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

[Thu N. <t.n...@un...>]

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 -