getting started with Slicer on linux trouble...

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getting started with Slicer on linux trouble...

Huge Ontoman
Good day slicer-users,

i tried to run the pre-built binary version of Slicer3 i recently downloaded,
Slicer3-3.4.2-2010-01-07-linux-x86, but running ./Slicer3 gives me errors.

Could not query slicer for module paths
couldn't open "/media/USB-HDD/_DATA/LINUX/slicer/Slicer3-3.4.2-2010-01-07-linux-x86/lib/Slicer3/Slicer3Version.txt": no such file or directory
/media/USB-HDD/_DATA/LINUX/slicer/Slicer3-3.4.2-2010-01-07-linux-x86/bin/Slicer3-real: error while loading shared libraries: libITKFEM.so.3.10: cannot open shared object file: No such file or directory

child process exited abnormally

I thought that installing the libinsighttoolkit3.6 would solve the problem, but that is not the case...after this, Slicer still wants version libITKFEM.so.3.10.

Digging deeper, ./bin/Slicer3-real doesn't find all of the required shared library dependencies, although the extracted directory contains all (?) of them..
Running ldd ./bin/Slicer3-real gave me a lot (!) of these missing dependencies, so probably i'm missing something too.

Obviously, i didn't do any installing of Slicer, simple case of extract-and-run.
I'm really starting to use Ubuntu.

My question is, is there a SAFE way to "configure" this extracted version of the application to use the shared libraries that come with the downloaded "pre-built" package?
Can i run it from my external usb drive (i simply don't have space to put Slicer on OS partition)?
Or do i have to build it from source to use my systems installed libraries?

Any advice would be welcome!
Cheers,
Huge.


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Re: getting started with Slicer on linux trouble...

Andrey Fedorov
On Sat, Feb 6, 2010 at 13:14, Huge Ontoman <[hidden email]> wrote:

> i tried to run the pre-built binary version of Slicer3 i recently
> downloaded,
> Slicer3-3.4.2-2010-01-07-linux-x86, but running ./Slicer3 gives me errors.
>
> Could not query slicer for module paths
> couldn't open
> "/media/USB-HDD/_DATA/LINUX/slicer/Slicer3-3.4.2-2010-01-07-linux-x86/lib/Slicer3/Slicer3Version.txt":
> no such file or directory
> /media/USB-HDD/_DATA/LINUX/slicer/Slicer3-3.4.2-2010-01-07-linux-x86/bin/Slicer3-real:
> error while loading shared libraries: libITKFEM.so.3.10: cannot open shared
> object file: No such file or directory
>

Huge,

it is hard to say what exactly caused this error in your case. I would
suggest first to make sure you have enough space on your USB drive,
and that all of the files were extracted properly. FYI, untarred
Slicer 3.4.2 linux binary tree takes about 600M. Did you try to grep
for ITKFEM library in SLICER_HOME?

> I thought that installing the libinsighttoolkit3.6 would solve the problem,
> but that is not the case...after this, Slicer still wants version
> libITKFEM.so.3.10.

You don't need to install ITK. Slicer binary build should be self-contained.

> Digging deeper, ./bin/Slicer3-real doesn't find all of the required shared
> library dependencies, although the extracted directory contains all (?) of
> them..
> Running ldd ./bin/Slicer3-real gave me a lot (!) of these missing
> dependencies, so probably i'm missing something too.
>

ldd gives you unresolved dependencies because Slicer3-real starts in
the different environment, which is set up by Slicer3 binary (NOT
bin/Slicer3 binary -- don't use this one). If you try "Slicer3
--launch xterm", and then run ldd in that xterm, you should see all
dependencies resolved (if your installation is not corrupted).


> Obviously, i didn't do any installing of Slicer, simple case of
> extract-and-run.
> I'm really starting to use Ubuntu.
>
> My question is, is there a SAFE way to "configure" this extracted version of
> the application to use the shared libraries that come with the downloaded
> "pre-built" package?
> Can i run it from my external usb drive (i simply don't have space to put
> Slicer on OS partition)?
> Or do i have to build it from source to use my systems installed libraries?
>
> Any advice would be welcome!
> Cheers,
> Huge.
>
> ________________________________
> Windows Live Hotmail: Your friends can get your Facebook updates, right from
> Hotmail®.
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
>
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Re: getting started with Slicer on linux trouble...

