Previous topic

Tutorials

This Page

TroubleshootingsΒΆ

This is an up-to-date of known issue with MARS-ALT. If a unknown bugs in MARS-ALT is not found, please send email .

Installation Issues

Installing on Mac OS X 10.6 “Snow Leopard”

If you see the following error message when you build MIPS on Mac OS X:

[  8%] Building CXX object StdPkgs/GuiPkg/Modules/CMakeFiles/tclModules.dir/Modules.o
In file included from /Users/admin/Work/mips/mips_src/StdPkgs/GuiPkg/Modules/Modules.C:18:
/Users/admin/Work/mips/mips_src/StdPkgs/GuiPkg/modules/togl.h:57:23: error: GL/gl.h: No such file or directory

Change the OPENGL build options in the CMake process. For that, type in your build shell:

make edit_cache

When ccmake is running, press ‘t’ to display all build options, and modify OPENGL build options :

OPENGL_INCLUDE_DIR          /usr/X11R6/include
OPENGL_gl_LIBRARY           /usr/X11R6/lib/libGL.dylib
OPENGL_glu_LIBRARY          /usr/X11R6/lib/libGLU.dylib

Configure [c], Generate [g] and re-build:

make

Installing on the Nef cluster

If you have the following error message when you build on the Nef Cluster:

Linking C shared library ../../../lib/libmipsZ.so
/usr/bin/ld: CMakeFiles/mipsZ.dir/adler32.o: relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
CMakeFiles/mipsZ.dir/adler32.o: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[2]: *** [lib/libmipsZ.so] Error 1
make[1]: *** [AuxPkgs/StdLibsPkg/Zlib/CMakeFiles/mipsZ.dir/all] Error 2
make: *** [all] Error 2

Change the CMAKE FLAGS build options in the CMake process. For that, type in your build shell:

make edit_cache

When ccmake is running, press ‘t’ to display all build options, and modify CMAKE FLAGS build options :

CMAKE_CXX_FLAGS     -fPIC
CMAKE_C_FLAGS       -fPIC

Configure [c], Generate [g] and re-build:

make

MARS-ALT Issues

Running lsm2inr.py

If you see the following error when you run :

Traceback (most recent call last):
File "lsm2inr.py", line 39, in <module>
  from openalea.vmanalysis import inrimage
ImportError: No module named vmanalysis

Install OpenAlea

If you see the following error when you run :

Traceback (most recent call last):
File "lsm2inr.py", line 42, in <module>
  from pylsm import lsmreader
ImportError: No module named pylsm

Install PyLSM

Running on Mac OS X 10.6 “Snow Leopard”

If you see the following error when you run zviewer on Mac OS X:

Segmentation fault

Install Tcl-Tk 8.5 from the sources.

Download and Uncompress the sources.

Compiling Tcl 8.5 on Mac OS X has two steps: configure and make.

cd tcl8.5.0/unix  # unix and not macosx
./configure --prefix=/Users/*your_username*/local/ --enable-framework --enable-threads
make
make test
make install

Compiling Tk 8.5 on Mac OS X has the same steps than Tcl: configure and make.

cd tk8.5.0/unix  # unix and not macosx
./configure --enable-threads --prefix=/Users/*your_username*/local/ --with-tcl=/Library/Frameworks/Tcl.framework/ --enable-framework --with-x
make
make test
make install

Then change the TCL-TK build options in the CMake process. For that, type in your build shell:

cd mips_build
make edit_cache

When ccmake is running, press ‘t’ to display all build options, and modify TCL-TK build options :

TCL_INCLUDE_PATH        /Library/Frameworks/Tcl.framework/Headers
TCL_LIBRARY             /Library/Frameworks/Tcl.framework
TCL_TCLSH               /Users/username/local/bin/tclsh8.5
TK_INCLUDE_PATH         /Library/Frameworks/Tk.framework/Headers
TK_LIBRARY              /Library/Frameworks/tk.framework

Configure [c], Generate [g] and re-build:

make

Running on Linux

cannot restore segment prot after reloc: Permission denied

If you see the following error when you try to use MARS-ALT :

cannot restore segment prot after reloc: Permission denied

This is likely due the the SE Linux setting being set to “enforcing”.

To Temporarily disable enforcement on a running system

/usr/sbin/setenforce 0

To permanently disable enforcement during a system startup

change “enforcing” to “disabled” in ‘’/etc/selinux/config’’ and reboot.

Aborted Error

If you see the following error when you run zviewer on Linux :

Aborted

It can be due to a bad link with the librairies of TK. Check the links:

ls -la /usr/lib/libtk.so

If you see the following link :

libtk.so -> libtk8.4.so

A solution can be to create a symbolic link to libtk8.5.so :

rm /usr/lib/libtk.so
ln -s /usr/lib/libtk8.5.so /usr/lib/libtk.so

X Error of failed request

If you see the following error when you run zviewer on Linux :

X Error of failed request:  BadValue (integer parameter out of range for operation)
Major opcode of failed request:  91 (X_QueryColors)
Value in failed request:  0xff141312
Serial number of failed request:  907
Current serial number in output stream:  907

Check and insert your xorg.conf file in /etc/X11 :

Section "Extensions"
     Option "Composite" "Disable"
EndSection

That means that your graphical card doesn’t manage the window draft.

SuperBaloo Not Installed

If Superbaloo is not installed, it means that GMM++ is missing.

see General Requirements

Edit the GMM build options in the CMake process. For that, type in your build shell :

cd mips_build
make edit_cache

When ccmake is running, press ‘t’ to display all build options, and modify GMM build options :

USE_GMM                          ON
GMM_INCLUDE_DIR                  /usr/local/include
Configure [c], Generate [g] and re-build : ::
make

DefInverse Not Installed

If DefInverse is not installed, it means that USE_MTL build option is desactivated.

Edit the USE_MTL build options in the CMake process. For that, type in your build shell :

cd mips_build
make edit_cache

When ccmake is running, press ‘t’ to display all build options, and modify USE_MTL build options :

USE_MTL                          ON

Configure [c], Generate [g] and re-build :

make

Running on Nef cluster

Permission denied (publickey)

If you see the following error when you run : * Script_5_Recalage_Rigide_Auto_sur_grille_1 * or Script_6_Recalage_Rigide_Auto_sur_grille_2 * or Script_8_Recalage_Dense_Auto_sur_grille_1 * or Script_9_Recalage_Dense_Auto_sur_grille_2

Permission denied (publickey).
lost connection

You have to edit the Script_5_Recalage_Rigide_Auto_sur_grille_1 with a text editor and add your username@ used on the cluster before nef.inria.fr:

vim Script_5_Recalage_Rigide_Auto_sur_grille_1
scp ScriptSubBaladin **username@** nef.inria.fr:~/tmpBaladin0/

Save and re-run the script.