Re: [scipion-users] [EXT] Re: Problem compiling xmipp in Scipion3 on Centos 7 cluster

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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 <+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 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.
>
>
>
>
>
>
> *----------------------------------------------------------------------------------------------------------------*
>
> *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
>
>
>
>
>
>
>
>
>
>
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>
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>
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>
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>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
> _______________________________________________
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>

Re: [scipion-users] [EXT] Re: Problem compiling xmipp in Scipion3 on Centos 7 cluster

Image processing framework to integrate EM software packages.

Re: [scipion-users] [EXT] Re: Problem compiling xmipp in Scipion3 on Centos 7 cluster