Andrey Fedorov
On Sun, Feb 7, 2010 at 06:58, Huge Ontoman <[hidden email]> wrote:
> command revealed that the symlinks can't be extracted/created, i get errors
> like
>
> tar:
> Slicer3-3.4.2-2010-01-07-linux-x86/lib/InsightToolkit/libITKIOReview.so:...can't
> make symbolik link for the following ..."libITKIOReview.so.3.10": Not
> permitted
>

Huge,

What is the filesystem you have on your USB drive? I suspect it's FAT,
in which case it may not be possible to create a symbolic link in the
directory where you install Slicer, and there are a lot of links in
lib/InsightToolkit, e.g.,

lrwxrwxrwx 1 andrey users      19 2010-01-21 08:28 libITKznz.so.3.10
-> libITKznz.so.3.10.2
-rwxr-xr-x 1 andrey users   13911 2009-05-20 13:47 libITKznz.so.3.10.2

You mentioned, you are using mounted USB drive, because you don't have
space on your main disk. If I were you, I would copy some files from
your main disk (which I assume is ext2), and try to untar Slicer in
that directory.

Another alternative is to format your USB disk as an ext filesystem.

hth

AF


> So i'm probably stuck at extracting it correctly, as these errors keep
> accumulating, and finaly tar exits (some 30 secs later after the first
> fail).
> Am i wrong with the extract command? What am i missing?
>
> I did try to launch Slicer3 with the --launch xterm, but (obviously) without
> all the files correctly extracted, it is a no go.
>
> Thanks for Your attention,
> Huge.
>
>> Date: Sat, 6 Feb 2010 13:41:55 -0500
>> Subject: Re: [slicer-users] getting started with Slicer on linux
>> trouble...
>> From: [hidden email]
>> To: [hidden email]
>> CC: [hidden email]
>>
>> On Sat, Feb 6, 2010 at 13:14, Huge Ontoman <[hidden email]> wrote:
>> > i tried to run the pre-built binary version of Slicer3 i recently
>> > downloaded,
>> > Slicer3-3.4.2-2010-01-07-linux-x86, but running ./Slicer3 gives me
>> > errors.
>> >
>> > Could not query slicer for module paths
>> > couldn't open
>> >
>> > "/media/USB-HDD/_DATA/LINUX/slicer/Slicer3-3.4.2-2010-01-07-linux-x86/lib/Slicer3/Slicer3Version.txt":
>> > no such file or directory
>> >
>> > /media/USB-HDD/_DATA/LINUX/slicer/Slicer3-3.4.2-2010-01-07-linux-x86/bin/Slicer3-real:
>> > error while loading shared libraries: libITKFEM.so.3.10: cannot open
>> > shared
>> > object file: No such file or directory
>> >
>>
>> Huge,
>>
>> it is hard to say what exactly caused this error in your case. I would
>> suggest first to make sure you have enough space on your USB drive,
>> and that all of the files were extracted properly. FYI, untarred
>> Slicer 3.4.2 linux binary tree takes about 600M. Did you try to grep
>> for ITKFEM library in SLICER_HOME?
>>
>> > I thought that installing the libinsighttoolkit3.6 would solve the
>> > problem,
>> > but that is not the case...after this, Slicer still wants version
>> > libITKFEM.so.3.10.
>>
>> You don't need to install ITK. Slicer binary build should be
>> self-contained.
>>
>> > Digging deeper, ./bin/Slicer3-real doesn't find all of the required
>> > shared
>> > library dependencies, although the extracted directory contains all (?)
>> > of
>> > them..
>> > Running ldd ./bin/Slicer3-real gave me a lot (!) of these missing
>> > dependencies, so probably i'm missing something too.
>> >
>>
>> ldd gives you unresolved dependencies because Slicer3-real starts in
>> the different environment, which is set up by Slicer3 binary (NOT
>> bin/Slicer3 binary -- don't use this one). If you try "Slicer3
>> --launch xterm", and then run ldd in that xterm, you should see all
>> dependencies resolved (if your installation is not corrupted).
>>
>>
>> > Obviously, i didn't do any installing of Slicer, simple case of
>> > extract-and-run.
>> > I'm really starting to use Ubuntu.
>> >
>> > My question is, is there a SAFE way to "configure" this extracted
>> > version of
>> > the application to use the shared libraries that come with the
>> > downloaded
>> > "pre-built" package?
>> > Can i run it from my external usb drive (i simply don't have space to
>> > put
>> > Slicer on OS partition)?
>> > Or do i have to build it from source to use my systems installed
>> > libraries?
>> >
>> > Any advice would be welcome!
>> > Cheers,
>> > Huge.
>> >
>> > ________________________________
>> > Windows Live Hotmail: Your friends can get your Facebook updates, right
>> > from
>> > Hotmail®.
>> > _______________________________________________
>> > slicer-users mailing list
>> > [hidden email]
>> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> > To unsubscribe: send email to
>> > [hidden email]
>> > with unsubscribe as the subject
>> >
>
> ________________________________
> New Windows 7: Find the right PC for you. Learn more.
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