[Gate-users] An error with my first rouch !!

M Albishri mohad1408 at hotmail.com
Fri Apr 4 12:25:44 CEST 2014





Hi everyone,
 
I haope you all in great health and happiness. The IT people in my uni have installed the GATE for me. It is GATE 6.2.0 and this is a list of required dependencies:
geant4 9.5 p02
root/5.34.10
gcc/4.81
gcc/4.7.3

I did strat using GATE two days ago; however, I have got an error by the first step, when I just inserted my first command /vis/open OGLSX . Yesterday, I realised that there are some differences between the versions I have for the required dependencies and that in GATE website, as I listed before. I have attached the error file, module display and module avail for you to see. I am seeking for your help and advice to fix this problem. Thank you and your support is highly appreciated.

Regards,
Mohammed 

------------------------------the error-----------------------------------------------

[msma7 at spectre02 ~]$ module load gate/6.2.0
[msma7 at spectre02 ~]$ Gate
[G4] 
[G4] *************************************************************
[G4]  Geant4 version Name: geant4-09-05-patch-02    (22-October-2012)
[G4]                       Copyright : Geant4 Collaboration
[G4]                       Reference : NIM A 506 (2003), 250-303
[G4]                             WWW : http://cern.ch/geant4
[G4] *************************************************************
[G4] 
[Core-0] Initialization of geometry
[Core-0] Initialization of physics
[Core-0] Initialization of actors
[Core-0] 
[Core-0] **********************************************************************
[Core-0]  GATE version name: gate_v6.2                                         
[Core-0]                     Copyright : OpenGATE Collaboration                
[Core-0]                     Reference : Phys. Med. Biol. 49 (2004) 4543-4561  
[Core-0]                     Reference : Phys. Med. Biol. 56 (2011) 881-901    
[Core-0]                     WWW : http://www.opengatecollaboration.org        
[Core-0] **********************************************************************
[Core-0] 
[Core-0] You are using a 9.5 version of Geant4
Idle> #VISUALIZATION
#VISUALIZATION
Idle> /vis/open OGLSX
libGL error: failed to load driver: swrast
libGL error: Try again with LIBGL_DEBUG=verbose for more details.
Idle> 



-------------------------------module display---------------------------------------------


[msma7 at spectre02 ~]$ module display gate/6.2.0
-------------------------------------------------------------------
/cm/shared/modulefiles/gate/6.2.0:

module-whatis     Loads the GATE 6.2.0 software environment 
prepend-path     LD_LIBRARY_PATH /cm/shared/apps/gcc/4.8.1/lib64 
prepend-path     LD_LIBRARY_PATH /cm/shared/apps/gate/deps/clhep/lib 
setenv         ROOTSYS /cm/shared/apps/gate/deps/root 
prepend-path     PATH /cm/shared/apps/gate/deps/root/bin 
prepend-path     MANPATH /cm/shared/apps/gate/deps/root/man 
prepend-path     PYTHONPATH /cm/shared/apps/gate/deps/root/lib 
prepend-path     LD_LIBRARY_PATH /cm/shared/apps/gate/deps/root/lib 
setenv         G4NEUTRONHPDATA /cm/shared/apps/gate/data/G4NDL4.4 
setenv         G4LEDATA /cm/shared/apps/gate/data/G4EMLOW6.35 
setenv         G4LEVELGAMMADATA /cm/shared/apps/gate/data/PhotonEvaporation3.0 
setenv         G4RADIOACTIVEDATA /cm/shared/apps/gate/data/RadioactiveDecay4.0 
setenv         G4NEUTRONXSDATA /cm/shared/apps/gate/data/G4NEUTRONXS1.4 
setenv         G4PIIDATA /cm/shared/apps/gate/data/G4PII1.3 
setenv         G4REALSURFACEDATA /cm/shared/apps/gate/data/RealSurface1.0 
setenv         G4SAIDXSDATA /cm/shared/apps/gate/data/G4SAIDDATA1.1 
setenv         G4ABLADATA /cm/shared/apps/gate/data/G4ABLA3.0 
prepend-path     LD_LIBRARY_PATH /cm/shared/apps/gate/deps/geant/lib64 
prepend-path     PATH /cm/shared/apps/gate/6.2.0/bin 
-------------------------------------------------------------------




