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Re: [scipion-users] [EXT] Re: Problem compiling xmipp in Scipion3 on Centos 7 cluster
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From: Alberto G. M. <alb...@cn...> - 2022-03-14 14:02:09
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Hello Thu Nguyen again (best to respond to the list so that everyone can follow up, sorry) To avoid issues related to hdf5 we recommend uninstalling all hdf5 version and install only the hdf5-devel version using/sudo yum install hdf5-devel./We have a installation guide for Centos <https://github.com/I2PC/xmipp/wiki/Installing-Xmipp-on-CentOS-7-9.2009>. After the installation of hdf5-devel, run ./xmipp config which should find the hdf5 path (usr/include/hdf5/serial) and should add this path on the INDIRFLAGS in the xmipp.config file, after checking this you could run ./xmipp and install it. On 14/3/22 14:52, Grigory Sharov wrote: > Hi Thu, > > Have you tried adding correct hdf5 paths to INCDIRFLAGS and > LIBDIRFLAGS in xmipp.conf? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... > > > On Mon, Mar 14, 2022 at 1:47 AM Thu Nguyen <t.n...@un...> > wrote: > > Thank you Pablo for your help, > > With your hints, I went ahead and install hdf5 and hdf5-dev > version 1.10.4 from a 3^rd party repo (Springdale computational, > Princeton), having to remove the centos’ 1.8.12 in the process. I > did try conda install hdf5 with the same version as well, but this > alone is not enough as it seems to need hdf5-dev > > The build could not find the new package at first, even after my > attempt to add PATH and LD_LIBRARY_PATH; however I was able to add > its include and the lib64 manually into xmipp.conf, then rerun > (after export XMIPP_NOCONFIG=True). > > The compiling seems to go further on, but then failed again with > the same error. > > /opt/gnu/gcc/bin/g++ -o bin/xmipp_micrograph_automatic_picking > -flto > applications/programs/micrograph_automatic_picking/micrograph_automatic_picking_main.o > -L/share/apps/scipion3/software/em/xmippSrc-v3.22.01.0/src/xmippCore/lib > -Llib -Llib -L/usr/local/hdf5/gcc/1.10.4/lib64 > -L/share/apps/anaconda3/envs/scipion3/lib > -L/usr/local/hdf5/gcc/1.10.4/lib64 -L/opt/cuda_10.2.89/lib64 > -L/opt/gnu/gcc/lib64 -L/opt/gnu/gmp/lib -L/opt/gnu/mpfr/lib > -L/opt/gnu/mpc/lib -L/opt/gridengine/lib/lx-amd64 > -L/opt/openmpi/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 > -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads > -lpython3.8 -lpthread -lsvm -lXmippCore > > lib/libXmipp.so: undefined reference to `non-virtual thunk to > H5::H5File::throwException(std::__cxx11::basic_string<char, > std::char_traits<char>, std::allocator<char> > const&, > std::__cxx11::basic_string<char, std::char_traits<char>, > std::allocator<char> > const&) const' > > I am a bit lost here, hoping for more hints. > > PS Scipion seems to be able to install other plugins with little > problem, it’s just xmipp3 that is the pain. > > *----------------------------------------------------------------------------------------------------------------* > > *Thu D. Nguyen* > > Bio21 Institute > > The University of Melbourne, Victoria 3010 Australia > > *From:*Pablo Conesa <pc...@cn...> > *Sent:* Saturday, 12 March 2022 2:12 AM > *To:* Mailing list for Scipion users > <sci...@li...>; Thu Nguyen > <t.n...@un...> > *Subject:* [EXT] Re: [scipion-users] Problem compiling xmipp in > Scipion3 on Centos 7 cluster > > *External email: *Please exercise caution > > ------------------------------------------------------------------------ > > Dear Thu! > > I soon (I hope) some Xmipp developer will give a better answer. > > All I can say is that in my case it is linked to a system hdf5 > lib, seems to be happy with v 10.3: > > pablo@youyou:~/software/scipion/software/lib$ ldd libXmippCore.so > linux-vdso.so.1 (0x00007ffe5a1e9000) > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 > (0x00007f6be37c7000) > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6be3678000) > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6be3486000) > libfftw3.