Hi Andre,
fantastic advice! You made my day! I followed instructions and so far so good, cvs is running.
Thanks a lot,
Martin
On Tue, Dec 3, 2013 at 12:09 AM, André Ribeiro andrefsr@gmail.com wrote:
Hi Martin,
In November 27 I posted a similar question, which later I found a solution. See if it works for you.
Hi Lilla,
Thank you for your reply. I have boost installed, yet it is not the version required (v. 1.49). Although, even after installing an older version such as the 1.41 it is not straightforward to use this libboost with freesurfer. The doc from libboost is not easy to understand and even if done correctly you will not be able to use this installation as there is no libboost_program_options.so.5. Nevertheless, I got it to work so here goes the solution that worked for me.
Download libboost v. 1.41 and untar cd libboost_folder mkdir libraries ./bootstrap.sh --prefix=./libraries ./bjam install cd libraries/lib ln -s libboost_program_options.so.1.41.0 libboost_program_options.so.5 export LD_LIBRARY_PATH=.../boost_1_41_0/libraries/lib:$LD_LIBRARY_PATH
Cheers, Andre Santos Ribeiro
regards
Andre Santos Ribeiro
On Mon, Dec 2, 2013 at 9:57 PM, Martin Kavec martin.kavec@gmail.comwrote:
Hi Zeke,
Thanks a lot for explanation. I think I will install centOS into a virtual machine for quick solution. I only need it to run CVS.
Thanks and best regards,
Martin
Sent from my iPad
On 2.12.2013, at 22:50, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Martin,
Upx (http://upx.sourceforge.net) is an executable packaging utility we
run on all our binaries before shipping to reduce their overall size. One consequence of upx is that it changes the way the "file" and "ld" commands process the binaries. In this case it makes the "file" command say they are statically linked when infact it is dynamically linked. You can view this for yourself by running upx in reverse (upx -d mris_resample) and indeed you will see that it says dynamically linked.
libboost1.41 is what comes by default on our centOS6_x86_64 platforms
and it is what freesurfer builds against. All I can suggest is that you install the same version, or one very close to it.
-Zeke
On 12/02/2013 02:50 PM, Martin Kavec wrote: Hi Zeke,
Thanks for response. Well it was the first thing for me to try to
compile boost on gentoo, which went fine. However the libraries were not compatible. Gentoo has 1.52 version, while the one needed is about 4 years old.
When I do "ldd mris_resample" I get "not a dynamic executable" and
when I do "file mris_resample" I get that it is a statically linked executable, stripped. I think something could have happened with when stripping the executable. I get the same output from file mris_rescale, but mris_rescale runs fine.
I am using Freesurfer-5.3.0 for Centos6 x86_64.
Thanks,
Martin
Sent from my iPad
On 2.12.2013, at 17:33, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Martin,
libboost is not a static library, it is a shared library. It comes by default on centOS platforms and freesurfer compiles against it during the the build process. Typing 'ldd mris_resample' and examining the output confirms this:
$>ldd mris_resample linux-vdso.so.1 => (0x00007fffd2773000) libboost_program_options.so.5 => /usr/lib64/libboost_program_options.so.5 (0x00007fe2e588d000) etc...
Also, many of the freesurfer binaries do require the libboost library.
Freesurfer works on most linux distribution, but we specifically build on and support centOS platforms. We do not have Gentoo linux machines
to
try and replicate your error but I am confident that if you get the libboost libraries on your machine, the program will work properly.
-Zeke
On 11/28/2013 05:09 PM, Martin Kavec wrote: Hi Lilla,
thanks for coming back. Unfortunately I was not able to compile appropriate boost for my operating system Gentoo linux. Nevertheless
I
do not understand why mris_resample misses the library if it should
be
statically linked. Other binaries do not need it. Could you please
check
if mris_resample in 64-bit linux version of CentOS is correct?
Otherwise I cannot run cvs.
Thanks a lot,
Martin
On Mon, Nov 25, 2013 at 5:32 PM, Lilla Zollei <lzollei@nmr.mgh.harvard.edu mailto:lzollei@nmr.mgh.harvard.edu>
wrote:
This is a bit delayed response (my apologies) to an earlier
question to
the list:
The boost library is installed by default on CentOS platforms. If
a user
gets the libboost error then they are using a different platform
which
doesn't have boost installed by default. On RedHat systems
libboost
can be installed by typing the follwing command: $>yum install boost-devel"
The version of libboost that we use for our latest release is
1.41.
Lilla
Martin Kavec Mon, 04 Nov 2013 14:10:53 -0800
Hi guys,
When running mri_cvs_register on linux (5.3.0), I get into
problem with
mris_resample, which cannot find libboost_programs_options.so.5. I installed the latest version of boost-1.52.0 for my system, but there are unresolved symbols.
Which version is suitable for mris_resample?
Thanks,
Martin
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