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Re: [scipion-users] [EXT] Re: Problem compiling xmipp in Scipion3 on Centos 7 cluster
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From: Thu N. <t.n...@un...> - 2022-03-14 01:46:58
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Thank you Pablo for your help,
With your hints, I went ahead and install hdf5 and hdf5-dev version 1.10.4 from a 3rd 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.
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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
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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
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Thu D. Nguyen
Bio21 Institute
The University of Melbourne, Victoria 3010 Australia
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Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team
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