Setup MIDAS experiment at TRIUMF

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Introduction

This page describes setting up a MIDAS experiment at TRIUMF. This information can be adapted for other sites.

Environment variables

  • MIDASSYS Base directory of the MIDAS package, midas and mxml should be at the same level.
  • MIDAS_EXPTAB Experiment definition file
  • MIDAS_SERVER_HOST MIDAS host server name for remote midas connections.
  • MIDAS_EXPT_NAME Experiment name

Standard layout of MIDAS experiment

The following shows the directory layout of a standard MIDAS experiment: 

/home/exptuser/
               packages/
                       root                   <---- ROOT
                       mxml
                       mscb
                       midas/                 <---- MIDAS
                             linux/{lib,bin}       <---- binaries matching the selected 64-bit/32-bit flavour of ROOT
                             linux-m32/{lib,bin}   <---- limited function 32-bit binaries for 32-bit frontend machines, build by "make linux32"
                             linux-m64/{lib,bin}   <---- limited function 64-bit binaries (only needed if ROOT and linux/bin are 32-bit)
                             linux-arm/{lib,bin}   <---- full function ARM cross-compiled using "make linuxarm"
                             linux-crosscompile/{lib,bin}  <---- cross-compiled limited function binaries for PPC and ARM frontends (see Makefile)
                       rootana                <---- ROOT analyzer
                       roody                  <---- graphical online histogram viewer for MIDAS and ROOTANA
                online/
                       exptab                         <---- experiment definition
                       {.ODB,.SYSTEM,.SYSMSG,etc}.SHM <---- MIDAS shared memory save files
                       src                            <---- experiment frontend sources
                       bin,scripts
                       elog                           <---- MIDAS elog
                       history                        <---- MIDAS history
                       data -> /data/exptname/current <---- symlink to the data directory
/data/exptname/current                                <---- experiment data directory with ODB save files and MIDAS .mid/.mid.gz data files

Prepare computers

On some operating systems, several MIDAS functions require administrator access:

Prepare the user account

NOTES
  • Instructions are given for recent MIDAS versions (August 2015 and later) which have enhanced Security. Instructions for older versions differ slightly.
    • follow the orange instructions for older versions
  • The Default Ports are different between the two versions:
    • default ports are mserver (1175), mhttpd (8080 and 8443)
    • default ports (older versions) are mserver (7071), mhttpd (8081)

The default port for ROODY is 9091.

  • Setup the user account for running this instance of midas. For machines part of the LADD cluster, follow these [1] instructions.
  • check that the account is using the /bin/bash shell
  • make $HOME/.profile look like this:
#!/bin/echo You must source

export SVN_EDITOR="emacs -nw"
export GIT_EDITOR="emacs -nw"
export MIDASSYS=$HOME/packages/midas
export ROOTANASYS=$HOME/packages/rootana
export MIDAS_EXPTAB=$HOME/online/exptab
#
# setup the MIDAS mserver
#
case `hostname` in
daq07*)
   unset MIDAS_SERVER_HOST
   ;;
*)
   export MIDAS_SERVER_HOST=daq07.triumf.ca:7070
   ;;
esac
#
# select 64-bit or 32-bit MIDAS and ROOT
#
case `uname -i` in
i386)
   source /daq/daqshare/olchansk/root/root_v5.34.01_SL62_32/bin/thisroot.sh
   export PATH=.:$MIDASSYS/linux-m32/bin:$PATH
   ;;
*)
   #source /daq/daqshare/olchansk/root/root_v5.34.34_SL67_64/bin/thisroot.sh
   source $HOME/packages/root/bin/thisroot.sh
   export PATH=.:$MIDASSYS/linux/bin:$PATH
   ;;
esac
#
export PATH=.:$HOME/online/bin:$HOME/packages/roody/bin:$PATH
#
#end
  • mkdir $HOME/packages
  • Logout and login again, for .cshrc changes to take effect

