External Email - Use Caution
Hello Jorge,
You can download a tar archive of the pre-built 3rd party packages with the
following command,
curl -O
http://surfer.nmr.mgh.harvard.edu/pub/data/fspackages/prebuilt/centos7-packages.tar.gz
- and the versions of the contained packages in that archive should work:
vtk=5.10.1, petsc=2.3.3; itk=4.13.0; gts=0.7.6; ann=1.1.2
You could set the individual cmake variables for each package, or instead try
setting -DFS_PACKAGES_DIR to point to the absolute path of where the ./packages
subdir is after expanding the archive; then you should not have to individually
set ITK_DIR, VTK_DIR, etc.
You could also try downloading “makefile.wiki” from,
https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view
to do this and other work for you.
Then if you type “make -f makefile.wiki pkg_download” it will try to download
that package archive for you, and also add a python3 (needed for freesurfer)
from anaconda python under the packages archive. If it finds everything,
it will generate the cmake command for you. You can see what the command
will be with "make -f makefile.wiki config_print”. You can also use
it to try and run cmake, then do the build and install passes - type “make -f
makefile.wiki help” to read more.
- R.
On May 26, 2019, at 04:25, Jorge Naranjo <jorge.nara...@nyu.edu>
wrote: External Email - Use
Caution Hi All,IM compiling
freesurfer, after many bumps reached a point i havent figured out how to
proceed.My setup:Centos7 GCC 4.8.5 Freesurfer 6.0.0 Dependencies
as in /usr/pubsw/packages/ - KWWWidgets : CVS-vtk560-
petsc : 2.3.3-p13- mni 1.5- tcltktixblt : 8.4.6 -
wxWidgets wxGTK-2.8.9 - xawplus: 3.1.0 Dependencies I built and
installed in /usr/pubsw/packages/- dcmtk: 3.6.4- itk: 4.9.1-
vxl: v1.17.0The rest of dependencies installed through RPM packages (yum)
system-wise.. including VTK, etc ... then I
do:FS_PACKAGES_DIR=/usr/pubsw/packagesVTK_DIR=/usrVTK_LIBRARIES=/usr/lib64PREFIX=/share/apps/NYUAD3/freesurfer/6..0.0CMAKE_BUILD_TYPE=ReleasePETSC_DIR=/usr/pubsw/packages/petsc/currentITK_DIR=/usr/pubsw/packages/itk/4.9.1/lib/cmake/ITK-4.9/OpenGL_GL_PREFERENCE=GLVNDDANN_LIBRARIES=/usr/lib64export
CPATH=$CPATH:/usr/pubsw/packages/itk/4.9.1/include/ITK-4.9/ cmake3
../freesurfer -DFS_PACKAGES_DIR=${FS_PACKAGES_DIR}
-DVTK_LIBRARIES=${VTK_LIBRARIES} -DVTK_DIR=${VTK_DIR}
-DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DPETSC_DIR=${PETSC_DIR} -DITK_DIR=${ITK_DIR}
-DOpenGL_GL_PREFERENCE=${OpenGL_GL_PREFERENCE}
-DANN_LIBRARIES=${DANN_LIBRARIES} -DUSE_PYTHON_INCLUDE_DIR=ON
-DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib64/ -lglut"makeNOTE: the glut thing is
because if I let the system use the libglut inside packages dir in the source
code ... compilation breaks with :/bin/ld:
../packages/glut/libglut.a(glut_win.c.o): undefined reference to symbol
'glXCreateContextWithConfigSGIX'Well, the thing is that will all the above, the
compilation breaks with this message:[ 57%] Built target trk_tools[ 57%] Built
target streamlineFilter[ 57%] Built target
testOrientationPlanesFromParcellation[ 57%] Building CXX object
anatomicuts/CMakeFiles/dmri_match.dir/AnatomiCuts_correspondences.cxx.o/scratch/apps/singularity-sandboxes/braimcore-sandbox/SOFTWARE/FREESURFER/freesurfer/anatomicuts/AnatomiCuts_correspondences.cxx:
In function ‘int main(int,
char**)’:/scratch/apps/singularity-sandboxes/braimcore-sandbox/SOFTWARE/FREESURFER/freesurfer/anatomicuts/AnatomiCuts_correspondences.cxx:648:62:
error: expected primary-expression before ‘double’
vcl_vector<unsigned int> assign = vnl_hungarian_algorithm<double>(
distances ); //.GetAssignmentVector();
^make[2]: ***
[anatomicuts/CMakeFiles/dmri_match.dir/AnatomiCuts_correspondences.cxx.o] Error
1make[1]: *** [anatomicuts/CMakeFiles/dmri_match.dir/all] Error 2make: ***
[all] Error 2Any help !?? will be highly appreciated thanks!Jorge A.
NaranjoHPC Computational SpecialistNYU Abu DhabiOffice Tel (UAE): +971 2 628
4750Mobile (UAE): +971 56 319 2814New York University - Abu Dhabi
(NYUAD) Saadiyat Campus - A2, Room-131 P.O. Box 129188Abu Dhabi,
United Arab Emirateshttp://nyuad.nyu.eduPlease consider the environment before
printing this email._______________________________________________Freesurfer
mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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