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Re: [scipion-users] Cloog library problem with Scipion 1.1 compilation on CentOS 6.9
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From: Juha H. <ju...@st...> - 2017-05-16 13:47:49
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Hi Pablo, I have these flags: CCFLAGS = -std=c99 CXXFLAGS = The missing file is on our system in /appl/opt/cloog/0.18.1/lib/ and this directory is in my LD_LIBRARY_PATH. Is it possible that the LD_LIBRARY_PATH is not carried out to scipion environment when it tries to compile Xmipp? Best wishes, Juha On Tue, May 16, 2017 at 2:34 PM, Pablo Conesa <pc...@cn...> wrote: > 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...> 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 >>>> >>>> >>>> ------------------------------------------------------------ >>>> ------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>> >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >> > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