Install ROOT

  • Identify the Linux version: RH9 (Red Hat Linux 9), FC3 (Fedora Core 3), RHEL4/SL4 (Red Hat Enterprise LInux 4/Scientific Linux 4), SL5x, SL6x, (CentOS/CC/SL) el7x: more /etc/redhat-release
  • Decide to use 32-bit or 64-bit ROOT ('uname -a')
  • cd $HOME/packages
  • ls -l /daq/daqshare/olchansk/root/ ### to see all available ROOT packages
  • ln -s /daq/daqshare/olchansk/root/root_vNNN_VVV_BB root, where NNN is the latest available version of ROOT ("ls -l /daq/daqshare/olchansk/root"), VVV is the Linux version code (RH9, FC3, SL4, etc) and BB is "_32" or "_64" for 32-bit or 64-bit ROOT. For example: /daq/daqshare/olchansk/root/root_v5.10.00_SL40
  • for example: ln -s /daq/daqshare/olchansk/root/root_v5.34.34_el72_64 $HOME/packages/root
  • Check that ROOT works: "source $HOME/packages/root/bin/thisroot.sh; root". Type ".q" to exit root.

Install MIDAS

You can see a list of other installation problems at Common problems & Debugging recipes.

NOTE
Optional features in MIDAS can be explicitly disabled if desired when making MIDAS using the NO_xxx feature (NO_ROOT,NO_MYSQL,NO_ODBC,NO_SQLITE,NO_MSCB), e.g. "make NO_ROOT=1" to disable ROOT. These NO_xxx Makefile variables are only used to control autodetection.

Install ROOTANA

Install ROODY

Build special versions of MIDAS

Build special versions of MIDAS for the case when some MIDAS programs, such as VME frontends, will run on a different computer that may have a different flavour of operating system, i.e. 32-bit linux or an older version of Scientific Linux.

  • login to the computer where the frontends will run and:
  • if it is a 32-bit linux: cd $HOME/packages/midas; make linux32
  • if it is a 64-bit linux: cd $HOME/packages/midas; make linux64
  • login to the host computer to cross-compile ARM code:
  • if it is an ARM linux: cd $HOME/packages/midas; make linuxarm # may need to install ARM cross compilers

Prepare VME hardware

Hardware check list:

Install Universe-II VME driver (V7648, V7750, V7805, V7851)

Install Tsi-148 VME driver (V7865)

Setup the experiment environment

  • Decide which computer will host MIDAS (where MIDAS shared memory buffers will reside).
This computer will run the mserver, mlogger and mhttpd applications. (It is usually the machine where the MIDAS,ROOT etc. packages have been downloaded). It will be referred to as the host machine (localhost).

The environment is slightly different depending on whether all programs run on the host machine, or whether some programs run on remote host(s) :

ALL programs run on localhost

If all programs run on the host machine (localhost), it is not necessary to run mserver. MIDAS_SERVER_HOST will not be assigned (see example .cshrc above).

Some programs run on REMOTE host(s)

IMPORTANT:
  1. Since August 2015 you must explicitly allow access for clients running on remote machines. To do this, follow the instructions here.
  2. The example code .cshrc (see above) should be present on both host and remote machine(s). This will ensure that MIDAS_SERVER_HOST will NOT be set for the host machine (localhost), but on a remote machine, MIDAS_SERVER_HOST will be set to the MIDAS host machine.
  3. The client mserver must be started on the MIDAS host machine. Note that multiple experiments can run on the same host machine by starting several instances of mserver (one for each experiment) running with different ports (and .cshrc would be edited so that MIDAS_SERVER_HOST is set to the appropriate port for the experiment).


On the host machine:

  • mkdir $HOME/online
  • cd $HOME/online
  • create directories for local programs, sources, elog and history: mkdir bin src elog history
  • create data directory: mkdir -p /ladd/data1/t2kvme5/data; ln -s /ladd/data1/t2kvme5/data $HOME/online
  • create the exptab file "$HOME/online/exptab" following the example below. The first entry (exptname) is the name if the DAQ system (MIDAS experiment name), the second entry (/home/USER/online) is the location of MIDAS shared memory buffers (by convention, $HOME/online), the third entry (kopio03) is your username.
exptname /home/kopio03/online kopio03
  • logout and login again for all changes to take effect

