/libm-2.12.1.so 00fdb000-00ff5000 r-xp 00000000 08:01 8781903 /lib/libgcc_s.so.1 00ff5000-00ff6000 r--p 00019000 08:01 8781903 /lib/libgcc_s.so.1 00ff6000-00ff7000 rw-p 0001a000 08:01 8781903 /lib/libgcc_s.so.1 08048000-0804b000 r-xp 00000000 08:01 8652645 /home/akg/Desktop/contest/a.out 0804b000-0804c000 r--p 00002000 08:01 8652645 /home/akg/Desktop/contest/a.out 0804c000-0804d000 rw-p 00003000 08:01 8652645 /home/akg/Desktop/contest/a.out 09f93000-09fb4000 rw-p 00000000 00:00 0 [heap] b7600000-b7621000 rw-p 00000000 00:00 0 b7621000-b7700000 ---p 00000000 00:00 0 b7765000-b7768000 rw-p 00000000 00:00 0 b7775000-b7779000 rw-p 00000000 00:00 0 bf9a7000-bf9c8000 rw-p 00000000 00:00 0 [stack] Aborted What does this mean? How can i get rid of it? I'm not using malloc or free , I'm just using vector!

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  • Debian apt dependency mismatch (libc6)

    - by Sean Gordon
    Earlier, I tried to install package via apt-get (cython), but it failed with the Errors were encountered while processing: message, and since then, apt is refusing to install anything. apt-get check output below: root@dix:~# apt-get check Reading package lists... Done Building dependency tree Reading state information... Done You might want to run 'apt-get -f install' to correct these. The following packages have unmet dependencies: libc6 : Depends: libc-bin (= 2.11.3-2) but 2.11.3-4 is installed libc6-dev : Depends: libc6 (= 2.11.3-4) but 2.11.3-2 is installed libc6-i386 : Depends: libc6 (= 2.11.3-4) but 2.11.3-2 is installed E: Unmet dependencies. Try using -f. Apt/aptitude don't seem to be able to fix this dependency issue, and I don't know what to do. Edit: Running apt-get -f install results in no change, and my sources are all squeeze. Running apt-get update then apt-get dist-upgrade show no change either. Edit 2: I went back to try this again in a new terminal and apt-get -f install gives this error: dpkg: error processing /var/cache/apt/archives/libc6_2.11.3-4_amd64.deb (--unpack): subprocess new pre-installation script killed by signal (Aborted) configured to not write apport reports Errors were encountered while processing: /var/cache/apt/archives/libc6_2.11.3-4_amd64.deb E: Sub-process /usr/bin/dpkg returned an error code (1) Edit 3: Using apt-get clean first, then the previous commands, results in the first error again. Using apt-get -f dist-upgrade gives the below. Reading package lists... Building dependency tree... Reading state information... Correcting dependencies... Done The following packages will be upgraded: apache2 apache2-mpm-prefork apache2-utils apache2.2-bin apache2.2-common at automake base-files bind9 bind9-doc bind9-host bind9utils debian-archive-keyring dnsutils dpkg-dev file host initscripts isc-dhcp-client isc-dhcp-common krb5-multidev libapr1 libbind9-60 libc6 libdns69 libdpkg-perl libexpat1 libexpat1-dev libgc1c2 libgssapi-krb5-2 libgssrpc4 libisc62 libisccc60 libisccfg62 libk5crypto3 libkadm5clnt-mit7 libkadm5srv-mit7 libkdb5-4 libkrb5-3 libkrb5-dev libkrb5support0 liblwres60 libmagic1 libmysqlclient16 libnss3-1d libssl-dev libssl0.9.8 libtiff4 libtiff4-dev libtiffxx0c2 libxi6 libxml2 linux-libc-dev lwresd mysql-client-5.1 mysql-common mysql-server mysql-server-5.1 mysql-server-core-5.1 openjdk-6-jre openjdk-6-jre-headless openjdk-6-jre-lib openssh-client openssh-server openssl procps python python-crypto python-minimal sudo sysv-rc sysvinit sysvinit-utils tzdata tzdata-java 75 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 5 not fully installed or removed. Need to get 0 B/79.9 MB of archives. After this operation, 1,411 kB of additional disk space will be used. (Reading database ... 52241 files and directories currently installed.) Preparing to replace libc6 2.11.3-2 (using .../libc6_2.11.3-4_amd64.deb) ... *** stack smashing detected ***: /usr/bin/perl terminated ======= Backtrace: ========= /lib/libc.so.6(__fortify_fail+0x37)[0x7fdaad9b9f87] /lib/libc.so.6(__fortify_fail+0x0)[0x7fdaad9b9f50] /usr/lib/libperl.so.5.10(Perl_yylex+0x5896)[0x7fdaae343346] [0x8e83a0] ======= Memory map: ======== 00400000-00402000 r-xp 00000000 08:01 525338 /usr/bin/perl 00601000-00602000 rw-p 00001000 08:01 525338 /usr/bin/perl 00602000-0091f000 rw-p 00000000 00:00 0 [heap] 7fdaaca54000-7fdaaca6a000 r-xp 00000000 08:01 393818 /lib/libgcc_s.so.1 7fdaaca6a000-7fdaacc69000 ---p 00016000 08:01 393818 /lib/libgcc_s.so.1 7fdaacc69000-7fdaacc6a000 rw-p 00015000 08:01 393818 /lib/libgcc_s.so.1 7fdaacc6a000-7fdaacc6f000 r-xp 00000000 08:01 524949 /usr/lib/perl5/auto/Locale/gettext/gettext.so 7fdaacc6f000-7fdaace6e000 ---p 00005000 08:01 524949 /usr/lib/perl5/auto/Locale/gettext/gettext.so 7fdaace6e000-7fdaace6f000 rw-p 00004000 08:01 524949 /usr/lib/perl5/auto/Locale/gettext/gettext.so 7fdaace6f000-7fdaace79000 r-xp 00000000 08:01 532753 /usr/lib/perl/5.10.1/auto/Encode/Encode.so 7fdaace79000-7fdaad078000 ---p 0000a000 08:01 532753 /usr/lib/perl/5.10.1/auto/Encode/Encode.so 7fdaad078000-7fdaad079000 rw-p 00009000 08:01 532753 /usr/lib/perl/5.10.1/auto/Encode/Encode.so 7fdaad079000-7fdaad07e000 r-xp 00000000 08:01 525444 /usr/lib/perl/5.10.1/auto/IO/IO.so 7fdaad07e000-7fdaad27d000 ---p 00005000 08:01 525444 /usr/lib/perl/5.10.1/auto/IO/IO.so 7fdaad27d000-7fdaad27e000 rw-p 00004000 08:01 525444 /usr/lib/perl/5.10.1/auto/IO/IO.so 7fdaad27e000-7fdaad299000 r-xp 00000000 08:01 525450 /usr/lib/perl/5.10.1/auto/POSIX/POSIX.so 7fdaad299000-7fdaad498000 ---p 0001b000 08:01 525450 /usr/lib/perl/5.10.1/auto/POSIX/POSIX.so 7fdaad498000-7fdaad49b000 rw-p 0001a000 08:01 525450 /usr/lib/perl/5.10.1/auto/POSIX/POSIX.so 7fdaad49b000-7fdaad49e000 r-xp 00000000 08:01 525436 /usr/lib/perl/5.10.1/auto/Fcntl/Fcntl.so 7fdaad49e000-7fdaad69e000 ---p 00003000 08:01 525436 /usr/lib/perl/5.10.1/auto/Fcntl/Fcntl.so 7fdaad69e000-7fdaad69f000 rw-p 00003000 08:01 525436 /usr/lib/perl/5.10.1/auto/Fcntl/Fcntl.so 7fdaad69f000-7fdaad6a7000 r-xp 00000000 08:01 393824 /lib/libcrypt-2.11.3.so 7fdaad6a7000-7fdaad8a6000 ---p 00008000 08:01 393824 /lib/libcrypt-2.11.3.so 7fdaad8a6000-7fdaad8a7000 r--p 00007000 08:01 393824 /lib/libcrypt-2.11.3.so 7fdaad8a7000-7fdaad8a8000 rw-p 00008000 08:01 393824 /lib/libcrypt-2.11.3.so 7fdaad8a8000-7fdaad8d6000 rw-p 00000000 00:00 0 7fdaad8d6000-7fdaada2f000 r-xp 00000000 08:01 393822 /lib/libc-2.11.3.so 7fdaada2f000-7fdaadc2e000 ---p 00159000 08:01 393822 /lib/libc-2.11.3.so 7fdaadc2e000-7fdaadc32000 r--p 00158000 08:01 393822 /lib/libc-2.11.3.so 7fdaadc32000-7fdaadc33000 rw-p 0015c000 08:01 393822 /lib/libc-2.11.3.so 7fdaadc33000-7fdaadc38000 rw-p 00000000 00:00 0 7fdaadc38000-7fdaadc4f000 r-xp 00000000 08:01 393248 /lib/libpthread-2.11.3.so 7fdaadc4f000-7fdaade4e000 ---p 00017000 08:01 393248 /lib/libpthread-2.11.3.so 7fdaade4e000-7fdaade4f000 r--p 00016000 08:01 393248 /lib/libpthread-2.11.3.so 7fdaade4f000-7fdaade50000 rw-p 00017000 08:01 393248 /lib/libpthread-2.11.3.so 7fdaade50000-7fdaade54000 rw-p 00000000 00:00 0 7fdaade54000-7fdaaded4000 r-xp 00000000 08:01 393826 /lib/libm-2.11.3.so 7fdaaded4000-7fdaae0d4000 ---p 00080000 08:01 393826 /lib/libm-2.11.3.so 7fdaae0d4000-7fdaae0d5000 r--p 00080000 08:01 393826 /lib/libm-2.11.3.so 7fdaae0d5000-7fdaae0d6000 rw-p 00081000 08:01 393826 /lib/libm-2.11.3.so 7fdaae0d6000-7fdaae0d8000 r-xp 00000000 08:01 393825 /lib/libdl-2.11.3.so 7fdaae0d8000-7fdaae2d8000 ---p 00002000 08:01 393825 /lib/libdl-2.11.3.so 7fdaae2d8000-7fdaae2d9000 r--p 00002000 08:01 393825 /lib/libdl-2.11.3.so 7fdaae2d9000-7fdaae2da000 rw-p 00003000 08:01 393825 /lib/libdl-2.11.3.so 7fdaae2da000-7fdaae43f000 r-xp 00000000 08:01 525387 /usr/lib/libperl.so.5.10.1 7fdaae43f000-7fdaae63e000 ---p 00165000 08:01 525387 /usr/lib/libperl.so.5.10.1 7fdaae63e000-7fdaae647000 rw-p 00164000 08:01 525387 /usr/lib/libperl.so.5.10.1 7fdaae647000-7fdaae665000 r-xp 00000000 08:01 393819 /lib/ld-2.11.3.so 7fdaae854000-7fdaae859000 rw-p 00000000 00:00 0 7fdaae862000-7fdaae864000 rw-p 00000000 00:00 0 7fdaae864000-7fdaae865000 r--p 0001d000 08:01 393819 /lib/ld-2.11.3.so 7fdaae865000-7fdaae866000 rw-p 0001e000 08:01 393819 /lib/ld-2.11.3.so 7fdaae866000-7fdaae867000 rw-p 00000000 00:00 0 7fff9616d000-7fff9618e000 rw-p 00000000 00:00 0 [stack] 7fff961ff000-7fff96200000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r--p 00000000 00:00 0 [vsyscall] dpkg: error processing /var/cache/apt/archives/libc6_2.11.3-4_amd64.deb (--unpack): subprocess new pre-installation script killed by signal (Aborted) Errors were encountered while processing: /var/cache/apt/archives/libc6_2.11.3-4_amd64.deb

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  • Error installing nginx with passenger-install-nginx-module on ubuntu 11.10 & rails 3.1.0

    - by user938363
    Here is the error message from installing nginx with passenger-install- nginx-module (rvmsudo). The nginx is 1.0.6 installed under /opt/nginx (default). gem install passenger successfully prior. Someone has idea about the problem? thanks. /usr/bin/ld: /home/dtt/.rvm/gems/ruby-1.9.2-p290/gems/passenger-3.0.9/ ext/nginx/../common/libpassenger_common.a(aggregate.o): undefined reference to symbol 'round@@GLIBC_2.2.5' /usr/bin/ld: note: 'round@@GLIBC_2.2.5' is defined in DSO /usr/lib/gcc/ x86_64-linux-gnu/4.6.1/../../../x86_64-linux-gnu/libm.so so try adding it to the linker command line /usr/lib/gcc/x86_64-linux-gnu/4.6.1/../../../x86_64-linux-gnu/libm.so: could not read symbols: Invalid operation collect2: ld returned 1 exit status make[1]: *** [objs/nginx] Error 1 make[1]: Leaving directory `/tmp/root-passenger-2135/nginx-1.0.6' make: *** [build] Error 2 -------------------------------------------- It looks like something went wrong

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  • HP-UX: libstd_v2 in stack trace of JNI code compiled with g++

    - by Miguel Rentes
    Hello, uname -mr: B.11.23 ia64 g++ --version: g++ (GCC) 4.4.0 java -version: Java(TM) SE Runtime Environment (build 1.6.0.06-jinteg_20_jan_2010_05_50-b00) Java HotSpot(TM) Server VM (build 14.3-b01-jre1.6.0.06-rc1, mixed mode) I'm trying to run a Java application that uses JNI. It is crashing inside the JNI code with the following (abbreviated) stack trace: (0) 0xc0000000249353e0 VMError::report_and_die{_ZN7VMError14report_and_dieEv} + 0x440 at /CLO/Components/JAVA_HOTSPOT/Src/src/share/vm/utilities/vmError.cpp:738 [/opt/java6/jre/lib/IA64W/server/libjvm.so] (1) 0xc000000024559240 os::Hpux::JVM_handle_hpux_signal{_ZN2os4Hpux22JVM_handle_hpux_signalEiP9 __siginfoPvi} + 0x760 at /CLO/Components/JAVA_HOTSPOT/Src/src/os_cpu/hp-ux_ia64/vm/os_hp-ux_ia64.cpp:1051 [/opt/java6/jre/lib/IA64W/server/libjvm.so] (2) 0xc0000000245331c0 os::Hpux::signalHandler{_ZN2os4Hpux13signalHandlerEiP9__siginfoPv} + 0x80 at /CLO/Components/JAVA_HOTSPOT/Src/src/os/hp-ux/vm/os_hp-ux.cpp:4295 [/opt/java6/jre/lib/IA64W/server/libjvm.so] (3) 0xe00000010e002620 ---- Signal 11 (SIGSEGV) delivered ---- (4) 0xc0000000000d2d20 __pthread_mutex_lock + 0x400 at /ux/core/libs/threadslibs/src/common/pthreads/mutex.c:3895 [/usr/lib/hpux64/libpthread.so.1] (5) 0xc000000000342e90 __thread_mutex_lock + 0xb0 at ../../../../../core/libs/libc/shared_em_64/../core/threads/wrappers1.c:273 [/usr/lib/hpux64/libc.so.1] (6) 0xc00000000177dff0 _HPMutexWrapper::lock{_ZN15_HPMutexWrapper4lockEPv} + 0x90 [/usr/lib/hpux64/libstd_v2.so.1] (7) 0xc0000000017e9960 std::basic_string,std::allocator{_ZNSsC1ERKSs} + 0x80 [/usr/lib/hpux64/libstd_v2.so.1] (8) 0xc000000008fd9fe0 JniString::str{_ZNK9JniString3strEv} + 0x50 at eg_handler_jni.cxx:50 [/soft/bus-7_0/lib/libbus_registry_jni.so.7.0.0] (9) 0xc000000008fd7060 pt_efacec_se_aut_frk_cmp_registry_REGHandler::getKey{_ZN44pt_efacec_se_aut_frk_cmp_registry_REGHandler6getKeyEP8_jstringi} + 0xa0 [/soft/bus-7_0/lib/libbus_registry_jni.so.7.0.0] (10) 0xc000000008fd17f0 Java_pt_efacec_se_aut_frk_cmp_registry_REGHandler_getKey__Ljava_lang_String_2I + 0xa0 [/soft/bus-7_0/lib/libbus_registry_jni.so.7.0.0] (11) 0x9fffffffdf400ed0 Internal error (-3) while unwinding stack [/CLO/Components/JAVA_HOTSPOT/Src/src/os_cpu/hp-ux_ia64/vm/thread_hp-ux_ia64.cpp:142] This JNI code and dependencies are being compiled using g++, are multithreaded and 64 bit (-pthread -mlp64 -shared -fPIC). The LD_LIBRARY_PATH environment variable is set the dependencies location, and running ldd on the JNI shared libraries finds them all: ldd libbus_registry_jni.so: libefa-d.so.7 = /soft/bus-7_0/lib/libefa-d.so.7 libbus_registry-d.so.7 = /soft/bus-7_0/lib/libbus_registry-d.so.7 libboost_thread-gcc44-mt-d-1_41.so = /usr/local/lib/libboost_thread-gcc44-mt-d-1_41.so libboost_system-gcc44-mt-d-1_41.so = /usr/local/lib/libboost_system-gcc44-mt-d-1_41.so libboost_regex-gcc44-mt-d-1_41.so = /usr/local/lib/libboost_regex-gcc44-mt-d-1_41.so librt.so.1 = /usr/lib/hpux64/librt.so.1 libstdc++.so.6 = /opt/hp-gcc-4.4.0/lib/gcc/ia64-hp-hpux11.23/4.4.0/../../../hpux64/libstdc++.so.6 libm.so.1 = /usr/lib/hpux64/libm.so.1 libgcc_s.so.0 = /opt/hp-gcc-4.4.0/lib/gcc/ia64-hp-hpux11.23/4.4.0/../../../hpux64/libgcc_s.so.0 libunwind.so.1 = /usr/lib/hpux64/libunwind.so.1 librt.so.1 = /usr/lib/hpux64/librt.so.1 libm.so.1 = /usr/lib/hpux64/libm.so.1 libunwind.so.1 = /usr/lib/hpux64/libunwind.so.1 libdl.so.1 = /usr/lib/hpux64/libdl.so.1 libunwind.so.1 = /usr/lib/hpux64/libunwind.so.1 libc.so.1 = /usr/lib/hpux64/libc.so.1 libuca.so.1 = /usr/lib/hpux64/libuca.so.1 Looking at the stack trace, it seams odd that, although ldd list g++'s libstdc++ is being used, the std:string copy c'tor being reported as used is the one in libstd_v2, the implementation provided by aCC. The crash happens in the following code, when method str() returns: class JniString { std::string m_utf8; public: JniString(JNIEnv* env, jstring instance) { const char* utf8Chars = env-GetStringUTFChars(instance, 0); if (utf8Chars == 0) { env-ExceptionClear(); // RPF throw std::runtime_error("GetStringUTFChars returned 0"); } m_utf8.assign(utf8Chars); env-ReleaseStringUTFChars(instance, utf8Chars); } std::string str() const { return m_utf8; } }; Simultaneous usage of the two C++ implementations could likely be a reason for the crash, but that should not be happening. Any ideas?

