Difference between revisions of "MNE CPP on Neuromag Linux"

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(Created page with "<pre style="color: red"> Warning: You should know what you are doing and be familiar with the Neuromag system! </pre> == Pre-Requisites == === Qt 5 === ./configure -no-x...")
 
Line 6: Line 6:
 
=== Qt 5 ===
 
=== Qt 5 ===
  
−
    ./configure -no-xcb -no-eglfs -no-directfb -no-linuxfb -no-kms -no-glib -no-gui -no-widgets -no-opengl -no-openssl -opensource -nomake examples -prefix /home/neuromag/RT_MNE_CPP/Qt/Qt5.3.0
+
<source lang=cpp>
−
    make
+
./configure -no-xcb -no-eglfs -no-directfb -no-linuxfb -no-kms -no-glib -no-gui -no-widgets -no-opengl -no-openssl -opensource -nomake examples -prefix /home/neuromag/RT_MNE_CPP/Qt/Qt5.3.0
 +
make
 +
</source>
  
 
It's likely that following error occurs:
 
It's likely that following error occurs:
Line 14: Line 16:
 
You can fix this error by replacing following line in src/corelib/thread/qmutex_linux.cpp
 
You can fix this error by replacing following line in src/corelib/thread/qmutex_linux.cpp
  
−
    # include <linux/futex.h>
+
<source lang=cpp>
 +
# include <linux/futex.h>
 +
</source>
  
 
with
 
with
  
−
    # define FUTEX_WAIT 0
+
<source lang=cpp>
−
    # define FUTEX_WAKE 1
+
# define FUTEX_WAIT 0
 +
# define FUTEX_WAKE 1
 +
</source>
  
 
You can ignore further Qt5 build errors. Since only qmake and the most important libraries are needed.
 
You can ignore further Qt5 build errors. Since only qmake and the most important libraries are needed.
 
Finish the installation with:
 
Finish the installation with:
  
−
    make install
+
<source lang=cpp>
 +
make install
 +
</source>
  
 
=== MNE-CPP ===
 
=== MNE-CPP ===
Line 31: Line 39:
 
Edit _mne-cpp.pri_ by commenting _withGui_ out:
 
Edit _mne-cpp.pri_ by commenting _withGui_ out:
  
−
    #MNECPP_CONFIG += withGui
+
<source lang=cpp>
 +
#MNECPP_CONFIG += withGui
 +
</source>
  
 
run:
 
run:
−
    qmake -r
+
 
−
    make
+
<source lang=cpp>
 +
qmake -r
 +
make
 +
</source>
  
 
==== Edit .bashrc ====
 
==== Edit .bashrc ====
 
After you compiled mne-cpp succesfully edit your .bashrc to make the shared libraries globally available:
 
After you compiled mne-cpp succesfully edit your .bashrc to make the shared libraries globally available:
  
−
    #
+
<source lang=cpp>
−
    # Qt
+
#
−
    #
+
# Qt
−
    export QT_HOME=/home/neuromag/RT_MNE_CPP/Qt/Qt5.3.0
+
#
−
    if [[ $QT_HOME && ${QT_HOME-_} ]]; then
+
export QT_HOME=/home/neuromag/RT_MNE_CPP/Qt/Qt5.3.0
−
        PATH=$PATH:$QT_HOME/bin
+
if [[ $QT_HOME && ${QT_HOME-_} ]]; then
−
        if [[ $LD_LIBRARY_PATH && ${LD_LIBRARY_PATH-_} ]]; then
+
    PATH=$PATH:$QT_HOME/bin
−
            LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$QT_HOME/lib
+
    if [[ $LD_LIBRARY_PATH && ${LD_LIBRARY_PATH-_} ]]; then
−
        else
+
      LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$QT_HOME/lib
−
            export LD_LIBRARY_PATH=$QT_HOME/lib
+
    else
−
        fi
+
      export LD_LIBRARY_PATH=$QT_HOME/lib
 
     fi
 
     fi
 +
fi
 
      
 
