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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...> - 2017-05-20 16:24:51
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Hi, I got it also working. Another change I needed to do was to change following line: software/em/xmipp/scipion_sconscript: kwargs['libs'] += ['mpi', 'mpi_cxx', 'XmippParallel'] to software/em/xmipp/scipion_sconscript: kwargs['libs'] += ['mpi', 'mpicxx', 'XmippParallel'] as it seems that cluster recommended intel mpi doesn't have underscore in library name. Thanks for the help, -vpk On 17.5.2017 12:47, Juha Huiskonen wrote: > 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... <mailto: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... <mailto: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... <mailto: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...> > > <mailto: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...> > <mailto: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...> > <mailto: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...> <mailto:vp...@gu... > <mailto:vp...@gu...>>> wrote: > >> > >> > >> Hi, > >> > >> I am trying to compile Scipion 1.1 for cluster > >> (taito.csc.fi <http://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> <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...> > >> > <mailto:sci...@li... > <mailto:sci...@li...>> > >> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > >> <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...> > >> <mailto:sci...@li... > <mailto:sci...@li...>> > >> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > >> <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...> > >> <mailto:sci...@li... > <mailto:sci...@li...>> > >> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > >> <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...> > > <mailto:sci...@li... > <mailto:sci...@li...>> > > > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > <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> > > -- Veli-Pekka Kestilä / vp...@gu... / +358503000014 |