Setup experiment startup scripts

  • login to the experiment host computer
  • echo $MIDAS_SERVER_HOST ### to check correct value - should be blank
  • create $HOME/online/bin/start_daq.sh, replacing XXX with the hostname of the machine running the experiment (and changing the mserver and mhttpd ports, as needed).
#!/bin/sh
# start_daq.sh
cd $HOME/online
#
case `hostname` in XXX*)
   echo "Good, we are on XXX!"
   ;;
*)
   echo "The start_daq script should be executed on XXX"
   exit 1
   ;;
esac
#
odbedit -c clean
#   start mhttpd on default port. (Mongoose https version - see mhttpd for other options)
mhttpd  -D  -a localhost -a XXX.triumf.ca # optionally restrict access to specified hosts
#
#   start mserver on default port (use argument -p to use a different port) 
mserver -D   # access must now be specifically allowed - see above

# OR (older MIDAS versions)
# mhttpd  -p 8081 -D -a localhost -a XXX.triumf.ca      # optionally restrict access to specified hosts
# mserver -p 7071 -D -a localhost -a lxdragon01.triumf.ca -a lxdragon02.triumf.ca -a XXX.triumf.ca # optionally restrict access to specified hosts

#
mlogger -D
#end file


Setup experiment database (ODB)

  • run $HOME/online/bin/start_daq.sh
  • odbedit, run these commands: (replace user names and directory names)
set "/Logger/Message file" "/home/kopio03/online/midas.log"
set "/Logger/Data Dir"     "/home/kopio03/online/data"
create STRING "/Logger/History dir"
set "/Logger/History dir"  "/home/kopio03/online/history"
create STRING "/Logger/Elog dir"
set "/Logger/Elog dir"     "/home/kopio03/online/elog"
set "/Logger/ODB dump file" "/home/kopio03/online/history/run%05d.xml"
set "/Logger/ODB dump" "y"
set "/Logger/Channels/0/Settings/Filename" "run%05dsub%03d.mid.gz"
set "/Logger/Channels/0/Settings/Subrun byte limit" "1000000000"
set "/Logger/Channels/0/Settings/Compression"   1
set "/Logger/Channels/0/Settings/ODB Dump" "y"
set "/Programs/Logger/Required" y
set "/Programs/Logger/Start command" "mlogger -D"
set "/Programs/fevme/Required" "y"
set "/Programs/fevme/Start command" "ssh -n lxdaq09 $HOME/online/src/fevme_gef.exe -O"
exit
  • open web browser e.g. firefox.
  • go to the midas status page at https://localhost:8443 (default port).
  • OR open the midas status page at http://localhost:8081 (older MIDAS versions)
  • midas status page will show most stuff "red" as nothing is running yet
  • DON'T DO THIS YET run ./fevme.exe (on the computer with the VME interface, could be different from computer hosting the experiment), observe that corresponding equipments have been created
  • save the url bookmark to the "personal toolbar"
  • go to the Programs page, stop mlogger, stop fevme, start mlogger, start fevme
  • go to the Status page, start run, stop run
  • go back to the Status page, everything should be green
  • start a run
  • send signals to the ADC gate
  • you should be getting events
  • to look at data, proceed with setting up the ROOT Analyzer.

Start DAQ programs at boot time

  • add this to /etc/rc.local (replace username and location of the start_daq script)
su - alpha -c /home/alpha/online/bin/start_daq.sh

Setup local software version control

Version control for experiment source code is setup using "git" (http://git-scm.com/)

  • cd $HOME/online
  • git init
  • git add exptab
  • git add bin/start_daq.sh
  • git add .gitignore ### contents can be
*~
*.o
*.exe
  • git add src/Makefile src/*.cxx ...
  • git commit -a

Adjust MIDAS buffer sizes

Default MIDAS SYSTEM buffer size is 8 Mbytes, fairly small for high-data-rate experiments. The rule of thumb is to have at least a few seconds worth of buffer space available. For example, if event size is 10 Kbytes and the event rate is 1 kHz, data rate is 10*10^3*1*10^3 = 10 Mbytes/sec. To buffer 10 seconds of data we need 100 Mbytes of buffer space.

