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Support Notice: SLES and CentOS/RHEL Bug Affects Vertica Process

This article explains specific issues you may experience when running Vertica on SUSE Linux Enterprise Server (SLES) and CentOS or Red Hat Enterprise Linux (RHEL) including affected version information, root cause, and resolution.

SLES

If you are running Vertica on SUSE Linux Enterprise Server (SLES), you may experience an issue when creating a new database. The following sections detail the versions of Vertica and SLES this issue impacts, root cause, and solution.

Environment

  • Vertica 9.1 and higher
  • SUSE Linux Enterprise Server 12 SP2 and higher
  • Server with Intel CPU that has Hardware Lock Elision (HLE) functionality similar to Haswell, Broadwell, etc.

    To check if the CPU has the HLE functionality, run the following command:

$ cat /proc/cpuinfo | grep flags | grep hle

flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall 
nx pdpe1gb rdtscp lm ibrs flush_l1d constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq 
dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave 
avx f16c rdrand lahf_lm abm 3dnowprefetch ida arat epb invpcid_single pln pts dtherm intel_pt ssbd ibpb stibp kaiser tpr_shadow vnmi flexpriority 
ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdseed adx smap xsaveopt cqm_llc cqm_occup_llc

Issue

Vertica cluster does not start up in the SLES environment. During start up, Vertica process crashes with the following messages in vertica.log:

nameless:1234567890ab [Init] <INFO> Catalog loaded
nameless:1234567890ab [Init] <INFO> Listening on port: 5433
nameless:1234567890ab [Init] <INFO> Initializing NodeInstanceId with random data.
nameless:1234567890ab [Init] <INFO> PID=12345
nameless:1234567890ab [Init] <INFO> Start reading DataCollector information
nameless:1234567890ac [Init] <INFO> NodeInstanceId initialized: 1234567890abcdefghijklmnopqrst.
nameless:1234567890ab [Init] <INFO> Startup [Read DataCollector] Inventory files (bytes) - 0 / 1375597933
nameless:1234567890ab [Init] <INFO> Done reading DataCollector information
Main:1234567890ab [EE] <INFO> The UDx zygote process is down, restarting it...
Main:1234567890ab [Main] <INFO> Handling signal: 11
Main:1234567890ab [Main] <ALL> Core dumped to /vertica01/DB/v_db_node0001_catalog/core.12345
Main:1234567890ab [Main] <PANIC> Received fatal signal SIGSEGV.
Main:1234567890ab [Main] <PANIC> Info: si_code: 128, si_pid: 0, si_uid: 0, si_addr: (nil)

Following is the backtrace in ErrorReport.txt:

Backtrace Generated by Error
Signal: [0x000000000000000b] PID: [0x00000000000010cd] PC: [0x00007f898d8c55e0] FP: [0x00007fff4910fe00] SIGSEGV: SI_ADDR : [0x0000000000000000]
(_ZNSt6vectorIPcSaIS0_EEaSERKS2_+0x2c6efc5) [0x39056b5]
(_ZNSt6vectorIPcSaIS0_EEaSERKS2_+0x2cbfd44) [0x3956434]
(_ZNSt6vectorIPcSaIS0_EEaSERKS2_+0x2cc10b6) [0x39577a6]
(_ZNSt6vectorIPcSaIS0_EEaSERKS2_+0x2cc11c9) [0x39578b9]
(__restore_rt+0x0) [0x7f898d8c3c10]
(__lll_unlock_elision+0x30) [0x7f898d8c55e0]
(_ZNSt6vectorIPcSaIS0_EEaSERKS2_+0x31cae81) [0x3e61571]
(__libc_fork+0x26e) [0x7f898d1be4be]
(_ZNSt6vectorIPcSaIS0_EEaSERKS2_+0x6010e5) [0x12977d5]
(_init+0x15114d) [0x5677d5]
(_init+0x476b9) [0x45dd41]
(__libc_start_main+0xf5) [0x7f898d122725]
(_init+0x14c1e9) [0x562871]
END BACKTRACE
THREAD CONTEXT
Thread type: Main Thread
Request: Unknown request
END THREAD CONTEXT

Cause

Some Intel CPUs do not handle the Hardware Lock Elision correctly.

Solution

The Hardware Lock Elision (HLE) functionality needs to be disabled.

To disable this, add an absolute path of the directory where the noelision libraries are located in the library load path.

