std::bad_alloc Loading SDK Sample Libraries

jpottsjpotts Registered User

My problem is very similar to these two unanswered questions, but with a different Vertica version:

https://forum.vertica.com/discussion/235890/rollback-3399-vsql-create-library-failure-in-udx-error

https://forum.vertica.com/discussion/238717/unable-to-create-library-rollback-3399-failure-in-udx-rpc-call-invokegetlibrarymanifest

I installed Vertica 9.0.1 on Ubuntu using vertica_9.0.1-0_amd64.deb and installed the following:

sudo apt-get install libboost-dev libboost-doc
sudo apt-get install libbz2-dev
sudo apt-get install libcurl4-openssl-dev
sudo apt-get install zlib1g-dev

Next I:
1. copied /opt/vertica/sdk/examples to a subfolder of my home folder
2. ran make
3. Ran vsql -f on a few of the sql scripts

All of them produced:

[Code: 3399, SQL State: VP001] [Vertica]VJDBC ROLLBACK: Failure in UDx RPC call InvokeGetLibraryManifest(): Exception calling getLibraryManifest() in User Defined Object [], message: std::bad_alloc

Vertica is running fine; I have some schema and data loaded.

Comments

  • For what it's worth, there may be some additional hints on what's happening (e.g. out of memory in PermGen space) in the UDxFencedProcessesJava.log which resides under your database catalog/UDxLogs dir.

  • Jim_KnicelyJim_Knicely Administrator, Moderator, Employee, Registered User, VerticaExpert

    Can you post the results of trying to compile just one of the Java example?

    Example:

    make JavaFunctions

  • jpottsjpotts Registered User

    See below for rerun results.

    I initially built using make. It gave warnings about skipping different components due to missing headers; the build appeared successful otherwise. I did not try loading it at this point; instead I installed headers using the apt-get commands above, rebuilt incrementially after each one, and then got a clean build from make. I have tried using make clean and then make again, and loading again, and still get bad_alloc.

    Log file is attached; interestingly there is only one failure directly related to the library file (I made multiple attempts on Jan 2).

    Rerun results from today:

    $ make clean

    rm -rf /home/jpotts/code/vertica-9-examples/build/tmp
    rm -f /home/jpotts/code/vertica-9-examples/build/.so
    rm -f /home/jpotts/code/vertica-9-examples/build/
    .jar
    rm -rf /home/jpotts/code/vertica-9-examples/build/Java*
    rmdir /home/jpotts/code/vertica-9-examples/build >/dev/null 2>&1 || true

    $ make

    (see attached; some folders obfuscated. appears successful)

    $ g++ --version

    g++ (Ubuntu 5.4.0-6ubuntu1~16.04.5) 5.4.0 20160609
    Copyright (C) 2015 Free Software Foundation, Inc.
    This is free software; see the source for copying conditions. There is NO
    warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

    $ java -version

    java version "1.8.0_151"
    Java(TM) SE Runtime Environment (build 1.8.0_151-b12)
    Java HotSpot(TM) 64-Bit Server VM (build 25.151-b12, mixed mode)

    $ javac -version

    javac 1.8.0_151

    $ free -m

              total        used        free      shared  buff/cache   available
    

    Mem: 15914 1629 10592 629 3693 13281
    Swap: 16251 0 16251

  • jpottsjpotts Registered User

    Error I get using vsql (error in first post is using DBVisualizer):

    vsql:AggregateFunctions.sql:12: ROLLBACK 3399: Failure in UDx RPC call InvokeGetLibraryManifest(): Exception calling getLibraryManifest() in User Defined Object [], message: std::bad_alloc

  • jpottsjpotts Registered User

    And a portion of the vertica.log file from the immediately above vsql run, attached.

  • sKwasKwa Registered User

    Hi!

    What is version of Ubuntu?

    $ lsb_release -a
    No LSB modules are available.
    Distributor ID: Ubuntu
    Description:    Ubuntu 14.04.5 LTS
    Release:    14.04
    Codename:   trusty
    

    Can you post full output of:

    $ ldd /opt/vertica/bin/vertica-udx-C++
        linux-vdso.so.1 =>  (0x00007ffc856a5000)
        libvmalloc.so => /opt/vertica/bin/../lib/libvmalloc.so (0x00007f0220724000)
        libncurses.so.5 => /lib/x86_64-linux-gnu/libncurses.so.5 (0x00007f02202e3000)
        libgssapi_krb5.so.2 => /opt/vertica/bin/../lib/libgssapi_krb5.so.2 (0x00007f02206b6000)
       ...
    

