[Paradiseo-help] [paradiseo-Bugs][5057] ParadisEO-PEO compilation problems on some configurations

paradiseo-bugs at gforge.inria.fr paradiseo-bugs at gforge.inria.fr
Mar 12 Fév 09:14:55 CET 2008


Bugs item #5057, was opened at 11/02/2008 13:05
You can respond by visiting: 
http://gforge.inria.fr/tracker/?func=detail&atid=663&aid=5057&group_id=145

>Status: Closed
Priority: 1
Submitted By: Tantar Alexandru-Adrian (atantar)
>Assigned to: thomas legrand (legrand)
Summary: ParadisEO-PEO compilation problems on some configurations 
>Resolution: Fixed
Group: v1.0 (example)
Category: CMake bug


Initial Comment:
There seems to be a trailing character in a file generated by cmake:

In src/rmc/mpi/CMakeFiles/rmc_mpi.dir/flags.make for the line

CXX_FLAGS = -O0 -g ... -I/tmp/paradiseo-ix86-1.0/paradiseo-peo/src/rmc/mpi/\ 

the '\' should not be there. It seems that for some reasons this breaks the compilation process on some systems.



The error messages with environment variables:

        # STEP 1

                --> Unpacking libxml2 (required for ParadisEO) ...

        # STEP 1 OK



        # STEP 2

                --> Unpacking mpich2 (required for ParadisEO) ...

        # STEP 2 OK



        # STEP 3

                --> Installing Paradiseo-EO. Please wait ...

        # STEP 3 OK



        # STEP 4

                --> Installing Paradiseo-MO. Please wait ...

        # STEP 4 OK



        # STEP 5

                --> Installing Paradiseo-MOEO. Please wait ...

        # STEP 5 OK



        # STEP 6

                --> Installing libxml2. Please wait ...

        # STEP 6 OK



        # STEP 7

                --> Removing libxml2 temp install directory ...

        # STEP 7 OK



        # STEP 8

                --> Installing mpich2. Please wait ...

        # STEP 8 OK



        # STEP 9

                --> Removing mpich2 temp install directory ...

        # STEP 9 OK



        # STEP 10

                --> Configuring environment variables for libxml2 and mpich2 ...

        # STEP 10 OK



        # STEP 11

                --> Installing Paradiseo-PEO. Please wait ...



                --> Error when installing Paradiseo-PEO

 ### END ###



  An error has occured : impossible to install Paradiseo-PEO.See /home/mswain/tmp3/install-paradiseo.20080207114152.log for more details

  Make sure you have the required variables in your environment (ex: by using "echo $PATH" for PATH variable) :

        -LD_LIBRARY_PATH=<libxml2 install path>/libxml2/lib:$LD_LIBRARY_PATH

        -PATH=<libxml2 install path>/libxml2/bin:<mpich2 install path>/mpich2/bin:$PATH



 => To report any problem or for help, please contact paradiseo-help at lists.gforge.inria.fr and join /home/mswain/tmp3/install-paradiseo.20080207114152.log



Terminated

mswain at BIO-INFO5:~/tmp3> echo $PATH

/usr/local/ant//bin:/usr/java/jdk1.6.0_02/bin:/home/mswain/bin:/sbin:/bin:/usr/sbin:/usr/share/:/usr/local/bin:/usr/bin:/opt/cmake-2.4.7/bin:/opt/openmpi-1.2.3/bin::.:.

