I fail to see Apache processes @ passenger-memory-stats

[Gabriel Lichtenstein‏]

Hello,

I do not see any Apache Processes, after running:

$ sudo /usr/sbin/passenger-memory-stats

I've checked the FAQ and troubleshooting guides but I do not found any hints, would you please help me find out what may be going on? Thank you very much in advance.

The output of the command is:
#############
Version: 5.1.5
Date : 2017-07-17 11:55:35 -0300
------- Apache processes --------
### Processes: 0
### Total private dirty RSS: 0.00 MB
-------- Nginx processes --------
### Processes: 0
### Total private dirty RSS: 0.00 MB
----- Passenger processes ------
PID VMSize Private Name
--------------------------------
11741 441.1 MB 1.3 MB Passenger watchdog
11744 1692.1 MB 7.7 MB Passenger core
11752 449.5 MB 1.4 MB Passenger ust-router
### Processes: 3
### Total private dirty RSS: 10.33 MB

I`ve started apache with:

sudo systemctl start apache2.service

and:

sudo systemctl status apache2.service

● apache2.service - LSB: Apache2 web server
   Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled)
  Drop-In: /lib/systemd/system/apache2.service.d
           └─apache2-systemd.conf
   Active: active (running) since lun 2017-07-17 14:52:08 ART; 19h ago
     Docs: man:systemd-sysv-generator(8)
   CGroup: /system.slice/apache2.service
           ├─2526 /usr/sbin/apache2 -k start
           ├─2529 Passenger watchdog                                            
           ├─2532 Passenger core                                                
           ├─2609 Passenger ust-router                                          
           ├─2647 /usr/sbin/apache2 -k start
           ├─2648 /usr/sbin/apache2 -k start
           ├─2650 /usr/sbin/apache2 -k start
           ├─2652 /usr/sbin/apache2 -k start
           ├─2653 /usr/sbin/apache2 -k start
           ├─2927 /usr/sbin/apache2 -k start
           ├─3189 /usr/sbin/apache2 -k start
           ├─3190 /usr/sbin/apache2 -k start
           ├─3490 /usr/sbin/apache2 -k start
           ├─3491 /usr/sbin/apache2 -k start
           ├─3493 /usr/sbin/apache2 -k start
           ├─3494 /usr/sbin/apache2 -k start

The web app I am executing is called sequenceserver:

and I have it online @:

impam2.fmed.uba.ar/blast

ruby and passenger were installed with:

sudo apt-get install ruby-full build-essential ruby-dev

sudo apt-get install -y libapache2-mod-passenger

I am under Ubuntu Xenial 16.04 x86_64

Thank you very much for any help,

Best regards!

[Camden Narzt‏]

Can you show the output of running the following command?

\ps -lp 2647 2648 2650 2652 2653 2927 3189 3190 3490 3491 3493 3494

It's possible that the passenger-memory-stats command is not matching the process names correctly, since apache does seem to be running.

[Gabriel Lichtenstein‏]

Hello Camden, 

Here I paste you the output:

\ps -lp 2647 2648 2650 2652 2653 2927 3189 3190 3490 3491 3493 3494

F S   UID   PID  PPID  C PRI  NI ADDR SZ WCHAN  TTY        TIME CMD

5 S    33  3490  2485  0  80   0 - 109287 -     ?          0:00 /usr/sbin/apache2 -k start

5 S    33  3491  2485  0  80   0 - 109287 -     ?          0:00 /usr/sbin/apache2 -k start

5 S    33  3493  2485  0  80   0 - 109287 -     ?          0:00 /usr/sbin/apache2 -k start

Thank you very much,

Cheers,

Gabriel

[Camden Narzt‏]

Thanks, can you also check the following?

which -a apxs2 apxs | xargs -I{} bash -c "echo -n {}': ' && {} -q TARGET"
passenger-config about detect-apache2

Cheers,

Cam

[Gabriel Lichtenstein‏]

Hello Camden, 

 yes, here is the output of those commands:

which -a apxs2 apxs | xargs -I{} bash -c "echo -n {}': ' && {} -q TARGET"