      
−
    #
+
#
−
    #  MNE-CPP
+
#  MNE-CPP
−
    #
+
#
−
    export MNE_CPP=/home/neuromag/RT_MNE_CPP/Git_Repos/mne-cpp
+
export MNE_CPP=/home/neuromag/RT_MNE_CPP/Git_Repos/mne-cpp
−
    if [[ $MNE_CPP && ${MNE_CPP-_} ]]; then
+
if [[ $MNE_CPP && ${MNE_CPP-_} ]]; then
−
        PATH=$PATH:$MNE_CPP/bin
+
    PATH=$PATH:$MNE_CPP/bin
−
        if [[ $LD_LIBRARY_PATH && ${LD_LIBRARY_PATH-_} ]]; then
+
    if [[ $LD_LIBRARY_PATH && ${LD_LIBRARY_PATH-_} ]]; then
−
            LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MNE_CPP/lib
+
        LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MNE_CPP/lib
−
        else
+
    else
−
            export LD_LIBRARY_PATH=$MNE_CPP/lib
+
        export LD_LIBRARY_PATH=$MNE_CPP/lib
−
        fi
+
 
     fi
 
     fi
 +
fi
 +
</source>
  
 
==== Firewall Configuration ====
 
==== Firewall Configuration ====
 
Open port 4217 & 4218 and add allowed clients by editing /etc/sysconfig/iptables. Insert the following:
 
Open port 4217 & 4218 and add allowed clients by editing /etc/sysconfig/iptables. Insert the following:
  
−
    -A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 4217 -j ACCEPT
+
<source lang=cpp>
−
    -A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 4218 -j ACCEPT
+
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 4217 -j ACCEPT
−
    -A RH-Firewall-1-INPUT -s ip.of.your.client -m tcp -p tcp --dport 4217 -j ACCEPT
+
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 4218 -j ACCEPT
−
    -A RH-Firewall-1-INPUT -s ip.of.your.client -m tcp -p tcp --dport 4218 -j ACCEPT
+
-A RH-Firewall-1-INPUT -s ip.of.your.client -m tcp -p tcp --dport 4217 -j ACCEPT
 +
-A RH-Firewall-1-INPUT -s ip.of.your.client -m tcp -p tcp --dport 4218 -j ACCEPT
 +
</source>
  
 
=== run _mne_rt_server_ ===
 
=== run _mne_rt_server_ ===
Line 80: Line 97:
 
=== The collectors ===
 
=== The collectors ===
 
You can use telnet to monitor the interaction of _mne_rt_server_ with the neuromag machine:
 
You can use telnet to monitor the interaction of _mne_rt_server_ with the neuromag machine:
−
Therefor connect to the collectors running on the real-time computers:
+
Therefore connect to the collectors running on the real-time computers:
  
−
    telnet megacq collector
+
<source lang=cpp>
 +
telnet megacq collector
 +
</source>
  
 
or
 
or
  
−
    telnet ip.of.megacq 11122
+
<source lang=cpp>
 +
telnet ip.of.megacq 11122
 +
</source>
  
 
Authorize your self:
 
Authorize your self:
−
    PASS ***
+
 
 +
<source lang=cpp>
 +
PASS ***
 +
</source>
  
 
Check the status by typing (They should be setup but not measuring. If this is not the case run a simple dummy project using the neuromag acqusition software, afterwards they will be setup.):
 
Check the status by typing (They should be setup but not measuring. If this is not the case run a simple dummy project using the neuromag acqusition software, afterwards they will be setup.):
−
    STAT
+
 
 +
<source lang=cpp>
 +
STAT
 +
</source>
  
 
Check the values of the variables by typing:
 
Check the values of the variables by typing:
−
    VARS
+
 
 +
<source lang=cpp>
 +
VARS
 +
</source>
  
 
Save the variables in a text file and make sure that they are the same after you have finished (your colleagues will appreciate this)
 
Save the variables in a text file and make sure that they are the same after you have finished (your colleagues will appreciate this)
  
 
You can change variable names by typing
 
You can change variable names by typing
−
    VARA ``<var> = <value>``
+
 
 +
<source lang=cpp>
 +
VARA ``<var> = <value>``
 +
</source>
  
 
Switch on the monitoring to follow all interactions with the real-time computers:
 
Switch on the monitoring to follow all interactions with the real-time computers:
−
    MONI ON
+
 
 +
<source lang=cpp>
 +
MONI ON
 +
</source>
  
 
You can start the acqusition manually with:
 
You can start the acqusition manually with:
−
    MEAS
+
 
 +
<source lang=cpp>
 +
MEAS
 +
</source>
  
 
And stopping it again with:
 
And stopping it again with:
−
    STOP
+
 
 +
<source lang=cpp>
 +
STOP
 +
</source>
  
 
All available commands you'll find by typing:
 
All available commands you'll find by typing:
−
    HELP
+
 
 +
<source lang=cpp>
 +
HELP
 +
</source>
  
 
You can leave the collectors by typing:
 
You can leave the collectors by typing:
−
    QUIT
+
 
 +
<source lang=cpp>
 +
QUIT
 +
</source>
  
 
=== Neuromag Acqusition ===
 
=== Neuromag Acqusition ===
  
 
It's recommended to start the Neuromag Acquisition program. The software will be remotely controlled by MNE-X since the collectors mirror the instructions received. You can use the Neuromag data display to check your MNE-X measurements.
 
