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Upgrade PHP-FPM Error uppgrading to PHP-FPM 5.6.30. Clang goes clunk...

Discussion in 'Install & Upgrades or Pre-Install Questions' started by jscott, Mar 4, 2017.

  1. jscott

    jscott Member

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    Please fill in any relevant information that applies to you:
    • CentOS Version: i.e. CentOS 6 64bit
    • Centmin Mod Version Installed: 123.09beta01
    • Nginx Version Installed: i.e. 1.11.10
    • PHP Version Installed: 5.6.30
    • MariaDB MySQL Version Installed:
    • When was last time updated Centmin Mod code base ? : just before problem

    • Persistent Config:
    Code:
    PHPFINFO='y'
    I was upgrading my Ramnode system (256mb). I did my centmin #23 #2, re-reran centmin & exited. Updated YUM.

    Decided to go ahead and update php-fpm to 5.6.30. CLUNK! PHP-FPM is DOWN!

    Code:
    /bin/sh /svr-setup/php-5.6.30/fpm-build/libtool --silent --preserve-dup-deps --mode=compile ccache /usr/bin/clang -m64 -mtune=native -I
    /svr-setup/php-5.6.30/ext/sqlite3/libsqlite -DSQLITE_ENABLE_FTS3=1 -DSQLITE_CORE=1 -DSQLITE_ENABLE_COLUMN_METADATA=1 -DSQLITE_THREADSAF
    E=0  -Iext/sqlite3/ -I/svr-setup/php-5.6.30/ext/sqlite3/ -DPHP_ATOM_INC -I/svr-setup/php-5.6.30/fpm-build/include -I/svr-setup/php-5.6.
    30/fpm-build/main -I/svr-setup/php-5.6.30 -I/svr-setup/php-5.6.30/fpm-build/ext/date/lib -I/svr-setup/php-5.6.30/ext/date/lib -I/svr-se
    tup/php-5.6.30/ext/ereg/regex -I/usr/include/libxml2 -I/usr/include/enchant -I/usr/X11 -I/usr/include/freetype2 -I/usr/include/imap -I/
    svr-setup/php-5.6.30/ext/mbstring/oniguruma -I/svr-setup/php-5.6.30/fpm-build/ext/mbstring/oniguruma -I/svr-setup/php-5.6.30/ext/mbstri
    ng/libmbfl -I/svr-setup/php-5.6.30/fpm-build/ext/mbstring/libmbfl -I/svr-setup/php-5.6.30/ext/mbstring/libmbfl/mbfl -I/svr-setup/php-5.
    6.30/fpm-build/ext/mbstring/libmbfl/mbfl -I/svr-setup/php-5.6.30/ext/sqlite3/libsqlite -I/usr/include/pspell -I/svr-setup/php-5.6.30/ex
    t/zip/lib -I/svr-setup/php-5.6.30/fpm-build/TSRM -I/svr-setup/php-5.6.30/fpm-build/Zend -I/svr-setup/php-5.6.30/main -I/svr-setup/php-5
    .6.30/Zend -I/svr-setup/php-5.6.30/TSRM -I/svr-setup/php-5.6.30/fpm-build/    -I/usr/include -g -O2  -c /svr-setup/php-5.6.30/ext/sqlit
    e3/libsqlite/sqlite3.c -o ext/sqlite3/libsqlite/sqlite3.lo 
    
    clang: error: unable to execute command: Killed
    clang: error: clang frontend command failed due to signal (use -v to see invocation)
    clang version 3.4.2 (tags/RELEASE_34/dot2-final)
    Target: x86_64-redhat-linux-gnu
    Thread model: posix
    clang: note: diagnostic msg: PLEASE submit a bug report to http://llvm.org/bugs/ and include the crash backtrace, preprocessed source, and associated run script.
    clang: note: diagnostic msg: 
    ********************
    
    PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
    Preprocessed source(s) and associated run script(s) are located at:
    clang: note: diagnostic msg: /tmp/sqlite3-f6785e.c
    clang: note: diagnostic msg: /tmp/sqlite3-f6785e.sh
    clang: note: diagnostic msg: 
    