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  • Stack Overflow problem in a recursive program in C

    - by Adi
    Hi all, I am getting a stack overflow in one of the recursive functions i am running.. Here is the code.. void* buddyMalloc(int req_size) { // Do something here return buddy_findout(original_index,req_size); // This is the recursive call } void *buddy_findout(int current_index,int req_size) { char *selected = NULL; if(front!=NULL) { if(current_index==original_index) { // Do something here return selected; } else { // Do Something here return buddy_findout(current_index+1,req_size); } } else { return buddy_findout(current_index-1,req_size); } } Consider the initial value of index to be 4. and it first do index-1 till it reaches 0 index. and then it comes back to index 4 by incrementing..This is wht i want to implement. But it gives a stack overflow with memory map in the command prompt : Here is the output from my shell : * glibc detected * ./473_mem: free(): invalid pointer: 0x00c274c0 * ======= Backtrace: ========= /lib/tls/i686/cmov/libc.so.6[0xb50ff1] /lib/tls/i686/cmov/libc.so.6[0xb526f2] /lib/tls/i686/cmov/libc.so.6(cfree+0x6d)[0xb557cd] ./473_mem[0x8048b44] ./473_mem[0x8048b74] ./473_mem[0x8048b74] ./473_mem[0x8048944] ./473_mem[0x8048c87] ./473_mem[0x8048d31] ./473_mem[0x8048f79] /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe6)[0xafcb56] ./473_mem[0x8048671] ======= Memory map: ======== 0017c000-00198000 r-xp 00000000 08:01 5224 /lib/libgcc_s.so.1 00198000-00199000 r--p 0001b000 08:01 5224 /lib/libgcc_s.so.1 00199000-0019a000 rw-p 0001c000 08:01 5224 /lib/libgcc_s.so.1 00260000-00284000 r-xp 00000000 08:01 1927 /lib/tls/i686/cmov/libm-2.10.1.so 00284000-00285000 r--p 00023000 08:01 1927 /lib/tls/i686/cmov/libm-2.10.1.so 00285000-00286000 rw-p 00024000 08:01 1927 /lib/tls/i686/cmov/libm-2.10.1.so 006cd000-006e8000 r-xp 00000000 08:01 6662 /lib/ld-2.10.1.so 006e8000-006e9000 r--p 0001a000 08:01 6662 /lib/ld-2.10.1.so 006e9000-006ea000 rw-p 0001b000 08:01 6662 /lib/ld-2.10.1.so 00aa9000-00aaa000 r-xp 00000000 00:00 0 [vdso] 00ae6000-00c24000 r-xp 00000000 08:01 1900 /lib/tls/i686/cmov/libc-2.10.1.so 00c24000-00c25000 ---p 0013e000 08:01 1900 /lib/tls/i686/cmov/libc-2.10.1.so 00c25000-00c27000 r--p 0013e000 08:01 1900 /lib/tls/i686/cmov/libc-2.10.1.so 00c27000-00c28000 rw-p 00140000 08:01 1900 /lib/tls/i686/cmov/libc-2.10.1.so 00c28000-00c2b000 rw-p 00000000 00:00 0 08048000-0804a000 r-xp 00000000 00:14 2176 /media/windows-share/OS/Project2/473_mem 0804a000-0804b000 r--p 00001000 00:14 2176 /media/windows-share/OS/Project2/473_mem 0804b000-0804c000 rw-p 00002000 00:14 2176 /media/windows-share/OS/Project2/473_mem 08483000-084a4000 rw-p 00000000 00:00 0 [heap] b7600000-b7621000 rw-p 00000000 00:00 0 b7621000-b7700000 ---p 00000000 00:00 0 b7716000-b7819000 rw-p 00000000 00:00 0 b7827000-b782a000 rw-p 00000000 00:00 0 bfb96000-bfbab000 rw-p 00000000 00:00 0 [stack] Aborted Thanks in advance adi

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  • CA SiteMinder Configuration for Ubuntu

    - by Matt Franklin
    I receive the following error when attempting to start apache through the init.d script: *apache2: Syntax error on line 186 of /etc/apache2/apache2.conf: Syntax error on line 4 of /etc/apache2/mods-enabled/auth_sm.conf: Cannot load /apps/netegrity/webagent/bin/libmod_sm22.so into server: libsmerrlog.so: cannot open shared object file: No such file or directory* SiteMinder does not officially support Ubuntu, so I am having trouble finding any configuration documentation to help me troubleshoot this issue. I successfully installed the SiteMinder binaries and registered the trusted host with the server, but I am having trouble getting the apache mod to load correctly. I have added the following lines to a new auth_sm.conf file in /etc/apache2/mods-available and symlinked to it in /etc/apache2/mods-enabled: SetEnv LD_LIBRARY_PATH /apps/netegrity/webagent/bin SetEnv PATH ${PATH}:${LD_LIBRARY_PATH} LoadModule sm_module /apps/netegrity/webagent/bin/libmod_sm22.so SmInitFile "/etc/apache2/WebAgent.conf" Alias /siteminderagent/pwcgi/ "/apps/netegrity/webagent/pw/" <Directory "/apps/netegrity/webagent/pw/"> Options Indexes MultiViews ExecCGI AllowOverride None Order allow,deny Allow from all </Directory> UPDATE: Output of ldd libmod_sm22.so: ldd /apps/netegrity/webagent/bin/libmod_sm22.so linux-gate.so.1 = (0xb8075000) libsmerrlog.so = /apps/netegrity/webagent/bin/libsmerrlog.so (0xb7ec0000) libsmeventlog.so = /apps/netegrity/webagent/bin/libsmeventlog.so (0xb7ebb000) libpthread.so.0 = /lib/tls/i686/cmov/libpthread.so.0 (0xb7e9a000) libdl.so.2 = /lib/tls/i686/cmov/libdl.so.2 (0xb7e96000) librt.so.1 = /lib/tls/i686/cmov/librt.so.1 (0xb7e8d000) libstdc++.so.5 = /usr/lib/libstdc++.so.5 (0xb7dd3000) libm.so.6 = /lib/tls/i686/cmov/libm.so.6 (0xb7dad000) libgcc_s.so.1 = /lib/libgcc_s.so.1 (0xb7d9e000) libc.so.6 = /lib/tls/i686/cmov/libc.so.6 (0xb7c3a000) libsmcommonutil.so = /apps/netegrity/webagent/bin/libsmcommonutil.so (0xb7c37000) /lib/ld-linux.so.2 (0xb8076000) UPDATE: The easiest way to set environment variables for the Apache run user in Ubuntu is to edit the /etc/apache2/envvars file and add export statements for any library paths you may need

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  • Install Python setuptools on CentOS 6

    - by Ivan
    I'm trying to install setuptools with no success so far. When I do python3.3 ez_setup.py I get the following error: Extracting in /tmp/tmp6nn4cz Traceback (most recent call last): File "ez_setup.py", line 370, in <module> sys.exit(main()) File "ez_setup.py", line 367, in main return _install(tarball, _build_install_args(options)) File "ez_setup.py", line 55, in _install tar = tarfile.open(tarball) File "/usr/local/lib/python3.3/tarfile.py", line 1571, in open raise ReadError("file could not be opened successfully") tarfile.ReadError: file could not be opened successfully I've been reading and it seems that zlib-devel was not installed when the python installation was done. However, I did uncomment line 358 on Modules/Setup to enable zlib before compiling and if I try to import zlib on python3.3 console it works. Also, in case it helps, here is the ldd python3.3: # ldd `which python3.3` linux-vdso.so.1 => (0x00007fff79fda000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b96092da000) libdl.so.2 => /lib64/libdl.so.2 (0x00002b96094f6000) libutil.so.1 => /lib64/libutil.so.1 (0x00002b96096fa000) libz.so.1 => /lib64/libz.so.1 (0x00002b96098fe000) libm.so.6 => /lib64/libm.so.6 (0x00002b9609b12000) libc.so.6 => /lib64/libc.so.6 (0x00002b9609d95000) /lib64/ld-linux-x86-64.so.2 (0x00002b96090bc000) What can I do?

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  • compile ntp without ssl

    - by Zulakis
    I need to deploy ntp to a very space-critical pxe-imaging-system. (Yes, each KB matters.) Footprint needs to be as small as possible, so I want to compile ntp without linking openssl. According to the manual this is should be possible: If available, the OpenSSL library from http://www.openssl.org is used to support public key cryptography. The library must be built and installed prior to building NTP. The procedures for doing that are included in the OpenSSL documentation. The library is found during the normal NTP configure phase and the interface routines compiled automatically. Only the libcrypto.a library file and openssl header files are needed. If the library is not available or disabled, this step is not required. I already tried out ./configure --without-openssl however, this didn't help. This is my ldd output: ldd ntpd/ntpd linux-gate.so.1 => (0xb7706000) libm.so.6 => /lib/i686/cmov/libm.so.6 (0xb76d5000) libcrypto.so.0.9.8 => /usr/lib/i686/cmov/libcrypto.so.0.9.8 (0xb7582000) librt.so.1 => /lib/i686/cmov/librt.so.1 (0xb7578000) libc.so.6 => /lib/i686/cmov/libc.so.6 (0xb741d000) /lib/ld-linux.so.2 (0xb7707000) libdl.so.2 => /lib/i686/cmov/libdl.so.2 (0xb7419000) libz.so.1 => /usr/lib/libz.so.1 (0xb7404000) libpthread.so.0 => /lib/i686/cmov/libpthread.so.0 (0xb73eb000) The system I am compiling on is 32-bit debian lenny using openssl 0.9.8g-15+lenny16. What is the correct configure option to compile ntp without openssl?

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  • g++ symbol versioning. Set it to GCC_3.0 using version 4 of g++

    - by Ismael
    Hi all I need to implemente a Java class which uses JNI to control a fiscal printer in XUbuntu 8.10 with sun-java6-jdk installed. The structure is the following: EpsonDriver.java loads libEpson.so libEpson is linked dynamically with EpsonFiscalProtocol.so ( provided by Epson, no source available ) and pthread I use javah to generate the header file, and the code compiles. Then I put the libEpson.so in $JAVA_HOME/jre/lib/i386, and EpsonDriver.java uses an static initializar System.loadLibrary("libEpson") That part works, however, when I try to use any of the methods I get an unsatisfiedLinkError exception. Some time ago, a coworker did a version that works, and using objdump -Dslx I got the following: Program Header: LOAD off 0x00000000 vaddr 0x00000000 paddr 0x00000000 align 2**12 filesz 0x0000ccc4 memsz 0x0000ccc4 flags r-x LOAD off 0x0000d000 vaddr 0x0000d000 paddr 0x0000d000 align 2**12 filesz 0x00000250 memsz 0x00044a5c flags rw- DYNAMIC off 0x0000d014 vaddr 0x0000d014 paddr 0x0000d014 align 2**2 filesz 0x000000f0 memsz 0x000000f0 flags rw- NOTE off 0x000000d4 vaddr 0x000000d4 paddr 0x000000d4 align 2**2 filesz 0x00000024 memsz 0x00000024 flags r-- STACK off 0x00000000 vaddr 0x00000000 paddr 0x00000000 align 2**2 filesz 0x00000000 memsz 0x00000000 flags rw- Dynamic Section: NEEDED EpsonFiscalProtocol.so NEEDED libpthread.so.0 NEEDED libstdc++.so.6 NEEDED libm.so.6 NEEDED libc.so.6 SONAME libcom_tichile_jpos_EpsonSerialDriver.so INIT 0x00007254 FINI 0x0000ba08 GNU_HASH 0x000000f8 STRTAB 0x00001f50 SYMTAB 0x00000ae0 STRSZ 0x00002384 SYMENT 0x00000010 PLTGOT 0x0000d108 PLTRELSZ 0x00000008 PLTREL 0x00000011 JMPREL 0x0000724c REL 0x000045c4 RELSZ 0x00002c88 RELENT 0x00000008 TEXTREL 0x00000000 VERNEED 0x00004564 VERNEEDNUM 0x00000002 VERSYM 0x000042d4 RELCOUNT 0x000000ac Version References: required from libstdc++.so.6: 0x056bafd3 0x00 05 CXXABI_1.3 0x08922974 0x00 04 GLIBCXX_3.4 required from libc.so.6: 0x0b792650 0x00 03 GCC_3.0 0x0d696910 0x00 02 GLIBC_2.0 In the recently compiled file I get: Program Header: LOAD off 0x00000000 vaddr 0x00000000 paddr 0x00000000 align 2**12 filesz 0x00005300 memsz 0x00005300 flags r-x LOAD off 0x00005300 vaddr 0x00006300 paddr 0x00006300 align 2**12 filesz 0x00000274 memsz 0x00010314 flags rw- DYNAMIC off 0x00005314 vaddr 0x00006314 paddr 0x00006314 align 2**2 filesz 0x000000e0 memsz 0x000000e0 flags rw- EH_FRAME off 0x00004a00 vaddr 0x00004a00 paddr 0x00004a00 align 2**2 filesz 0x00000154 memsz 0x00000154 flags r-- Dynamic Section: NEEDED libstdc++.so.5 NEEDED libm.so.6 NEEDED libgcc_s.so.1 NEEDED libc.so.6 SONAME EpsonFiscalProtocol.so INIT 0x00001cb4 FINI 0x00004994 HASH 0x000000b4 STRTAB 0x00000da4 SYMTAB 0x000004f4 STRSZ 0x00000acf SYMENT 0x00000010 PLTGOT 0x0000640c PLTRELSZ 0x00000270 PLTREL 0x00000011 JMPREL 0x00001a44 REL 0x000019dc RELSZ 0x00000068 RELENT 0x00000008 VERNEED 0x0000198c VERNEEDNUM 0x00000002 VERSYM 0x00001874 RELCOUNT 0x00000004 Version References: required from libstdc++.so.5: 0x056bafd2 0x00 04 CXXABI_1.2 required from libc.so.6: 0x09691f73 0x00 03 GLIBC_2.1.3 0x0d696910 0x00 02 GLIBC_2.0 So I suspect the main diference is the GCC_3.0 symbol I compile libcom_tichile_EpsonSerialDriver.so with the following command ( from memory as I not at work right now ) g++ -Wl,-soname=.... -shared -I/*jni libraries*/ -o libcom_tichile_jpos_EpsonSerialDriver -lEpsonFiscalProtocol -lpthread Is there any way to tell g++ to use that symbol version? Or any idea in how to make it work? EDIT: I have another non-working version with the followin dump: Program Header: LOAD off 0x00000000 vaddr 0x00000000 paddr 0x00000000 align 2**12 filesz 0x0000bf68 memsz 0x0000bf68 flags r-x LOAD off 0x0000cc0c vaddr 0x0000cc0c paddr 0x0000cc0c align 2**12 filesz 0x000005e8 memsz 0x00044df0 flags rw- DYNAMIC off 0x0000cc20 vaddr 0x0000cc20 paddr 0x0000cc20 align 2**2 filesz 0x000000f8 memsz 0x000000f8 flags rw- EH_FRAME off 0x0000b310 vaddr 0x0000b310 paddr 0x0000b310 align 2**2 filesz 0x000002bc memsz 0x000002bc flags r-- STACK off 0x00000000 vaddr 0x00000000 paddr 0x00000000 align 2**2 filesz 0x00000000 memsz 0x00000000 flags rw- RELRO off 0x0000cc0c vaddr 0x0000cc0c paddr 0x0000cc0c align 2**0 filesz 0x000003f4 memsz 0x000003f4 flags r-- Dynamic Section: NEEDED EpsonFiscalProtocol.so NEEDED libpthread.so.0 NEEDED libstdc++.so.6 NEEDED libm.so.6 NEEDED libgcc_s.so.1 NEEDED libc.so.6 SONAME libcom_tichile_jpos_EpsonSerialDriver.so INIT 0x000055d8 FINI 0x0000a968 HASH 0x000000f4 GNU_HASH 0x00000a30 STRTAB 0x00002870 SYMTAB 0x00001410 STRSZ 0x00002339 SYMENT 0x00000010 PLTGOT 0x0000cff4 PLTRELSZ 0x00000168 PLTREL 0x00000011 JMPREL 0x00005470 REL 0x00004ea8 RELSZ 0x000005c8 RELENT 0x00000008 VERNEED 0x00004e38 VERNEEDNUM 0x00000002 VERSYM 0x00004baa RELCOUNT 0x00000001 Version References: required from libstdc++.so.6: 0x056bafd3 0x00 05 CXXABI_1.3 0x08922974 0x00 03 GLIBCXX_3.4 required from libc.so.6: 0x09691f73 0x00 06 GLIBC_2.1.3 0x0d696914 0x00 04 GLIBC_2.4 0x0d696910 0x00 02 GLIBC_2.0 Now I think the main difference is in the GCC_3.0 symbol/ABI EDIT: Luckily, a coworker found a way to talk to the printer using Java

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  • How to I do install DB2 ODBC?