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3.so.3 > (0x00007f6be3280000) > libfftw3_threads.so.3 => > /usr/lib/x86_64-linux-gnu/libfftw3_threads.so.3 (0x00007f6be3276000) > libhdf5_serial.so.103 => > /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103 (0x00007f6be2ef9000) > libhdf5_cpp.so.103 => > /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103 (0x00007f6be2e7a000) > libtiff.so.5 => /usr/lib/x86_64-linux-gnu/libtiff.so.5 > (0x00007f6be2df9000) > libjpeg.so.8 => /usr/lib/x86_64-linux-gnu/libjpeg.so.8 > (0x00007f6be2d74000) > libsqlite3.so.0 => /usr/lib/x86_64-linux-gnu/libsqlite3.so.0 > (0x00007f6be2c4b000) > libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 > (0x00007f6be2a69000) > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 > (0x00007f6be2a4e000) > /lib64/ld-linux-x86-64.so.2 (0x00007f6be4046000) > libsz.so.2 => /usr/lib/x86_64-linux-gnu/libsz.so.2 > (0x00007f6be2a47000) > libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f6be2a2b000) > libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 > (0x00007f6be2a25000) > libwebp.so.6 => /usr/lib/x86_64-linux-gnu/libwebp.so.6 > (0x00007f6be29bb000) > libzstd.so.1 => /usr/lib/x86_64-linux-gnu/libzstd.so.1 > (0x00007f6be2912000) > liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 > (0x00007f6be28e9000) > libjbig.so.0 => /usr/lib/x86_64-linux-gnu/libjbig.so.0 > (0x00007f6be26d9000) > libaec.so.0 => /usr/lib/x86_64-linux-gnu/libaec.so.0 > (0x00007f6be26d0000) > > Based on the xmipp doc > <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> > : > "In addition, if hdf5 is not found there, Xmipp will look for it > in /usr/lib and /usr/include/hdf5/serial. If found it, the paths > are appended to the INCDIRFLAGS and LIBDIRFLAGS. If not found and > a specific conda environ is present, Xmipp will try to install > hdf5 through conda under the current conda-environ." > > Not sure if conda hdf5 version can be fixed? > > On 11/3/22 1:49, Thu Nguyen wrote: > > Hi Scipion experts ! > > I administer a cluster built with Centos 7. The cluster has > scipion2 and users want to have scipion3 installed, mainly to > use the topography plugins. > > I followed the instructions and have Scipion3 core installed > fine, but when it comes to building xmipp, I always have this > error: > > libXmipp.so: undefined reference to `non-virtual > thunk to H5::H5File::throwException … > > I guess it relates to hdf5. I do have hdf5 and hdf5-devel > install via yum, and make sure than ‘conda list’ does not have > any hdf5 installed, but it makes no differences. > > As centos 7 has them up to version 1.8.12 only, I wonder if > this is the cause of the problem. I seem to have read > somewhere that xmipp requires at least hdf5 1.10.4 but could > not confirm it. > > I hope anyone has a solution for this. Being a cluster, I do > not have the freedom as stand-alone servers: whatever changes > has to be implemented on all the nodes. > > FYI, I have tried gcc 7.2.0 and 8.5.0, cuda 10,11 , they made > no differences. Installing hdf5 in conda (different versions) > also made no difference as well. > > Thank you all in advance > > *----------------------------------------------------------------------------------------------------------------* > > *Thu D. Nguyen* > > Bio21 Institute > > The University of Melbourne, Victoria 3010 Australia > > > > > _______________________________________________ > > scipion-users mailing list > > sci...@li... > > https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- - Alberto GM - |