    ********************
    make: *** [ext/sqlite3/libsqlite/sqlite3.lo] Error 1
    
    real    2m39.525s
    user    2m14.727s
    sys     0m8.105s
    
    /bin/sh /svr-setup/php-5.6.30/fpm-build/libtool --silent --preserve-dup-deps --mode=compile ccache /usr/bin/clang -m64 -mtune=native -I/svr-setup/php-5.6.30/ext/sqlite3/libsqlite -DSQLITE_ENABLE_FTS3=1 -DSQLITE_CORE=1 -DSQLITE_ENABLE_COLUMN_METADATA=1 -DSQLITE_THREADSAFE=0  -Iext/sqlite3/ -I/svr-setup/php-5.6.30/ext/sqlite3/ -DPHP_ATOM_INC -I/svr-setup/php-5.6.30/fpm-build/include -I/svr-setup/php-5.6.30/fpm-build/main -I/svr-setup/php-5.6.30 -I/svr-setup/php-5.6.30/fpm-build/ext/date/lib -I/svr-setup/php-5.6.30/ext/date/lib -I/svr-setup/php-5.6.30/ext/ereg/regex -I/usr/include/libxml2 -I/usr/include/enchant -I/usr/X11 -I/usr/include/freetype2 -I/usr/include/imap -I/svr-setup/php-5.6.30/ext/mbstring/oniguruma -I/svr-setup/php-5.6.30/fpm-build/ext/mbstring/oniguruma -I/svr-setup/php-5.6.30/ext/mbstring/libmbfl -I/svr-setup/php-5.6.30/fpm-build/ext/mbstring/libmbfl -I/svr-setup/php-5.6.30/ext/mbstring/libmbfl/mbfl -I/svr-setup/php-5.6.30/fpm-build/ext/mbstring/libmbfl/mbfl -I/svr-setup/php-5.6.30/ext/sqlite3/libsqlite -I/usr/include/pspell -I/svr-setup/php-5.6.30/ext/zip/lib -I/svr-setup/php-5.6.30/fpm-build/TSRM -I/svr-setup/php-5.6.30/fpm-build/Zend -I/svr-setup/php-5.6.30/main -I/svr-setup/php-5.6.30/Zend -I/svr-setup/php-5.6.30/TSRM -I/svr-setup/php-5.6.30/fpm-build/    -I/usr/include -g -O2  -c /svr-setup/php-5.6.30/ext/sqlite3/libsqlite/sqlite3.c -o ext/sqlite3/libsqlite/sqlite3.lo 
    
    clang: error: unable to execute command: Killed
    clang: error: clang frontend command failed due to signal (use -v to see invocation)
    clang version 3.4.2 (tags/RELEASE_34/dot2-final)
    Target: x86_64-redhat-linux-gnu
    Thread model: posix
    clang: note: diagnostic msg: PLEASE submit a bug report to http://llvm.org/bugs/ and include the crash backtrace, preprocessed source, and associated run script.
    clang: note: diagnostic msg: 
    ********************
    
    PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
    Preprocessed source(s) and associated run script(s) are located at:
    clang: note: diagnostic msg: /tmp/sqlite3-1807c8.c
    clang: note: diagnostic msg: /tmp/sqlite3-1807c8.sh
    clang: note: diagnostic msg: 
    
    ********************
    make: *** [ext/sqlite3/libsqlite/sqlite3.lo] Error 1
    
    
    This is why we have test servers!!! :))

    -John
     
  2. pamamolf

    pamamolf Well-Known Member

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    Nginx-1.13.x
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    Out of ram maybe or use a heavy Centos latest version on it?
     
    • Agree Agree x 1
  3. eva2000

    eva2000 Administrator Staff Member

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    For 123.09beta01 and higher, you need at least 1023000 kilobytes of total swap space and 780000 kilobytes of memory to enable fileinfo php extension due to fileinfo's native high memory compilation requirements.

    If you meet the swap disk and minimum memory requirements, set in persistent config file /etc/centminmod/custom_config.inc
    Code (Text):
    PHPFINFO=y
    

    then run centmin.sh menu option 5 to recompile your php version
     
  4. jscott

    jscott Member

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    looks like it is time to bump the minimum specs again.

    I removed phpfinfo and tried to scale back to 5.6.25 which was what was running before. No joy. The Beast is Raging!! and started ravaging the system. Looks like sqlite3 is something of a pig as well. I think that is what the Beast was after.

    Code:
    [623160.582092] OOM killer in rage, 1 tasks killed
    [623160.582365] Out of memory in UB 41774: OOM killed process 28615 (nginx) score 0 vm:120116kB, rss:12660kB, swap:5308kB
    [623160.621893] OOM killer in rage, 1 tasks killed
    [623160.622162] Out of memory in UB 41774: OOM killed process 28616 (nginx) score 0 vm:120116kB, rss:12444kB, swap:5308kB
    [623160.661612] OOM killer in rage, 1 tasks killed
    [623160.661884] Out of memory in UB 41774: OOM killed process 28617 (nginx) score 0 vm:120116kB, rss:12700kB, swap:5308kB
    
    I even killed off every service I could and it did not help.

    -John
     
    Last edited: Mar 4, 2017
  5. eva2000

    eva2000 Administrator Staff Member

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    @jscott what is output for this command
    Code (Text):
    ps -e -o pid,user,cpu,size,rss,cmd --sort -size,-rss | head
    

    and
    Code (Text):
    free -m
    df -HT
    

    Might want to use CODE tags for code How to use forum BBCODE code tags :)
     
  6. jscott

    jscott Member

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    Hi George,

    Here is the information you requested.

