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From: Lugmayr, W. <w.l...@uk...> - 2022-03-17 11:32:52
|
dear all, just to finalize - it worked also for me in a fresh scipion install when i did: conda activate scipion3 conda install -y hdf5 # load my gcc10.3, cuda 11.5, and openmpi with cuda11 enabled scipion3 installp -p scipion-em-xmipp -j 12 | tee -a install.log all went fine except the -mtune/march parameters do not fit to our environment. we have intel and amd nodes in the cluster. so i did in the same environment as above: cd to_xmipp_location ./xmipp cleanBin vi ./scripts/config.py changed: #self.configDict["CXXFLAGS"] += " -mtune=native -march=native -flto" to: self.configDict["CXXFLAGS"] += " -mavx2" ./xmipp config noAsk | tee config.log ./xmipp compile | tee compile.log ./xmipp install | tee install.log cheers, wolfgang From: "Alberto Garcia Mena" <alb...@cn...> To: "Thu Nguyen" <t.n...@un...>, "Mailing list for Scipion users" <sci...@li...> Cc: "Irene" <isa...@cn...> Sent: Thursday, 17 March, 2022 11:51:35 Subject: Re: [scipion-users] [EXT] Re: Problem compiling xmipp in Scipion3 on Centos 7 cluster Glad to hear it. I'm sure hdf5 creates some problems, also the compiler version. Thanks for your patience and for your installation report. [ https://github.com/I2PC/xmipp/wiki/Installing-Xmipp-on-CentOS-7-9.2009 | I have updated the wiki page ] for installing Xmipp on Centos7, reporting the problems with hdf5. Thanks again for your patience and I hope you enjoy Scipion&Xmipp. If you have any other problems related to Scipion / xmipp, please write to us. BR On 17/3/22 11:18, Thu Nguyen wrote: Dear All, BQ_BEGIN Thanks to All that have responded and helped. For a whole week, I have tried without success with countless combinations of gcc, cuda and hdf5. Now I can report that I have "sort-of" solved my own problem. I hope this will help someone who might have the same issue. * Asumming the centos 7 hdf5-devel installed with yum (1.8.12) was not doing its job, I uninstalled it. No trace of hdf5* in /usr/include of /usr/lib64. * I used gcc 8.5.0 to compile and install hdf 1.10.3 from source, installed at /usr/local/hdf5. Please note, I have used this version before, but as rpms from a 3 rd party (Springdale Computational, Princeton); this time I built my own. * I ran ./xmipp cleanAll. This erase averything including contents of the src folder I think. * then ./xmipp config. This time the config said it could not find hdf5 and asked me to put it in, so I was able to specify the include and lib paths to the new hdf5 (usr/local/hdf5/include and lib) * ./xmipp all will redownload everything, compile and install I am so glad to finally see the line that said xmipp installed sucessfully. In the process I learned to clean up after a failed build; how to rebuild the xmipp.config file and do other things with the ./xmipp. Also when trying with gcc5.3, I got a message complaining about "inline variables", which on my search I read that it is a C++17 feature that gcc only fully supports in their version 8's. That confirms the need for gcc8; I am not sure if my previous use of gcc 7.2.0 contributed to the failure or not (would not have the energy to go back and try !) In saying I sort-of solve the problem, the cluster needs packages to be in rpm form to be auto-deployed to compute nodes, so I will have to find a way to get my hdf5 to them, but this is outside the focus of this forum Again thank for all your help, specially those who have email me personally with plenty of hints. ___________________________________________________ Thu D. Nguyen Bio21 Institute The University of Melbourne BQ_END -- - Alberto GM - _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Alberto G. M. <alb...@cn...> - 2022-03-17 10:52:49
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Glad to hear it. I'm sure hdf5 creates some problems, also the compiler version. Thanks for your patience and for your installation report. I have updated the wiki page <https://github.com/I2PC/xmipp/wiki/Installing-Xmipp-on-CentOS-7-9.2009> for installing Xmipp on Centos7, reporting the problems with hdf5. Thanks again for your patience and I hope you enjoy Scipion&Xmipp. If you have any other problems related to Scipion / xmipp, please write to us. BR On 17/3/22 11:18, Thu Nguyen wrote: > Dear All, > >> Thanks to All that have responded and helped. For a whole week, I >> have tried without success with countless combinations of gcc, cuda >> and hdf5. Now I can report that I have "sort-of" solved my own >> problem. I hope this will help someone who might have the same issue. >> >> * Asumming the centos 7 hdf5-devel installed with yum (1.8.12) was >> not doing its job, I uninstalled it. No trace of hdf5* in >> /usr/include of /usr/lib64. >> * I used gcc 8.5.0 to compile and install hdf 1.10.3 from source, >> installed at /usr/local/hdf5. Please note, I have used this >> version before, but as rpms from a 3^rd party (Springdale >> Computational, Princeton); this time I built my own. >> * I ran ./xmipp cleanAll. This erase averything including contents >> of the src folder I think. >> * then ./xmipp config. This time the config said it could not find >> hdf5 and asked me to put it in, so I was able to specify the >> include and lib paths to the new hdf5 (usr/local/hdf5/include and >> lib) >> * ./xmipp all will redownload everything, compile and install >> >> I am so glad to finally see the line that said xmipp installed >> sucessfully. > In the process I learned to clean up after a failed build; > how to rebuild the xmipp.config file and do other things with the > ./xmipp. Also when trying with gcc5.3, I got a message complaining > about "inline variables", which on my search I read that it is a C++17 > feature that gcc only fully supports in their version 8's. That > confirms the need for gcc8; I am not sure if my previous use of gcc > 7.2.0 contributed to the failure or not (would not have the energy to > go back and try !) > > In saying I sort-of solve the problem, the cluster needs packages to > be in rpm form to be auto-deployed to compute nodes, so I will have to > find a way to get my hdf5 to them, but this is outside the focus of > this forum > > Again thank for all your help, specially those who have email me > personally with plenty of hints. > > > > ___________________________________________________ > > Thu D. Nguyen > > Bio21 Institute > > The University of Melbourne > > > > -- - Alberto GM - |
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From: Thu N. <t.n...@un...> - 2022-03-17 10:19:18
|
Dear All,
Thanks to All that have responded and helped. For a whole week, I have tried without success with countless combinations of gcc, cuda and hdf5. Now I can report that I have "sort-of" solved my own problem. I hope this will help someone who might have the same issue.