To resize the MIDAS event buffers (SYSTEM, etc) do this:

  • stop all frontends, stop mlogger
  • start odbedit:
    • cd "/Experiment/Buffer sizes"
    • set SYSTEM 100000000
  • run "mdump -z SYSTEM"
  • if mdump complains about the size of .SYSTEM.SHM, remove it, try again.
  • ls -l /dev/shm ### to observe that the size of shared memory is correct



Secure MIDAS and ELOG Web access

In versions prior to May 2015, the default web access to MIDAS and ELOG uses the "http:" protocol which is insecure. In this case, all information is transmitted as clear text meaning that secret, confidential and sensitive information (such as the MIDAS and ELOG passwords and usernames) can be stolen "easily". This means that even "password protected" MIDAS and ELOG pages are not really protected if accessed using the "http" method.

Better security for HTTP is gained by using a password protected SSL (https) proxy. (It does not provide absolute security because of remaining problems with the security of SSL certificates, security of passwords, etc). Setting up an SSL (https) proxy is described below.

Since May 2015, an alternative secure option to setting up an HTTP proxy is available to users of MIDAS. Recent versions of elogd (ELOG) do support SSL https:// connections, and #mhttpd with HTTPS/SSL server (Mongoose) is now available. This option is the default, and provides a similar level of security to an HTTP proxy.

See Security#Web Access for a comparison of these two secure options.

mhttpd with HTTPS/SSL server (Mongoose)

Since May 2015 the MIDAS web server mhttpd is explicitly linked with OpenSSL to provide secure HTTPS connections via the Mongoose web server (see mhttpd). With this version, default web access to MIDAS uses the "https" protocol. Web access to mhttpd can be restricted by using the "-a hostname" switch of mhttpd. The first time mhttpd is run, a password file must be created. An SSL certificate is also required. See HTTPS/SSL server (Mongoose) for instructions.


mhttpd using an HTTPS/SSL proxy

An HTTP proxy must be set up. This is the only way of securing older version of mhttpd (pre August 2015). Older versions of mhttpd are started using the -p port option e.g.

  • mhttpd -D -p 8080

To run a new version of mhttpd using an HTTP proxy, use the options provided to run the old (non-Mongoose) webserver on a given port, i.e.

  • mhttpd --oldserver 8080 --nomg -D

When using an SSL proxy, only access from the SSL proxy (and maybe some special trusted machines) should be permitted. This is done using the "-a hostname" switch of mhttpd. Normally there will be only "-a localhost" switch, enabling access only for the local machine (where the SSL proxy is running). Additional "-a hostname" switches enable access from listed local machines. No "-a xxx" enables access from everywhere (defeating the purpose of the SSL proxy, unless access controls are enforced elsewhere, i.e. by a site firewall or by local firewall rules).

Setting up an HTTP proxy

In this example, we use APACHE HTTPD to password-protect a typical midas/mhttpd and elog installation.

In this configuration, one uses the Linux stock httpd that accepts encrypted https:// connections and forwards them to mhttpd and elogd. Instead of (or in addition to) using mhttpd and elogd passwords, one configures password protection in httpd via the regular apache httpd password mechanisms (htpasswd, etc).

Recent versions of elogd do support SSL https:// connections, but if one is running an SSL proxy for anyway, it is simpler to run both through the same SSL proxy using the same SSL host certificate and the same httpd password file.

Restricting http: access to elogd

Note
Recent versions of elogd do support SSL https:// connections. The following information is for those using an HTTP proxy (see above).

For elogd, this is done using the "-n localhost" switch with enables only access from the same machine if present, or access from anywhere is absent (defeating the purpose of the SSL proxy, unless access controls are enforced elsewhere).

(It is recommended to run elogd from the same user as the main daq user and to keep elogd.cfg and all logbooks in the home directory of this user, where they are captured by the normal site backup system)

Install standalone elog

  • login into the user account that will run the elog
  • cd $HOME/packages
  • git clone https://bitbucket.org/ritt/elog
  • cd elog
  • make
  • create new file start_elogd with this contents:
#!/bin/sh

killall elogd
sleep 1
killall -KILL elogd
sleep 1
$HOME/packages/elog/elogd -n localhost -x -c $HOME/packages/elog/elogd.cfg -p 8082 -D

