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

[Grigory S. <sha...@gm...>]

Hi Thu,

I think the actual problem is before that. I see that you are compiling
apps, while I believe the xmippCore compiled before that has problems
finding hdf5

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 Tue, Mar 15, 2022 at 10:17 AM Thu Nguyen <t.n...@un...> wrote:

> I am sorry to report it made no differences.
>
> It's not gcc, as I switched to gcc 8.5.0, the error is still there.  Here
> is where it came out in my latest attempt:
>
> g++ -o bindings/python/python_metadata.os -c -mtune=native -march=native
> -flto -std=c++17 -O3 -I../ -I/share/apps/anaconda3/envs/scipion3/include
> -I/usr/include -fPIC
> -I/share/apps/anaconda3/envs/scipion3/include/python3.8
> -I/share/apps/anaconda3/envs/scipion3/lib/python3.8/site-packages/numpy/core/include
> -Iexternal -Ilibraries
> -I/share/apps/scipion3/software/em/xmippSrc-v3.22.01.0/src/xmippCore
> bindings/python/python_metadata.cpp
>
>
> g++ -o bin/xmipp_transform_mirror -flto
> applications/programs/transform_mirror/transform_mirror_main.o
> -L/share/apps/scipion3/software/em/xmippSrc-v3.22.01.0/src/xmippCore/lib
> -Llib -Llib -L/share/apps/anaconda3/envs/scipion3/lib -L/usr/lib64
> -L/share/apps/gcc/8.5.0/lib64 -L/share/apps/gcc/8.5.0/lib
> -L/opt/cuda_10.2.89/lib64 -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'
> collect2: error: ld returned 1 exit status
> scons: *** [bin/xmipp_pdb_analysis] Error 1
>
>
>
> ___________________________________________________
>
> Thu D. Nguyen
>
>
>
>
>
>
>
>
> ------------------------------
> *From:* Alberto Garcia Mena <alb...@cn...>
> *Sent:* Tuesday, 15 March 2022 5:50 PM
> *To:* Thu Nguyen <t.n...@un...>; Mailing list for Scipion
> users <sci...@li...>
> *Subject:* Re: [scipion-users] [EXT] Re: Problem compiling xmipp in
> Scipion3 on Centos 7 cluster
>
> * External email: Please exercise caution *
> ------------------------------
>
> Hi again Thu,
>
> Xmipp looks for libhdf5* and hdf5.h files. For Centos7 libhdf5* are in*
> /usr/lib64/ *and hdf5.h is in* /usr/include/.* Please verify that you
> have the files in those paths and add them to INCDIRFLAGS and LIBDIRFLAGS
> in xmipp.config as
>
> LIBDIRFLAGS= ... -L/usr/lib64
> INCDIRFLAGS= ... -I/usr/include
>
> After that run *./xmipp compileAndInstall*
>
> Thank you for your detailed report. (It seems that for Centos7 Xmipp is
> not able to find hdf5 by default)
>
>
> On 14/3/22 23:59, Thu Nguyen wrote:
>
> Thanks to all that responded.
>
>
>
> Unfortunately I am not faring any better.  I have tried different versions
> of hdf5-devel (1.8.12, 1.10.0,1.10.4,1.10.6), correctly edit xmipp.conf for
> INCDIRFLAGS and LIBDIRFLAGS each time (as shown in my latest error post),
> and even tried the 20.07 release as some suggested.
>
>
>
> The error seemed to turn up at different stages each time.
>
>
>
> One thing I just notice, in all my hdf5-devel installs, I never seem to
> get the “serial” folder as shown in some discussions.  What does this
> folder have?
>
>
>
>
>
>
> *----------------------------------------------------------------------------------------------------------------*
>
> *Thu D. Nguyen*
>
>
>
> Bio21 Institute
>
> The University of Melbourne, Victoria 3010 Australia
>
>
>
> *From:* Alberto Garcia Mena <alb...@cn...>
> <alb...@cn...>
> *Sent:* Monday, 14 March 2022 6:49 PM
> *To:* Thu Nguyen <t.n...@un...> <t.n...@un...>
> *Subject:* Re: [scipion-users] [EXT] Re: Problem compiling xmipp in
> Scipion3 on Centos 7 cluster
>
>
>
> *External email: *Please exercise caution
>
>
> ------------------------------
>
> Hello thu Nguyen,
>
> 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.
>
>
>
> --
> - Alberto GM -
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