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

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One thing I changed is in NVCC_CXXFLAGS (besides cc7.5): I put -std=c++14
instead of -std=c++11

Otherwise I had some errors (not related to 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 Wed, Mar 16, 2022 at 12:44 PM Grigory Sharov <sha...@gm...>
wrote:

> Dear Wolfgang,
>
> cc 8.6 certainly requires CUDA11
> <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>, since this is for
> RTX30xx cards. There's no cc8.6 suggestions by default (see here
> <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)#cuda-configuration>),
> so I believe you have added this argument.
>
> I have xmipp compiled on Scientific Linux 7.9 with gcc10.2.0, cuda 11.4 (
> cc7.5 max, since I have Tesla T4 cards) and hdf5 1.12.1 installed via conda.
>
> 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 Wed, Mar 16, 2022 at 12:24 PM Lugmayr, Wolfgang <w.l...@uk...>
> wrote:
>
>> Dear Grigory,
>>
>> I have the same problem and tried a complete fresh install of scipion3.
>> In your
>> https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install.html
>> you say CUDA 10 but it seems you need CUDA 11
>>
>> Checking CUDA configuration ...
>>  /beegfs/cssb/software/spack/opt/spack/linux-centos7-x86_64/gcc-10.3.0/cuda-10.2.89-4fkqx2xzcctfvrzwzuqiylwdrxhdywro/bin/nvcc
>> -c -w --x cu -D_FORCE_INLINES -Xcompiler -fPIC -ccbin
>> /beegfs/cssb/software/spack/opt/spack/linux-centos7-x86_64/gcc-10.3.0/gcc-8.5.0-vo5ghaznhl5vu4k77vimk2bqs5e53kil/bin/g++
>> -std=c++14 --expt-extended-lambda -gencode=arch=compute_60,code=compute_60
>> -gencode=arch=compute_61,code=compute_61
>> -gencode=arch=compute_75,code=compute_75
>> -gencode=arch=compute_86,code=compute_86 -I../
>> -I/beegfs/cssb/software/em/scipion/3.0/miniconda/envs/scipion3/include
>> xmipp_cuda_test.cpp -o xmipp_cuda_test.o
>> nvcc fatal   : Unsupported gpu architecture 'compute_86'
>>  Check the NVCC, NVCC_CXXFLAGS and INCDIRFLAGS
>>  Cannot compile with NVCC, continuing without CUDA
>>
>> And then later i have problems with the hdf5 libraries. The ondes from
>> the distribution do not seem to have the cxx bindings and hdf5 1.12 is too
>> new. So I assume you need hdf5 1.8?
>>
>> cheers,
>> Wolfgang
>>
>>
>> ------------------------------
>> *From: *"Grigory Sharov" <sha...@gm...>
>> *To: *"Mailing list for Scipion users" <
>> sci...@li...>
>> *Sent: *Wednesday, 16 March, 2022 11:09:42
>> *Subject: *Re: [scipion-users] [EXT] Re: Problem compiling xmipp in
>> Scipion3 on Centos 7 cluster
>>
>> Also, what do you have in:
>>
>>> ls /usr/lib64/libhdf*
>>> ls /usr/include/hdf*
>>> ls /share/apps/anaconda3/envs/scipion3/lib/libhdf*
>>
>> ls /share/apps/anaconda3/envs/scipion3/include/*
>>
>>
>>
>> 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
>> e-mail: gs...@mr...
>>
>>
>> On Wed, Mar 16, 2022 at 9:50 AM Grigory Sharov <sha...@gm...>
>> wrote:
>>
>>> 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
>>> 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
>>>>
>>>
>>
>> _______________________________________________
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>>
>

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