mswain at BIO-INFO5:~/tmp3> echo $LD_LIBRARY_PATH

/opt/openmpi-1.2.3/lib:/opt/ego/soam/3.1/linux2.4-glibc2.3-x86/lib:

mswain at BIO-INFO5:~/tmp3> ls

AUTHORS                               lib           paradiseo-mo

INSTALL                               libxml2       paradiseo-moeo

install.cmake                         LICENSE       paradiseo-peo

install-paradiseo.20080207114152.log  mpich2        README

installParadiseo.sh                   paradiseo-eo

mswain at BIO-INFO5:~/tmp3> export LD_LIBRARY_PATH=/home/mswain/tmp3/libxml2/lib:$LD_LIBRARY_PATH

mswain at BIO-INFO5:~/tmp3> export PATH=/home/mswain/tmp3/libxml2/bin:$PATH

mswain at BIO-INFO5:~/tmp3> echo $PATH



 ### ParadisEO install starting .... ###



Installing the environment for ParadisEO...Note that the librairies "libxml2" ans "mpich2" required for ParadisEO are provided with this package.





        # STEP 2

                --> Unpacking libxml2 (required for ParadisEO) ...

        # STEP 2 OK



        # STEP 3

                --> Installing libxml2. Please wait ...

        # STEP 3 OK



        # STEP 4

                --> Removing libxml2 temp install directory ...

        # STEP 4 OK



        # STEP 5

                --> Installing Paradiseo-PEO. Please wait ...



                --> Error when installing Paradiseo-PEO

 ### END ###



  An error has occured : impossible to install Paradiseo-PEO.See /home/mswain/tmp3/install-paradiseo.20080207120027.log for more details

  Make sure you have the required variables in your environment (ex: by using "echo $PATH" for PATH variable) :

        -LD_LIBRARY_PATH=<libxml2 install path>/libxml2/lib:$LD_LIBRARY_PATH

        -PATH=<libxml2 install path>/libxml2/bin:<mpich2 install path>/mpich2/bin:$PATH



 => To report any problem or for help, please contact paradiseo-help at lists.gforge.inria.fr and join /home/mswain/tmp3/install-paradiseo.20080207120027.log



Terminated



mswain at BIO-INFO5:~/tmp3> echo $LD_LIBRARY_PATH

/opt/openmpi-1.2.3/lib:/opt/ego/soam/3.1/linux2.4-glibc2.3-x86/lib::/home/mswain/tmp3/libxml2/lib::/home/mswain/tmp3/libxml2/lib

mswain at BIO-INFO5:~/tmp3> ls /home/mswain/tmp3/libxml2/lib

libxml2.a   libxml2.so    libxml2.so.2.6.0  xml2Conf.sh

libxml2.la  libxml2.so.2  pkgconfig

mswain at BIO-INFO5:~/tmp3> echo $PATH

/usr/local/ant//bin:/usr/java/jdk1.6.0_02/bin:/home/mswain/bin:/sbin:/bin:/usr/sbin:/usr/share/:/usr/local/bin:/usr/bin:/opt/cmake-2.4.7/bin:/opt/openmpi-1.2.3/bin::.:.:/home/mswain/tmp3/libxml2/bin:/home/mswain/tmp3/mpich2/bin:/home/mswain/tmp3/libxml2/bin:/home/mswain/tmp3/mpich2/bin

mswain at BIO-INFO5:~/tmp3> ls /home/mswain/tmp3/libxml2/bin

xml2-config  xmlcatalog  xmllint





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

>Comment By: thomas legrand (legrand)
Date: 12/02/2008 08:14

Message:
The problem was due to the include flag set by CMake for the "libxml2 cflags". A trailing space was introcuded :



(paradiseo-peo/CMakeLists.txt) 

# set libxml2 cflags in XML2_CFLAGS

EXECUTE_PROCESS(COMMAND ${XML2_CONFIG_PROGRAM} --cflags  OUTPUT_VARIABLE XML2_CFLAGS OUTPUT_STRIP_TRAILING_WHITESPACE)	  

SET(XML2_CFLAGS_WITH_WHITESPACE " ${XML2_CFLAGS}")



The "include" in src/rmc/mpi/CMakeLists.txt:



INCLUDE_DIRECTORIES(${XML2_CFLAGS_WITH_WHITESPACE})



has been replaced by :



SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${XML2_CFLAGS}")



The bug seems to be fixed.



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