/usr/bin/apxs2: apache2
/usr/bin/apxs: apache2

passenger-config about detect-apache2:

Looking for possible Apache installations...
 --> Looking for /usr/local/sbin/apxs2: not found
 --> Looking for /usr/local/bin/apxs2: not found
 --> Looking for /usr/sbin/apxs2: not found
 --> Looking for /usr/bin/apxs2: found
 --> Looking for /sbin/apxs2: not found
 --> Looking for /bin/apxs2: not found
 --> Looking for /snap/bin/apxs2: not found
 --> Looking for /usr/local/maui/bin/apxs2: not found
 --> Looking for /usr/local/maui/sbin/apxs2: not found
 --> Looking for /usr/local/sbin/apxs: not found
 --> Looking for /usr/local/bin/apxs: not found
 --> Looking for /usr/sbin/apxs: not found
 --> Looking for /usr/bin/apxs: found
 --> Looking for /sbin/apxs: not found
 --> Looking for /bin/apxs: not found
 --> Looking for /snap/bin/apxs: not found
 --> Looking for /usr/local/maui/bin/apxs: not found
 --> Looking for /usr/local/maui/sbin/apxs: not found
1 symlink duplicate(s) detected; ignoring them.
Analyzing /usr/bin/apxs...
Detecting main Apache executable...
 --> Looking for /usr/bin/apache2: not found
 --> Looking for /usr/sbin/apache2: found
Detecting version...
 --> 2.4.18
Detecting control command...
 --> Looking for /usr/bin/apache2ctl: not found
 --> Looking for /usr/bin/apachectl2: not found
 --> Looking for /usr/bin/apachectl: not found
 --> Looking for /usr/sbin/apache2ctl: found
Detecting configuration file location...
 --> Looking for /usr/bin/apache2ctl: not found
 --> Looking for /usr/bin/apachectl2: not found
 --> Looking for /usr/bin/apachectl: not found
 --> Looking for /usr/sbin/apache2ctl: found
 --> Looking for /usr/bin/apache2ctl: not found
 --> Looking for /usr/bin/apachectl2: not found
 --> Looking for /usr/bin/apachectl: not found
 --> Looking for /usr/sbin/apache2ctl: found
 --> /etc/apache2/apache2.conf
Detecting error log file...
 --> Looking for /usr/bin/apache2ctl: not found
 --> Looking for /usr/bin/apachectl2: not found
 --> Looking for /usr/bin/apachectl: not found
 --> Looking for /usr/sbin/apache2ctl: found
 --> Looking for /usr/bin/apache2ctl: not found
 --> Looking for /usr/bin/apachectl2: not found
 --> Looking for /usr/bin/apachectl: not found
 --> Looking for /usr/sbin/apache2ctl: found
 --> Attempting to substitute environment variables in Apache config value "${APACHE_LOG_DIR}/error.log"...
 --> Substituted "${APACHE_LOG_DIR}" -> "/var/log/apache2"
 --> /var/log/apache2/error.log
Detecting a2enmod and a2dismod...
 --> Looking for /usr/bin/a2enmod: not found
 --> Looking for /usr/sbin/a2enmod: found
 --> Looking for /usr/bin/a2dismod: not found
 --> Looking for /usr/sbin/a2dismod: found
 --> Looking for /usr/bin/apache2ctl: not found
 --> Looking for /usr/bin/apachectl2: not found
 --> Looking for /usr/bin/apachectl: not found
 --> Looking for /usr/sbin/apache2ctl: found
Found a usable Apache installation using /usr/bin/apxs.
Final autodetection results
 * Found Apache 2.4.18!
   Information:
      apxs2          : /usr/bin/apxs
      Main executable: /usr/sbin/apache2
      Control command: /usr/sbin/apache2ctl
      Config file    : /etc/apache2/apache2.conf
      Error log file : /var/log/apache2/error.log
   To install Phusion Passenger against this specific Apache version:
      /usr/bin/ruby2.3 /usr/bin/passenger-install-apache2-module --apxs2-path='/usr/bin/apxs'
   To start, stop or restart this specific Apache version:
      /usr/sbin/apache2ctl start
      /usr/sbin/apache2ctl stop
      /usr/sbin/apache2ctl restart
   To troubleshoot, please read the logs in this file:
      /var/log/apache2/error.log

 

[Camden Narzt‏]

Did you install passenger from the Ubuntu repos or the Phusion repos? Ubuntu makes changes when they package Passenger that can cause this problem.