    - by Justin
    I have been trying, with no success, to install a IBM DB2 ODBC driver so that my PHP server can connect to a database. I've tried installing the db2_connect and get all sorts of problems, I tried install I Access for Linux and the RPM did not install right nor did using alien breed any useful results. I've also tried the DB2 Runtime v8.1, no success. If I attempt to run the rpm it claims I need dependencies that I can't find in apt-get. Yum is also not very helpful as it appears I don't have any repositories installed or lists... Running the simple RPM gives me this result in terminal: # rpm -ivh iSeriesAccess-7.1.0-1.0.x86_64.rpm rpm: RPM should not be used directly install RPM packages, use Alien instead! rpm: However assuming you know what you are doing... error: Failed dependencies: /bin/ln is needed by iSeriesAccess-7.1.0-1.0.x86_64 /sbin/ldconfig is needed by iSeriesAccess-7.1.0-1.0.x86_64 /bin/rm is needed by iSeriesAccess-7.1.0-1.0.x86_64 /bin/sh is needed by iSeriesAccess-7.1.0-1.0.x86_64 libc.so.6()(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 libc.so.6(GLIBC_2.2.5)(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 libc.so.6(GLIBC_2.3)(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 libdl.so.2()(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 libdl.so.2(GLIBC_2.2.5)(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 libgcc_s.so.1()(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 libm.so.6()(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 libm.so.6(GLIBC_2.2.5)(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 libodbcinst.so.1()(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 libodbc.so.1()(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 libpthread.so.0()(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 libpthread.so.0(GLIBC_2.2.5)(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 libpthread.so.0(GLIBC_2.3.2)(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 librt.so.1()(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 librt.so.1(GLIBC_2.2.5)(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 libstdc++.so.6()(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 libstdc++.so.6(CXXABI_1.3)(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 libstdc++.so.6(GLIBCXX_3.4)(64bit) is needed by iSeriesAccess-7.1.0-1.0.x86_64 Using alien and running the dkpg gives me thes headaque: $ alien iSeriesAccess-7.1.0-1.0.x86_64.rpm --scripts # dpkg -i iseriesaccess_7.1.0-2_amd64.deb (Reading database ... 127664 files and directories currently installed.) Preparing to replace iseriesaccess 7.1.0-2 (using iseriesaccess_7.1.0-2_amd64.deb) ... Unpacking replacement iseriesaccess ... post uninstall processing for iSeriesAccess 1.0...upgrade /var/lib/dpkg/info/iseriesaccess.postrm: line 8: [: upgrade: integer expression expected Setting up iseriesaccess (7.1.0-2) ... post install processing for iSeriesAccess 1.0...configure iSeries Access ODBC Driver has been deleted (if it existed at all) because its usage count became zero odbcinst: Driver installed. Usage count increased to 1. Target directory is /etc odbcinst: Driver installed. Usage count increased to 3. Target directory is /etc Processing triggers for libc-bin ... ldconfig deferred processing now taking place So it seems the files installed right, well my odbc driver shows up but db2cli.ini is no where to be found. So several questions. Is there a better alternative to connect php to db2, say an ubuntu package I can just install? Can someone direct me to the steps that makes my ubuntu server works well with the RPM so I can build my db2 instance? Also remember I'm connection to an I Series remotely. I'm not using the DB2 Express C thing, even if I did try it to get the db2 php functions to work. And I don't have zend but I think I have every other package on the ubuntu repositories. Help, thank you!

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  • ELF: linking: Why do I get undefined references in .so files

    - by ki.lya.online.fr
    Hi, I'm trying to build a program against wxWidgets, and I get a linker error. I'd like to really understand what it means. The error is: /usr/lib/libwx_baseu-2.8.so: undefined reference to `std::ctype<char>::_M_widen_init() const@GLIBCXX_3.4.11' What I don't understand is why the error is at libwx_baseu-2.8.so. I thought that .so files had all its symbols resolved, contrary to .o files that still need linking. When I ldd the .so, I get can resolve all its linked libraries, so there is no problem there: $ ldd /usr/lib/libwx_baseu-2.8.so linux-gate.so.1 => (0x00476000) libz.so.1 => /lib/libz.so.1 (0x00d9c000) libdl.so.2 => /lib/libdl.so.2 (0x002a8000) libm.so.6 => /lib/libm.so.6 (0x00759000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x002ad000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x0068d000) libpthread.so.0 => /lib/libpthread.so.0 (0x006f0000) libc.so.6 => /lib/libc.so.6 (0x00477000) /lib/ld-linux.so.2 (0x007f6000) Does it means that the .so file was not compiled correctly (in that case, it's a bug in my distribution package) or does it means that there are missing libraries on the linker command line for my particular program? Additionally, do you know how I can get a list on undefined symbols in an ELF file. I tried readelf -s but I can't find the missing symbol. Thank you. Mildred

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  • Finding missing symbols in libstd++ on Debian/squeeze

    - by Florian Le Goff
    I'm trying to use a pre-compiled library provided as a .so file. This file is dynamically linked against a few librairies : $ ldd /usr/local/test/lib/libtest.so linux-gate.so.1 = (0xb770d000) libstdc++-libc6.1-1.so.2 = not found libm.so.6 = /lib/i686/cmov/libm.so.6 (0xb75e1000) libc.so.6 = /lib/i686/cmov/libc.so.6 (0xb7499000) /lib/ld-linux.so.2 (0xb770e000) libgcc_s.so.1 = /lib/libgcc_s.so.1 (0xb747c000) Unfortunately, in Debian/squeeze, there is no libstdc++-libc6.1-1.so.* file. Only a libstdc++.so.* file provided by the libstdc++6 package. I tried to link (using ln -s) libstdc++-libc6.1-1.so.2 to the libstdc++.so.6 file. It does not work, a batch of symbols seems to be lacking when I'm trying to ld my .o files with this lib. /usr/local/test/lib/libtest.so: undefined reference to `__builtin_vec_delete' /usr/local/test/lib/libtest.so: undefined reference to `istrstream::istrstream(int, char const *, int)' /usr/local/test/lib/libtest.so: undefined reference to `__rtti_user' /usr/local/test/lib/libtest.so: undefined reference to `__builtin_new' /usr/local/test/lib/libtest.so: undefined reference to `istream::ignore(int, int)' What would you do ? How may I find in which lib those symbols are exported ?

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  • Error loading shared libraries

    - by user459811
    Hi, I'm running eclipse on Ubuntu using a g++ compiler and I'm trying to run a sample program that utilizes xerces. The build produced no errors however, when i attempted to run the program, I would receive this error: "error while loading shared libraries: libxerces-c-3.1.so: cannot open shared object file: No such file or directory" libxerces-c-3.1.so is in the directory /opt/lib which I have included as a library in eclipse. The file is there when I checked the folder. When I perform an 'echo $LD_LIBRARY_PATH', /opt/lib is also listed. Any ideas into where the problem lies? Thanks. An 'ldd libxerces-c-3.1.so' command yields the following output: linux-vdso.so.1 => (0x00007fffeafff000) libnsl.so.1 => /lib/libnsl.so.1 (0x00007fa3d2b83000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007fa3d2966000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007fa3d265f000) libm.so.6 => /lib/libm.so.6 (0x00007fa3d23dc000) libc.so.6 => /lib/libc.so.6 (0x00007fa3d2059000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007fa3d1e42000) /lib64/ld-linux-x86-64.so.2 (0x00007fa3d337d000)

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  • How to fix Ogre3d segfault with std::_Rb_tree_insert_and_rebalance ?

    - by Balázs Béla
    Hello all. I'm working on a 3d music visualizer using Ogre3d, basically it's a spectrum analizer, a lot like the old xmms plugin: (http)://www.youtube.com/watch?v=_6NKBiwYN24 It works well, the bars are drawn and updated, there are no framerate issues, but it crashes randomly. Sometimes it can run without problems, finish the song, other times it crashes instantly, other times the music just stops, without a crash. Here is the source code for the main class : https://github.com/balazsbela/OgreVisualizer/blob/master/src/VisualizerApplication.cpp#L221 Also the crashes seem to happen less often when I display the framerate overlay from Ogre samples. Would limiting the framerate help ? The crashes are seemingly random. Is it a performance issue ? Please help me out, I'm quite lost on this one, I also posted on Ogre3d forums but I received no responses. (http)://www.ogre3d.org/forums/viewtopic.php?f=2&t=63207 I also tried stackoverflow: (http)://stackoverflow.com/questions/5050147/how-to-fix-ogre3d-segfault-with-std-rb-tree-insert-and-rebalance Thank you. Backtrace: balazsbela@darknet:~/workspace/OgreVisualizer/Release$ gdb OgreVisualizer core GNU gdb (GDB) 7.2-debian Copyright (C) 2010 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "i486-linux-gnu". For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>... Reading symbols from /home/balazsbela/workspace/OgreVisualizer/Release/OgreVisualizer...done. [New Thread 17705] [New Thread 17702] [New Thread 17703] [New Thread 17700] Reading symbols from /usr/lib/libv4l/v4l1compat.so...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libv4l/v4l1compat.so Reading symbols from /usr/local/lib/libOgreMain.so.1.7.1...done. Loaded symbols for /usr/local/lib/libOgreMain.so.1.7.1 Reading symbols from /usr/lib/libfftw3.so.3...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libfftw3.so.3 Reading symbols from /usr/lib/libSDL_sound-1.0.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libSDL_sound-1.0.so.1 Reading symbols from /usr/lib/libSDL-1.2.so.0...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libSDL-1.2.so.0 Reading symbols from /usr/lib/libSDL_mixer-1.2.so.0...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libSDL_mixer-1.2.so.0 Reading symbols from /usr/lib/libOIS-1.2.0.so...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libOIS-1.2.0.so Reading symbols from /usr/lib/libstdc++.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libstdc++.so.6 Reading symbols from /lib/i686/cmov/libm.so.6...Reading symbols from /usr/lib/debug/lib/i686/cmov/libm-2.11.2.so...done. done. Loaded symbols for /lib/i686/cmov/libm.so.6 Reading symbols from /lib/libgcc_s.so.1...(no debugging symbols found)...done. Loaded symbols for /lib/libgcc_s.so.1 Reading symbols from /lib/i686/cmov/libc.so.6...Reading symbols from /usr/lib/debug/lib/i686/cmov/libc-2.11.2.so...done. done. Loaded symbols for /lib/i686/cmov/libc.so.6 Reading symbols from /lib/i686/cmov/libpthread.so.0...Reading symbols from /usr/lib/debug/lib/i686/cmov/libpthread-2.11.2.so...done. done. Loaded symbols for /lib/i686/cmov/libpthread.so.0 Reading symbols from /usr/local/lib/libv4l1.so.0...done. Loaded symbols for /usr/local/lib/libv4l1.so.0 Reading symbols from /usr/lib/libfreetype.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libfreetype.so.6 Reading symbols from /usr/lib/libSM.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libSM.so.6 Reading symbols from /usr/lib/libICE.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libICE.so.6 Reading symbols from /usr/lib/libX11.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libX11.so.6 Reading symbols from /usr/lib/libXext.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libXext.so.6 Reading symbols from /usr/lib/libXt.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libXt.so.6 Reading symbols from /usr/lib/libXaw.so.7...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libXaw.so.7 Reading symbols from /lib/i686/cmov/libdl.so.2...Reading symbols from /usr/lib/debug/lib/i686/cmov/libdl-2.11.2.so...done. done. Loaded symbols for /lib/i686/cmov/libdl.so.2 Reading symbols from /usr/lib/libboost_thread.so.1.42.0...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libboost_thread.so.1.42.0 Reading symbols from /usr/lib/libboost_date_time.so.1.42.0...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libboost_date_time.so.1.42.0 Reading symbols from /usr/lib/libfreeimage.so.3...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libfreeimage.so.3 Reading symbols from /usr/lib/libzzip-0.so.13...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libzzip-0.so.13 Reading symbols from /usr/lib/libz.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libz.so.1 Reading symbols from /usr/lib/libsmpeg-0.4.so.0...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libsmpeg-0.4.so.0 Reading symbols from /usr/lib/libmikmod.so.2...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libmikmod.so.2 Reading symbols from /usr/lib/libvorbis.so.0...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libvorbis.so.0 Reading symbols from /usr/lib/libvorbisfile.so.3...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libvorbisfile.so.3 Reading symbols from /usr/lib/libFLAC.so.8...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libFLAC.so.8 Reading symbols from /usr/lib/libogg.so.0...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libogg.so.0 Reading symbols from /usr/lib/sse2/libspeex.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib/sse2/libspeex.so.1 Reading symbols from /usr/lib/libasound.so.2...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libasound.so.2 Reading symbols from /lib/i686/cmov/librt.so.1...Reading symbols from /usr/lib/debug/lib/i686/cmov/librt-2.11.2.so...done. done. Loaded symbols for /lib/i686/cmov/librt.so.1 Reading symbols from /usr/lib/libdirectfb-1.2.so.9...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libdirectfb-1.2.so.9 Reading symbols from /usr/lib/libfusion-1.2.so.9...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libfusion-1.2.so.9 Reading symbols from /usr/lib/libdirect-1.2.so.9...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libdirect-1.2.so.9 Reading symbols from /usr/lib/libvga.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libvga.so.1 Reading symbols from /lib/ld-linux.so.2...Reading symbols from /usr/lib/debug/lib/ld-2.11.2.so...done. done. Loaded symbols for /lib/ld-linux.so.2 Reading symbols from /usr/local/lib/libv4l2.so.0...done. Loaded symbols for /usr/local/lib/libv4l2.so.0 Reading symbols from /lib/libuuid.so.1...(no debugging symbols found)...done. Loaded symbols for /lib/libuuid.so.1 Reading symbols from /usr/lib/libxcb.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libxcb.so.1 Reading symbols from /usr/lib/libXmu.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libXmu.so.6 Reading symbols from /usr/lib/libXpm.so.4...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libXpm.so.4 Reading symbols from /usr/lib/libjpeg.so.62...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libjpeg.so.62 Reading symbols from /usr/lib/libmng.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libmng.so.1 Reading symbols from /usr/lib/libopenjpeg.so.2...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libopenjpeg.so.2 Reading symbols from /lib/libpng12.so.0...(no debugging symbols found)...done. Loaded symbols for /lib/libpng12.so.0 Reading symbols from /usr/lib/libIlmImf.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libIlmImf.so.6 Reading symbols from /usr/lib/libImath.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libImath.so.6 Reading symbols from /usr/lib/libHalf.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libHalf.so.6 Reading symbols from /usr/lib/libIex.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libIex.so.6 Reading symbols from /usr/lib/libIlmThread.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libIlmThread.so.6 Reading symbols from /lib/libx86.so.1...(no debugging symbols found)...done. Loaded symbols for /lib/libx86.so.1 Reading symbols from /usr/local/lib/libv4lconvert.so.0...done. Loaded symbols for /usr/local/lib/libv4lconvert.so.0 Reading symbols from /usr/lib/libXau.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libXau.so.6 Reading symbols from /usr/lib/libXdmcp.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libXdmcp.so.6 Reading symbols from /usr/lib/liblcms.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib/liblcms.so.1 Reading symbols from /usr/local/lib/OGRE/RenderSystem_GL.so...done. Loaded symbols for /usr/local/lib/OGRE/RenderSystem_GL.so Reading symbols from /usr/lib/libGLU.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libGLU.so.1 Reading symbols from /usr/lib/libGL.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libGL.so.1 Reading symbols from /usr/lib/libXrandr.so.2...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libXrandr.so.2 Reading symbols from /usr/lib/libGLcore.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libGLcore.so.1 Reading symbols from /usr/lib/tls/libnvidia-tls.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib/tls/libnvidia-tls.so.1 Reading symbols from /usr/lib/libXrender.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libXrender.so.1 Reading symbols from /usr/lib/libXcursor.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libXcursor.so.1 Reading symbols from /usr/lib/libXfixes.so.3...(no debugging symbols found)...done. Loaded symbols for /usr/lib/libXfixes.so.3 Reading symbols from /lib/i686/cmov/libnss_compat.so.2...Reading symbols from /usr/lib/debug/lib/i686/cmov/libnss_compat-2.11.2.so...done. done. Loaded symbols for /lib/i686/cmov/libnss_compat.so.2 Reading symbols from /lib/i686/cmov/libnsl.so.1...Reading symbols from /usr/lib/debug/lib/i686/cmov/libnsl-2.11.2.so...done. done. Loaded symbols for /lib/i686/cmov/libnsl.so.1 Reading symbols from /lib/i686/cmov/libnss_nis.so.2...Reading symbols from /usr/lib/debug/lib/i686/cmov/libnss_nis-2.11.2.so...done. done. Loaded symbols for /lib/i686/cmov/libnss_nis.so.2 Reading symbols from /lib/i686/cmov/libnss_files.so.2...Reading symbols from /usr/lib/debug/lib/i686/cmov/libnss_files-2.11.2.so...done. done. Loaded symbols for /lib/i686/cmov/libnss_files.so.2 Reading symbols from /usr/lib/alsa-lib/libasound_module_rate_speexrate.so...(no debugging symbols found)...done. Loaded symbols for /usr/lib/alsa-lib/libasound_module_rate_speexrate.so Reading symbols from /usr/lib/sse2/libspeexdsp.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib/sse2/libspeexdsp.so.1 Core was generated by `./OgreVisualizer'. Program terminated with signal 11, Segmentation fault. #0 0xb6dc563d in std::_Rb_tree_insert_and_rebalance(bool, std::_Rb_tree_node_base*, std::_Rb_tree_node_base*, std::_Rb_tree_node_base&) () from /usr/lib/libstdc++.so.6 (gdb) bt #0 0xb6dc563d in std::_Rb_tree_insert_and_rebalance(bool, std::_Rb_tree_node_base*, std::_Rb_tree_node_base*, std::_Rb_tree_node_base&) () from /usr/lib/libstdc++.so.6 #1 0xb73bb3c2 in std::_Rb_tree<Ogre::Node*, Ogre::Node*, std::_Identity<Ogre::Node*>, std::less<Ogre::Node*>, Ogre::STLAllocator<Ogre::Node*, Ogre::CategorisedAllocPolicy<(Ogre::MemoryCategory)0> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, Ogre::Node* const&) () from /usr/local/lib/libOgreMain.so.1.7.1 #2 0xb73b5a52 in _M_insert_unique (this=0xb6157ea0, child=0xb616aff8, forceParentUpdate=false) at /usr/include/c++/4.4/bits/stl_tree.h:1182 #3 insert (this=0xb6157ea0, child=0xb616aff8, forceParentUpdate=false) at /usr/include/c++/4.4/bits/stl_set.h:411 #4 Ogre::Node::requestUpdate (this=0xb6157ea0, child=0xb616aff8, forceParentUpdate=false) at /home/balazsbela/Downloads/ogre_src_v1-7-1/OgreMain/src/OgreNode.cpp:805 #5 0xb73b6a40 in Ogre::Node::needUpdate (this=0xb616aff8, forceParentUpdate=92) at /home/balazsbela/Downloads/ogre_src_v1-7-1/OgreMain/src/OgreNode.cpp:789 #6 0xb73b5038 in Ogre::Node::setScale (this=0x1825c, scale=...) at /home/balazsbela/Downloads/ogre_src_v1-7-1/OgreMain/src/OgreNode.cpp:638 #7 0x0805d306 in VisualizerApplication::adjustNodes (this=0x9cd4808) at ../src/VisualizerApplication.cpp:236 #8 0xb6e867f0 in ?? () from /usr/lib/libSDL_mixer-1.2.so.0 #9 0xb6e8719a in ?? () from /usr/lib/libSDL_mixer-1.2.so.0 #10 0xb6ed9b0d in ?? () from /usr/lib/libSDL-1.2.so.0 #11 0xb6ee185e in ?? () from /usr/lib/libSDL-1.2.so.0 #12 0xb6f2e0bd in ?? () from /usr/lib/libSDL-1.2.so.0 #13 0xb6bc7955 in start_thread (arg=0xb198ab70) at pthread_create.c:300 #14 0xb6ca6e7e in clone () at ../sysdeps/unix/sysv/linux/i386/clone.S:130 (gdb) Ogre.log: (http)://pastie.org/1581790

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  • Can RPM packages be installed into Cygwin?