    Is there something wrong with my code blocks? Everything looks fine in my preview, but this is the second time you have mentioned it to me. I am wondering if there is something wrong that I am not seeing.

    Thanks
    -John



    Code:
    [00:27][root@atlonenet ~]# ps -e -o pid,user,cpu,size,rss,cmd --sort -size,-rss | head
      PID USER     CPU    SZ   RSS CMD
     1258 root       - 634872 4424 /usr/bin/nrserver
     1050 mysql      - 354196 17388 /usr/sbin/mysqld --basedir=/usr --datadir=/var/lib/mysql --plugin-dir=/usr/lib64/mysql/plugin --user=mysql --log-error=/var/lib/mysql/atlonenet.err --open-files-limit=8192 --pid-file=/var/lib/mysql/atlonenet.pid --socket=/var/lib/mysql/mysql.sock
     1109 503        - 280116 13624 /usr/local/bin/memcached -d -m 8 -l 127.0.0.1 -p 11211 -c 2048 -b 2048 -R 200 -t 4 -n 72 -f 1.25 -u memcached -o slab_reassign,slab_automove,lru_crawler,lru_maintainer,maxconns_fast,hash_algorithm=murmur3 -P /var/run/memcached/memcached1.pid
     1268 root       - 259032 1768 /usr/bin/nrservice
      570 root       - 198644  872 /sbin/rsyslogd -i /var/run/syslogd.pid -c 5
     1220 nginx      - 29508 21516 nginx: worker process                                   
     4362 root       - 22280 21564 lfd - sleeping
     1214 root       - 17220  4844 nginx: master process /usr/local/sbin/nginx -c /usr/local/nginx/conf/nginx.conf
    10885 munin      - 14528 16664 /usr/share/munin/munin-update [Munin::Master::UpdateWorker<compute-1.amazonaws.com;ec2-52-23-160-25.compute-1.amazonaws.com>]
    
    Code:
    [00:33][root@atlonenet ~]# free -m
                 total       used       free     shared    buffers     cached
    Mem:           256        202         53         29          0        120
    -/+ buffers/cache:         82        173
    Swap:          128         54         73
    [00:33][root@atlonenet ~]# df -HT
    Filesystem     Type      Size  Used Avail Use% Mounted on
    /dev/simfs     reiserfs  129G   18G  112G  14% /
    none           devtmpfs  135M  4.1k  135M   1% /dev
    
    
     
  7. eva2000

    eva2000 Administrator Staff Member

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    Nothing wrong just my posts for troubleshooting are for benefit for all readers of the post not just you - so lurkers and other members are aware of it :D

    Is this an OpenVZ VPSes ? if that is the case it reports used memory to include Virtual memory size unlike non-OpenVZ systems, should your usage of memory seen by system will be larger. That /usr/bin/nrserver is neo router or something it's total size is large and probably what is tipping things over. You can check Virtual memory size with vsz column form output of
    Code (Text):
    ps -e -o pid,user,cpu,vsz,size,rss,cmd --sort -size,-rss | head
    


    So try upgrading PHP on low memory systems via disabling nginx, php-fpm, mysql and memcached services first

    To prevent errors for visitors do it like this
    Code (Text):
    npstop
    mysqlstop
    memcachedstop
    

    also stop nrserver service

    then update nginx

    Code (Text):
    mysqlstart
    memcachedstart
    nprestart
    

    then start nrserver again
     
    Last edited: Mar 4, 2017
  8. jscott

    jscott Member

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    Are you saying you want me to use CODEB blocks instead of CODE blocks so my code looks like

    Code (Text):
    Code block with black background
    


    Instead of
    Code:
    Code block with white background
    
     
  9. eva2000

    eva2000 Administrator Staff Member

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    corrected your post, but you can use either CODE or CODEB tags.. just better than no CODE tags at all :)
     
  10. jscott

    jscott Member

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    Thats what I am trying to figure out.... You have mentioned that I should use them a couple of times, but as far as I know I have always used them... So I am just confused... I want to do things the "right" way....

    -john
     
  11. eva2000

    eva2000 Administrator Staff Member

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    no worries, when i reply i keep in mind that posts are read by other folks too so what i state is for those readers as much as yourself. I should change the way I mention that in future :)
     
  12. jscott

    jscott Member

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    AH, now I understand. Yes, when you mentioned using CODE tags in a reply to me, I assumed it was a recomendation to ME. So I thought I was missing something.

    Thanks for the clarification, and everything you do here. You are a great contributor to the linux community.

    -John

     
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