#end
  • chmod a+x start_elogd
  • edit elogd.cfg to read:
[global]
port = 8082
SMTP host = smtp.triumf.ca
URL = https://titan00.triumf.ca/elog/

Reverse sort = 1
Display Mode = full

#List Menu commands = New, Find, Admin, Help
#Menu commands = New, Edit, Reply, Find, Duplicate, Help

Entries Per Page = 30
Supress Email on edit = 1
Default encoding = 1
Page title = TITAN ELOG
Resolve host names = 1

Logfile = /home/titan/packages/elog/elogd.log
#Logging level = 3

[midas]

List page Title = T2K M11 MIDAS ELOG
Comment = T2K M11 MIDAS ELOG
Page Title = T2K M11 MIDAS ELOG
RSS Title = [$logbook - $type - $system] $subject, posted by $author

Attributes = Author, Subject, Run, Type, System
Show Attributes Edit = Run, Author, Subject, Type, System
Required Attributes = Author, Type, System, Subject

Options Type = Routine, Reply, Shift Summary, Modification, Question, Info, Problem
Options System = General, DAQ, Beamline

Preset Run = $shell(MIDASSYS=. /home/t2km11/packages/midas/linux/bin/odbedit -d Runinfo -c 'ls -v \"run number\"')

Preset On Reply Type = Reply
Preset On Reply Run = $shell(MIDASSYS=. /home/t2km11/packages/midas/linux/bin/odbedit -d Runinfo -c 'ls -v \"run number\"')

List Display = Date, Subject, Type, System, Author, ID
Quick Filter = Date, Type, ID

Remove on reply = Author
Quote on reply = 1

Use lock = 1

************* Email Functionality ****************

Use Email Subject = [T2KM11 - $System] $Subject
Omit Email To = 1

Email System General = xxx

To start elogd automatically when the machine is rebooted, login as root and

  • add this text to /etc/rc.local:
su - titan -c "/home/titan/packages/elog/start_elogd"
  • chmod a+x /etc/rc.local
  • systemctl start rc-local

To import elog entries from the mhttpd elog, do this:

  • cd ~/packages/elog/logbooks
  • ln -s /home/t2km11/online/elog midas
  • cd midas
  • ~/packages/elog/elconv)

Install https proxy

  • login as root to the https proxy machine
  • cd ~root
  • yum install mod_ssl
  • yum install crypto-utils # see http://www.triumf.info/wiki/DAQwiki/index.php/SLinstall#Enable_monitoring_of_HTTPS_certificates
  • create a certificate request (replace ladd09 with your hostname): openssl req -new -nodes -newkey rsa:2048 -sha256 -out ladd09.csr -keyout ladd09.key (answer: CA, BC, Vancouver, TRIUMF, DAQ, ladd09.triumf.ca, email@email.com
  • sign it by TRIUMF:
    • mail -s "Certificate request" yourself@email.com < ladd09.csr
    • forward this request to Andrew Daviel
    • he will email the signed crt file, copy it to this system as ladd09.crt
  • sign it yourself: openssl x509 -req -days 365 -sha256 -in ladd09.csr -signkey ladd09.key -out ladd09.crt
  • (if the certificate expires, renew it by signing it again)
  • Additional commands for working with certificates:
    • explore the private key: openssl pkey -in ladd09.key -text -noout
    • explore the certificate request: openssl req -in ladd00.csr -text -noout
    • explore the certificate: openssl x509 -in ladd09.crt -noout -text
  • move certificate files to proper system locations:
  • mv ladd09.key /etc/pki/tls/private/
  • mv ladd09.crt /etc/pki/tls/certs/
  • if selinux is enabled, do this:
    • restorecon -Rv /etc/pki/tls/certs/
    • restorecon -Rv /etc/pki/tls/private/
    • /usr/sbin/setsebool -P httpd_can_network_connect 1
  • open /etc/httpd/conf.d/ssl.conf in a text editor, go to the very bottom and right before the "</VirtualHost>" entry, add following text:
...
SSLCertificateFile /etc/pki/tls/certs/ladd09.crt 
SSLCertificateKeyFile /etc/pki/tls/private/ladd09.key 

ProxyPass /elog/ http://localhost:8082/ retry=1
ProxyPass /      http://localhost:8080/ retry=1

