Re: [scipion-users] Cloog library problem with Scipion 1.1 compilation on CentOS 6.9

[Juha H. <ju...@st...>]

Hi Jose Miguel,

I am trying to install on the same cluster as Veli-Pekka. I had created the
directory in March the 13th, but I am not sure if that's when I last time
successfully installed release-1.1 branch.

Best wishes,
Juha

On Mon, May 15, 2017 at 2:21 PM, Jose Miguel de la Rosa Trevin <
del...@gm...> wrote:

> Dear Veli-Pekka and Juha,
>
> Thanks for the feedback. Juha, do you remember (approximately) when do you
> successfully installed the branch release-1.1? Is you OS also a CentOS
> distribution?
>
> I have been looking into the logs but none of the recent commits looks
> like causing such error.
>
> Bests,
> Jose Miguel
>
>
> On Mon, May 15, 2017 at 3:14 PM, Juha Huiskonen <ju...@st...>
> wrote:
>
>> Hi All,
>>
>> Just to confirm, I have the same issue as Veli-Pekka reported.  I had
>> earlier installed release-1.1 successfully but now after doing "git pull;
>> scipion install" I get an error that it cannot find libcloog-isl.so.4. Any
>> ideas? Perhaps this is something that the the local sysadmins should
>> install?
>>
>> Best wishes,
>> Juha
>>
>> On Sun, May 14, 2017 at 10:21 PM, Veli-Pekka Kestilä <vp...@gu...>
>> wrote:
>>
>>>
>>> Hi,
>>>
>>> I am trying to compile Scipion 1.1 for cluster (taito.csc.fi) where
>>> computing nodes are running CentOS 6.9 unfortunately compilation fails
>>> when compiling Xmipp as the alg-library it contains needs newer version
>>> of cloog library than the system has.
>>>
>>> I tried to fix the problem by compiling Cloog library myself, but this
>>> didn't work with SCons as it for some reason makes g++ to ignore shared
>>> library infomation. Same compilation on commanline works without problem
>>>
>>> scons: done reading SConscript files.
>>> scons: Building targets ...
>>> g++ -o software/em/xmipp/external/alglib/src/ap.os -c -DCLOOG_INT_GMP=1
>>> -I/proj/group/taito/scipion-1.1-fixes/software/include
>>> -L/proj/group/taito/scipion-1.1-fixes/software/lib -L/lib -lcloog-isl
>>> -lgmp -O3 -fPIC -Isoftware/include -Isoftware/em/xmipp/external
>>> -Isoftware/em/xmipp/libraries -Isoftware/include
>>> software/em/xmipp/external/alglib/src/ap.cpp
>>> /homeappl/appl_taito/opt/gcc/4.9.3/bin/../libexec/gcc/x86_64
>>> -unknown-linux-gnu/4.9.3/cc1plus:
>>> error while loading shared libraries: libcloog-isl.so.4: cannot open
>>> shared object file: No such file or directory
>>> scons: *** [software/em/xmipp/external/alglib/src/ap.os] Error 1
>>> scons: building terminated because of errors.
>>>
>>> As as can be seen from the directory listing file is in given libpath.
>>>
>>> [user@taito-login4 scipion-1.1-fixes]$ ls -la
>>> /proj/group/taito/scipion-1.1-fixes/software/lib/libcloo*
>>> ..../lib/libcloog-isl.a
>>> ..../lib/libcloog-isl.la
>>> ..../lib/libcloog-isl.so -> libcloog-isl.so.4.0.0
>>> ..../lib/libcloog-isl.so.4 -> libcloog-isl.so.4.0.0
>>> ..../lib/libcloog-isl.so.4.0.0
>>>
>>> I have also tried other ways to give the shared library to the Scons but
>>> they have also failed. Any help on the matter is appreciated.
>>>
>>> Best Regards,
>>> Veli-Pekka Kestilä
>>>
>>>
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>>
>>
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