    - by Dejian Zhao
    I noticed that there is a command - rpm - under Cygwin 1.7. Does that mean RPM packages can be installed into Cygwin? I tried to install ncbi-blast-2.2.26+-3.i686.rpm (see: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ ) into Cygwin 1.7.13 with the command "install -i ncbi-blast-2.2.26+-3.i686.rpm". However, error message appeared as below. I tried to search for the missing libs using the setup.exe of Cygwin. It seems that some of them were not present, such as libc.so.6, libdl.so.2, libm.so.6, libnsl.so.1, and libz.so.1. Where can I get these libs? Thanks! $ rpm -i ncbi-blast-2.2.26+-3.i686.rpm error: Failed dependencies: /usr/bin/perl is needed by ncbi-blast-2.2.26+-3 libbz2.so.1 is needed by ncbi-blast-2.2.26+-3 libc.so.6 is needed by ncbi-blast-2.2.26+-3 libc.so.6(GLIBC_2.0) is needed by ncbi-blast-2.2.26+-3 libc.so.6(GLIBC_2.1) is needed by ncbi-blast-2.2.26+-3 libc.so.6(GLIBC_2.1.2) is needed by ncbi-blast-2.2.26+-3 libc.so.6(GLIBC_2.1.3) is needed by ncbi-blast-2.2.26+-3 libc.so.6(GLIBC_2.2) is needed by ncbi-blast-2.2.26+-3 libc.so.6(GLIBC_2.3) is needed by ncbi-blast-2.2.26+-3 libdl.so.2 is needed by ncbi-blast-2.2.26+-3 libdl.so.2(GLIBC_2.0) is needed by ncbi-blast-2.2.26+-3 libdl.so.2(GLIBC_2.1) is needed by ncbi-blast-2.2.26+-3 libgcc_s.so.1 is needed by ncbi-blast-2.2.26+-3 libgcc_s.so.1(GCC_3.0) is needed by ncbi-blast-2.2.26+-3 libgcc_s.so.1(GLIBC_2.0) is needed by ncbi-blast-2.2.26+-3 libm.so.6 is needed by ncbi-blast-2.2.26+-3 libnsl.so.1 is needed by ncbi-blast-2.2.26+-3 libpthread.so.0 is needed by ncbi-blast-2.2.26+-3 libpthread.so.0(GLIBC_2.0) is needed by ncbi-blast-2.2.26+-3 libpthread.so.0(GLIBC_2.1) is needed by ncbi-blast-2.2.26+-3 libpthread.so.0(GLIBC_2.2) is needed by ncbi-blast-2.2.26+-3 libpthread.so.0(GLIBC_2.3.2) is needed by ncbi-blast-2.2.26+-3 librt.so.1 is needed by ncbi-blast-2.2.26+-3 libstdc++.so.6 is needed by ncbi-blast-2.2.26+-3 libstdc++.so.6(CXXABI_1.3) is needed by ncbi-blast-2.2.26+-3 libstdc++.so.6(GLIBCXX_3.4) is needed by ncbi-blast-2.2.26+-3 libstdc++.so.6(GLIBCXX_3.4.5) is needed by ncbi-blast-2.2.26+-3 libz.so.1 is needed by ncbi-blast-2.2.26+-3 perl(Archive::Tar) is needed by ncbi-blast-2.2.26+-3 perl(Digest::MD5) is needed by ncbi-blast-2.2.26+-3 perl(File::Temp) is needed by ncbi-blast-2.2.26+-3 perl(File::stat) is needed by ncbi-blast-2.2.26+-3 perl(Getopt::Long) is needed by ncbi-blast-2.2.26+-3 perl(Net::FTP) is needed by ncbi-blast-2.2.26+-3 perl(Pod::Usage) is needed by ncbi-blast-2.2.26+-3 perl(constant) is needed by ncbi-blast-2.2.26+-3 perl(strict) is needed by ncbi-blast-2.2.26+-3 perl(warnings) is needed by ncbi-blast-2.2.26+-3

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  • Unable to install rubygems in ubuntu 10.04

    - by loganathan
    I had installed the ruby 1.8.7 with patch level 253 successfully on my ubuntu 10.04, but while installing ruby gems I am facing the below error, can anybody help me on this. ruby -v ruby 1.8.7 (2010-04-19 patchlevel 253) [i686-linux], MBARI 0x8770, Ruby Enterprise Edition 2010.02 gem install mongrel *** longjmp causes uninitialized stack frame ***: /usr/bin/ruby terminated ======= Backtrace: ========= /lib/tls/i686/cmov/libc.so.6(__fortify_fail+0x50)[0x3612d0] /lib/tls/i686/cmov/libc.so.6(+0xe223a)[0x36123a] /usr/bin/ruby[0x80577b9] /usr/bin/ruby[0x80577d5] /usr/bin/ruby(rb_thread_schedule+0x9fc)[0x80652ac] /usr/bin/ruby(rb_thread_kill+0x14)[0x8066c74] /usr/bin/ruby[0x806071d] /usr/bin/ruby[0x80608b9] /usr/bin/ruby[0x806a869] /usr/bin/ruby[0x806a290] /usr/bin/ruby[0x8060601] /usr/bin/ruby[0x80608b9] /usr/bin/ruby[0x806a869] /usr/bin/ruby[0x806995b] /usr/bin/ruby[0x8060601] /usr/bin/ruby[0x80608b9] /usr/bin/ruby[0x806aaa5] /usr/bin/ruby[0x8069d54] /usr/bin/ruby[0x8060601] /usr/bin/ruby[0x80608b9] /usr/bin/ruby[0x805df2d] /usr/bin/ruby[0x8069581] /usr/bin/ruby[0x805de52] /usr/bin/ruby[0x806a0eb] /usr/bin/ruby[0x805e630] /usr/bin/ruby[0x8060601] /usr/bin/ruby[0x80608b9] /usr/bin/ruby[0x806aaa5] /usr/bin/ruby[0x806a715] /usr/bin/ruby[0x8060601] /usr/bin/ruby[0x80608b9] /usr/bin/ruby[0x806a869] /usr/bin/ruby[0x805e48b] /usr/bin/ruby[0x805de52] /usr/bin/ruby[0x8060601] /usr/bin/ruby[0x80608b9] /usr/bin/ruby[0x806aaa5] /usr/bin/ruby[0x805e58a] /usr/bin/ruby[0x805e4aa] /usr/bin/ruby[0x805de52] /usr/bin/ruby[0x8060601] /usr/bin/ruby[0x80608b9] /usr/bin/ruby[0x806a869] /usr/bin/ruby[0x805e48b] /usr/bin/ruby[0x80693f1] /usr/bin/ruby[0x805de52] /usr/bin/ruby[0x806a0eb] /usr/bin/ruby[0x805e630] /usr/bin/ruby[0x805de52] /usr/bin/ruby[0x8060601] /usr/bin/ruby[0x80608b9] /usr/bin/ruby[0x806a869] /usr/bin/ruby[0x805e48b] /usr/bin/ruby[0x805de52] /usr/bin/ruby[0x806a0eb] /usr/bin/ruby[0x805e630] /usr/bin/ruby[0x805de52] /usr/bin/ruby[0x8060601] /usr/bin/ruby[0x80608b9] /usr/bin/ruby[0x806aaa5] /usr/bin/ruby[0x805e48b] /usr/bin/ruby[0x805de52] /usr/bin/ruby[0x8060601] ======= Memory map: ======== 00110000-00112000 r-xp 00000000 08:06 3805677 /usr/lib/ruby/1.8/i686-linux/etc.so 00112000-00113000 r--p 00001000 08:06 3805677 /usr/lib/ruby/1.8/i686-linux/etc.so 00113000-00114000 rw-p 00002000 08:06 3805677 /usr/lib/ruby/1.8/i686-linux/etc.so 00114000-0012e000 r-xp 00000000 08:06 3805682 /usr/lib/ruby/1.8/i686-linux/syck.so 0012e000-0012f000 r--p 00019000 08:06 3805682 /usr/lib/ruby/1.8/i686-linux/syck.so 0012f000-00130000 rw-p 0001a000 08:06 3805682 /usr/lib/ruby/1.8/i686-linux/syck.so 00130000-00131000 r-xp 00000000 08:06 3805666 /usr/lib/ruby/1.8/i686-linux/fcntl.so 00131000-00132000 r--p 00000000 08:06 3805666 /usr/lib/ruby/1.8/i686-linux/fcntl.so 00132000-00133000 rw-p 00001000 08:06 3805666 /usr/lib/ruby/1.8/i686-linux/fcntl.so 00133000-00150000 r-xp 00000000 08:06 11403438 /lib/libgcc_s.so.1 00150000-00151000 r--p 0001c000 08:06 11403438 /lib/libgcc_s.so.1 00151000-00152000 rw-p 0001d000 08:06 11403438 /lib/libgcc_s.so.1 001e2000-00206000 r-xp 00000000 08:06 11403697 /lib/tls/i686/cmov/libm-2.11.1.so 00206000-00207000 r--p 00023000 08:06 11403697 /lib/tls/i686/cmov/libm-2.11.1.so 00207000-00208000 rw-p 00024000 08:06 11403697 /lib/tls/i686/cmov/libm-2.11.1.so 0024d000-00256000 r-xp 00000000 08:06 11403688 /lib/tls/i686/cmov/libcrypt-2.11.1.so 00256000-00257000 r--p 00008000 08:06 11403688 /lib/tls/i686/cmov/libcrypt-2.11.1.so 00257000-00258000 rw-p 00009000 08:06 11403688 /lib/tls/i686/cmov/libcrypt-2.11.1.so 00258000-0027f000 rw-p 00000000 00:00 0 0027f000-003d2000 r-xp 00000000 08:06 11403695 /lib/tls/i686/cmov/libc-2.11.1.so 003d2000-003d4000 r--p 00153000 08:06 11403695 /lib/tls/i686/cmov/libc-2.11.1.so 003d4000-003d5000 rw-p 00155000 08:06 11403695 /lib/tls/i686/cmov/libc-2.11.1.so 003d5000-003d8000 rw-p 00000000 00:00 0 0047e000-00488000 r-xp 00000000 08:06 3805680 /usr/lib/ruby/1.8/i686-linux/socket.so 00488000-00489000 r--p 00009000 08:06 3805680 /usr/lib/ruby/1.8/i686-linux/socket.so 00489000-0048a000 rw-p 0000a000 08:06 3805680 /usr/lib/ruby/1.8/i686-linux/socket.so 004f2000-00507000 r-xp 00000000 08:06 11403690 /lib/tls/i686/cmov/libpthread-2.11.1.so 00507000-00508000 r--p 00014000 08:06 11403690 /lib/tls/i686/cmov/libpthread-2.11.1.so 00508000-00509000 rw-p 00015000 08:06 11403690 /lib/tls/i686/cmov/libpthread-2.11.1.so 00509000-0050b000 rw-p 00000000 00:00 0 00524000-00525000 r-xp 00000000 00:00 0 [vdso] 00544000-00557000 r-xp 00000000 08:06 11403553 /lib/libz.so.1.2.3.3 00557000-00558000 r--p 00012000 08:06 11403553 /lib/libz.so.1.2.3.3 00558000-00559000 rw-p 00013000 08:06 11403553 /lib/libz.so.1.2.3.3 00639000-0063c000 r-xp 00000000 08:06 3805679 /usr/lib/ruby/1.8/i686-linux/thread.so 0063c000-0063d000 r--p 00002000 08:06 3805679 /usr/lib/ruby/1.8/i686-linux/thread.so 0063d000-0063e000 rw-p 00003000 08:06 3805679 /usr/lib/ruby/1.8/i686-linux/thread.so 00649000-0064d000 r-xp 00000000 08:06 11403714 /lib/tls/i686/cmov/libnss_dns-2.11.1.so 0064d000-0064e000 r--p 00004000 08:06 11403714 /lib/tls/i686/cmov/libnss_dns-2.11.1.so 0064e000-0064f000 rw-p 00005000 08:06 11403714 /lib/tls/i686/cmov/libnss_dns-2.11.1.so 00663000-006a3000 r-xp 00000000 08:06 4329500 /usr/lib/ruby/site_ruby/1.8/i686-linux/openssl.so 006a3000-006a4000 r--p 0003f000 08:06 4329500 /usr/lib/ruby/site_ruby/1.8/i686-linux/openssl.so 006a4000-006a5000 rw-p 00040000 08:06 4329500 /usr/lib/ruby/site_ruby/1.8/i686-linux/openssl.so 006a5000-006a6000 rw-p 00000000 00:00 0 0070d000-0070f000 r-xp 00000000 08:06 11403689 /lib/tls/i686/cmov/libdl-2.11.1.so 0070f000-00710000 r--p 00001000 08:06 11403689 /lib/tls/i686/cmov/libdl-2.11.1.so 00710000-00711000 rw-p 00002000 08:06 11403689 /lib/tls/i686/cmov/libdl-2.11.1.so 00711000-0084b000 r-xp 00000000 08:06 11403909 /lib/libcrypto.so.0.9.8 0084b000-00853000 r--p 00139000 08:06 11403909 /lib/libcrypto.so.0.9.8 00853000-00861000 rw-p 00141000 08:06 11403909 /lib/libcrypto.so.0.9.8 00861000-00864000 rw-p 00000000 00:00 0 00864000-00865000 ---p 00000000 00:00 0 00865000-00966000 rwxp 00000000 00:00 0 00977000-00979000 r-xp 00000000 08:06 11403476 /lib/libnss_mdns4_minimal.so.2 00979000-0097a000 r--p 00001000 08:06 11403476 /lib/libnss_mdns4_minimal.so.2 0097a000-0097b000 rw-p 00002000 08:06 11403476 /lib/libnss_mdns4_minimal.so.2 009fa000-00a04000 r-xp 00000000 08:06 11403691 /lib/tls/i686/cmov/libnss_files-2.11.1.so 00a04000-00a05000 r--p 00009000 08:06 11403691 /lib/tls/i686/cmov/libnss_files-2.11.1.so 00a05000-00a06000 rw-p 0000a000 08:06 11403691 /lib/tls/i686/cmov/libnss_files-2.11.1.so 00ac0000-00ac4000 r-xp 00000000 08:06 3805670 /usr/lib/ruby/1.8/i686-linux/stringio.so 00ac4000-00ac5000 r--p 00003000 08:06 3805670 /usr/lib/ruby/1.8/i686-linux/stringio.so 00ac5000-00ac6000 rw-p 00004000 08:06 3805670 /usr/lib/ruby/1.8/i686-linux/stringio.so 00af3000-00b0e000 r-xp 00000000 08:06 11403607 /lib/ld-2.11.1.so 00b0e000-00b0f000 r--p 0001a000 08:06 11403607 /lib/ld-2.11.1.so 00b0f000-00b10000 rw-p 0001b000 08:06 11403607 /lib/ld-2.11.1.so 00c35000-00c45000 r-xp 00000000 08:06 11403692 /lib/tls/i686/cmov/libresolv-2.11.1.so 00c45000-00c46000 r--p 00010000 08:06 11403692 /lib/tls/i686/cmov/libresolv-2.11.1.so 00c46000-00c47000 rw-p 00011000 08:06 11403692 /lib/tls/i686/cmov/libresolv-2.11.1.so 00c47000-00c49000 rw-p 00000000 00:00 0 00d51000-00d59000 r-xp 00000000 08:06 4329502 /usr/lib/ruby/site_ruby/1.8/i686-linux/zlib.so 00d59000-00d5a000 r--p 00007000 08:06 4329502 /usr/lib/ruby/site_ruby/1.8/i686-linux/zlib.so 00d5a000-00d5b000 rw-p 00008000 08:06 4329502 /usr/lib/ruby/site_ruby/1.8/i686-linux/zlib.so 00d60000-00d61000 r-xp 00000000 08:06 3805664 /usr/lib/ruby/1.8/i686-linux/rational.so 00d61000-00d62000 r--p 00000000 08:06 3805664 /usr/lib/ruby/1.8/i686-linux/rational.so 00d62000-00d63000 rw-p 00001000 08:06 3805664 /usr/lib/ruby/1.8/i686-linux/rational.so 00de6000-00de9000 r-xp 00000000 08:06 3805691 /usr/lib/ruby/1.8/i686-linux/digest.so 00de9000-00dea000 r--p 00002000 08:06 3805691 /usr/lib/ruby/1.8/i686-linux/digest.so 00dea000-00deb000 rw-p 00003000 08:06 3805691 /usr/lib/ruby/1.8/i686-linux/digest.so 00e63000-00e6a000 r-xp 00000000 08:06 11403700 /lib/tls/i686/cmov/librt-2.11.1.so 00e6a000-00e6b000 r--p 00006000 08:06 11403700 /lib/tls/i686/cmov/librt-2.11.1.so 00e6b000-00e6c000 rw-p 00007000 08:06 11403700 /lib/tls/i686/cmov/librt-2.11.1.so 00f70000-00fb4000 r-xp 00000000 08:06 11403907 /lib/libssl.so.0.9.8Aborted

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  • RHEL server Yum dependencies not working

