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Author Topic: error abou tomoalign-gui
awesome91@-
163.com
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Post error abou tomoalign-gui
on: November 3, 2015, 05:32
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When I practised protomo with its tutorial, there was something wrong with tomoalign-gui. When I type "$tomoalign-gui", it prints "tomoalign-gui: undefined or invalid library path".
I thought it may be something wrong in environment setting. However, I checked them again and this error still appeared. Here is my workstation env setting. (My shell is c-shell)
set ROOT = /usr/local/eman
set LOCAL = $ROOT
set I3ROOT = "/home/shanghailocal/app_install/protomo-2.3.1"

setenv EMANDIR $LOCAL/EMAN
setenv EMAN2DIR $LOCAL/EMAN2
setenv LD_LIBRAY_PATH ""
setenv PYTHONPATH ""
setenv I3LIB $I3ROOT/lib/linux/x86-64
setenv I3DEPLIB /usr/lib64:/home/shanghailocal/locallib/lib/linux/x86-64:/usr/local/lib
setenv I3LIBPATH ${I3LIB}:${I3DEPLIB}:${EMAN2DIR}/lib
setenv I3EXEPATH ${I3ROOT}/bin/linux/x86-64:${I3ROOT}/bin:${EMAN2DIR}/bin
setenv I3PYPATH ${I3LIB}:${EMAN2DIR}/lib

if ( ! $?PATH ) then
setenv PATH ""
endif

if ( ! $?LD_LIBRARY_PATH ) then
setenv LD_LIBRARY_PATH ""
endif

if ( ! $?PYTHONPATH ) then
setenv PYTHONPATH ""
endif

setenv LD_LIBRARY_PATH /usr/local/OpenMPI/lib:${I3LIBPATH}:${EMANDIR}/lib:${EMAN2DIR}/lib:${EMAN2DIR}/extlib/lib:$LOCAL/lib:/usr/lib64:/home/shanghailocal/app_install/ccp4mg-2.10.4/pythondist/lib/python2.7/site-packages/ccp4mg/lib:$LD_LIBRARY_PATH
#package include:coot, relion, hkl2map, rave_linux, mpi, erraser, IHRSR, eman, eman2, spider
setenv PATH .:/usr/local/coot-Linux-x86_64-rhel-6-gtk2-python/bin:/home/shanghailocal/app_install/relion-1.3/bin:/home/shanghailocal/app_install/hkl2map:/usr/local/tools/rave_linux/bin64/bin:/usr/local/OpenMPI/bin:/home/shanghailocal/Downloads/rosetta_bin_linux_2015.09.57646_bundle/tools/ERRASER:/home/shanghailocal/app_install/IHRSR_v1.5:${SPBIN_DIR}:$EMANDIR/bin:$EMAN2DIR/bin:$EMANDIR/python:$EMAN2DIR/Python/bin:$LOCAL/bin:${I3EXEPATH}:$PATH
setenv PYTHONPATH ${EMANDIR}/lib:${EMAN2DIR}/lib:${EMAN2DIR}/bin:${LOCAL}/lib/python:${LOCAL}/lib:/home/shanghailocal/app_install/ccp4mg-2.10.4/pythondist/lib/python2.7/site-packages/ccp4mg/lib:/home/shanghailocal/app_install/ccp4mg-2.10.4/pythondist/lib/python:${I3PYPATH}:${PYTHONPATH}

