External Email - Use Caution
Hi, I'm Kazuhiro.
I also met trouble for compilation of freesurfer stable6 repository under my
Ubuntu 18.04 LTS machine.
Even the binary package of
freesurfer6.0(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz) can work
under Ubuntu 18.04, option of '-use-gpu' required cuda runtime library of ver
5.0(libcudart.so.5.0).
I have tried to link cuda runtime library of Ubuntu 18.04 (ver9.1) to ver5.0
filename.
(ln -s libcudart.so.9.0 libcudart.so.5.0 )
It cannot work well.
In my case, after eight steps below, it was successfully compiled and
run normally with CUDA-GPU.
(1) use library of centos7-packages. It was installed to /usr/pubsw/packages
(2) vxl library build regard as instruction of develop_reposiory/packages/vxl.
libvxl have not yet included in Ubuntu 18.04 packages.
vxl library were installed to /usr/pubsw/vxl.
(3) use library of tcltktixblt from binary package of freesurfer6.0
distribution (lib/tcltktixblt)
tcltktixblt packages copy to /usr/pubsw/tcltktixblt
(4) Cuda development packages were installed to /usr/local/cuda
Download cuda_cluster_pkgs_8.0.61_ubuntu1604.tar.gz from NVIDA web site
after extraction of above archive
sudo dpkg -i cuda-cluster-runtime-8-0_8.0.61-1_amd64.deb
sudo dpkg -i cuda-cluster-devel-8-0_8.0.61-1_amd64.deb
My GPU card is fermi architecture of TESLA C2070
Therefore the final support packages is CUDA ver 8.0
(5) two files were changed in stable 6 repository for non-GUI build
configure.in
expat/xmlparse.c
and additional ten files were changed for GUI build regarding as compile
error
GEMS/Makefile.am
glut/glut_cmap.c
glut/glut_util.c
lineprof/LineProf.cpp
lineprof/LineProf.h
lineprof/Makefile.am
lineprof/Preprocessor.cpp
lineprof/Tracer.cpp
lineprof/Traceh.h
freeview/main.cpp
(6) configure with
./configure --prefix=/usr/local/freesurfer --with-vxl-dir=/usr/pubsw/vxl \
--with-tcl-dir=/usr/pubsw/tcltktixblt --disable-Werror\
--with-vtk-dir=/usr/pubsw/packages/vtk/5.6
--with-mni-dir=/usr/pubsw/packages/mni/current \
--with-petsc-dir=/usr/pubsw/packages/petsc/2.3.3 --with-cuda=/usr/local/cuda
--enable-fermi-gpu \
--with-itk-4.13=/usr/pubsw/packages/itk/4.13.0
--with-kwwidgets-dir=/usr/pubsw/packages/KWWidgets/CVS
(7) make -j 8
(8) make install
difference source code as follows
configure.in, add blas and lapack library path and ITK4.13 configurlation
--------------------------------------------------------------------------
--- configure.in_dist 2018-11-01 14:55:56.087117356 +0900
+++ configure.in 2018-10-05 17:31:04.451989866 +0900
@@ -397,6 +397,10 @@ fi
if test -e /usr/lib64/libblas.a ; then
LIB_BLAS="/usr/lib64/libblas.a"
fi
+if test -e /usr/lib/x86_64-linux-gnu/libblas.a ; then
+ LIB_BLAS="/usr/lib/x86_64-linux-gnu/libblas.a"
+fi
+
if test "$host" = "powerpc64-suse-linux"; then
if test -e /usr/lib/libblas.a ; then
LIB_BLAS="/usr/lib/libblas.a"
@@ -413,6 +417,8 @@ elif test -e /usr/lib64/liblapack.a ; th
LIB_LAPACK="/usr/lib64/liblapack.a"
elif test -e /usr/lib/lapack/liblapack.a ; then
LIB_LAPACK="/usr/lib/lapack/liblapack.a"
+elif test -e /usr/lib/x86_64-linux-gnu/liblapack.a ; then
+ LIB_LAPACK="/usr/lib/x86_64-linux-gnu/liblapack.a"
fi
if test "$host" = "powerpc64-suse-linux"; then
if test -e /usr/lib/liblapack.a ; then
@@ -557,7 +563,7 @@ case "${target}" in
OS=Linux
OS_CPPFLAGS="$DEADCODE_STRIP"
OS_LDFLAGS="$DEADCODE_STRIP"
- LDFLAGS="-L/usr/lib64 -L/usr/X11R6/lib64 $LDFLAGS"
+ LDFLAGS="-L/usr/lib/x86_64-linux-gnu $LDFLAGS"
DYNAMIC_LIB_EXT=".so"
SHARED_CFLAGS="-fPIC"
SHARED_LDFLAGS="-shared"