    - by Tony
    I have a redhat server that isnt resolving dependencies correctly. I want to install httpd via yum "yum install httpd" and it installs correctly, but when i go to start httpd I get the following error: /sbin/service httpd restart Stopping httpd: [FAILED] Starting httpd: /usr/sbin/httpd: error while loading shared libraries: libaprutil-1.so.0: cannot open shared object file: No such file or directory [FAILED] It is missing the dependency for apr-util package. Weirdly the i386 package is installed and not the x86_64 package. Can anyone shed any light on why the dependencies might not be resolved correctly? ldd /usr/sbin/httpd libm.so.6 => /lib64/libm.so.6 (0x00002b02370db000) libpcre.so.0 => /lib64/libpcre.so.0 (0x00002b023735e000) libselinux.so.1 => /lib64/libselinux.so.1 (0x00002b023757a000) libaprutil-1.so.0 => not found libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00002b0237793000) libldap-2.3.so.0 => /usr/lib64/libldap-2.3.so.0 (0x00002b02379cb000) liblber-2.3.so.0 => /usr/lib64/liblber-2.3.so.0 (0x00002b0237c06000) libdb-4.3.so => /lib64/libdb-4.3.so (0x00002b0237e14000) libexpat.so.0 => /lib64/libexpat.so.0 (0x00002b0238109000) libapr-1.so.0 => not found libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b023832c000) libdl.so.2 => /lib64/libdl.so.2 (0x00002b0238547000) libc.so.6 => /lib64/libc.so.6 (0x00002b023874c000) libsepol.so.1 => /lib64/libsepol.so.1 (0x00002b0238aa3000) /lib64/ld-linux-x86-64.so.2 (0x00002b0236ebe000) libresolv.so.2 => /lib64/libresolv.so.2 (0x00002b0238ce9000) libsasl2.so.2 => /usr/lib64/libsasl2.so.2 (0x00002b0238eff000) libssl.so.6 => /lib64/libssl.so.6 (0x00002b0239118000) libcrypto.so.6 => /lib64/libcrypto.so.6 (0x00002b0239364000) libgssapi_krb5.so.2 => /usr/lib64/libgssapi_krb5.so.2 (0x00002b02396b6000) libkrb5.so.3 => /usr/lib64/libkrb5.so.3 (0x00002b02398e4000) libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00002b0239b79000) libk5crypto.so.3 => /usr/lib64/libk5crypto.so.3 (0x00002b0239d7c000) libz.so.1 => /usr/lib64/libz.so.1 (0x00002b0239fa1000) libkrb5support.so.0 => /usr/lib64/libkrb5support.so.0 (0x00002b023a1b5000) libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00002b023a3be000) yet this is the i386 package apr-util-1.2.7-11.el5.i386 : Apache Portable Runtime Utility library Repo : installed Matched from: Filename : /usr/lib/libaprutil-1.so.0

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  • Unable to start Android emulator > 1.5

    - by Cicatrice
    Hi ! I got this trace when I tried to launch android 1.6 or 2.1. Android 1.5 is working fine. I tried to reinstall each SDK, but there is no way to get it working. I created those AVD with Eclipse plugin. geo@geo-laptop:~> android/android-sdk-linux_86/tools/emulator -avd a16 *** glibc detected *** android/android-sdk-linux_86/tools/emulator: free(): invalid pointer: 0x45454545 *** ======= Backtrace: ========= /lib/libc.so.6(+0x6df7b)[0xb748cf7b] /lib/libc.so.6(cfree+0xd9)[0xb7491ac9] android/android-sdk-linux_86/tools/emulator[0x80db20c] android/android-sdk-linux_86/tools/emulator[0x840eb38] ======= Memory map: ======== 08048000-08246000 r-xp 00000000 08:06 5693701 /home/geo/android/android-sdk-linux_86/tools/emulator 08246000-08249000 rw-p 001fd000 08:06 5693701 /home/geo/android/android-sdk-linux_86/tools/emulator 08249000-08445000 rw-p 00000000 00:00 0 08445000-08447000 rwxp 00000000 00:00 0 08447000-0874c000 rw-p 00000000 00:00 0 [heap] ad8e9000-ada86000 rw-s 00000000 00:04 85229580 /SYSV00000000 (deleted) ada86000-adced000 rw-p 00000000 00:00 0 adced000-add0d000 rw-s 00000000 00:04 84770825 /SYSV0056a4d6 (deleted) add0d000-adde4000 r-xp 00000000 08:05 22591 /usr/lib/libasound.so.2.0.0 adde4000-adde5000 ---p 000d7000 08:05 22591 /usr/lib/libasound.so.2.0.0 adde5000-adde8000 r--p 000d7000 08:05 22591 /usr/lib/libasound.so.2.0.0 adde8000-adde9000 rw-p 000da000 08:05 22591 /usr/lib/libasound.so.2.0.0 adde9000-ade09000 rw-s 00000000 00:05 3268 /dev/snd/pcmC0D0p ade09000-b3e0b000 rw-p 00000000 00:00 0 b3e0b000-b3e0c000 ---p 00000000 00:00 0 b3e0c000-b55cd000 rw-p 00000000 00:00 0 b55cd000-b6dcd000 rwxp 00000000 00:00 0 b6dcd000-b6ea3000 rw-p 00000000 00:00 0 b6ea4000-b7205000 rw-p 00000000 00:00 0 b7205000-b7209000 r-xp 00000000 08:05 22491 /usr/lib/libXfixes.so.3.1.0 b7209000-b720a000 r--p 00003000 08:05 22491 /usr/lib/libXfixes.so.3.1.0 b720a000-b720b000 rw-p 00004000 08:05 22491 /usr/lib/libXfixes.so.3.1.0 b7212000-b7222000 rw-s 00000000 00:05 3269 /dev/snd/pcmC0D0c b7222000-b7226000 r-xp 00000000 08:05 22588 /usr/lib/alsa-lib/libasound_module_rate_speexrate.so b7226000-b7227000 r--p 00003000 08:05 22588 /usr/lib/alsa-lib/libasound_module_rate_speexrate.so b7227000-b7228000 rw-p 00004000 08:05 22588 /usr/lib/alsa-lib/libasound_module_rate_speexrate.so b7228000-b7229000 rw-s 81000000 00:05 3268 /dev/snd/pcmC0D0p b7229000-b722a000 r--s 80000000 00:05 3268 /dev/snd/pcmC0D0p b722a000-b722b000 rw-s 00000000 00:04 84738056 /SYSV0056a4d5 (deleted) b722b000-b7276000 r--p 00000000 08:05 85242 /var/cache/libx11/compose/l4_024_313cb605_00280cc0 b7276000-b72b5000 r--p 00000000 08:05 20724 /usr/lib/locale/en_US.utf8/LC_CTYPE b72b5000-b73d2000 r--p 00000000 08:05 101088 /usr/lib/locale/en_US.utf8/LC_COLLATE b73d2000-b73d9000 r-xp 00000000 08:05 22991 /usr/lib/libXrandr.so.2.2.0 b73d9000-b73da000 r--p 00006000 08:05 22991 /usr/lib/libXrandr.so.2.2.0 b73da000-b73db000 rw-p 00007000 08:05 22991 /usr/lib/libXrandr.so.2.2.0 b73db000-b73e4000 r-xp 00000000 08:05 4146 /usr/lib/libXrender.so.1.3.0 b73e4000-b73e5000 r--p 00008000 08:05 4146 /usr/lib/libXrender.so.1.3.0 b73e5000-b73e6000 rw-p 00009000 08:05 4146 /usr/lib/libXrender.so.1.3.0 b73e6000-b73f7000 r-xp 00000000 08:05 3705 /usr/lib/libXext.so.6.4.0 b73f7000-b73f8000 r--p 00010000 08:05 3705 /usr/lib/libXext.so.6.4.0 b73f8000-b73f9000 rw-p 00011000 08:05 3705 /usr/lib/libXext.so.6.4.0 b73f9000-b73fa000 rw-p 00000000 00:00 0 b73fa000-b73fc000 r-xp 00000000 08:05 8573 /usr/lib/libXau.so.6.0.0 b73fc000-b73fd000 r--p 00001000 08:05 8573 /usr/lib/libXau.so.6.0.0 b73fd000-b73fe000 rw-p 00002000 08:05 8573 /usr/lib/libXau.so.6.0.0 b73fe000-b73ff000 rw-p 00000000 00:00 0 b73ff000-b741d000 r-xp 00000000 08:05 3862 /usr/lib/libxcb.so.1.1.0 b741d000-b741e000 r--p 0001d000 08:05 3862 /usr/lib/libxcb.so.1.1.0 b741e000-b741f000 rw-p 0001e000 08:05 3862 /usr/lib/libxcb.so.1.1.0 b741f000-b7583000 r-xp 00000000 08:05 39690 /lib/libc-2.11.1.so b7583000-b7584000 ---p 00164000 08:05 39690 /lib/libc-2.11.1.so b7584000-b7586000 r--p 00164000 08:05 39690 /lib/libc-2.11.1.so b7586000-b7587000 rw-p 00166000 08:05 39690 /lib/libc-2.11.1.so b7587000-b758a000 rw-p 00000000 00:00 0 b758a000-b75a6000 r-xp 00000000 08:05 11519 /lib/libgcc_s.so.1 b75a6000-b75a7000 r--p 0001b000 08:05 11519 /lib/libgcc_s.so.1 b75a7000-b75a8000 rw-p 0001c000 08:05 11519 /lib/libgcc_s.so.1 b75a8000-b768b000 r-xp 00000000 08:05 85419 /usr/lib/libstdc++.so.6.0.14 b768b000-b768c000 ---p 000e3000 08:05 85419 /usr/lib/libstdc++.so.6.0.14 b768c000-b7690000 r--p 000e3000 08:05 85419 /usr/lib/libstdc++.so.6.0.14 b7690000-b7691000 rw-p 000e7000 08:05 85419 /usr/lib/libstdc++.so.6.0.14 b7691000-b7698000 rw-p 00000000 00:00 0 b7698000-b76c0000 r-xp 00000000 08:05 39698 /lib/libm-2.11.1.so b76c0000-b76c1000 r--p 00027000 08:05 39698 /lib/libm-2.11.1.so b76c1000-b76c2000 rw-p 00028000 08:05 39698 /lib/libm-2.11.1.so b76c2000-b76d9000 r-xp 00000000 08:05 39716 /lib/libpthread-2.11.1.so b76d9000-b76da000 r--p 00016000 08:05 39716 /lib/libpthread-2.11.1.so b76da000-b76db000 rw-p 00017000 08:05 39716 /lib/libpthread-2.11.1.so b76db000-b76de000 rw-p 00000000 00:00 0 b76de000-b76e1000 r-xp 00000000 08:05 39696 /lib/libdl-2.11.1.so b76e1000-b76e2000 r--p 00002000 08:05 39696 /lib/libdl-2.11.1.so b76e2000-b76e3000 rw-p 00003000 08:05 39696 /lib/libdl-2.11.1.so b76e3000-b76eb000 r-xp 00000000 08:05 39720 /lib/librt-2.11.1.so b76eb000-b76ec000 r--p 00007000 08:05 39720 /lib/librt-2.11.1.so b76ec000-b76ed000 rw-p 00008000 08:05 39720 /lib/librt-2.11.1.so b76ed000-b76ef000 r-xp 00000000 08:05 39725 /lib/libutil-2.11.1.so b76ef000-b76f0000 r--p 00001000 08:05 39725 /lib/libutil-2.11.1.so b76f0000-b76f1000 rw-p 00002000 08:05 39725 /lib/libutil-2.11.1.so b76f1000-b7828000 r-xp 00000000 08:05 4550 /usr/lib/libX11.so.6.3.0 b7828000-b7829000 r--p 00136000 08:05 4550 /usr/lib/libX11.so.6.3.0 b7829000-b782c000 rw-p 00137000 08:05 4550 /usr/lib/libX11.so.6.3.0 b782c000-b782d000 rw-s 81000000 00:05 3269 /dev/snd/pcmC0D0c b782d000-b782e000 r--s 80000000 00:05 3269 /dev/snd/pcmC0D0c b782e000-b782f000 rw-s 00000000 00:04 82771979 /SYSV0056a4d7 (deleted) b782f000-b7839000 r-xp 00000000 08:05 22208 /usr/lib/libXcursor.so.1.0.2 b7839000-b783a000 r--p 00009000 08:05 22208 /usr/lib/libXcursor.so.1.0.2 b783a000-b783b000 rw-p 0000a000 08:05 22208 /usr/lib/libXcursor.so.1.0.2 b783b000-b783c000 r--p 00000000 08:05 20194 /usr/lib/locale/en_US.utf8/LC_NUMERIC b783c000-b783d000 r--p 00000000 08:05 100190 /usr/lib/locale/en_US.utf8/LC_TIME b783d000-b783e000 r--p 00000000 08:05 100189 /usr/lib/locale/en_US.utf8/LC_MONETARY[1] 24082 abort android/android-sdk-linux_86/tools/emulator -avd a16

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  • Segfaulting Java process