  1. Edit /etc/ld.so.conf as in the following. Add the first line to the command:

    /lib64/noelision
    /usr/local/lib64
    /usr/local/lib
    include /etc/ld.so.conf.d/*.conf
  2. Run ldconfig command.
  3. Run ldconfig -p | grep noel command. You should get the following result that includes "noelision" in the target path.

    libpthread.so.0 (libc6,x86-64, OS ABI: Linux 3.0.0) => /lib64/noelision/libpthread.so.0
  4. Run ldd /opt/vertica/bin/vertica | grep libpthread command. You should get the following result that includes "noelision" in the target path again.

    libpthread.so.0 => /lib64/noelision/libpthread.so.0 (0x00007fd4c0275000)
  5. Create the database again.

CENTOS/RHEL

Update: Issue Resolved In Red Hat 7.x

In February 2016, we released a support notice about a glibc bug that was causing failures in Vertica databases running on Red Hat Enterprise Linux 7.x and CentOS 7.x. (See Details below)

This update notes that Red Hat has released a fix for these issues. For more information, see the Red Hat site.  

Users can upgrade glibc to the following version (or a later version) to avoid this problem: 

glibc-2.17-106.el7_2.6.x86_64.rpm

To upgrade glibc, you must perform the following:

1. Restart Vertica as dbadmin: 

admintools -t stop_db -d <database_name> 

2. Run the following command as root on all nodes: 

yum update glibc

3. Run the following command as dbadmin: 

admintools -t start_db -d <database_name>

Original Notice (Published 2/2016)

If you are running Vertica on Red Hat Enterprise Linux 7.x (or CentOS 7.x), be aware that you may experience a Vertica server process failure due to a known issue in RHEL/CentOS. This article explains the root cause of the RHEL/CentOS bug, details the symptoms you’ll see if you encounter this Red Hat bug, and provides guidance on how to proceed.

 

Root Cause of the RHEL/CentOS Bug

The problem that causes the Vertica failure stems from the fact that an important glibc bug fix has not been applied to several distributions of RHEL 7.x and downstream distributions like CentOS 7.x.

The glibc bug fix that is missing is described here: 

https://www.sourceware.org/bugzilla/show_bug.cgi?id=15073

Update: Red Hat has released a fix, available here:

https://rhn.redhat.com/errata/RHBA-2016-1030.html

 

The fix is not yet available on CentOS. We will publish an update as soon as this fix is available on CentOS.

 

Note This issue appears in Vertica running on RHEL and CentOS 7.x distributions only. The issue does not appear with Ubuntu and Debian distributions of Linux.

 

What you’ll see if this problem occurs

  1. If this problem occurs, the Vertica server process will fail, and you’ll see the following error in the <CATALOG_DIRECTORY>/dbLog file.

*** Error in `/opt/vertica/bin/vertica': invalid fastbin entry (free): 0x00007ef70f209800 ***

 

======= Backtrace: =========

0x7f0614f0efe1(/lib64/libc.so.6):  + 0x7cfe1

0x2a1e014(/opt/vertica/bin/vertica) CAT::TabColPair_pairToBytes2(void const*, void*, unsigned long) 

  1. In addition, you’ll notice that the vertica.log file appears as if was truncated at an arbitrary place, sometime in the middle of a line.

  2. Finally, on the core file for the failure, the following pattern appears at the top of the stack 

raise

    abort

    __libc_message

    _int_free          <==========

    CAT::TabColPair_pairToBytes2(void const*, void*, unsigned long)

 

How to determine whether you have the affected glibc

To determine whether the patch has been applied to your glibc, you can either:

  • Run the objdump utility, or
  • Examine the libc.so file manually

Run the objdump utility

  1. Find your libc.so file using the following command:

ldd /opt/vertica/bin/vertica | grep libc.so

libc.so.6 => /lib64/libc.so.6 (0x00007ff6dd99e000

 

  1. Run the objdump utility as shown below to determine whether fix has been applied:

## example of buggy lib.c

objdump -r -d /lib64/libc.so.6 | grep -C 20 _int_free | grep -C 10 cmpxchg | head -21 | grep -A 3 cmpxchg | tail -1 | (grep '%r' && echo "Your libc is likely buggy." || echo "Your libc looks OK.")

   7ca16: 48 85 c9                test   %rcx,%rcx

Your libc is likely buggy.

