[Gate-users] Installing GATE on Ubuntu 9.04 - linking error

Tue Oct 20 20:23:23 CEST 2009

Dear Fares,

You’re running into all 64-bit system issues one possibly can… :-). Your new problem is related to the fact that on all current linux distributions I have been dealing with the static “gsl” library (GNU scientific library) against which ROOT is linked has been compiled without the “-fPIC” option. This means that there are two solution to the problem, one being to link against the shared library, the other to create a static one which has been compiled using the needed switch:

a)      Easy one: Use the ROOT configure option --enable-gsl-shared in order to be able to build MathMore using GSL shared libraries when issuing the “./configure” command.

b)      Download and install “gsl” from source (you can use the latest version from http://www.gnu.org/software/gsl/ ). Configure the build of “gsl” with
“./configure --prefix=somewhere --with-pic” and when you re-configure ROOT specify the GSL location
“./configure --with-gsl-incdir=somewhere/include --with-gsl-libdir=somewhere/lib”

Have fun…

Best regards,

Wolfram

Dr. Wolfram Stiller, Dipl.-Phys.

Universitätsklinikum Heidelberg

Abteilung für Diagnostische und Interventionelle Radiologie

Im Neuenheimer Feld 110

D-69120 Heidelberg

Germany

E-mail: wolfram.stiller at med.uni-heidelberg.de

Tel.: +49 (0) 6221 56 37240 or

       +49 (0) 6221 56 6434

Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte Informationen. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den Absender und vernichten Sie diese E-Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail ist nicht gestattet.

This e-mail may contain confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden.

-----Ursprüngliche Nachricht-----
Von: gate-users-bounces at lists.healthgrid.org [mailto:gate-users-bounces at lists.healthgrid.org] Im Auftrag von Fares Alhassen
Gesendet: Dienstag, 20. Oktober 2009 19:33
An: gate-users at lists.healthgrid.org
Betreff: Re: [Gate-users] Installing GATE on Ubuntu 9.04 - linking error

Thank you for your suggestions Cheick, Chris, and Wolfram. I think your explanation Wolfram makes sense as I am trying to install on a 64-bit system and am still getting the same errors even with the environment variables set as Cheick suggested. I used the SVN checkout method to get my own root source and I tried to compile it, but I'm having compilation issues. I know this is a GATE mailing list so I'm not sure if I can discuss getting root compiled correctly on this board.

Anyway, just in case, here's the compilation error I get:

/usr/lib64/libgslcblas.a

/usr/bin/ld: /usr/lib64/libgslcblas.a(sasum.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC

/usr/lib64/libgslcblas.a: could not read symbols: Bad value

collect2: ld returned 1 exit status

make: *** [lib/libMathMore.so] Error 1

make: *** Waiting for unfinished jobs....

rm core/utils/src/RStl_tmp.cxx core/utils/src/rootcint_tmp.cxx

I used the following line to configure my root make:

./configure linuxx8664gcc

I used the following make command for my Intel Core Duo system:

make -j 2

Sincerely,

Fares

On Mon, 19 Oct 2009 13:12:03 +0200

 "Stiller, Wolfram" <Wolfram.Stiller at med.uni-heidelberg.de> wrote:

>Dear Fares,

>

>

>

>Errors flagged as "/usr/bin/ld: skipping incompatible /home/fares/root/lib/libCore.so when searching for..." usually are caused by the linker finding the library it is searching for but that library being compiled for a different kind of system. Normally these errors are seen on 64 bit linux systems when compiling for 64 bit if the libraries installed which are linked against are 32 bit. On some systems you will see the warning without getting an error: in that case the linker first finds the 32 bit library, e.g. installed for compatibility reasons; then it comes across the 64 bit library which it links against. I suspect you are trying to install on a 64 bit system, but you probably have installed a version of Root which has been compiled for 32 bit. Please check for that. If so, the solution is simple: either download and install a 64 bit pre-compiled Root version or download the Root sources and compile from scratch. I'd do the latter...

>

>

>

>Hope the given information is of use.

>

>

>

>Best regards,

>

>

>

>Wolfram

>

>

>

>

>

>

>

>Dr. Wolfram Stiller, Dipl.-Phys.