    - by zenmonkey
    I've a java process that is working on some large data set in memory. I've seen it crash with a SIGSEGV signal sometimes, so i was wondering some potential causes and fixes could do. Caues: - JVM bug - Native library bug (e.g pthreads etc) - JNI bug in user code Fixes: - Upgrade to new JVM In my particular case, this is the output form the log file (pruned) A fatal error has been detected by the Java Runtime Environment: # SIGSEGV (0xb) at pc=0x00002aaaaacd1b94, pid=32116, tid=1086544208 # JRE version: 6.0_14-b08 Java VM: Java HotSpot(TM) 64-Bit Server VM (14.0-b16 mixed mode linux-amd64 ) Problematic frame: C [libpthread.so.0+0xab94] pthread_cond_timedwait+0x154 # If you would like to submit a bug report, please visit: http://java.sun.com/webapps/bugreport/crash.jsp # --------------- T H R E A D --------------- Current thread (0x00002aacaad41000): WatcherThread [stack: 0x0000000040b35000,0x0000000040c36000] [id=32141] siginfo:si_signo=SIGSEGV: si_errno=0, si_code=1 (SEGV_MAPERR), si_addr=0x00002aabc40008c0 Registers: RAX=0x0000000000000000, RBX=0x0000000000000000, RCX=0x0000000000000000, RDX=0x0000000000000002 RSP=0x0000000040c34cc0, RBP=0x0000000040c34d80, RSI=0x0000000000000001, RDI=0x00002aabc40008c0 R8 =0x00002aacaad42528, R9 =0x0000000000000000, R10=0x0000000040c34cd8, R11=0x0000000000000202 R12=0x0000000000000001, R13=0x0000000040c34d40, R14=0xffffffffffffff92, R15=0x00002aacaad42550 RIP=0x00002aaaaacd1b94, EFL=0x0000000000010246, CSGSFS=0x000000000000e033, ERR=0x0000000000000006 TRAPNO=0x000000000000000e Top of Stack: (sp=0x0000000040c34cc0) 0x0000000040c34cc0: 0000000000000000 00002aabc40008c0 0x0000000040c34cd0: 00002aacaad42528 0000000000000000 0x0000000040c34ce0: 0000000002fae0e0 0000000000000000 0x0000000040c34cf0: 00002aaaaacd1750 0000000040c34cc0 0x0000000040c34d00: 00002aacaad42528 0000000000000000 0x0000000040c34d10: 00002aacaad42528 00002aacaad42500 0x0000000040c34d20: 0000000000000032 00002aaaabadf876 0x0000000040c34d30: fffffffdaad40e80 0000000040c34d40 0x0000000040c34d40: 000000004bbb7166 0000000015f07098 0x0000000040c34d50: 0000000040c34d80 00138cd32df59cce 0x0000000040c34d60: 431bde82d7b634db 00002aacaad429c0 0x0000000040c34d70: 0000000000000032 00002aacaad429c0 0x0000000040c34d80: 0000000040c34e00 00002aaaabadda6d 0x0000000040c34d90: 0000000040c34da0 00002aacaad42500 0x0000000040c34da0: 00002aacaad429c0 00002aaa00000002 0x0000000040c34db0: 0000000000000001 0000000000000002 0x0000000040c34dc0: 0000000040c34dd0 00002aaaabb6f613 0x0000000040c34dd0: 0000000040c34e00 00002aacaad41000 0x0000000040c34de0: 0000000000000032 00002aacaad429c0 0x0000000040c34df0: 00002aacaad41000 0000000000001000 0x0000000040c34e00: 0000000040c34e60 00002aaaabbc39fb 0x0000000040c34e10: 0000000040c34e40 00002aaaabab868f 0x0000000040c34e20: 00002aacaad41000 00002aacaad42aa0 0x0000000040c34e30: 00002aacaad42aa0 00002aaaabe10630 0x0000000040c34e40: 00002aaaabe10630 00002aacaad42aa0 0x0000000040c34e50: 00002aacaad429c0 00002aacaad41000 0x0000000040c34e60: 0000000040c35130 00002aaaabadff9f 0x0000000040c34e70: 0000000000000000 0000000000000000 0x0000000040c34e80: 0000000000000000 0000000000000000 0x0000000040c34e90: 0000000000000000 0000000000000000 0x0000000040c34ea0: 0000000000000000 0000000000000000 0x0000000040c34eb0: 0000000000000000 0000000000000000 Instructions: (pc=0x00002aaaaacd1b94) 0x00002aaaaacd1b84: 88 22 00 00 48 8b 7c 24 08 be 01 00 00 00 31 c0 0x00002aaaaacd1b94: f0 0f b1 37 0f 85 e8 00 00 00 8b 57 2c 48 8b 47 Stack: [0x0000000040b35000,0x0000000040c36000], sp=0x0000000040c34cc0, free space=1023k Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code) C [libpthread.so.0+0xab94] pthread_cond_timedwait+0x154 V [libjvm.so+0x594a6d] V [libjvm.so+0x67a9fb] V [libjvm.so+0x596f9f] --------------- P R O C E S S --------------- Java Threads: ( = current thread ) 0x00002aacaad3f000 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=32140, stack(0x0000000040a34000,0x0000000040b35000)] 0x00002aacaad3c000 JavaThread "CompilerThread1" daemon [_thread_blocked, id=32139, stack(0x0000000040933000,0x0000000040a34000)] 0x00002aacaad37800 JavaThread "CompilerThread0" daemon [_thread_blocked, id=32138, stack(0x0000000040832000,0x0000000040933000)] 0x00002aacaad36800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=32137, stack(0x0000000040731000,0x0000000040832000)] 0x00002aacaab7d800 JavaThread "Finalizer" daemon [_thread_blocked, id=32136, stack(0x0000000040630000,0x0000000040731000)] 0x00002aacaab7b800 JavaThread "Reference Handler" daemon [_thread_blocked, id=32135, stack(0x000000004052f000,0x0000000040630000)] 0x0000000040115800 JavaThread "main" [_thread_blocked, id=32117, stack(0x000000004012b000,0x000000004022c000)] Other Threads: 0x00002aacaab75000 VMThread [stack: 0x000000004042e000,0x000000004052f000] [id=32134] =0x00002aacaad41000 WatcherThread [stack: 0x0000000040b35000,0x0000000040c36000] [id=32141] VM state:at safepoint (normal execution) VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event]) [0x0000000040112e80] Threads_lock - owner thread: 0x00002aacaab75000 [0x0000000040113380] Heap_lock - owner thread: 0x0000000040115800 Heap PSYoungGen total 1854528K, used 1029248K [0x00002aac025a0000, 0x00002aaca8340000, 0x00002aaca9040000) eden space 1029248K, 100% used [0x00002aac025a0000,0x00002aac412c0000,0x00002aac412c0000) from space 825280K, 0% used [0x00002aac412c0000,0x00002aac412c0000,0x00002aac738b0000) to space 812800K, 0% used [0x00002aac76980000,0x00002aac76980000,0x00002aaca8340000) PSOldGen total 4423680K, used 4423651K [0x00002aaab5040000, 0x00002aabc3040000, 0x00002aac025a0000) object space 4423680K, 99% used [0x00002aaab5040000,0x00002aabc3038fe8,0x00002aabc3040000) PSPermGen total 21248K, used 5848K [0x00002aaaafc40000, 0x00002aaab1100000, 0x00002aaab5040000) object space 21248K, 27% used [0x00002aaaafc40000,0x00002aaab01f61f0,0x00002aaab1100000) Dynamic libraries: 40000000-40009000 r-xp 00000000 08:01 313415 /usr/java/jdk1.6.0_14/bin/java 40108000-4010a000 rwxp 00008000 08:01 313415 /usr/java/jdk1.6.0_14/bin/java 4010a000-4012b000 rwxp 4010a000 00:00 0 [heap] 4012b000-4012e000 ---p 4012b000 00:00 0 4012e000-4022c000 rwxp 4012e000 00:00 0 4022c000-4022d000 ---p 4022c000 00:00 0 4022d000-4032d000 rwxp 4022d000 00:00 0 4032d000-4032e000 ---p 4032d000 00:00 0 4032e000-4042e000 rwxp 4032e000 00:00 0 4042e000-4042f000 ---p 4042e000 00:00 0 4042f000-4052f000 rwxp 4042f000 00:00 0 4052f000-40532000 ---p 4052f000 00:00 0 40532000-40630000 rwxp 40532000 00:00 0 40630000-40633000 ---p 40630000 00:00 0 40633000-40731000 rwxp 40633000 00:00 0 40731000-40734000 ---p 40731000 00:00 0 40734000-40832000 rwxp 40734000 00:00 0 40832000-40835000 ---p 40832000 00:00 0 40835000-40933000 rwxp 40835000 00:00 0 40933000-40936000 ---p 40933000 00:00 0 40936000-40a34000 rwxp 40936000 00:00 0 40a34000-40a37000 ---p 40a34000 00:00 0 40a37000-40b35000 rwxp 40a37000 00:00 0 40b35000-40b36000 ---p 40b35000 00:00 0 40b36000-40c36000 rwxp 40b36000 00:00 0 2aaaaaaab000-2aaaaaac6000 r-xp 00000000 08:01 49198 /lib64/ld-2.7.so 2aaaaaac6000-2aaaaaac7000 rwxp 2aaaaaac6000 00:00 0 2aaaaaac7000-2aaaaaad0000 r-xs 0006d000 08:10 29851669 /mnt/home/jatten/workspace/common/build/lib/common.jar 2aaaaaad2000-2aaaaaad3000 rwxp 2aaaaaad2000 00:00 0 2aaaaaad3000-2aaaaaae0000 r-xp 00000000 08:01 315357 /usr/java/jdk1.6.0_14/jre/lib/amd64/libverify.so 2aaaaaae0000-2aaaaabdf000 ---p 0000d000 08:01 315357 /usr/java/jdk1.6.0_14/jre/lib/amd64/libverify.so 2aaaaabdf000-2aaaaabe2000 rwxp 0000c000 08:01 315357 /usr/java/jdk1.6.0_14/jre/lib/amd64/libverify.so 2aaaaabe2000-2aaaaac0a000 rwxp 2aaaaabe2000 00:00 0 2aaaaac0a000-2aaaaac0f000 r-xs 0003a000 08:10 30326840 /mnt/home/jatten/workspace/common_ml20010405/build/lib/common_ml.jar 2aaaaac0f000-2aaaaac12000 r-xs 00020000 08:10 29786222 /mnt/home/jatten/pagescorer.jar 2aaaaacc5000-2aaaaacc6000 r-xp 0001a000 08:01 49198 /lib64/ld-2.7.so 2aaaaacc6000-2aaaaacc7000 rwxp 0001b000 08:01 49198 /lib64/ld-2.7.so 2aaaaacc7000-2aaaaacdd000 r-xp 00000000 08:01 49280 /lib64/libpthread-2.7.so 2aaaaacdd000-2aaaaaedc000 ---p 00016000 08:01 49280 /lib64/libpthread-2.7.so 2aaaaaedc000-2aaaaaedd000 r-xp 00015000 08:01 49280 /lib64/libpthread-2.7.so 2aaaaaedd000-2aaaaaede000 rwxp 00016000 08:01 49280 /lib64/libpthread-2.7.so 2aaaaaede000-2aaaaaee2000 rwxp 2aaaaaede000 00:00 0 2aaaaaee2000-2aaaaaee9000 r-xp 00000000 08:01 315360 /usr/java/jdk1.6.0_14/jre/lib/amd64/jli/libjli.so 2aaaaaee9000-2aaaaafea000 ---p 00007000 08:01 315360 /usr/java/jdk1.6.0_14/jre/lib/amd64/jli/libjli.so 2aaaaafea000-2aaaaafec000 rwxp 00008000 08:01 315360 /usr/java/jdk1.6.0_14/jre/lib/amd64/jli/libjli.so 2aaaaafec000-2aaaaafee000 r-xp 00000000 08:01 49240 /lib64/libdl-2.7.so 2aaaaafee000-2aaaab1ee000 ---p 00002000 08:01 49240 /lib64/libdl-2.7.so 2aaaab1ee000-2aaaab1ef000 r-xp 00002000 08:01 49240 /lib64/libdl-2.7.so 2aaaab1ef000-2aaaab1f0000 rwxp 00003000 08:01 49240 /lib64/libdl-2.7.so 2aaaab1f0000-2aaaab1f1000 rwxp 2aaaab1f0000 00:00 0 2aaaab1f1000-2aaaab33e000 r-xp 00000000 08:01 49219 /lib64/libc-2.7.so 2aaaab33e000-2aaaab53e000 ---p 0014d000 08:01 49219 /lib64/libc-2.7.so 2aaaab53e000-2aaaab542000 r-xp 0014d000 08:01 49219 /lib64/libc-2.7.so 2aaaab542000-2aaaab543000 rwxp 00151000 08:01 49219 /lib64/libc-2.7.so 2aaaab543000-2aaaab549000 rwxp 2aaaab543000 00:00 0 2aaaab549000-2aaaabca7000 r-xp 00000000 08:01 315371 /usr/java/jdk1.6.0_14/jre/lib/amd64/server/libjvm.so 2aaaabca7000-2aaaabda6000 ---p 0075e000 08:01 315371 /usr/java/jdk1.6.0_14/jre/lib/amd64/server/libjvm.so 2aaaabda6000-2aaaabf1e000 rwxp 0075d000 08:01 315371 /usr/java/jdk1.6.0_14/jre/lib/amd64/server/libjvm.so 2aaaabf1e000-2aaaabf5c000 rwxp 2aaaabf1e000 00:00 0 2aaaabf67000-2aaaabfe9000 r-xp 00000000 08:01 49263 /lib64/libm-2.7.so 2aaaabfe9000-2aaaac1e8000 ---p 00082000 08:01 49263 /lib64/libm-2.7.so 2aaaac1e8000-2aaaac1e9000 r-xp 00081000 08:01 49263 /lib64/libm-2.7.so 2aaaac1e9000-2aaaac1ea000 rwxp 00082000 08:01 49263 /lib64/libm-2.7.so 2aaaac1ea000-2aaaac1f2000 r-xp 00000000 08:01 49283 /lib64/librt-2.7.so 2aaaac1f2000-2aaaac3f1000 ---p 00008000 08:01 49283 /lib64/librt-2.7.so 2aaaac3f1000-2aaaac3f2000 r-xp 00007000 08:01 49283 /lib64/librt-2.7.so 2aaaac3f2000-2aaaac3f3000 rwxp 00008000 08:01 49283 /lib64/librt-2.7.so 2aaaac3f3000-2aaaac41c000 r-xp 00000000 08:01 315336 /usr/java/jdk1.6.0_14/jre/lib/amd64/libjava.so 2aaaac41c000-2aaaac51b000 ---p 00029000 08:01 315336 /usr/java/jdk1.6.0_14/jre/lib/amd64/libjava.so 2aaaac51b000-2aaaac522000 rwxp 00028000 08:01 315336 /usr/java/jdk1.6.0_14/jre/lib/amd64/libjava.so 2aaaac522000-2aaaac523000 ---p 2aaaac522000 00:00 0 2aaaac523000-2aaaac524000 rwxp 2aaaac523000 00:00 0 2aaaac52d000-2aaaac542000 r-xp 00000000 08:01 49265 /lib64/libnsl-2.7.so 2aaaac542000-2aaaac741000 ---p 00015000 08:01 49265 /lib64/libnsl-2.7.so 2aaaac741000-2aaaac742000 r-xp 00014000 08:01 49265 /lib64/libnsl-2.7.so 2aaaac742000-2aaaac743000 rwxp 00015000 08:01 49265 /lib64/libnsl-2.7.so 2aaaac743000-2aaaac745000 rwxp 2aaaac743000 00:00 0 2aaaac745000-2aaaac74c000 r-xp 00000000 08:01 315362 /usr/java/jdk1.6.0_14/jre/lib/amd64/native_threads/libhpi.so 2aaaac74c000-2aaaac84d000 ---p 00007000 08:01 315362 /usr/java/jdk1.6.0_14/jre/lib/amd64/native_threads/libhpi.so 2aaaac84d000-2aaaac84f000 rwxp 00008000 08:01 315362 /usr/java/jdk1.6.0_14/jre/lib/amd64/native_threads/libhpi.so 2aaaac84f000-2aaaac850000 rwxp 2aaaac84f000 00:00 0 2aaaac850000-2aaaac858000 rwxs 00000000 08:01 229379 /tmp/hsperfdata_jatten/32116 2aaaac85b000-2aaaac865000 r-xp 00000000 08:01 49269 /lib64/libnss_files-2.7.so 2aaaac865000-2aaaaca64000 ---p 0000a000 08:01 49269 /lib64/libnss_files-2.7.so 2aaaaca64000-2aaaaca65000 r-xp 00009000 08:01 49269 /lib64/libnss_files-2.7.so 2aaaaca65000-2aaaaca66000 rwxp 0000a000 08:01 49269 /lib64/libnss_files-2.7.so 2aaaaca66000-2aaaaca74000 r-xp 00000000 08:01 315358 /usr/java/jdk1.6.0_14/jre/lib/amd64/libzip.so 2aaaaca74000-2aaaacb76000 ---p 0000e000 08:01 315358 /usr/java/jdk1.6.0_14/jre/lib/amd64/libzip.so 2aaaacb76000-2aaaacb79000 rwxp 00010000 08:01 315358 /usr/java/jdk1.6.0_14/jre/lib/amd64/libzip.so 2aaaacb79000-2aaaacdea000 rwxp 2aaaacb79000 00:00 0 2aaaacdea000-2aaaafb7a000 rwxp 2aaaacdea000 00:00 0 2aaaafb7a000-2aaaafb84000 rwxp 2aaaafb7a000 00:00 0 2aaaafb84000-2aaaafc3a000 rwxp 2aaaafb84000 00:00 0 2aaaafc40000-2aaab1100000 rwxp 2aaaafc40000 00:00 0 2aaab1100000-2aaab5040000 rwxp 2aaab1100000 00:00 0 2aaab5040000-2aabc3040000 rwxp 2aaab5040000 00:00 0 2aac025a0000-2aaca8340000 rwxp 2aac025a0000 00:00 0 2aaca8340000-2aaca9040000 rwxp 2aaca8340000 00:00 0 2aaca9040000-2aaca904b000 rwxp 2aaca9040000 00:00 0 2aaca904b000-2aaca906a000 rwxp 2aaca904b000 00:00 0 2aaca906a000-2aaca98da000 rwxp 2aaca906a000 00:00 0 2aaca98da000-2aaca9ad4000 rwxp 2aaca98da000 00:00 0 2aaca9ad4000-2aacaa004000 rwxp 2aaca9ad4000 00:00 0 2aacaa004000-2aacaa00a000 rwxp 2aacaa004000 00:00 0 2aacaa00a000-2aacaa87b000 rwxp 2aacaa00a000 00:00 0 2aacaa87b000-2aacaaa76000 rwxp 2aacaa87b000 00:00 0 2aacaaa76000-2aacaaa81000 rwxp 2aacaaa76000 00:00 0 2aacaaa81000-2aacaaaa0000 rwxp 2aacaaa81000 00:00 0 2aacaaaa0000-2aacaaba0000 rwxp 2aacaaaa0000 00:00 0 2aacaaba0000-2aacaad36000 r-xs 02fb1000 08:01 315318 /usr/java/jdk1.6.0_14/jre/lib/rt.jar 2aacaad36000-2aacaaf36000 rwxp 2aacaad36000 00:00 0 2aacaaf36000-2aacaaf49000 r-xp 00000000 08:01 315349 /usr/java/jdk1.6.0_14/jre/lib/amd64/libnet.so 2aacaaf49000-2aacab04a000 ---p 00013000 08:01 315349 /usr/java/jdk1.6.0_14/jre/lib/amd64/libnet.so 2aacab04a000-2aacab04d000 rwxp 00014000 08:01 315349 /usr/java/jdk1.6.0_14/jre/lib/amd64/libnet.so 2aacab058000-2aacab05c000 r-xp 00000000 08:01 49268 /lib64/libnss_dns-2.7.so 2aacab05c000-2aacab25b000 ---p 00004000 08:01 49268 /lib64/libnss_dns-2.7.so 2aacab25b000-2aacab25c000 r-xp 00003000 08:01 49268 /lib64/libnss_dns-2.7.so 2aacab25c000-2aacab25d000 rwxp 00004000 08:01 49268 /lib64/libnss_dns-2.7.so 2aacab25d000-2aacab26e000 r-xp 00000000 08:01 49282 /lib64/libresolv-2.7.so 2aacab26e000-2aacab46e000 ---p 00011000 08:01 49282 /lib64/libresolv-2.7.so 2aacab46e000-2aacab46f000 r-xp 00011000 08:01 49282 /lib64/libresolv-2.7.so 2aacab46f000-2aacab470000 rwxp 00012000 08:01 49282 /lib64/libresolv-2.7.so 2aacab470000-2aacab572000 rwxp 2aacab470000 00:00 0 2aacab572000-2aacab57e000 r-xs 00081000 08:10 29851828 /mnt/home/jatten/workspace/common/lib/google-collect-1.0.jar 2aacab57e000-2aacab585000 r-xs 000aa000 08:10 29851946 /mnt/home/jatten/workspace/common/lib/mysql-connector-java-5.1.8-bin.jar 2aacab585000-2aacab58d000 r-xs 00028000 08:10 29851949 /mnt/home/jatten/workspace/common/lib/xml-apis.jar 2aacab58d000-2aacab591000 r-xs 0002f000 08:10 29851947 /mnt/home/jatten/workspace/common/lib/commons-beanutils-core-1.8.2.jar 2aacab591000-2aacab59e000 r-xs 0007f000 08:10 29851943 /mnt/home/jatten/workspace/common/lib/commons-collections-3.2.jar 2aacab59e000-2aacab5a3000 r-xs 00026000 08:10 29851942 /mnt/home/jatten/workspace/common/lib/httpcore-4.0.jar 2aacab5a3000-2aacab5a9000 r-xs 00030000 08:10 29851932 /mnt/home/jatten/workspace/common/lib/junit-dep-4.8.1.jar 2aacab5a9000-2aacab5ac000 r-xs 00011000 08:10 29851922 /mnt/home/jatten/workspace/common/lib/servlet.jar 2aacab5ac000-2aacab5ae000 r-xs 00009000 08:10 29851937 /mnt/home/jatten/workspace/common/lib/gsb.jar 2aacab5ae000-2aacab5b5000 r-xs 00059000 08:10 29851930 /mnt/home/jatten/workspace/common/lib/log4j-1.2.15.jar 2aacab5b5000-2aacab6b5000 rwxp 2aacab5b5000 00:00 0 2aacab6b5000-2aacab6b7000 r-xs 00009000 08:10 29851956 /mnt/home/jatten/workspace/common/lib/gsb-src.jar 2aacab6b7000-2aacab7b7000 rwxp 2aacab6b7000 00:00 0 2aacab7b7000-2aacab7cf000 r-xs 00115000 08:10 29851938 /mnt/home/jatten/workspace/common/lib/xercesImpl.jar 2aacab7cf000-2aacab7d1000 r-xs 00009000 08:10 29851957 /mnt/home/jatten/workspace/common/lib/velocity-tools-view-1.0.jar 2aacab7d1000-2aacab7d3000 r-xs 00009000 08:10 29851939 /mnt/home/jatten/workspace/common/lib/commons-cli-1.2.jar 2aacab7d3000-2aacab7d9000 r-xs 00034000 08:10 29851955 /mnt/home/jatten/workspace/common/lib/junit-4.8.1.jar 2aacab7d9000-2aacab7db000 r-xs 0000e000 08:10 29851917 /mnt/home/jatten/workspace/common/lib/jakarta-oro-2.0.8.jar 2aacab7db000-2aacab858000 r-xs 0031d000 08:10 29851916 /mnt/home/jatten/workspace/common/lib/poi-ooxml-schemas-3.6-20091214.jar 2aacab858000-2aacab85c000 r-xs 00028000 08:10 29851936 /mnt/home/jatten/workspace/common/lib/httpcore-nio-4.0.jar 2aacab85c000-2aacab85e000 r-xs 00005000 08:10 29851940 /mnt/home/jatten/workspace/common/lib/commons-beanutils-bean-collections-1.8.2.jar 2aacab85e000-2aacab864000 r-xs 00059000 08:10 29851919 /mnt/home/jatten/workspace/common/lib/mail-1.4.jar 2aacab864000-2aacab866000 r-xs 0000d000 08:10 29851950 /mnt/home/jatten/workspace/common/lib/commons-logging-1.1.1.jar 2aacab866000-2aacab86c000 r-xs 00045000 08:10 29851924 /mnt/home/jatten/workspace/common/lib/commons-httpclient-3.1.jar 2aacab86c000-2aacab877000 r-xs 00074000 08:10 29851931 /mnt/home/jatten/workspace/common/lib/velocity-dep-1.4.jar 2aacab877000-2aacab87f000 r-xs 00051000 08:10 29851954 /mnt/home/jatten/workspace/common/lib/velocity-1.4.jar 2aacab87f000-2aacab884000 r-xs 00034000 08:10 29851958 /mnt/home/jatten/workspace/common/lib/commons-beanutils-1.8.2.jar 2aacab884000-2aacab889000 r-xs 00048000 08:10 29851918 /mnt/home/jatten/workspace/common/lib/dom4j-1.6.1.jar 2aacab889000-2aacab8c6000 r-xs 0024f000 08:10 29851914 /mnt/home/jatten/workspace/common/lib/xmlbeans-2.3.0.jar 2aacab8c6000-2aacab8cb000 r-xs 00033000 08:10 29851929 /mnt/home/jatten/workspace/common/lib/xmemcached-1.2.3.jar 2aacab8cb000-2aacab8cd000 r-xs 00005000 08:10 29851928 /mnt/home/jatten/workspace/common/lib/org.hamcrest.core_1.1.0.v20090501071000.jar 2aacab8cd000-2aacab8d0000 r-xs 0000a000 08:10 29851944 /mnt/home/jatten/workspace/common/lib/persistence-api-1.0.jar 2aacab8d0000-2aacab8d6000 r-xs 0005f000 08:10 29851926 /mnt/home/jatten/workspace/common/lib/poi-ooxml-3.6-20091214.jar 2aacab8d6000-2aacab8d7000 r-xs 0002b000 08:10 29851951 /mnt/home/jatten/workspace/common/lib/maxmind.jar 2aacab8d7000-2aacab8d8000 r-xs 00002000 08:10 29851935 /mnt/home/jatten/workspace/common/lib/jackson-jaxrs-1.2.0.jar 2aacab8d8000-2aacab8d9000 r-xs 00002000 08:10 29851913 /mnt/home/jatten/workspace/common/lib/slf4j-log4j12-1.5.6.jar 2aacab8d9000-2aacab8dd000 r-xs 00025000 08:10 29851945 /mnt/home/jatten/workspace/common/lib/yanf4j-1.1.1.jar 2aacab8dd000-2aacab8df000 r-xs 00003000 08:10 29851952 /mnt/home/jatten/workspace/common/lib/clickstream-1.0.2.jar 2aacab8df000-2aacab8e1000 r-xs 00004000 08:10 29851953 /mnt/home/jatten/workspace/common/lib/slf4j-api-1.5.6.jar 2aacab8e1000-2aacab8e9000 r-xs 0004d000 08:10 29851920 /mnt/home/jatten/workspace/common/lib/jackson-mapper-asl-1.2.0.jar 2aacab8e9000-2aacab8ed000 r-xs 0001f000 08:10 29851925 /mnt/home/jatten/workspace/common/lib/jackson-core-asl-1.2.0.jar 2aacab8ed000-2aacab8f1000 r-xs 0001b000 08:10 29851912 /mnt/home/jatten/workspace/common/lib/oscache-2.3.jar 2aacab8f1000-2aacab90c000 r-xs 0015d000 08:10 29851927 /mnt/home/jatten/workspace/common/lib/poi-3.6-20091214.jar 2aacab90c000-2aacab911000 r-xs 00040000 08:10 29851831 /mnt/home/jatten/workspace/common/lib/commons-lang-2.5.jar 2aacab911000-2aacab914000 r-xs 00012000 08:10 29851923 /mnt/home/jatten/workspace/common/lib/jgooglesafebrowser-0.1a.2.jar 2aacab914000-2aacab918000 r-xs 00023000 08:10 29851933 /mnt/home/jatten/workspace/common/lib/gson-1.3.jar 2aacab918000-2aacabb18000 rwxp 2aacab918000 00:00 0 2aacabb82000-2aacabd82000 rwxp 2aacabb82000 00:00 0 2aacabe05000-2aacaf204000 rwxp 2aacabe05000 00:00 0 7fffaa12a000-7fffaa141000 rwxp 7fffaa12a000 00:00 0 [stack] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vdso] VM Arguments: jvm_args: -Xmx8000M java_command: com.scorers.ModelImplementingPageScorer -t data/data/golds/adult.all.json -b 18 -s data/models/pagetext.binary. adult.april6.all.model -m com.models.MultiClassUpdateableModel -p 30 --goldsilver -v --cat adult --fakeinput -e /mnt/tmp/xyz.15647.pageo bjects.txt -o Launcher Type: SUN_STANDARD Environment Variables: JAVA_HOME=/usr/java/jdk1.6.0_14 PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/jatten/bin LD_LIBRARY_PATH=/usr/java/jdk1.6.0_14/jre/lib/amd64/server:/usr/java/jdk1.6.0_14/jre/lib/amd64:/usr/java/jdk1.6.0_14/jre/../lib/amd64 SHELL=/bin/bash Signal Handlers: SIGSEGV: [libjvm.so+0x6bd980], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGBUS: [libjvm.so+0x6bd980], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGFPE: [libjvm.so+0x594cc0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGPIPE: [libjvm.so+0x594cc0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGXFSZ: [libjvm.so+0x594cc0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGILL: [libjvm.so+0x594cc0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGUSR1: SIG_DFL, sa_mask[0]=0x00000000, sa_flags=0x00000000 SIGUSR2: [libjvm.so+0x597480], sa_mask[0]=0x00000000, sa_flags=0x10000004 SIGHUP: [libjvm.so+0x5971d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGINT: [libjvm.so+0x5971d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGTERM: [libjvm.so+0x5971d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGQUIT: [libjvm.so+0x5971d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 --------------- S Y S T E M --------------- OS:Fedora release 8 (Werewolf) uname:Linux 2.6.21.7-2.fc8xen #1 SMP Fri Feb 15 12:34:28 EST 2008 x86_64 libc:glibc 2.7 NPTL 2.7 rlimit: STACK 10240k, CORE 0k, NPROC 61504, NOFILE 1024, AS infinity load average:2.83 2.73 2.78 CPU:total 2 (4 cores per cpu, 1 threads per core) family 6 model 23 stepping 10, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1 Memory: 4k page, physical 7872040k(14540k free), swap 0k(0k free) vm_info: Java HotSpot(TM) 64-Bit Server VM (14.0-b16) for linux-amd64 JRE (1.6.0_14-b08), built on May 21 2009 01:11:11 by "java_re" with gcc 3.2.2 (SuSE Lin ux) [error occurred during error reporting (printing date and time), id 0xb]