 

## example of good lib.c

objdump -r -d /lib/x86_64-linux-gnu/libc.so.6 | grep -C 20 _int_free | grep -C 10 cmpxchg | head -21 | grep -A 3 cmpxchg | tail -1 | (grep '%r' && echo "Your libc is likely buggy." || echo "Your libc looks OK.")

 

Your libc looks OK.

 

Examine the libc.so file manually

You can also choose to examine your libc in its entirety and identify whether the fix has been applied or not. The following example contains the string ‘test   %dil,%dil’. This means that the fix has been applied:

objdump -r -d /lib64/libc-2.12.so | grep -C 20 _int_free | grep -C 10 cmpxchg | head -21

 32cd8786cb:   40 20 f7                and    %sil,%dil

 32cd8786ce:   74 0c                   je     32cd8786dc <_int_free+0xec>

 32cd8786d0:   4c 8b 42 08             mov    0x8(%rdx),%r8

 32cd8786d4:   41 c1 e8 04             shr    $0x4,%r8d

 32cd8786d8:   41 83 e8 02             sub    $0x2,%r8d

 32cd8786dc:   48 89 53 10             mov    %rdx,0x10(%rbx)

 32cd8786e0:   48 89 d0                mov    %rdx,%rax

 32cd8786e3:   64 83 3c 25 18 00 00    cmpl   $0x0,%fs:0x18

 32cd8786ea:   00 00

 32cd8786ec:   74 01                   je     32cd8786ef <_int_free+0xff>

 32cd8786ee:   f0 48 0f b1 19          lock cmpxchg %rbx,(%rcx)

 32cd8786f3:   48 39 c2                cmp    %rax,%rdx

 32cd8786f6:   75 c0                   jne    32cd8786b8 <_int_free+0xc8>

 32cd8786f8:   40 84 ff                test   %dil,%dil             <==** likely good**==

 32cd8786fb:   74 09                   je     32cd878706 <_int_free+0x116>

 32cd8786fd:   41 39 e8                cmp    %ebp,%r8d

 32cd878700:   0f 85 05 07 00 00       jne    32cd878e0b <_int_free+0x81b>

 32cd878706:   48 83 c4 28             add    $0x28,%rsp

 32cd87870a:   5b                      pop    %rbx

 32cd87870b:   5d                      pop    %rbp

 32cd87870c:   41 5c                   pop    %r12

The following example does not contain the string ‘test   %dil,%dil’ . This means the fix has not been applied:

objdump -r -d /lib64/libc-2.17.so | grep -C 20 _int_free | grep -C 10 cmpxchg | head -21

 

 7c9ec:       48 85 c9                test   %rcx,%rcx

 7c9ef:       74 09                   je     7c9fa <_int_free+0xda>

 7c9f1:       8b 41 08                mov    0x8(%rcx),%eax

 7c9f4:       c1 e8 04                shr    $0x4,%eax

 7c9f7:       8d 70 fe                lea    -0x2(%rax),%esi

 7c9fa:       48 89 4b 10             mov    %rcx,0x10(%rbx)

 7c9fe:       48 89 c8                mov    %rcx,%rax

 7ca01:       64 83 3c 25 18 00 00    cmpl   $0x0,%fs:0x18

 7ca08:       00 00

 7ca0a:       74 01                   je     7ca0d <_int_free+0xed>

 7ca0c:       f0 48 0f b1 1a          lock cmpxchg %rbx,(%rdx)

 7ca11:       48 39 c1                cmp    %rax,%rcx

 7ca14:       75 ca                   jne    7c9e0 <_int_free+0xc0>

 7ca16:       48 85 c9                test   %rcx,%rcx               <==**likely buggy**===

 7ca19:       74 09                   je     7ca24 <_int_free+0x104>

 7ca1b:       44 39 e6                cmp    %r12d,%esi

 7ca1e:       0f 85 84 08 00 00       jne    7d2a8 <_int_free+0x988>

 7ca24:       48 83 c4 48             add    $0x48,%rsp

 7ca28:       5b                      pop    %rbx

 7ca29:       5d                      pop    %rbp

 7ca2a:       41 5c                   pop    %r12

What you should do

If the problem occurs, and you are using Red Hat Enterprise Linux, download this glibc fix here:

https://rhn.redhat.com/errata/RHBA-2016-1030.html

If you are on CentOS, you should contact your operating system vendor and request a fix for this issue.

You can also choose to build the latest GLIBC 2.17 from source. Vertica recommends testing this process in a staging area before implementing it in production. As with any major operation on your system, Vertica recommends backing up your system before this operation.

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