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Re: [scipion-users] Problem compiling xmipp in Scipion3 on Centos 7 cluster
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From: Pablo C. <pc...@cn...> - 2022-03-11 15:12:30
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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* |
