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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...> - 2017-05-17 09:48:23
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Hi Jose Miguel Thanks, this worked for me. Best wishes, Juha On Wed, May 17, 2017 at 10:55 AM, Jose Miguel de la Rosa Trevin < del...@gm...> wrote: > Hi Veli-Pekka, > > I have found a line that can be causing that LD_LIBRARY_PATH is not > propagated. > > In line 227 of scipion/SConstruct file, a new Environment is created and > it seems that propagating the whole system environment has broken other > compilations. > So, in the next line the PATH is explicitly propagated. > > Could you try to add the following code in line 229: > > env2['ENV']['LD_LIBRARY_PATH'] = env['ENV']['LD_LIBRARY_PATH'] > > > And check if this solves the specific problem you are having. If it does, > then we will need to consider this change > and if it does not affect other systems. > > > Cheers, > Jose Miguel > > > > On Tue, May 16, 2017 at 10:39 PM, Jose Miguel de la Rosa Trevin < > del...@gm...> wrote: > >> Hum, this seems weird. To the best of my knowledge Scons should preserve >> the system LD_LIBRARY_PATH, but it seems that is not working in this way. I >> will take a look at it tomorrow and think in a workaround for you can >> proceed with the installation. >> >> Veli-Pekka, I'm afraid that now you need to compile all the required >> libraries before getting into the Xmipp part. I would like to improve this >> for the future, but we are not there yet. >> >> Bests, >> Jose Miguel >> >> >> On Tue, May 16, 2017 at 10:31 PM, Veli-Pekka Kestilä <vp...@gu...> >> wrote: >> >>> >>> 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.ne >>> t/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.ne >>> t/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 >>> > >>> >>> ------------------------------------------------------------ >>> ------------------ >>> 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 > > |