Cam

[Gabriel Lichtenstein‏]

I followed this guide:

https://www.phusionpassenger.com/library/install/apache/install/oss/zesty/

so I add the repo and:

sudo apt-get install -y libapache2-mod-passenger

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[Camden Narzt‏]

Just to be clear did you follow the zesty guide or the xenial guide?

You linked the zesty guide but said earlier that you are using ubuntu xenial.

[Gabriel Lichtenstein‏]

oh yes you are very right, sorry, I indeed used the xenial guide in the server, zesty is in my laptop.

https://www.phusionpassenger.com/library/install/apache/install/oss/xenial/

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[Gabriel Lichtenstein‏]

Hello Camden,

From: 

$ man /usr/sbin/passenger-memory-stats

I read this:

ENVIRONMENT VARIABLES

       HTTPD  The full filename to the Apache executable. By default, Passenger will attempt to autodetect the Apache executable. If

              autodetection fails for whatever reason, then Apache processes will not be shown in the  memory  statistics.  In  that

              case, you may manually specify the location to the Apache executable using this environment variable.

I did it and got the same result with no apache processes showing, but in this regard I wanted to ask you if the following syntax is ok:

sudo /usr/sbin/passenger-memory-stats --HTTPD=='/usr/bin/apxs'

Thank you very much,

BRGDS,

Gabriel

[Camden Narzt‏]

The syntax you want is as follows:

HTTPD=`which apache2` sudo -E /usr/sbin/passenger-memory-stats

apxs is not the apache executable it is a helper tool for finding the apache components, and you set env vars separate from the flags.

[Gabriel Lichtenstein‏]

Oh, thanks a lot, the command worked but the result was the same :/

HTTPD=`which apache2` sudo -E /usr/sbin/passenger-memory-stats

Version: 5.1.6
Date   : 2017-07-24 14:45:38 -0300

------- Apache processes --------
### Processes: 0
### Total private dirty RSS: 0.00 MB

-------- Nginx processes --------
### Processes: 0
### Total private dirty RSS: 0.00 MB

----- Passenger processes ------
PID    VMSize     Private  Name
--------------------------------

32099  441.0 MB   1.2 MB   Passenger watchdog
32104  1692.1 MB  7.7 MB   Passenger core
32114  449.4 MB   1.3 MB   Passenger ust-router
### Processes: 3
### Total private dirty RSS: 10.23 MB

[Camden Narzt‏]

Did you install the apache2 meta-package?

sudo apt-get install apache2

just to be sure all the pieces are in place.

[Gabriel Lichtenstein‏]

Yeap:

Reading package lists... Done

Building dependency tree       

Reading state information... Done

apache2 is already the newest version (2.4.18-2ubuntu3.3).

I am running this wordpress website with apache2:

impam2.fmed.uba.ar

Thanks for your help and patience,

BRGDS,

Gabriel

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[Camden Narzt‏]

Well, you could try adding some logging to `passenger-config about ruby-libdir`/phusion_passenger/admin_tools/memory_stats.rb and see what executable passenger is looking for and the output from ps that it sees. The apache_processes method is the one you'll want to start with.

[Gabriel Lichtenstein‏]

Hello Camden,

I don´t know how to achieve what you suggested, you are saying I should edit the file:

/usr/lib/ruby/vendor_ruby/phusion_passenger/admin_tools/memory_stats.rb

to add some logging to it? how may I do it?

Thank for your patience,

Best Regards,

Gabriel

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[Camden Narzt‏]

What do you need help with? Opening the file in your editor, writing the ruby to print out some variables, or something else?

