[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 ~]$
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