It's recommended to start the Neuromag Acquisition program. The software will be remotely controlled by MNE-X since the collectors mirror the instructions received. You can use the Neuromag data display to check your MNE-X measurements.

Revision as of 17:29, 21 January 2016

Warning: You should know what you are doing and be familiar with the Neuromag system!

Pre-Requisites

Qt 5

./configure -no-xcb -no-eglfs -no-directfb -no-linuxfb -no-kms -no-glib -no-gui -no-widgets -no-opengl -no-openssl -opensource -nomake examples -prefix /home/neuromag/RT_MNE_CPP/Qt/Qt5.3.0
make

It's likely that following error occurs: Futex Error (RHEL 5.1 with gcc 4.1.2 compiler)

You can fix this error by replacing following line in src/corelib/thread/qmutex_linux.cpp 

# include <linux/futex.h>

with 

# define FUTEX_WAIT 0
# define FUTEX_WAKE 1

You can ignore further Qt5 build errors. Since only qmake and the most important libraries are needed. Finish the installation with: 

make install

MNE-CPP

Download MNE-CPP

Edit _mne-cpp.pri_ by commenting _withGui_ out: 

#MNECPP_CONFIG += withGui

run: 

qmake -r
make

Edit .bashrc

After you compiled mne-cpp succesfully edit your .bashrc to make the shared libraries globally available: 

#
# Qt
#
export QT_HOME=/home/neuromag/RT_MNE_CPP/Qt/Qt5.3.0
if [[ $QT_HOME && ${QT_HOME-_} ]]; then
    PATH=$PATH:$QT_HOME/bin
    if [[ $LD_LIBRARY_PATH && ${LD_LIBRARY_PATH-_} ]]; then
       LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$QT_HOME/lib
    else
       export LD_LIBRARY_PATH=$QT_HOME/lib
    fi
fi
 
#
#  MNE-CPP
#
export MNE_CPP=/home/neuromag/RT_MNE_CPP/Git_Repos/mne-cpp
if [[ $MNE_CPP && ${MNE_CPP-_} ]]; then
    PATH=$PATH:$MNE_CPP/bin
    if [[ $LD_LIBRARY_PATH && ${LD_LIBRARY_PATH-_} ]]; then
        LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MNE_CPP/lib
    else
        export LD_LIBRARY_PATH=$MNE_CPP/lib
    fi
fi

Firewall Configuration

Open port 4217 & 4218 and add allowed clients by editing /etc/sysconfig/iptables. Insert the following: 

-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 4217 -j ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 4218 -j ACCEPT
-A RH-Firewall-1-INPUT -s ip.of.your.client -m tcp -p tcp --dport 4217 -j ACCEPT
-A RH-Firewall-1-INPUT -s ip.of.your.client -m tcp -p tcp --dport 4218 -j ACCEPT

run _mne_rt_server_

If all previous steps were successfully processed you are now able to run _mne_rt_server_ - well done :)!

Hints

The collectors

You can use telnet to monitor the interaction of _mne_rt_server_ with the neuromag machine: Therefore connect to the collectors running on the real-time computers: 

telnet megacq collector

or 

telnet ip.of.megacq 11122

Authorize your self: 

PASS ***

Check the status by typing (They should be setup but not measuring. If this is not the case run a simple dummy project using the neuromag acqusition software, afterwards they will be setup.): 

STAT

Check the values of the variables by typing: 

VARS

Save the variables in a text file and make sure that they are the same after you have finished (your colleagues will appreciate this)

You can change variable names by typing 

VARA ``<var> = <value>``

Switch on the monitoring to follow all interactions with the real-time computers: 

MONI ON

You can start the acqusition manually with: 

MEAS

And stopping it again with: 

STOP

All available commands you'll find by typing: 

HELP

You can leave the collectors by typing: 

QUIT

Neuromag Acqusition

It's recommended to start the Neuromag Acquisition program. The software will be remotely controlled by MNE-X since the collectors mirror the instructions received. You can use the Neuromag data display to check your MNE-X measurements.

Retrieved from "http://wiki.mne-cpp.org/index.php?title=MNE_CPP_on_Neuromag_Linux&oldid=173"