and I also ran the ldd to check the libraries used in tomoalign-gui.
the result was:
linux-vdso.so.1 => (0x00007fff2b1ff000)
libi3gtk.so.2 => /home/shanghailocal/app_install/protomo-2.3.1/lib/linux/x86-64/libi3gtk.so.2 (0x00007f01aecc8000)
libi3gui.so.2 => /home/shanghailocal/app_install/protomo-2.3.1/lib/linux/x86-64/libi3gui.so.2 (0x00007f01aeac4000)
libi3tomoalign.so.2 => /home/shanghailocal/app_install/protomo-2.3.1/lib/linux/x86-64/libi3tomoalign.so.2 (0x00007f01ae8b6000)
libi3tomoseries.so.2 => /home/shanghailocal/app_install/protomo-2.3.1/lib/linux/x86-64/libi3tomoseries.so.2 (0x00007f01ae6a3000)
libi3tomo.so.2 => /home/shanghailocal/app_install/protomo-2.3.1/lib/linux/x86-64/libi3tomo.so.2 (0x00007f01ae476000)
libi3fourierop.so.2 => /home/shanghailocal/app_install/protomo-2.3.1/lib/linux/x86-64/libi3fourierop.so.2 (0x00007f01ae271000)
libi3fourier.so.2 => /home/shanghailocal/app_install/protomo-2.3.1/lib/linux/x86-64/libi3fourier.so.2 (0x00007f01ae06a000)
libi3imageio.so.2 => /home/shanghailocal/app_install/protomo-2.3.1/lib/linux/x86-64/libi3imageio.so.2 (0x00007f01ade52000)
libi3io.so.2 => /home/shanghailocal/app_install/protomo-2.3.1/lib/linux/x86-64/libi3io.so.2 (0x00007f01adc40000)
libi3approx.so.2 => /home/shanghailocal/app_install/protomo-2.3.1/lib/linux/x86-64/libi3approx.so.2 (0x00007f01ada3c000)
libi3image.so.2 => /home/shanghailocal/app_install/protomo-2.3.1/lib/linux/x86-64/libi3image.so.2 (0x00007f01ad832000)
libi3array.so.2 => /home/shanghailocal/app_install/protomo-2.3.1/lib/linux/x86-64/libi3array.so.2 (0x00007f01ad5ab000)
libi3core.so.2 => /home/shanghailocal/app_install/protomo-2.3.1/lib/linux/x86-64/libi3core.so.2 (0x00007f01ad391000)
libtiff.so.4 => /home/shanghailocal/locallib/lib/linux/x86-64/libtiff.so.4 (0x000000308a400000)
libgtkglext-x11-1.0.so.0 => /usr/local/lib/libgtkglext-x11-1.0.so.0 (0x00007f01ad18d000)
libgdkglext-x11-1.0.so.0 => /usr/local/lib/libgdkglext-x11-1.0.so.0 (0x00007f01acf29000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x0000003973800000)
libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003973400000)
libXmu.so.6 => /usr/lib64/libXmu.so.6 (0x00000037d2a00000)
libXt.so.6 => /usr/lib64/libXt.so.6 (0x00000037dc200000)
libSM.so.6 => /usr/lib64/libSM.so.6 (0x00000037dde00000)
libICE.so.6 => /usr/lib64/libICE.so.6 (0x00000037dd600000)
libgtk-x11-2.0.so.0 => /usr/lib64/libgtk-x11-2.0.so.0 (0x00000037e8200000)
libpangox-1.0.so.0 => /usr/lib64/libpangox-1.0.so.0 (0x00000037cfa00000)
libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000037d1600000)
libgdk-x11-2.0.so.0 => /usr/lib64/libgdk-x11-2.0.so.0 (0x00000037e8a00000)
libatk-1.0.so.0 => /usr/lib64/libatk-1.0.so.0 (0x00000037d5e00000)
libgio-2.0.so.0 => /lib64/libgio-2.0.so.0 (0x00000037d1200000)
libpangoft2-1.0.so.0 => /usr/lib64/libpangoft2-1.0.so.0 (0x00000037d6600000)
libgdk_pixbuf-2.0.so.0 => /usr/lib64/libgdk_pixbuf-2.0.so.0 (0x00000037d6a00000)
libm.so.6 => /lib64/libm.so.6 (0x00000037cda00000)
libpangocairo-1.0.so.0 => /usr/lib64/libpangocairo-1.0.so.0 (0x00000037e8e00000)
libcairo.so.2 => /usr/lib64/libcairo.so.2 (0x00000037e7a00000)
libpango-1.0.so.0 => /usr/lib64/libpango-1.0.so.0 (0x00000037d4e00000)
libfreetype.so.6 => /usr/lib64/libfreetype.so.6 (0x00000037d1a00000)
libfontconfig.so.1 => /usr/lib64/libfontconfig.so.1 (0x00000037d3600000)
libgobject-2.0.so.0 => /lib64/libgobject-2.0.so.0 (0x00000037d0200000)
libgmodule-2.0.so.0 => /lib64/libgmodule-2.0.so.0 (0x00000037d0600000)
libgthread-2.0.so.0 => /lib64/libgthread-2.0.so.0 (0x00000037cfe00000)
librt.so.1 => /lib64/librt.so.1 (0x00000037cee00000)
libglib-2.0.so.0 => /lib64/libglib-2.0.so.0 (0x00000037cf200000)
libdl.so.2 => /lib64/libdl.so.2 (0x00000037ce600000)
libc.so.6 => /lib64/libc.so.6 (0x00000037cde00000)
libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x000000398f800000)
libz.so.1 => /lib64/libz.so.1 (0x00000037cea00000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00000037ce200000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000037d9600000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000037d7a00000)
libnvidia-tls.so.331.20 => /usr/lib64/tls/libnvidia-tls.so.331.20 (0x0000003970600000)
libnvidia-glcore.so.331.20 => /usr/lib64/libnvidia-glcore.so.331.20 (0x0000003970a00000)
libXext.so.6 => /usr/lib64/libXext.so.6 (0x00000037d2600000)
libuuid.so.1 => /lib64/libuuid.so.1 (0x00000037d8e00000)
libXfixes.so.3 => /usr/lib64/libXfixes.so.3 (0x00000037d3a00000)
libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00000037d0a00000)
libXrender.so.1 => /usr/lib64/libXrender.so.1 (0x00000037d3200000)
libXinerama.so.1 => /usr/lib64/libXinerama.so.1 (0x00000037d4200000)
libXi.so.6 => /usr/lib64/libXi.so.6 (0x00000037d2e00000)
libXrandr.so.2 => /usr/lib64/libXrandr.so.2 (0x00000037d4600000)
libXcursor.so.1 => /usr/lib64/libXcursor.so.1 (0x00000037d3e00000)
libXcomposite.so.1 => /usr/lib64/libXcomposite.so.1 (0x00000037d5200000)
libXdamage.so.1 => /usr/lib64/libXdamage.so.1 (0x00000037d7200000)
libresolv.so.2 => /lib64/libresolv.so.2 (0x00007f01acce0000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x00000037cf600000)
libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00000037d1e00000)
libpixman-1.so.0 => /usr/lib64/libpixman-1.so.0 (0x00000037e6c00000)
libexpat.so.1 => /lib64/libexpat.so.1 (0x00000037d2200000)
/lib64/ld-linux-x86-64.so.2 (0x00000037cd600000)
libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000037d0e00000)
So I can not figure out what is wrong in running tomoalign-gui.
Please help me.

awesome91@-
163.com
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Posts: 2
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Post Re: error abou tomoalign-gui
on: November 5, 2015, 08:05
Quote

Finally, I have solved this problem. I changed the shell from c-shell to bash and source the setup environment. However, I still do not understand why there is a big difference when the protomo is running in csh and bash.

winkler
Administrator
Posts: 69
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Post Re: error abou tomoalign-gui
on: November 11, 2015, 09:47
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I am not so familiar with the c-shell, but the error message indicates that an environment variable was not correctly set or exported. From your post I guess that it could be I3ROOT.

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