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Re: [scipion-users] Cloog library problem with Scipion 1.1 compilation on CentOS 6.9
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From: Veli-Pekka K. <vp...@gu...> - 2017-05-16 20:31:54
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Hi, I checked this and Juha was correct in his theory on missing LD_LIBRARY_PATH. It seems that CSC has changed their environment so that for g++ it's mandatory to have libcloog in LD_LIBRARY_PATH and scipion or scons strips it away from it. If I manually remove libcloog from the LD_LIBRARY_PATH the error also manifested itself in command line. I think the easiest fix for us would be that scipion/scons would respect the system LD_LIBRARY_PATH and would not change it. Is there easy way to skip all the other compilations and just try compile xmipp so that I could check if other compilers provided in the cluster environment would work? Greetings, -vpk On 16.5.2017 16:46, Juha Huiskonen wrote: > 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... > <mailto: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... <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 >> >> >> ------------------------------------------------------------------------------ >> 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... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> <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... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> <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... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> <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... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <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 > |