Camden

[Gabriel Lichtenstein‏]

Hi Camden,

I could open the file with geany, but I do not how to write the ruby to print out some variables,

Thanks again,

Cheers,

Gabriel

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[Camden Narzt‏]

Ok, so search for `def apache_processes` in that file and between the `def` line and the `@apache_processes` line add this:

puts "\n"*3
puts "httpd: #{PlatformInfo.httpd}"
puts "procs: #{list_processes(:exe => PlatformInfo.httpd)}"
puts "\n"*3

Then call passenger-memory-stats to print the output.

[Gabriel Lichtenstein‏]

Ok, thanks!

I`ve done this:

      def apache_processes

        puts "\n"*3

        puts "httpd: #{PlatformInfo.httpd}"

        puts "procs: #{list_processes(:exe => PlatformInfo.httpd)}"

        puts "\n"*3

        @apache_processes ||= begin

          if PlatformInfo.httpd

            processes = list_processes(:exe => PlatformInfo.httpd)

            if processes.empty?

              # On some Linux distros, the Apache worker processes

              # are called "httpd.worker"

              processes = list_processes(:exe => "#{PlatformInfo.httpd}.worker")

            end

            processes

          else

            nil

          end

        end

      end

and executed:

glichtenstein@impam2:~$ sudo /usr/sbin/passenger-memory-stats

and it resulted in:

Version: 5.1.6

Date   : 2017-07-31 11:28:20 -0300

httpd: /usr/sbin/apache2

procs: []

httpd: /usr/sbin/apache2

procs: []

------- Apache processes --------

### Processes: 0

### Total private dirty RSS: 0.00 MB

-------- Nginx processes --------

### Processes: 0

### Total private dirty RSS: 0.00 MB

----- Passenger processes ------

PID    VMSize     Private  Name

--------------------------------

11843  441.0 MB   1.2 MB   Passenger watchdog

11854  1756.6 MB  7.5 MB   Passenger core

11861  449.4 MB   3.3 MB   Passenger ust-router

### Processes: 3

### Total private dirty RSS: 12.09 MB

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[Camden Narzt‏]

ok so now you'll want to search for `def list_processes` and replace the method with the following:

def list_processes(options)
        if options[:exe]
          name = options[:exe].sub(/.*\/(.*)/, '\1')
          puts "name: #{name}"
          puts "os: #{os_name_simple}"
          if os_name_simple == "linux"
            ps = "ps -C '#{name}'"
          else
            ps = "ps -A"
            options[:match] = Regexp.new(Regexp.escape(name))
          end
          puts "ps: #{ps}"
        elsif options[:name]
          if os_name_simple == "linux"
            ps = "ps -C '#{options[:name]}'"
          else
            ps = "ps -A"
            options[:match] = Regexp.new(" #{Regexp.escape(options[:name])}")
          end
        elsif options[:match]
          ps = "ps -A"
        else
          raise ArgumentError, "Invalid options."
        end

        processes = []
        case os_name_simple
        when "solaris"
          ps_output = `#{ps} -o pid,ppid,nlwp,vsz,rss,pcpu,comm`
          threads_known = true
        when "macosx"
          ps_output = `#{ps} -w -o pid,ppid,vsz,rss,%cpu,command`
          threads_known = false
        else
          ps_output = `#{ps} -w -o pid,ppid,nlwp,vsz,rss,%cpu,command`
          threads_known = true
        end
puts "ps_output: #{ps_output}"
        list = force_binary(ps_output).split("\n")
puts "list: #{list}"
        list.shift
        list.each do |line|
puts "raw line: #{line}"
          line.gsub!(/^ */, '')
          line.gsub!(/ *$/, '')
puts "line modded: #{line}"
          p = Process.new
          if threads_known
            p.pid, p.ppid, p.threads, p.vm_size, p.rss, p.cpu, p.name = line.split(/ +/, 7)
          else
            p.pid, p.ppid, p.vm_size, p.rss, p.cpu, p.name = line.split(/ +/, 6)
          end
puts "process: #{p}"
          p.name.sub!(/\Aruby: /, '')
          p.name.sub!(/ \(ruby\)\Z/, '')
          if p.name !~ /^ps/ && (!options[:match] || p.name.match(options[:match]))
            # Convert some values to integer.
            [:pid, :ppid, :vm_size, :rss].each do |attr|
              p.send("#{attr}=", p.send(attr).to_i)
            end
            p.threads = p.threads.to_i if threads_known

            if platform_provides_private_dirty_rss_information?
              p.private_dirty_rss = determine_private_dirty_rss(p.pid)
            end
            processes << p
          end
        end
        return processes
      end

And then check the output again

[Gabriel Lichtenstein‏]

Ok, done.