--------------------------------module avail------------------------------------------------

[msma7 at spectre02 ~]$ module avail

---------------------------- /cm/local/modulefiles -----------------------------
cluster-tools/6.1              openldap
cmd                            openmpi/gcc/64/1.4.3-mlnx-ofed
dot                            shared
freeipmi/1.2.6                 torque/4.1.6
ipmitool/1.8.12                torque/4.2.4(default)
module-git                     torque/4.2.6.1
module-info                    use.own
mvapich/gcc/64/1.2.0-mlnx-ofed version
null

---------------------------- /cm/shared/modulefiles ----------------------------
abinit/7.2.2                      intel/impi/4.1.0
abinit/7.2.2par                   intel/impi/4.1.1
abinit/7.6.2                      intel/impi/4.1.3
abyss/1.3.6                       intel/license
abyss/1.3.7                       intel/mkl/10.3.11
amber/12                          intel/mkl/11.0.0
amos/3.1.0                        intel/tac/8.0.3
apt/21.2.2                        intel/tac/8.1.4
apt/21.2.3                        intel/tbb/4.0.5
apt/21.4.1                        intel/tbb/4.1.1
apt/21.4.2                        iozone/3_414
apt/22.0                          iraf/2.16
apt/22.0.2                        isis/1.6.2-27
arb/5.1-6213                      java/1.7.0_25
avid/2.1                          lapack/gcc/3.4.2
bcrypt/1.1                        lapack/intel/3.4.2
beast/1.8.0                       llvm/3.4
beat/6.7.0                        lua/5.2
bedtools/2.17.0                   makedepf90/2.8.8
bioperl/1.6.1                     mam/7.2.3
biopython/1.63                    maple/17
blas/gcc/1                        matlab/2013a
blas/intel/1                      maven/3.1.0
blast+/2.2.28                     mira/3.4.1.1
blat/3.5                          mira/3.9.18
bonnie++/1.97.1                   moab/6.0.0
boost/gcc/1.49.0                  moab/7.2.4
boost/gcc/1.53.0                  moab/7.2.5(default)
boost/gcc/1.55.0                  mothur/1.32.1
boost/intel/1.53.0                mpiexec/0.84_432
boost/intel/1.55.0                mrcanavar/0.41
bwa/0.7.5a                        mrfast/2.6.0
cdo/1.6.1                         mrsfast-ultra/3.2.0
cfitsio/3.360                     mummer/3.23
cfitsio/gcc/3.350                 mysql/5.6.15
cfitsio/intel/3.350               nag/cll6a09dhl
CGAL/4.3                          nag/cll6a23dhl
ciao/ciao-4.6                     nag/fdl6i03dcl
circos/0.64                       nag/fll6a22dfl
cmake/2.8.10.2                    nag/fll6a23dfl
cmgui/6.1                         nag/fll6i22dcl
cns/1.3                           nag/fll6i23dcl
coda/2.2                          nag/fnl6i04dcl
coda/2.5                          nag/fsl6i22dcl
conifer/0.2.2                     nag/gpulib
cuda55/blas/5.5.22                nag/npl6a52n
cuda55/fft/5.5.22                 nag/npl6a53n
cuda55/profiler/5.5.22            nasa-baselibs/2.2.0
cuda55/tdk/5.319.43               nco/4.3.0
cuda55/toolkit/5.5.22             ncview/2.1.2
cufflinks/2.1.1                   netcdf/gcc/4.2.1.1
cutadapt/1.2.1                    netcdf/gcc/all
dart/5.4.5-20130620               netcdf/gcc/c/4.3.0
default-environment               netcdf/gcc/cxx/4.2.1
ds9/7.2                           netcdf/gcc/fortran/4.2
eigen/5097c01bcdc4                netcdf/intel/4.2.1.1
emboss/6.6.0                      netperf/2.6.0
envi/4.7                          njplot/2.3
exonerate/2.2.0a                  openblas/bulldozer/0.2.6
fasta/3.6                         openblas/dynamic/0.2.6
fastqc/0.10.1                     openblas/istanbul/0.2.6
fastx-toolkit/0.0.13              openblas/nehalem/0.2.6
fcgene/1.0.7                      openblas/sandybridge/0.2.6
fcm/2014-02                       openfoam/2.2.2
fermi/9.31.1                      openmpi/gcc/1.6.5