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  • JNI 'problmatic frame' causes JVM to crash

    - by HJED
    Hi I'm using JNI to access the exiv2 library (written in C++) in Java and I'm getting a weird runtime error in the JNI code. I've tried using various -Xms and -Xmx options, but that seems to have no affect. I've also tried running this code on JDK1.7.0 with the same result. # A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0x00007ff31807757f, pid=4041, tid=140682078746368 # # JRE version: 6.0_20-b20 # Java VM: OpenJDK 64-Bit Server VM (19.0-b09 mixed mode linux-amd64 ) # Derivative: IcedTea6 1.9.2 # Distribution: Ubuntu 10.10, package 6b20-1.9.2-0ubuntu2 # Problematic frame: # V [libjvm.so+0x42757f] # # If you would like to submit a bug report, please include # instructions how to reproduce the bug and visit: # https://bugs.launchpad.net/ubuntu/+source/openjdk-6/ # --------------- T H R E A D --------------- Current thread (0x000000000190d000): JavaThread "main" [_thread_in_Java, id=4043, stack(0x00007ff319447000,0x00007ff319548000)] siginfo:si_signo=SIGSEGV: si_errno=0, si_code=1 (SEGV_MAPERR), si_addr=0x0000000000000024 Registers: ... Register to memory mapping: RAX=0x0000000000000002 0x0000000000000002 is pointing to unknown location RBX=0x000000000190db90 0x000000000190db90 is pointing to unknown location RCX=0x0000000000000000 0x0000000000000000 is pointing to unknown location RDX=0x00007ff3195463f8 0x00007ff3195463f8 is pointing into the stack for thread: 0x000000000190d000 "main" prio=10 tid=0x000000000190d000 nid=0xfcb runnable [0x0000000000000000] java.lang.Thread.State: RUNNABLE RSP=0x00007ff319546270 0x00007ff319546270 is pointing into the stack for thread: 0x000000000190d000 "main" prio=10 tid=0x000000000190d000 nid=0xfcb runnable [0x0000000000000000] java.lang.Thread.State: RUNNABLE RBP=0x00007ff319546270 0x00007ff319546270 is pointing into the stack for thread: 0x000000000190d000 "main" prio=10 tid=0x000000000190d000 nid=0xfcb runnable [0x0000000000000000] java.lang.Thread.State: RUNNABLE RSI=0x0000000000000024 0x0000000000000024 is pointing to unknown location RDI=0x00007ff3195463e0 0x00007ff3195463e0 is pointing into the stack for thread: 0x000000000190d000 "main" prio=10 tid=0x000000000190d000 nid=0xfcb runnable [0x0000000000000000] java.lang.Thread.State: RUNNABLE R8 =0x000000000190d000 "main" prio=10 tid=0x000000000190d000 nid=0xfcb runnable [0x0000000000000000] java.lang.Thread.State: RUNNABLE R9 =0x000000000190db88 0x000000000190db88 is pointing to unknown location R10=0x00007ff319546300 0x00007ff319546300 is pointing into the stack for thread: 0x000000000190d000 "main" prio=10 tid=0x000000000190d000 nid=0xfcb runnable [0x0000000000000000] java.lang.Thread.State: RUNNABLE R11=0x0000000000000002 0x0000000000000002 is pointing to unknown location R12=0x000000000190d000 "main" prio=10 tid=0x000000000190d000 nid=0xfcb runnable [0x0000000000000000] java.lang.Thread.State: RUNNABLE R13=0x00007ff319546560 0x00007ff319546560 is pointing into the stack for thread: 0x000000000190d000 "main" prio=10 tid=0x000000000190d000 nid=0xfcb runnable [0x0000000000000000] java.lang.Thread.State: RUNNABLE R14=0x00007ff3195463e0 0x00007ff3195463e0 is pointing into the stack for thread: 0x000000000190d000 "main" prio=10 tid=0x000000000190d000 nid=0xfcb runnable [0x0000000000000000] java.lang.Thread.State: RUNNABLE R15=0x0000000000000003 0x0000000000000003 is pointing to unknown location Top of Stack: (sp=0x00007ff319546270) ... Instructions: (pc=0x00007ff31807757f) 0x00007ff31807756f: e2 03 48 03 57 58 31 c9 48 8b 32 48 85 f6 74 03 0x00007ff31807757f: 48 8b 0e 48 89 0a 8b 77 68 83 c0 01 39 f0 7c d1 Stack: [0x00007ff319447000,0x00007ff319548000], sp=0x00007ff319546270, free space=1020k Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code) V [libjvm.so+0x42757f] V [libjvm.so+0x42866b] V [libjvm.so+0x4275c8] V [libjvm.so+0x4331bd] V [libjvm.so+0x44e5c7] C [libExiff2-binding.so+0x1f16] _ZN7JNIEnv_15CallVoidMethodAEP8_jobjectP10_jmethodIDPK6jvalue+0x40 C [libExiff2-binding.so+0x1b96] _Z8loadIPTCSt8auto_ptrIN5Exiv25ImageEEPKcP7JNIEnv_P8_jobject+0x2ba C [libExiff2-binding.so+0x1d3f] _Z7getVarsPKcP7JNIEnv_P8_jobject+0x176 C [libExiff2-binding.so+0x1de7] Java_photo_exiv2_Exiv2MetaDataStore_impl_1loadFromExiv+0x4b j photo.exiv2.Exiv2MetaDataStore.impl_loadFromExiv(Ljava/lang/String;Lphoto/exiv2/Exiv2MetaDataStore;)V+0 j photo.exiv2.Exiv2MetaDataStore.loadFromExiv2()V+9 j photo.exiv2.Exiv2MetaDataStore.loadData()V+1 j photo.exiv2.Exiv2MetaDataStore.<init>(Lphoto/ImageFile;)V+10 j test.Main.main([Ljava/lang/String;)V+76 v ~StubRoutines::call_stub V [libjvm.so+0x428698] V [libjvm.so+0x4275c8] V [libjvm.so+0x432943] V [libjvm.so+0x447f91] C [java+0x3495] JavaMain+0xd75 --------------- P R O C E S S --------------- Java Threads: ( => current thread ) 0x00007ff2c4027800 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=4060, stack(0x00007ff2c9052000,0x00007ff2c9153000)] 0x00007ff2c4025000 JavaThread "CompilerThread1" daemon [_thread_blocked, id=4059, stack(0x00007ff2c9153000,0x00007ff2c9254000)] 0x00007ff2c4022000 JavaThread "CompilerThread0" daemon [_thread_blocked, id=4058, stack(0x00007ff2c9254000,0x00007ff2c9355000)] 0x00007ff2c401f800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=4057, stack(0x00007ff2c9355000,0x00007ff2c9456000)] 0x00007ff2c4001000 JavaThread "Finalizer" daemon [_thread_blocked, id=4056, stack(0x00007ff2c994d000,0x00007ff2c9a4e000)] 0x0000000001984000 JavaThread "Reference Handler" daemon [_thread_blocked, id=4055, stack(0x00007ff2c9a4e000,0x00007ff2c9b4f000)] =>0x000000000190d000 JavaThread "main" [_thread_in_Java, id=4043, stack(0x00007ff319447000,0x00007ff319548000)] Other Threads: 0x000000000197d800 VMThread [stack: 0x00007ff2c9b4f000,0x00007ff2c9c50000] [id=4054] 0x00007ff2c4032000 WatcherThread [stack: 0x00007ff2c8f51000,0x00007ff2c9052000] [id=4061] VM state:not at safepoint (normal execution) VM Mutex/Monitor currently owned by a thread: None Heap PSYoungGen total 18432K, used 316K [0x00007ff2fed30000, 0x00007ff3001c0000, 0x00007ff313730000) eden space 15808K, 2% used [0x00007ff2fed30000,0x00007ff2fed7f0b8,0x00007ff2ffca0000) from space 2624K, 0% used [0x00007ff2fff30000,0x00007ff2fff30000,0x00007ff3001c0000) to space 2624K, 0% used [0x00007ff2ffca0000,0x00007ff2ffca0000,0x00007ff2fff30000) PSOldGen total 42240K, used 0K [0x00007ff2d5930000, 0x00007ff2d8270000, 0x00007ff2fed30000) object space 42240K, 0% used [0x00007ff2d5930000,0x00007ff2d5930000,0x00007ff2d8270000) PSPermGen total 21248K, used 2827K [0x00007ff2cb330000, 0x00007ff2cc7f0000, 0x00007ff2d5930000) object space 21248K, 13% used [0x00007ff2cb330000,0x00007ff2cb5f2f60,0x00007ff2cc7f0000) Dynamic libraries: 00400000-00409000 r-xp 00000000 08:03 141899 /usr/lib/jvm/java-6-openjdk/jre/bin/java 00608000-00609000 r--p 00008000 08:03 141899 /usr/lib/jvm/java-6-openjdk/jre/bin/java 00609000-0060a000 rw-p 00009000 08:03 141899 /usr/lib/jvm/java-6-openjdk/jre/bin/java 01904000-019ad000 rw-p 00000000 00:00 0 [heap] ... 7ff2c820c000-7ff2c8232000 r-xp 00000000 08:03 917704 /lib/libexpat.so.1.5.2 7ff2c8232000-7ff2c8432000 ---p 00026000 08:03 917704 /lib/libexpat.so.1.5.2 7ff2c8432000-7ff2c8434000 r--p 00026000 08:03 917704 /lib/libexpat.so.1.5.2 7ff2c8434000-7ff2c8435000 rw-p 00028000 08:03 917704 /lib/libexpat.so.1.5.2 7ff2c8435000-7ff2c844a000 r-xp 00000000 08:03 917708 /lib/libgcc_s.so.1 7ff2c844a000-7ff2c8649000 ---p 00015000 08:03 917708 /lib/libgcc_s.so.1 7ff2c8649000-7ff2c864a000 r--p 00014000 08:03 917708 /lib/libgcc_s.so.1 7ff2c864a000-7ff2c864b000 rw-p 00015000 08:03 917708 /lib/libgcc_s.so.1 7ff2c864b000-7ff2c8733000 r-xp 00000000 08:03 134995 /usr/lib/libstdc++.so.6.0.14 7ff2c8733000-7ff2c8932000 ---p 000e8000 08:03 134995 /usr/lib/libstdc++.so.6.0.14 7ff2c8932000-7ff2c893a000 r--p 000e7000 08:03 134995 /usr/lib/libstdc++.so.6.0.14 7ff2c893a000-7ff2c893c000 rw-p 000ef000 08:03 134995 /usr/lib/libstdc++.so.6.0.14 7ff2c893c000-7ff2c8951000 rw-p 00000000 00:00 0 7ff2c8951000-7ff2c8af3000 r-xp 00000000 08:03 134599 /usr/lib/libexiv2.so.6.0.0 7ff2c8af3000-7ff2c8cf2000 ---p 001a2000 08:03 134599 /usr/lib/libexiv2.so.6.0.0 7ff2c8cf2000-7ff2c8d0f000 r--p 001a1000 08:03 134599 /usr/lib/libexiv2.so.6.0.0 7ff2c8d0f000-7ff2c8d10000 rw-p 001be000 08:03 134599 /usr/lib/libexiv2.so.6.0.0 7ff2c8d10000-7ff2c8d23000 rw-p 00000000 00:00 0 7ff2c8d42000-7ff2c8d45000 r-xp 00000000 08:03 800718 /home/hjed/libExiff2-binding.so 7ff2c8d45000-7ff2c8f44000 ---p 00003000 08:03 800718 /home/hjed/libExiff2-binding.so 7ff2c8f44000-7ff2c8f45000 r--p 00002000 08:03 800718 /home/hjed/libExiff2-binding.so 7ff2c8f45000-7ff2c8f46000 rw-p 00003000 08:03 800718 /home/hjed/libExiff2-binding.so 7ff2c8f46000-7ff2c8f49000 r--s 0000f000 08:03 141333 /usr/lib/jvm/java-6-openjdk/jre/lib/ext/pulse-java.jar 7ff2c8f49000-7ff2c8f51000 r--s 00066000 08:03 408472 /usr/share/java/gnome-java-bridge.jar ... 7ff2ca559000-7ff2ca55b000 r--s 0001d000 08:03 141354 /usr/lib/jvm/java-6-openjdk/jre/lib/plugin.jar 7ff2ca55b000-7ff2ca560000 r--s 00044000 08:03 141353 /usr/lib/jvm/java-6-openjdk/jre/lib/netx.jar 7ff2ca560000-7ff2ca592000 rw-p 00000000 00:00 0 7ff2ca592000-7ff2ca720000 r--s 038af000 08:03 141833 /usr/lib/jvm/java-6-openjdk/jre/lib/rt.jar ... 7ff31673b000-7ff316742000 r-xp 00000000 08:03 141867 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/libzip.so 7ff316742000-7ff316941000 ---p 00007000 08:03 141867 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/libzip.so 7ff316941000-7ff316942000 r--p 00006000 08:03 141867 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/libzip.so 7ff316942000-7ff316943000 rw-p 00007000 08:03 141867 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/libzip.so 7ff316943000-7ff31694f000 r-xp 00000000 08:03 921396 /lib/libnss_files-2.12.1.so 7ff31694f000-7ff316b4e000 ---p 0000c000 08:03 921396 /lib/libnss_files-2.12.1.so 7ff316b4e000-7ff316b4f000 r--p 0000b000 08:03 921396 /lib/libnss_files-2.12.1.so 7ff316b4f000-7ff316b50000 rw-p 0000c000 08:03 921396 /lib/libnss_files-2.12.1.so 7ff316b50000-7ff316b5a000 r-xp 00000000 08:03 921398 /lib/libnss_nis-2.12.1.so 7ff316b5a000-7ff316d59000 ---p 0000a000 08:03 921398 /lib/libnss_nis-2.12.1.so 7ff316d59000-7ff316d5a000 r--p 00009000 08:03 921398 /lib/libnss_nis-2.12.1.so 7ff316d5a000-7ff316d5b000 rw-p 0000a000 08:03 921398 /lib/libnss_nis-2.12.1.so 7ff316d5b000-7ff316d63000 r-xp 00000000 08:03 921393 /lib/libnss_compat-2.12.1.so 7ff316d63000-7ff316f62000 ---p 00008000 08:03 921393 /lib/libnss_compat-2.12.1.so 7ff316f62000-7ff316f63000 r--p 00007000 08:03 921393 /lib/libnss_compat-2.12.1.so 7ff316f63000-7ff316f64000 rw-p 00008000 08:03 921393 /lib/libnss_compat-2.12.1.so 7ff316f64000-7ff316f6c000 r-xp 00000000 08:03 141869 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/native_threads/libhpi.so 7ff316f6c000-7ff31716b000 ---p 00008000 08:03 141869 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/native_threads/libhpi.so 7ff31716b000-7ff31716c000 r--p 00007000 08:03 141869 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/native_threads/libhpi.so 7ff31716c000-7ff31716d000 rw-p 00008000 08:03 141869 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/native_threads/libhpi.so 7ff31716d000-7ff317184000 r-xp 00000000 08:03 921392 /lib/libnsl-2.12.1.so 7ff317184000-7ff317383000 ---p 00017000 08:03 921392 /lib/libnsl-2.12.1.so 7ff317383000-7ff317384000 r--p 00016000 08:03 921392 /lib/libnsl-2.12.1.so 7ff317384000-7ff317385000 rw-p 00017000 08:03 921392 /lib/libnsl-2.12.1.so 7ff317385000-7ff317387000 rw-p 00000000 00:00 0 7ff317387000-7ff3173b2000 r-xp 00000000 08:03 141850 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/libjava.so 7ff3173b2000-7ff3175b1000 ---p 0002b000 08:03 141850 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/libjava.so 7ff3175b1000-7ff3175b2000 r--p 0002a000 08:03 141850 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/libjava.so 7ff3175b2000-7ff3175b5000 rw-p 0002b000 08:03 141850 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/libjava.so 7ff3175b5000-7ff3175c3000 r-xp 00000000 08:03 141866 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/libverify.so 7ff3175c3000-7ff3177c2000 ---p 0000e000 08:03 141866 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/libverify.so 7ff3177c2000-7ff3177c4000 r--p 0000d000 08:03 141866 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/libverify.so 7ff3177c4000-7ff3177c5000 rw-p 0000f000 08:03 141866 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/libverify.so 7ff3177c5000-7ff3177cc000 r-xp 00000000 08:03 921405 /lib/librt-2.12.1.so 7ff3177cc000-7ff3179cb000 ---p 00007000 08:03 921405 /lib/librt-2.12.1.so 7ff3179cb000-7ff3179cc000 r--p 00006000 08:03 921405 /lib/librt-2.12.1.so 7ff3179cc000-7ff3179cd000 rw-p 00007000 08:03 921405 /lib/librt-2.12.1.so 7ff3179cd000-7ff317a4f000 r-xp 00000000 08:03 921390 /lib/libm-2.12.1.so 7ff317a4f000-7ff317c4e000 ---p 00082000 08:03 921390 /lib/libm-2.12.1.so 7ff317c4e000-7ff317c4f000 r--p 00081000 08:03 921390 /lib/libm-2.12.1.so 7ff317c4f000-7ff317c50000 rw-p 00082000 08:03 921390 /lib/libm-2.12.1.so 7ff317c50000-7ff3184c4000 r-xp 00000000 08:03 141871 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server/libjvm.so 7ff3184c4000-7ff3186c3000 ---p 00874000 08:03 141871 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server/libjvm.so 7ff3186c3000-7ff318739000 r--p 00873000 08:03 141871 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server/libjvm.so 7ff318739000-7ff318754000 rw-p 008e9000 08:03 141871 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server/libjvm.so 7ff318754000-7ff31878d000 rw-p 00000000 00:00 0 7ff31878d000-7ff318907000 r-xp 00000000 08:03 921385 /lib/libc-2.12.1.so 7ff318907000-7ff318b06000 ---p 0017a000 08:03 921385 /lib/libc-2.12.1.so 7ff318b06000-7ff318b0a000 r--p 00179000 08:03 921385 /lib/libc-2.12.1.so 7ff318b0a000-7ff318b0b000 rw-p 0017d000 08:03 921385 /lib/libc-2.12.1.so 