I am attaching you the output in a file:

sudo /usr/sbin/passenger-memory-stats > passenger-memory-stats.log

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[Camden Narzt‏]

There is only the header line in the output for `ps -C 'apache2' -w -o pid,ppid,nlwp,vsz,rss,%cpu,command` in the script, can you check that command manually?

Is there anything unusual about your ps executable? Or do you have some sort of SELinux like system in place?

Camden

[Gabriel Lichtenstein‏]

Ok, I executed this:

glichtenstein@impam2:~$ ps -C 'apache2' -w -o pid,ppid,nlwp,vsz,rss,%cpu,command

  PID  PPID NLWP    VSZ   RSS %CPU COMMAND

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[Camden Narzt‏]

Ok so the ps command cannot find the apache processes, and that's why Passenger cannot see them either. I don't know what's going on with your ps, but it's not a passenger problem.

[Gabriel Lichtenstein‏]

Oh, ok. I do not know what could be, I thought about implementing a virtualbox machine with ubuntu as a workaround and so reinstall everything there and see if I can launch the sequenceserver (ruby-apache-phusion app I need) from the VM, and well somehow configure the website that is hosted in the main server to point to this new installation, I don't know if its is possible but it may work I guess.

On the other hand when I ran this command, apache2 is there running:

ps aux | grep apache2

root     11840  0.0  0.0 437124 34556 ?        Ss   jul28   0:11 /usr/sbin/apache2 -k start

www-data 11896  0.0  0.0 437080 14836 ?        S    jul28   0:00 /usr/sbin/apache2 -k start

www-data 11897  0.0  0.0 515908 37948 ?        S    jul28   0:00 /usr/sbin/apache2 -k start

www-data 11900  0.0  0.0 516292 38856 ?        S    jul28   0:00 /usr/sbin/apache2 -k start

www-data 11901  0.0  0.0 442276 37104 ?        S    jul28   0:00 /usr/sbin/apache2 -k start

www-data 11902  0.0  0.0 516300 41788 ?        S    jul28   0:00 /usr/sbin/apache2 -k start

www-data 12040  0.0  0.0 518256 42276 ?        S    jul28   0:00 /usr/sbin/apache2 -k start

www-data 12138  0.0  0.0 517128 44504 ?        S    jul28   0:00 /usr/sbin/apache2 -k start

www-data 12139  0.0  0.0 516212 40548 ?        S    jul28   0:00 /usr/sbin/apache2 -k start

www-data 12383  0.0  0.0 517272 44816 ?        S    jul28   0:00 /usr/sbin/apache2 -k start

www-data 12384  0.0  0.0 516124 40580 ?        S    jul28   0:00 /usr/sbin/apache2 -k start

www-data 12385  0.0  0.0 516720 40892 ?        S    jul28   0:00 /usr/sbin/apache2 -k start

www-data 12386  0.0  0.0 516120 39436 ?        S    jul28   0:00 /usr/sbin/apache2 -k start

glichte+ 25678  0.0  0.0  15760  1040 pts/8    S+   13:32   0:00 grep --color=auto apache2

Thanks for your time Camden I do not know how can I thank you enough,

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[Camden Narzt‏]

No need to thank me, and if you can find a way to get ps to filter the apache processes correctly then I'll see what I can do about getting that incorporated into Passenger.

Just a heads up, and I don't want to be alarmist but processes missing from ps output can, but certainly doesn't have to, be a sign of a malware infection. It can be many other things, notably such as SELinux or kernel level isolation technologies like cgroups but it is something that I felt I should mention.