>

>

>

>Universitätsklinikum Heidelberg

>

>Abteilung für Diagnostische und Interventionelle Radiologie

>

>Im Neuenheimer Feld 110

>

>D-69120 Heidelberg

>

>Germany

>

>

>

>E-mail: wolfram.stiller at med.uni-heidelberg.de

>

>

>

>Tel.: +49 (0) 6221 56 37240 or

>

>       +49 (0) 6221 56 6434

>

>-----Ursprüngliche Nachricht-----

>Von: gate-users-bounces at lists.healthgrid.org [mailto:gate-users-bounces at lists.healthgrid.org] Im Auftrag von Fares Alhassen

>Gesendet: Freitag, 16. Oktober 2009 23:42

>An: Chris Reynolds

>Cc: gate-users at lists.healthgrid.org

>Betreff: Re: [Gate-users] Installing GATE on Ubuntu 9.04 - linking error

>

>

>

>Thanks for the advice, Chris. I tried making GATE again but I still received the same error message:

>

>

>

>Using granular libraries ...

>

>Linking Gate

>

>/usr/bin/ld: skipping incompatible /home/fares/root/lib/libCore.so when searching for -lCore

>

>/usr/bin/ld: cannot find -lCore

>

>collect2: ld returned 1 exit status

>

>make: *** [bin/Linux-g++/Gate] Error 1

>

>

>

>Maybe your version of ROOT is different or the way you installed ROOT is different? My ROOT version is 5.20 and I think I installed it using the binary for RedHat Linux:

>

>http://root.cern.ch/root/Version520.html

>

>

>

>Sincerely,

>

>Fares

>

>

>

>

>

>On Fri, 16 Oct 2009 12:13:44 +0100

>

> Chris Reynolds <C.Reynolds at westminster.ac.uk> wrote:

>

>>I had linker errors for the same platform, which were solved with a

>

>>simple: make clean

>

>>

>

>>before re-making: make

>

>>

>

>>sounds simple but, worked for me!

>

>>

>

>>Chris

>

>>

>

>>On Thu, 2009-10-15 at 11:43 -0700, Fares Alhassen wrote:

>

>>> Dear all,

>

>>>

>

>>> Hi, I'm trying to install GATE on my Ubuntu 9.04 system. I have already installed CLHEP, geant4, and root. When I try to compile GATE, everything works fine except for a few warning messages. However, I get an error message during linking. Here's the output after the compilation is complete:

>

>>>

>

>>> Using granular libraries ...

>

>>> Linking Gate

>

>>> /usr/bin/ld: skipping incompatible /home/fares/root/lib/libCore.so when searching for -lCore

>

>>> /usr/bin/ld: cannot find -lCore

>

>>> collect2: ld returned 1 exit status

>

>>> make: *** [bin/Linux-g++/Gate] Error 1

>

>>>

>

>>> Any suggestions? Please let me know if you need more info.

>

>>>

>

>>> Sincerely,

>

>>> Fares

>

>>>

>

>>>

>

>>> ------------------------------------------------

>

>>> Fares Alhassen

>

>>> Associate Specialist

>

>>> UCSF Physics Research Laboratory

>

>>> Department of Radiology and Biomedical Imaging

>

>>> University of California, San Francisco

>

>>> web: http://radiology.ucsf.edu/physics

>

>>>

>

>>> _______________________________________________

>

>>> Gate-users mailing list

>

>>> Gate-users at lists.healthgrid.org

>

>>> http://lists.healthgrid.org/mailman/listinfo/gate-users

>

>>

>

>>

>

>>--

>

>>The University of Westminster is a charity and a company limited by

>

>>guarantee.  Registration number: 977818 England.  Registered Office:

>

>>309 Regent Street, London W1B 2UW, UK.

>

>

>

>------------------------------------------------

>

>Fares Alhassen

>

>Associate Specialist

>

>UCSF Physics Research Laboratory

>

>Department of Radiology and Biomedical Imaging

>

>University of California, San Francisco

>

>185 Berry Street, Suite 350 BOX # 0946

>

>San Francisco, CA 94143-0946 (94107 UPS/FedEx/DHL)

>

>email: fares.alhassen at radiology.ucsf.edu

>

>T: (415) 353-9438

>

>F: (415) 353-9421

>

>web: http://radiology.ucsf.edu/physics

>

>

>

>_______________________________________________

>

>Gate-users mailing list

>

>Gate-users at lists.healthgrid.org

>

>http://lists.healthgrid.org/mailman/listinfo/gate-users

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

Fares Alhassen

Associate Specialist

UCSF Physics Research Laboratory

Department of Radiology and Biomedical Imaging

University of California, San Francisco

185 Berry Street, Suite 350 BOX # 0946

San Francisco, CA 94143-0946 (94107 UPS/FedEx/DHL)

email: fares.alhassen at radiology.ucsf.edu

T: (415) 353-9438

F: (415) 353-9421

web: http://radiology.ucsf.edu/physics

_______________________________________________

Gate-users mailing list

Gate-users at lists.healthgrid.org

http://lists.healthgrid.org/mailman/listinfo/gate-users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20091020/4ca44a99/attachment.htm>