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

Sun Oct 25 16:26:10 CET 2009

Hello Fares,

your new problem is no longer linked to 64bit. You seem to have overcome these issues by recompiling "gsl" successfully. This new problem is linked to Root - here a needed package, namely "xrootd" is not compiled correctly. I had the same problem. You can install Root without this package, then you have to state this in your "./configure" command line options. I am pretty sure this part of Root is not needed for Gate - you'll have to look up what functionality will be missing in Root if you do that . However, should you need it or simply have the will to solve this as well, then I can look up on my system at work what has to be changed in the Root makefiles resp. configure-files to compile xrootd because I ran into the same problem which apparently is caused by a mistake/omission in the Root configuration. Should you want to know I can look it up, this might take two or three days. Until then I suggest to disable "xrootd".

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

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________________________________________
Von: gate-users-bounces at lists.healthgrid.org [gate-users-bounces at lists.healthgrid.org] im Auftrag von Fares Alhassen [fares.alhassen at radiology.ucsf.edu]
Gesendet: Samstag, 24. Oktober 2009 01:35
An: gate-users at lists.healthgrid.org
Betreff: Re: [Gate-users] Installing GATE on Ubuntu 9.04 - linking error

Thanks for the advice. I tried both methods, and I think they both address the issues you mentioned, but for some reason I'm running into other issues now.

a) Using the easy method, I ran into these errors during my make of root:

g++: net/xrootd/src/xrootd/lib/libXrd.a: No such file or directory

g++: net/xrootd/src/xrootd/lib/libXrdClient.a: No such file or directory

g++: net/xrootd/src/xrootd/lib/libXrdNet.a: No such file or directory

g++: net/xrootd/src/xrootd/lib/libXrdOuc.a: No such file or directory

g++: net/xrootd/src/xrootd/lib/libXrdSys.a: No such file or directory

g++: net/xrootd/src/xrootd/lib/libXrdSut.a: No such file or directory

b) I was able to download, compile, and install gsl. I tried the following ./configure commands:
./configure linuxx8664gcc --with-gsl-incdir=/home/fares/gsl/include --with-gsl-libdir=/home/fares/gsl/lib
./configure --with-gsl-incdir=/home/fares/gsl/include --with-gsl-libdir=/home/fares/gsl/lib

And making using these two commands (I have a dual core system)
make -j 2
make

But I still received an error during compilation:

/usr/bin/ld: cannot find -lXrdOuc

Any ideas? Thank you so much for your help!

Fares

On Tue, 20 Oct 2009 20:23:23 +0200
 "Stiller, Wolfram" <Wolfram.Stiller at med.uni-heidelberg.de> wrote:
>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

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

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