Best of luck,

Camden

[Gabriel Lichtenstein‏]

Camden, 

I've found something odd, if I do the ps query but with the apache full path I get:

glichtenstein@impam2:~$ ps -C '/usr/sbin/apache2' -w -o pid,ppid,nlwp,vsz,rss,%cpu,command

  PID  PPID NLWP    VSZ   RSS %CPU COMMAND

11840     1    1 437124 34556  0.0 /usr/sbin/apache2 -k start

11896 11840    1 437080 14836  0.0 /usr/sbin/apache2 -k start

11897 11840    1 515908 37948  0.0 /usr/sbin/apache2 -k start

11900 11840    1 516308 40260  0.0 /usr/sbin/apache2 -k start

11901 11840    1 442468 37580  0.0 /usr/sbin/apache2 -k start

11902 11840    1 516300 41788  0.0 /usr/sbin/apache2 -k start

12040 11840    1 518256 42276  0.0 /usr/sbin/apache2 -k start

12138 11840    1 517320 45508  0.0 /usr/sbin/apache2 -k start

12139 11840    1 516212 40548  0.0 /usr/sbin/apache2 -k start

12383 11840    1 517272 44816  0.0 /usr/sbin/apache2 -k start

12384 11840    1 516124 40580  0.0 /usr/sbin/apache2 -k start

12385 11840    1 516720 40892  0.0 /usr/sbin/apache2 -k start

12386 11840    1 516120 39436  0.0 /usr/sbin/apache2 -k start

12410 11840    1 518532 41396  0.0 /usr/sbin/apache2 -k start

12411 11840    1 516216 40136  0.0 /usr/sbin/apache2 -k start

12412 11840    1 516208 40308  0.0 /usr/sbin/apache2 -k start

12413 11840    1 516700 40904  0.0 /usr/sbin/apache2 -k start

12414 11840    1 516468 39192  0.0 /usr/sbin/apache2 -k start

12415 11840    1 517336 45620  0.0 /usr/sbin/apache2 -k start

12416 11840    1 442444 39288  0.0 /usr/sbin/apache2 -k start

12417 11840    1 517432 44656  0.0 /usr/sbin/apache2 -k start

12518 11840    1 516192 39440  0.0 /usr/sbin/apache2 -k start

12520 11840    1 516280 39284  0.0 /usr/sbin/apache2 -k start

12521 11840    1 516720 39592  0.0 /usr/sbin/apache2 -k start

12522 11840    1 516652 40996  0.0 /usr/sbin/apache2 -k start

12524 11840    1 516432 40208  0.0 /usr/sbin/apache2 -k start

12526 11840    1 516348 39516  0.0 /usr/sbin/apache2 -k start

12527 11840    1 517284 45428  0.0 /usr/sbin/apache2 -k start

12528 11840    1 516196 38512  0.0 /usr/sbin/apache2 -k start

12530 11840    1 516576 41500  0.0 /usr/sbin/apache2 -k start

12531 11840    1 516468 39296  0.0 /usr/sbin/apache2 -k start

12532 11840    1 442396 35604  0.0 /usr/sbin/apache2 -k start

12533 11840    1 516140 39008  0.0 /usr/sbin/apache2 -k start

12534 11840    1 442364 36216  0.0 /usr/sbin/apache2 -k start

12535 11840    1 515960 40476  0.0 /usr/sbin/apache2 -k start

12536 11840    1 442468 36368  0.0 /usr/sbin/apache2 -k start

12537 11840    1 516192 39348  0.0 /usr/sbin/apache2 -k start

To view this discussion on the web visit https://groups.google.com/d/msgid/phusion-passenger/1fda950e-953d-4722-82ca-8dedbc8a6e66%40googlegroups.com.

[Camden Narzt‏]

You might want to check your env for any of these variables:

COLUMNS
LINES
PS_PERSONALITY
CMD_ENV
I_WANT_A_BROKEN_PS
LC_TIME
PS_COLORS
PS_FORMAT
PS_SYSMAP
PS_SYSTEM_MAP
POSIXLY_CORRECT
POSIX2
UNIX95
_XPG

They can change ps' behavior in surprising ways.