fermi/9.32.5                      paraview/4.1.0
ferret/6.84                       partek/6.13.0516
ffmpeg/1.2.3                      pgplot/5.2.2
fftw2/gcc/2.1.5                   phase/2.1.1
fftw2/intel/2.1.5                 picard/1.93
fftw2/openmpi/gcc/64/double/2.1.5 plato/1.2.6
fftw2/openmpi/gcc/64/float/2.1.5  plink/1.07
fftw3/openmpi/gcc/64/3.3.3        plinkseq/0.08
finchtv/1.3.1                     prokka/1.7
fl/0.79a                          python/2.4.6
fluent/13.0                       python/2.7.3
freebayes/9.9.2-43                python/3.2.3
g95/0.93                          qctool/1.1
gamma/20130717                    qctool/1.3
gamma/20130902                    qdoas/2.0
gate/6.2.0                        qdoas/2.103
gatk/2.6-5                        qiime/1.7.0
gatk/2.7-2                        qt/4.8.4
gauss/gauss11                     qt/4.8.5
gauss/gauss12                     qwt/6.0.0
gauss/gauss12.1                   R/3.0.1
gauss/gauss12-test                R/3.0.2
gauss/gaussruntime11              raremetalworker/0.3.4
gauss/gaussruntime12              ray/2.3.1
gauss/gaussruntime12.1            reflex/2.4
gaussian/g03e01                   reflex/2.5
gcc/4.7.3                         root/5.34.10
gcc/4.8.1                         rsem/1.2.9
gdal/1.10.1                       ruby/2.0.0
gdl/0.9.3                         samtools/0.1.19
gdl/0.9.4                         sas/9.3
genemark                          shapeit/1.416
ghc/7.6.3                         shapeit/2.644
glimmer/3.02                      snptest/2.4.1
grace/5.1.23                      snptest/2.5.b4
gromacs/4.6.2                     soapdenovo/2.04
gs454/2.6                         solar/7.2.5
gsl/1.16                          spex/2.03
gtool/0.7.5                       stacks/1.06
hdf4/gcc/4.2.9                    staden/2.0.0b9
hdf4/intel/4.2.9                  stampy/1.0.22
hdf5/1.6.10                       stampy/1.0.23
hdf5/gcc/1.8.11                   starlink/2013-04-16
hdf5/intel/1.8.11                 stata/11/mp8
heasoft/6.14                      stata/12/mp8
heasoft/6.15                      stsci_python/2.14
heasoft/6.15.1                    subversion/1.8.3
hpl/2.1                           supermongo/2.4.38
hwloc/1.7                         szip/gcc/2.1
hydra/3.0.1(default)              szip/intel/2.1
idl/idl70                         tabix/0.2.6
idl/idl80                         tablet/1.13.07.31
idl/idl82                         topcat/4.0-1
idlastro/20131029                 topcat/4.1-0
idlastro/20131105                 tophat/2.1.0
idlastro/20140114                 transabyss/1.4.8
idlastro/20140403                 trans-abyss/1.3.7
igv/2.0.15                        trinityRNA/20131110
igv/2.3.18                        ureka/1
impute2/2.3.0                     vcflib/20140203
intel/compilers/12.1.0            vcftools/0.1.11
intel/compilers/12.1.5            velvet/1.2.10
intel/compilers/13.0.0            vista/1.4.26
intel/compilers/13.1.1            wcstools/3.8.7
intel/compilers/13.1.3            xds/20130330
intel/compilers/14.0.1            xmmsas/13.0.1
intel/compilers/14.0.2            xmmsas/13.5.0
intel/impi/4.0.3
[msma7 at spectre02 ~]$ 


 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140404/d1c3ba95/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: module avail
Type: application/octet-stream
Size: 6997 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140404/d1c3ba95/attachment-0003.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: module display
Type: application/octet-stream
Size: 1416 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140404/d1c3ba95/attachment-0004.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: the error
Type: application/octet-stream
Size: 1378 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140404/d1c3ba95/attachment-0005.obj>


More information about the Gate-users mailing list