@@ -1219,8 +1225,8 @@ if test "x$x_includes" = "xNONE"; then
x_includes=
fi
if test "x$x_includes" = "x"; then
- if test -d "/usr/X11R6/include" ; then
- x_includes=/usr/X11R6/include
+ if test -d "/usr/include/X11" ; then
+ x_includes=/usr/include/X11
fi
fi
AC_MSG_NOTICE([x_includes set to $x_includes \
@@ -2772,6 +2778,19 @@ AC_ARG_WITH(itk-4.5.1,
])
# end NJS HACK
+# knam: --with-itk-4.13 is a temporary hack to allow building against ITK v4.13
+AC_ARG_WITH(itk-4.13,
+ [ --with-itk-4.13=DIR set paths to use ITK v4.13.],
+ [ ac_itk_includes="$withval"/include/ITK-4.13
+ ac_itk_libraries="$withval"/lib
+ ITK_DIR="$withval"
+ itk_apps="yes"
+ itk_413="yes"
+ AC_SUBST(ITK_DIR)
+ ])
+# end NJS HACK
+
+
AC_ARG_WITH(itk-include,
[ --with-itk-include=DIR root of ITK include directory.],
[ itk_i="$withval"
@@ -2863,6 +2882,21 @@ if test "$itk_apps" = "yes"; then
$ac_itk_libraries/libitkopenjpeg-4.5.a \
$ac_itk_libraries/libITKDICOMParser-4.5.a"
fi
+ if test "x$itk_413" = "xyes"; then
+ LIBS_ITK="\
+ $ac_itk_libraries/libITKIONRRD-4.13.a \
+ $ac_itk_libraries/libITKIOImageBase-4.13.a \
+ $ac_itk_libraries/libITKCommon-4.13.a \
+ $ac_itk_libraries/libITKMetaIO-4.13.a \
+ $ac_itk_libraries/libITKniftiio-4.13.a \
+ $ac_itk_libraries/libITKNrrdIO-4.13.a \
+ $ac_itk_libraries/libitkpng-4.13.a \
+ $ac_itk_libraries/libitksys-4.13.a \
+ $ac_itk_libraries/libitktiff-4.13.a \
+ $ac_itk_libraries/libitkv3p_netlib-4.13.a \
+ $ac_itk_libraries/libitkzlib-4.13.a \
+ $ac_itk_libraries/libITKTransform-4.13.a"
+fi
# ITK v3.16.0 needs libuuid for function `gdcm::Util::GenerateUUID'
if test -e /usr/lib/libuuid.a ; then
@@ -2885,6 +2919,10 @@ fi
AM_CONDITIONAL(ENABLE_ITK_APPS, test "$itk_apps" = "yes")
AM_CONDITIONAL(HAVE_ITK_LIBS, test "$itk_apps" = "yes")
+AM_CONDITIONAL(HAVE_ITK45, test "$itk_45" = "yes")
+AM_CONDITIONAL(HAVE_ITK45, test "$itk_413" = "yes")
+AM_CONDITIONAL(HAVE_ITK413, test "$itk_413" = "yes")
+
AC_SUBST(ITK_CFLAGS)
AC_SUBST(ITK_LIBS)
-------------------------------------------------------------------------
expat/xmlparse.c, correspond to memmove error
--------------------------------------------------------------------------
--- xmlparse.c_dist 2018-11-01 14:54:25.554818570 +0900
+++ xmlparse.c 2018-10-04 10:31:10.246153077 +0900
@@ -79,14 +79,14 @@ typedef char ICHAR;
/* Round up n to be a multiple of sz, where sz is a power of 2. */
#define ROUND_UP(n, sz) (((n) + ((sz) - 1)) & ~((sz) - 1))
-/* Handle the case where memmove() doesn't exist. */
-#ifndef HAVE_MEMMOVE
-#ifdef HAVE_BCOPY
-#define memmove(d,s,l) bcopy((s),(d),(l))
-#else
-#error memmove does not exist on this platform, nor is a substitute available
-#endif /* HAVE_BCOPY */
-#endif /* HAVE_MEMMOVE */
+/*Handle the case where memmove() doesn't exist. */
+//#ifndef HAVE_MEMMOVE
+//#ifdef HAVE_BCOPY
+//#define memmove(d,s,l) bcopy((s),(d),(l))
+//#else
+//#error memmove does not exist on this platform, nor is a substitute available
+//#endif /* HAVE_BCOPY */
+//#endif /* HAVE_MEMMOVE */
#include "internal.h"
#include "xmltok.h"
-------------------------------------------------------------------------
GEMS/Makefile.am was override by GEMS/Makefile.kvlN4ITK.am
--------------------------------------------------------------------------
-------------------------------------------------------------------------
glut/glut_cmap.c, correspond to XmuLookupStandardColormap error
--------------------------------------------------------------------------
--- glut_cmap.c_dist 2018-11-01 14:58:58.199666598 +0900
+++ glut_cmap.c 2018-10-05 10:06:39.501707105 +0900
