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Re: [scipion-users] Cloog library problem with Scipion 1.1 compilation on CentOS 6.9
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From: Pablo C. <pc...@cn...> - 2017-05-16 11:34:53
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Dear all, we don't think we have committed any recent change here that
might has cause the issue.
Does anyone know which binary requires the missing library?
And ldd of software/lib/libXmippAlglib.so doesn't seem to depend on it:
linux-vdso.so.1 => (0x00007ffeefd72000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
(0x00007f026fc53000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f026f94a000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
(0x00007f026f733000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f026f36a000)
/lib64/ld-linux-x86-64.so.2 (0x000055cc2c957000)
Am I missing (probably since I'm out of my comfort zone here, this is
C++) anything?
All the best, Pablo.
Could you also send what is the content of the below variables at
<SCIPIOn_HOME>/config/scipion.conf ?
CCFLAGS, CXXFLAGS
and Does an /echo $CCFLAGS $CXXFLAGS///print something?
On 15/05/17 15:35, Juha Huiskonen wrote:
> 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... <mailto: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... <mailto: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... <mailto:vp...@gu...>> wrote:
>
>
> Hi,
>
> I am trying to compile Scipion 1.1 for cluster
> (taito.csc.fi <http://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 <http://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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