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

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Hi Thu,

xmipp script needs a second parameter, but anyway I suggest going step by
step:

1) conda activate scipion3
2) cd /share/apps/scipion3/software/em/xmippSrc-v3.22.01.0/
3) ./xmipp cleanBin
4) edit xmipp.conf and set Verified=False
5) ./xmipp check_config -> check what it returns
6) ./xmipp compile | tee -a compile.log -> attach here compile.log

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 11:16 AM Thu Nguyen <t.n...@un...> wrote:

> Running:
>
>  /share/apps/scipion3/scipion3 run
> /share/apps/scipion3/software/em/xmippSrc-v3.22.01.0/xmipp
> Scipion v3.0.10 - Eugenius
>
>  >>> WARNING: Image library not found!
>   > Please install Xmipp to get full functionality.
> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin
> manager window)
>
>
> ** Running command:
>  /share/apps/scipion3/software/em/xmippSrc-v3.22.01.0/xmipp
>  'xmipp.conf' detected.
> Checking configuration ------------------------------
>  'xmipp.conf' is already checked. Set VERIFIED=False to re-checked
> Getting Dependencies -------------------------------------
>  Checkouting cuFFTAdvisor:master ...
>  Repository contains uncommitted changes.
>  Use 'compileAndInstall' mode to keep developing.
>  Cannot checkout branch 'master'. Remaining on the branch 'None'.
>  Cannot get dependencies
> Traceback (most recent call last):
>   File "/share/apps/anaconda3/envs/scipion3/bin/emprogram", line 8, in
> <module>
>     sys.exit(main())
>   File
> "/share/apps/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/cmd/program.py",
> line 43, in main
>     runProgram(program, params)
>   File
> "/share/apps/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/utils.py",
> line 73, in runProgram
>     pwutils.runJob(None, program, params, env=env)
>   File
> "/share/apps/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 52, in runJob
>     return runCommand(command, env, cwd)
>   File
> "/share/apps/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 67, in runCommand
>     check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
>   File "/share/apps/anaconda3/envs/scipion3/lib/python3.8/subprocess.py",
> line 364, in check_call
>     raise CalledProcessError(retcode, cmd)
> subprocess.CalledProcessError: Command '
> /share/apps/scipion3/software/em/xmippSrc-v3.22.01.0/xmipp ' returned
> non-zero exit status 1.
>
> ---------------------------------
>
> And here is my xmipp.conf:
>
> [BUILD]
> BUILD_TESTS=False
> CC=gcc
> CCFLAGS=-std=c99
> CONFIG_VERSION=release-22.01 (97a0c0dc)
> CUDA=True
> CXX=/share/apps/gcc/8.5.0/bin/g++
> CXXFLAGS=-mtune=native -march=native -flto -std=c++17 -O3
> CXX_CUDA=/share/apps/gcc/8.5.0/bin
> DEBUG=False
> INCDIRFLAGS=-I../ -I/share/apps/anaconda3/envs/scipion3/include
> -I/usr/include
> JAR=/usr/java/latest/bin/jar
> JAVAC=/usr/java/latest/bin/javac
> JAVA_BINDIR=/usr/java/latest/bin
> JAVA_HOME=/usr/java/latest
> JNI_CPPPATH=/usr/java/latest/include:/usr/java/latest/include/linux
> LIBDIRFLAGS=-L/share/apps/anaconda3/envs/scipion3/lib -L/usr/lib64
> LINKERFORPROGRAMS=/share/apps/gcc/8.5.0/bin/g++
> LINKFLAGS=-flto
> MATLAB=False
> MATLAB_DIR=
> MPI_CC=mpicc
> MPI_CXX=mpicxx
> MPI_CXXFLAGS=
> MPI_LINKERFORPROGRAMS=mpicxx
> MPI_LINKFLAGS=
> MPI_RUN=mpirun
> NVCC=/opt/cuda_10.2.89/bin/nvcc
> NVCC_CXXFLAGS=--x cu -D_FORCE_INLINES -Xcompiler -fPIC -ccbin
> /share/apps/gcc/8.5.0/bin -std=c++11 --expt-extended-lambda
> -gencode=arch=compute_35,code=compute_35
> -gencode=arch=compute_50,code=compute_50
> -gencode=arch=compute_60,code=compute_60
> -gencode=arch=compute_61,code=compute_61
> NVCC_LINKFLAGS=-L/opt/cuda_10.2.89/targets/x86_64-linux/lib
> -L/opt/cuda_10.2.89/targets/x86_64-linux/lib/stubs
> OPENCV=False
> OPENCV3=False
> OPENCVSUPPORTSCUDA=False
> PYTHONINCFLAGS=-I/share/apps/anaconda3/envs/scipion3/include/python3.8
> -I/share/apps/anaconda3/envs/scipion3/lib/python3.8/site-packages/numpy/core/include
> PYTHON_LIB=python3.8
> STARPU=False
> STARPU_HOME=
> STARPU_INCLUDE=/include/starpu/1.3
> STARPU_LIB=/lib
> STARPU_LIBRARY=libstarpu-1.3
> USE_DL=False
> VERIFIED=True
>
> Thank you.
>
>
>
> ___________________________________________________
>
> Thu D. Nguyen
>
> Bio21 Institute
>
> Thu University of Melbourne
>
>
>
>
>
>
>
>
> ------------------------------
> *From:* Alberto Garcia Mena <alb...@cn...>
> *Sent:* Tuesday, 15 March 2022 9:36 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,
>
>
> 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...>
> <alb...@cn...>
> *Sent:* Tuesday, 15 March 2022 5:50 PM
> *To:* Thu Nguyen <t.n...@un...> <t.n...@un...>;
> Mailing list for Scipion users <sci...@li...>
> <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 -
>
> --
> - Alberto GM -
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

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