@@ -238,6 +238,7 @@ __glutSetupColormap(XVisualInfo * vi, GL
XFree(standardCmaps);
}
}
+#define SOLARIS_2_4_BUG
#ifndef SOLARIS_2_4_BUG
/* Solaris 2.4 and 2.5 have a bug in their
XmuLookupStandardColormap implementations. Please
-------------------------------------------------------------------------
glut/glut_util.c, correspond to gluErrorString error
--------------------------------------------------------------------------
--- glut_util.c_dist 2018-11-01 14:59:08.407695685 +0900
+++ glut_util.c 2018-10-05 10:04:38.821442922 +0900
@@ -48,7 +48,8 @@ glutReportErrors(void)
GLenum error;
while ((error = glGetError()) != GL_NO_ERROR)
- __glutWarning("GL error: %s", gluErrorString(error));
+ // __glutWarning("GL error: %s", gluErrorString(error));
+ __glutWarning("GL error: %s gluErrorString(error)");
}
/* ENDCENTRY */
-------------------------------------------------------------------------
files in lineprof directory were copied from developed repositry
-------------------------------------------------------------------------
lineprof/LineProf.cpp
lineprof/LineProf.h
lineprof/Makefile.am
lineprof/Preprocessor.cpp
lineprof/Tracer.cpp
lineprof/Traceh.h
-------------------------------------------------------------------------
freeview/main.cpp was changed for files in lineprof directory
--------------------------------------------------------------------------
--- main.cpp_dist 2018-11-01 14:57:56.591487516 +0900
+++ main.cpp 2018-10-05 10:43:10.374280172 +0900
@@ -122,7 +122,7 @@ int main(int argc, char *argv[])
qInstallMsgHandler(myMessageOutput);
#endif
- LineProf::InitializePetsc();
+ LineProf::InitializePetsc(true);
CmdLineEntry cmdLineDesc[] =
{
>
>Hi there,
>
>
>Thank you for directing me to the CMake fswiki. I was able to install the
>third party packages and execute the command `cmake . -DFS_PACKAGES_DIR="path
>/to/pkgs"`.
>
>
>However, when I run `make -j4` (after adjusting a few bash files in various
>libraries to find (#include) other libraries) I am met with numerous
>similarly-worded link error lines under the step "Linking Fortran executable
>t4imgs_4dfp" with the general schema:
>
>
>/usr/bin/ld: path/to/fortran-related/filename: relocation R_X86_64_32 against
>`some.variable.or.file.name` can not be used when making a PIE object;
>recompile with -fPIC
>
>
>where path/to/fortran-related/filename is either CMakeFiles/t4imgs_4dfp.dir/
>some-file.c.o or /usr/lib/gcc/x86_64-linux-gnu/4.8/libgfortran.a(some-
>function.o)
>
>
>I tried finding a solution online and found the suggestion to add a global -
>fPIC flag via export CXXFLAGS="$CXXFLAGS -fPIC" ( https://stackoverflow.com/
>questions/13812185/how-to-recompile-with-fpic ). I tried this by starting
>completely over with a new clone of the freesurfer repo and calling cmake . -
>DFS_PACKAGES_DIR="path/to/pkgs" and the make still failed at the same point.
>
>
>Other suggestions (e.g., to add --enable-shared at ./configure(in that same
>thread linked above)) suggest adding arguments when configuring, but since
>this is all part of the make process I'm not sure whether that's possible.
>
>
>Any advice? I did not find any similar issues in the archive.
>
>Thank you very much,
>Christian McDaniel
--------------------------------------------------------------
Kazuhiro Nakamura, Ph.D.
Research Institute for Brain and Blood Vessels-Akita
6-10 Senshukubota machi, Akita 010-0874 JAPAN
phone +81-18-833-0115 ext 769, fax +81-18-833-2104
E-mail: [email protected]
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