7ff318b0b000-7ff318b10000 rw-p 00000000 00:00 0 7ff318b10000-7ff318b12000 r-xp 00000000 08:03 921388 /lib/libdl-2.12.1.so 7ff318b12000-7ff318d12000 ---p 00002000 08:03 921388 /lib/libdl-2.12.1.so 7ff318d12000-7ff318d13000 r--p 00002000 08:03 921388 /lib/libdl-2.12.1.so 7ff318d13000-7ff318d14000 rw-p 00003000 08:03 921388 /lib/libdl-2.12.1.so 7ff318d14000-7ff318d18000 r-xp 00000000 08:03 141838 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/jli/libjli.so 7ff318d18000-7ff318f17000 ---p 00004000 08:03 141838 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/jli/libjli.so 7ff318f17000-7ff318f18000 r--p 00003000 08:03 141838 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/jli/libjli.so 7ff318f18000-7ff318f19000 rw-p 00004000 08:03 141838 /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/jli/libjli.so 7ff318f19000-7ff318f31000 r-xp 00000000 08:03 921401 /lib/libpthread-2.12.1.so 7ff318f31000-7ff319130000 ---p 00018000 08:03 921401 /lib/libpthread-2.12.1.so 7ff319130000-7ff319131000 r--p 00017000 08:03 921401 /lib/libpthread-2.12.1.so 7ff319131000-7ff319132000 rw-p 00018000 08:03 921401 /lib/libpthread-2.12.1.so 7ff319132000-7ff319136000 rw-p 00000000 00:00 0 7ff319136000-7ff31914c000 r-xp 00000000 08:03 917772 /lib/libz.so.1.2.3.4 7ff31914c000-7ff31934c000 ---p 00016000 08:03 917772 /lib/libz.so.1.2.3.4 7ff31934c000-7ff31934d000 r--p 00016000 08:03 917772 /lib/libz.so.1.2.3.4 7ff31934d000-7ff31934e000 rw-p 00017000 08:03 917772 /lib/libz.so.1.2.3.4 7ff31934e000-7ff31936e000 r-xp 00000000 08:03 921379 /lib/ld-2.12.1.so 7ff319387000-7ff319391000 rw-p 00000000 00:00 0 7ff319391000-7ff319447000 rw-p 00000000 00:00 0 7ff319447000-7ff31944a000 ---p 00000000 00:00 0 7ff31944a000-7ff31954d000 rw-p 00000000 00:00 0 7ff319562000-7ff31956a000 rw-s 00000000 08:03 1966453 /tmp/hsperfdata_hjed/4041 7ff31956a000-7ff31956b000 rw-p 00000000 00:00 0 7ff31956b000-7ff31956c000 r--p 00000000 00:00 0 7ff31956c000-7ff31956e000 rw-p 00000000 00:00 0 7ff31956e000-7ff31956f000 r--p 00020000 08:03 921379 /lib/ld-2.12.1.so 7ff31956f000-7ff319570000 rw-p 00021000 08:03 921379 /lib/ld-2.12.1.so 7ff319570000-7ff319571000 rw-p 00000000 00:00 0 7fff0fb03000-7fff0fb24000 rw-p 00000000 00:00 0 [stack] 7fff0fbff000-7fff0fc00000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] VM Arguments: jvm_args: -Dfile.encoding=UTF-8 java_command: test.Main Launcher Type: SUN_STANDARD Environment Variables: PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games USERNAME=hjed LD_LIBRARY_PATH=/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server:/usr/lib/jvm/java-6-openjdk/jre/lib/amd64:/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 SHELL=/bin/bash DISPLAY=:0.0 Signal Handlers: SIGSEGV: [libjvm.so+0x712700], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGBUS: [libjvm.so+0x712700], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGFPE: [libjvm.so+0x5d4020], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGPIPE: [libjvm.so+0x5d4020], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGXFSZ: [libjvm.so+0x5d4020], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGILL: [libjvm.so+0x5d4020], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGUSR1: SIG_DFL, sa_mask[0]=0x00000000, sa_flags=0x00000000 SIGUSR2: [libjvm.so+0x5d3730], sa_mask[0]=0x00000004, sa_flags=0x10000004 SIGHUP: [libjvm.so+0x5d61a0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGINT: SIG_IGN, sa_mask[0]=0x00000000, sa_flags=0x00000000 SIGTERM: [libjvm.so+0x5d61a0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 SIGQUIT: [libjvm.so+0x5d61a0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004 --------------- S Y S T E M --------------- OS:Ubuntu 10.10 (maverick) uname:Linux 2.6.35-24-generic #42-Ubuntu SMP Thu Dec 2 02:41:37 UTC 2010 x86_64 libc:glibc 2.12.1 NPTL 2.12.1 rlimit: STACK 8192k, CORE 0k, NPROC infinity, NOFILE 1024, AS infinity load average:0.25 0.16 0.21 /proc/meminfo: MemTotal: 4048200 kB MemFree: 1230476 kB Buffers: 589572 kB Cached: 911132 kB SwapCached: 0 kB Active: 1321712 kB Inactive: 1202272 kB Active(anon): 1023852 kB Inactive(anon): 7168 kB Active(file): 297860 kB Inactive(file): 1195104 kB Unevictable: 64 kB Mlocked: 64 kB SwapTotal: 7065596 kB SwapFree: 7065596 kB Dirty: 632 kB Writeback: 0 kB AnonPages: 1023368 kB Mapped: 145832 kB Shmem: 7728 kB Slab: 111136 kB SReclaimable: 66316 kB SUnreclaim: 44820 kB KernelStack: 3824 kB PageTables: 27736 kB NFS_Unstable: 0 kB Bounce: 0 kB WritebackTmp: 0 kB CommitLimit: 9089696 kB Committed_AS: 2378396 kB VmallocTotal: 34359738367 kB VmallocUsed: 332928 kB VmallocChunk: 34359397884 kB HardwareCorrupted: 0 kB HugePages_Total: 0 HugePages_Free: 0 HugePages_Rsvd: 0 HugePages_Surp: 0 Hugepagesize: 2048 kB DirectMap4k: 67136 kB DirectMap2M: 4118528 kB CPU:total 8 (4 cores per cpu, 2 threads per core) family 6 model 26 stepping 5, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, ht Memory: 4k page, physical 4048200k(1230476k free), swap 7065596k(7065596k free) vm_info: OpenJDK 64-Bit Server VM (19.0-b09) for linux-amd64 JRE (1.6.0_20-b20), built on Dec 10 2010 19:45:55 by "buildd" with gcc 4.4.5 time: Sat Jan 1 14:12:27 2011 elapsed time: 0 seconds The java code is: ... public class Main { public static void main(String[] args) { ... ImageFile img = new ImageFile(System.getProperty("user.home") + "/PC100001.JPG"); Exiv2MetaDataStore e = new Exiv2MetaDataStore(img); Iterator<Entry<String, String>> i = e.entrySet().iterator(); while (i.hasNext()) { Entry<String, String> entry = i.next(); System.out.println(entry.getKey() + ":" + entry.getValue()); } //if you switch this print statment with the while loop you get the same error. // System.out.print(e.toString()); } } and /** NB: MetaDataStore is an abstract class that extends HashMap<String,String> */ public class Exiv2MetaDataStore extends MetaDataStore{ ... private final ImageFile F; /** * Creates an meta data store from an ImageFile using Exiv2 * this calls loadData(); * @param f */ public Exiv2MetaDataStore(ImageFile f) { F = f; loadData(); } ... @Override protected void loadData() { loadFromExiv2(); } ... private void loadFromExiv2() { impl_loadFromExiv(F.getAbsolutePath(), this); } private native void impl_loadFromExiv(String path, Exiv2MetaDataStore str); //this method called by the C++ code public void exiv2_reciveElement(String key, String value) { super.put(key,value); } static { Runtime.getRuntime().load("/home/hjed/libExiff2-binding.so"); } } C++ code: #include <exif.hpp> #include <image.hpp> #include <iptc.hpp> #include <exiv2/exiv2.hpp> #include <exiv2/error.hpp> #include <iostream> #include <iomanip> #include <cassert> void loadIPTC(Exiv2::Image::AutoPtr image, const char * path, JNIEnv * env, jobject obj) { Exiv2::IptcData &iptcData = image->iptcData(); //load method jclass cls = env->GetObjectClass(obj); jmethodID mid = env->GetMethodID(cls, "exiv2_reciveElement", "(Ljava/lang/String;Ljava/lang/String;)V"); //is there any IPTC data AND check that method exists if (iptcData.empty() | (mid == NULL)) { std::string error(path); error += ": failed loading IPTC data, there may not be any data"; } else { Exiv2::IptcData::iterator end = iptcData.end(); for (Exiv2::IptcData::iterator md = iptcData.begin(); md != end; ++md) { jvalue values[2]; const char* key = md->key().c_str(); values[0].l = env->NewStringUTF(key); md->value().toString().c_str(); const char* value = md->typeName(); values[2].l = env->NewStringUTF(value); //If I replace the code for values[2] with the commented out code I get the same error. //const char* type = md->typeName(); //values[2].l = env->NewStringUTF(type); env->CallVoidMethodA(obj, mid, values); } } } void getVars(const char* path, JNIEnv * env, jobject obj) { //Load image Exiv2::Image::AutoPtr image = Exiv2::ImageFactory::open(path); assert(image.get() != 0); image->readMetadata(); //Load IPTC data loadIPTC(image, path, env, obj); } JNIEXPORT void JNICALL Java_photo_exiv2_Exiv2MetaDataStore_impl_1loadFromExiv(JNIEnv * env, jobject obj, jstring path, jobject obj2) { const char* path2 = env->GetStringUTFChars(path, NULL); getVars(path2, env, obj); env->ReleaseStringUTFChars(path, path2); } I've searched for a fix for this, but I can't find one. I don't have much experience using C++ so if I've made an obvious mistake in the C code I apologies. Thanks for any help, HJED P.S. This is my first post on this site and I wasn't sure how much of the code I needed to show. Sorry if I've put to much up.

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  • How do I install Geomatica?

    - by Chethan S.
    I wanted to try the latest version(trial) of Geomatica, Geomatica 2012 on Ubuntu 11.10 beta. When I tried to run the bin file I got a whole list of dependencies. It also seems that it is a RPM package. Instead of going through each entry manually, is there any easy way to search and install a list of dependencies? Here is the list what I got - rpm: RPM should not be used directly install RPM packages, use Alien instead! rpm: However assuming you know what you are doing... error: Failed dependencies: glibc >= 2.9 is needed by geomatica-2012-12.0-0.x86_64 libstdc++43 is needed by geomatica-2012-12.0-0.x86_64 libgcc43 is needed by geomatica-2012-12.0-0.x86_64 libgomp43 is needed by geomatica-2012-12.0-0.x86_64 libgfortran43 is needed by geomatica-2012-12.0-0.x86_64 openmotif-libs >= 2.3.1 is needed by geomatica-2012-12.0-0.x86_64 /bin/sh is needed by geomatica-2012-12.0-0.x86_64 libatk-1.0.so.0()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libcairo.so.2()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libcrypto.so.0.9.8()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libcrypt.so.1()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libc.so.6()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libc.so.6(GLIBC_2.2.5)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libc.so.6(GLIBC_2.3.2)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libc.so.6(GLIBC_2.3.4)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libc.so.6(GLIBC_2.3)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libc.so.6(GLIBC_2.7)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libdl.so.2()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libdl.so.2(GLIBC_2.2.5)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libexpat.so.1()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libfontconfig.so.1()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgcc_s.so.1()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgcc_s.so.1(GCC_3.0)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgcc_s.so.1(GCC_4.0.0)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgdk_pixbuf-2.0.so.0()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgdk-x11-2.0.so.0()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgd.so.2()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgfortran.so.3()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgfortran.so.3(GFORTRAN_1.0)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgio-2.0.so.0()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libglib-2.0.so.0()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libGL.so.1()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgmodule-2.0.so.0()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgobject-2.0.so.0()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgomp.so.1()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgomp.so.1(GOMP_1.0)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgomp.so.1(OMP_1.0)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgthread-2.0.so.0()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libgtk-x11-2.0.so.0()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libjpeg.so.62()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libm.so.6()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libm.so.6(GLIBC_2.2.5)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libnsl.so.1()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libpango-1.0.so.0()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libpangocairo-1.0.so.0()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libpangoft2-1.0.so.0()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libpng12.so.0()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libpng12.so.0(PNG12_0)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libpthread.so.0()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libpthread.so.0(GLIBC_2.2.5)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libpthread.so.0(GLIBC_2.3.2)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libpthread.so.0(GLIBC_2.3.4)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libpython2.6.so.1.0()(64bit) is needed by geomatica-2012-12.0-0.x86_64 librt.so.1()(64bit) is needed by geomatica-2012-12.0-0.x86_64 librt.so.1(GLIBC_2.2.5)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libSM.so.6()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libssl.so.0.9.8()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libstdc++.so.6()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libstdc++.so.6(CXXABI_1.3.1)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libstdc++.so.6(CXXABI_1.3)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libstdc++.so.6(GLIBCXX_3.4)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libstdc++.so.6(GLIBCXX_3.4.9)(64bit) is needed by geomatica-2012-12.0-0.x86_64 libtiff.so.3()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libutil.so.1()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libX11.so.6()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libXinerama.so.1()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libXm.so.4()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libXt.so.6()(64bit) is needed by geomatica-2012-12.0-0.x86_64 libXxf86vm.so.1()(64bit) is needed by geomatica-2012-12.0-0.x86_64

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