    ???

  • jpottsjpotts Registered User

    $ lsb_release -a
    No LSB modules are available.
    Distributor ID: Ubuntu
    Description: Ubuntu 16.04.3 LTS
    Release: 16.04
    Codename: xenial

    $ ldd /opt/vertica/bin/vertica-udx-C++

    linux-vdso.so.1 =>  (0x00007ffc2bd4e000)
    libvmalloc.so => /opt/vertica/bin/../lib/libvmalloc.so (0x00007fc0c7a5e000)
    libncurses.so.5 => /lib/x86_64-linux-gnu/libncurses.so.5 (0x00007fc0c7823000)
    libgssapi_krb5.so.2 => /opt/vertica/bin/../lib/libgssapi_krb5.so.2 (0x00007fc0c77c9000)
    libkrb5.so.3 => /opt/vertica/bin/../lib/libkrb5.so.3 (0x00007fc0c76d8000)
    libkrb5support.so.0 => /opt/vertica/bin/../lib/libkrb5support.so.0 (0x00007fc0c76ca000)
    libk5crypto.so.3 => /opt/vertica/bin/../lib/libk5crypto.so.3 (0x00007fc0c7684000)
    libcom_err.so.3 => /opt/vertica/bin/../lib/libcom_err.so.3 (0x00007fc0c7680000)
    libcrypto.so.10 => /opt/vertica/bin/../lib/libcrypto.so.10 (0x00007fc0c729d000)
    libssl.so.10 => /opt/vertica/bin/../lib/libssl.so.10 (0x00007fc0c7030000)
    libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fc0c6cae000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fc0c69a5000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fc0c6787000)
    librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fc0c657f000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fc0c637b000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fc0c5fb0000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fc0c5d9a000)
    libtinfo.so.5 => /lib/x86_64-linux-gnu/libtinfo.so.5 (0x00007fc0c5b71000)
    libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1 (0x00007fc0c596c000)
    libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007fc0c5751000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fc0c5536000)
    libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2 (0x00007fc0c5332000)
    /lib64/ld-linux-x86-64.so.2 (0x000055ca7058d000)
    

    tldr: java fixed now; c++ sample still not working

    $ vsql -U dbadmin -f JavaFunctions.sql

    vsql:JavaFunctions.sql:14: ROLLBACK 5702: Couldn't create new UDx side process: Java Binary not found: /usr/bin/java/bin/java

    $ sudo -u dbadmin printenv | grep JAVA_HOME
    JAVA_HOME=/usr/bin/java

    The JAVA_HOME variable above is incorrect; it points at an executable rather than a folder. It wasn't obvious because it was only affecting the dbadmin user rather than my user account.

    How I found where JAVA_HOME was set
    grep -r JAVA_HOME /etc/* 2>&1 | grep -v "Permission denied"
    grep -r JAVA_HOME ~/.*

    JAVA_HOME was being set correctly here:

    • /etc/profile.d/jdk.sh
    • /etc/profile.d/jdk.csh

    But I had set it incorrectly here:

    • /etc/environment

    The profile.d flavor was loading into my personal login, but the /etc/environment flavor was being used for the dbadmin user.

    Fixed it by setting JAVA_HOME in /home/dbadmin/.bashrc

    Still getting std::bad_alloc for C++ example

  • sKwasKwa Registered User
    edited January 5

    Hi!

    Ubuntu 16.04.3 LTS is unsupported platform, try 14.04 LTS.

    ps: I got same error on 16.04(just checked).

  • jpottsjpotts Registered User

    That's disappointing.

  • Sergey_Cherepan_1Sergey_Cherepan_1 Registered User

    Hi Josh,
    Hope you are doing well.
    I got same error... on CentOS 7.3.... on gcc 7.3.1... and I can load properly with gcc 7.2.1... and it completely unexplainable.
    Statement that Ubuntu version is desupported is not relevant here, just a way to send you out.
    Try to compile on different box, may be luck will be with you.

  • jpottsjpotts Registered User

    Great to hear from you, hope all is well. We should grab a beer soon.

    I may try compiling on Ubuntu 14 with the default packages and see if I can get the binary to run on Ubuntu 16.

    Reach out to me through LinkedIn.

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