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Re: [scipion-users] [EXT] Re: Problem compiling xmipp in Scipion3 on Centos 7 cluster
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From: Thu N. <t.n...@un...> - 2022-03-15 11:16:08
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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...><mailto:alb...@cn...>
Sent: Tuesday, 15 March 2022 5:50 PM
To: Thu Nguyen <t.n...@un...><mailto:t.n...@un...>; Mailing list for Scipion users <sci...@li...><mailto: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 -
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- Alberto GM -
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