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

[Alberto G. M. <alb...@cn...>]

Hi again,


Could you share the xmipp.config file? You can try to install xmipp with 
scipion scipion3 by running: */./scipion3 run pathToXmipp/xmipp /*to run 
it with the scipion enviroment.



On 15/3/22 11:15, Thu Nguyen 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...> 
>> <mailto:alb...@cn...>
>> *Sent:* Monday, 14 March 2022 6:49 PM
>> *To:* Thu Nguyen <t.n...@un...> 
>> <mailto: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 -
-- 
- Alberto GM -