<Location />

SSLRequireSSL
AuthType Basic
AuthName "password protected site"
Require valid-user

# create password file: touch /etc/httpd/htpasswd
# to add new user or change password: htpasswd /etc/httpd/htpasswd username
AuthUserFile /etc/httpd/htpasswd

</Location>
</VirtualHost>
...
  • comment out duplicate "SSLCertificateFile" and "SSLCertificateKeyFile" elsewhere in the file
  • (optionally) If you got a certificate that is signed by DigiCert or RapidSSL then you'll need to add a line specifying the certificate chain file:
...
SSLCertificateChainFile /etc/pki/tls/certs/DigiCertCA.crt
...
  • touch /etc/httpd/htpasswd
  • htpasswd /etc/httpd/htpasswd midas # enter password midas
  • chkconfig httpd on
  • service httpd restart
  • firewall-cmd --add-port=443/tcp --permanent
  • firewall-cmd --reload
  • firewall-cmd --list-all
  • test it
  • in ODB, set "/Elog/URL" to "https://host/elog/"
  • now from the midas status page, the "Elog" button should take us to the https Elog URL

In needed, enable user directories: https://blah/~user in ~user/public_html

  • edit /etc/httpd/conf.d/userdir.conf, replace "UserDir disabled" with "UserDir enabled"
  • setsebool -P httpd_enable_homedirs true
  • systemctl restart httpd

Setup the history mhttpd for faster access to history plots

When running an SSL proxy,

  • start the main mhttpd (orange command for old mhttpd, green for new mhttpd with Mongoose(post August2015):
    • "mhttpd -p 8071 -D" or
    • "mhttpd -D --oldserver 8071 --nomg"
  • start the history mhttpd
    • "mhttpd -p 8072 -D -H" or
    • "mhttpd -D -H --oldserver 8072 --nomg"
  • set ODB /History/URL to "http://alphacpc09.cern.ch:8072/HS/"
  • open the MIDAS status page
  • go to the history section, try to open any history plot, observe that the history plot gif image loads correctly, inspect it's URL (use "copy image URL" or "view source", etc), it should point to port 8072 causing connection to the history mhttpd.
  • continue with these instructions to setup history mhttpd access through an SSL proxy:
  • setup SSL proxy access (required mod_proxy_html)
    • login as root to the SSL proxy machine
    • on SL5, install the missing mod_proxy_html httpd module:
    • yum install httpd-devel libxml2-devel
    • wget http://apache.webthing.com/mod_proxy_html/mod_proxy_html.tar.bz2
    • tar xjvf mod_proxy_html.tar.bz2
    • cd mod_proxy_html
    • apxs -c -I. -I/usr/include/libxml2 -i mod_proxy_html.c
    • apxs -c -I. -I/usr/include/libxml2 -i mod_xml2enc.c
    • cd /etc/httpd/conf.d, add this to ssl.conf:
before the ProxyPass statements
# proxy the MIDAS web servers  
LoadModule  xml2enc_module       modules/mod_xml2enc.so  
LoadModule  proxy_html_module    modules/mod_proxy_html.so  
ProxyHTMLLinks  a               href  
ProxyHTMLLinks  link            href  
ProxyHTMLLinks  img             src  
#ProxyHTMLEnable On  
ProxyRequests off
after the ProxyPass statements
# ALPHA1 history access 
ProxyPass /alpha1/history/   http://alphacpc09.cern.ch:8072/HS/  retry=1 
ProxyPass /alpha1/           http://alphacpc09.cern.ch:8071/     retry=1 
 
ProxyHTMLEnable On  
ProxyHTMLURLMap http://alphacpc09.cern.ch:8072/HS/ /alpha1/history/
adjust
  • "alpha1" is the experiment name
  • "alphacpc09.cern.ch" is the machine running mhttpd
  • "8071" is the port number of the main mhttpd
    • "mhttpd -p 8071 -D" or
    • "mhttpd -D --oldserver 8071 --nomg"
  • "8072" is the port number of the history mhttpd
    • "mhttpd -p 8072 -D -H" or
    • "mhttpd -D -H --oldserver 8072 --nomg"
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