* Asumming the centos 7 hdf5-devel installed with yum (1.8.12) was not doing its job, I uninstalled it. No trace of hdf5* in /usr/include of /usr/lib64.
* I used gcc 8.5.0 to compile and install hdf 1.10.3 from source, installed at /usr/local/hdf5. Please note, I have used this version before, but as rpms from a 3rd party (Springdale Computational, Princeton); this time I built my own.
* I ran ./xmipp cleanAll. This erase averything including contents of the src folder I think.
* then ./xmipp config. This time the config said it could not find hdf5 and asked me to put it in, so I was able to specify the include and lib paths to the new hdf5 (usr/local/hdf5/include and lib)
* ./xmipp all will redownload everything, compile and install
I am so glad to finally see the line that said xmipp installed sucessfully.
In the process I learned to clean up after a failed build; how to rebuild the xmipp.config file and do other things with the ./xmipp. Also when trying with gcc5.3, I got a message complaining about "inline variables", which on my search I read that it is a C++17 feature that gcc only fully supports in their version 8's. That confirms the need for gcc8; I am not sure if my previous use of gcc 7.2.0 contributed to the failure or not (would not have the energy to go back and try !)
In saying I sort-of solve the problem, the cluster needs packages to be in rpm form to be auto-deployed to compute nodes, so I will have to find a way to get my hdf5 to them, but this is outside the focus of this forum
Again thank for all your help, specially those who have email me personally with plenty of hints.
___________________________________________________
Thu D. Nguyen
Bio21 Institute
The University of Melbourne
|
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From: Thu N. <t.n...@un...> - 2022-03-17 00:32:12
|
Thank you for taking the time to help. Despite so many trials, the problem is still showings. Here are some more details in response to your query: cd /usr/lib64; ls -la libhdf* lrwxrwxrwx 1 root root 20 Mar 17 09:56 libhdf5_cpp.so -> libhdf5_cpp.so.8.0.1 lrwxrwxrwx 1 root root 20 Mar 17 09:56 libhdf5_cpp.so.8 -> libhdf5_cpp.so.8.0.1 -rwxr-xr-x 1 root root 347960 Sep 16 12:28 libhdf5_cpp.so.8.0.1 lrwxrwxrwx 1 root root 24 Mar 17 09:56 libhdf5_fortran.so -> libhdf5_fortran.so.8.0.1 lrwxrwxrwx 1 root root 24 Mar 17 09:56 libhdf5_fortran.so.8 -> libhdf5_fortran.so.8.0.1 -rwxr-xr-x 1 root root 266216 Sep 16 12:28 libhdf5_fortran.so.8.0.1 lrwxrwxrwx 1 root root 23 Mar 17 09:56 libhdf5_hl_cpp.so -> libhdf5_hl_cpp.so.8.0.1 lrwxrwxrwx 1 root root 23 Mar 17 09:56 libhdf5_hl_cpp.so.8 -> libhdf5_hl_cpp.so.8.0.1 -rwxr-xr-x 1 root root 11352 Sep 16 12:28 libhdf5_hl_cpp.so.8.0.1 lrwxrwxrwx 1 root root 26 Mar 17 09:56 libhdf5hl_fortran.so -> libhdf5hl_fortran.so.8.0.1 lrwxrwxrwx 1 root root 26 Mar 17 09:56 libhdf5hl_fortran.so.8 -> libhdf5hl_fortran.so.8.0.1 -rwxr-xr-x 1 root root 82808 Sep 16 12:28 libhdf5hl_fortran.so.8.0.1 lrwxrwxrwx 1 root root 19 Mar 17 09:56 libhdf5_hl.so -> libhdf5_hl.so.8.0.1 lrwxrwxrwx 1 root root 19 Mar 17 09:56 libhdf5_hl.so.8 -> libhdf5_hl.so.8.0.1 -rwxr-xr-x 1 root root 132536 Sep 16 12:28 libhdf5_hl.so.8.0.1 -rw-r--r-- 1 root root 4283 Sep 16 12:28 libhdf5.settings lrwxrwxrwx 1 root root 16 Mar 17 09:56 libhdf5.so -> libhdf5.so.8.0.1 lrwxrwxrwx 1 root root 16 Mar 17 09:56 libhdf5.so.8 -> libhdf5.so.8.0.1 -rwxr-xr-x 1 root root 2796496 Sep 16 12:28 libhdf5.so.8.0.1 cd /usr/include; ls -la hdf* -rw-r--r-- 1 root root 2655 Sep 16 12:28 hdf5.h -rw-r--r-- 1 root root 1604 Sep 16 12:28 hdf5_hl.h cd /share/apps/anaconda3/envs/scipion3/lib; ls -la libhdf* ls: cannot access libhdf*: No such file or directory cd /share/apps/anaconda3/envs/scipion3/include; ls curses.h form.h ks_names.h ncurses.h sqlite3ext.h tclOO.h tclUnixPort.h tk3d.h tkEntry.h tkIntXlibDecls.h tkMacOSX.h tkMenu.h tkUnixDefault.h default.h itcl2TclOO.h lzma ncursesw sqlite3.h tclOOIntDecls.h tdbcDecls.h tkArray.h tkFileFilter.h tkMacOSXColor.h tkMacOSXInt.h tkPlatDecls.h tkUnixInt.h eti.h itclDecls.h lzma.h odbcStubs.h tclDecls.h tclOOInt.h tdbc.h tkBusy.h tkFont.h tkMacOSXConstants.h tkMacOSXKeysyms.h tkPort.h tkUnixPort.h fakemysql.h itcl.h menu.h openssl tcl.h tclPlatDecls.h tdbcInt.h tkButton.h tk.h tkMacOSXCursors.h tkMacOSXPort.h tkScale.h unctrl.h fakepq.h itclIntDecls.h mysqlStubs.h panel.h tclIntDecls.h tclPort.h termcap.h tkCanvas.h tkImgPhoto.h tkMacOSXDebug.h tkMacOSXPrivate.h tkScrollbar.h zconf.h fakesql.h itclInt.h nc_tparm.h pqStubs.h tclInt.h tclThread.h term_entry.h tkColor.h tkIntDecls.h tkMacOSXDefault.h tkMacOSXWm.h tkSelect.h zlib.h ffi.h itclMigrate2TclCore.h ncurses python3.8 tclIntPlatDecls.h tclTomMathDecls.h term.h tkDecls.h tkInt.h tkMacOSXEvent.h tkMacOSXXCursors.h tkText.h ffitarget.h itclTclIntStubsFcn.h ncurses_dll.h readline tclOODecls.h tclTomMath.h tic.h tkDList.h tkIntPlatDecls.h tkMacOSXFont.h tkMenubutton.h tkUndo.h I am also attaching the compile.log . ---------------------------------------------------------------------------------------------------------------- Thu D. Nguyen Bio21 Institute The University of Melbourne, Victoria 3010 Australia 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 <sharo...@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 >>> |
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From: Grigory S. <sha...@gm...> - 2022-03-16 12:51:10
|
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 >>> >> > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Grigory S. <sha...@gm...> - 2022-03-16 12:49:36
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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 >>>> >>> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > |
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From: Lugmayr, W. <w.l...@uk...> - 2022-03-16 12:23:58
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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 | 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* BQ_BEGIN ls /share/apps/anaconda3/envs/scipion3/include/* BQ_END 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: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Mar 16, 2022 at 9:50 AM Grigory Sharov < [ mailto:sha...@gm... | sha...@gm... ] > wrote: BQ_BEGIN 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: [ mailto:gs...@mr... | gs...@mr... ] On Tue, Mar 15, 2022 at 11:16 AM Thu Nguyen < [ mailto:t.n...@un... | t.n...@un... ] > wrote: BQ_BEGIN 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 < [ mailto:alb...@cn... | alb...@cn... ] > Sent: Tuesday, 15 March 2022 9:36 PM To: Thu Nguyen < [ mailto:t.n...@un... | t.n...@un... ] >; Mailing list for Scipion users < [ mailto: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, 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: BQ_BEGIN 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 [ mailto:alb...@cn... | <alb...@cn...> ] Sent: Tuesday, 15 March 2022 5:50 PM To: Thu Nguyen [ mailto:t.n...@un... | <t.n...@un...> ] ; Mailing list for Scipion users [ mailto: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: BQ_BEGIN 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 [ mailto:alb...@cn... | <alb...@cn...> ] Sent: Monday, 14 March 2022 6:49 PM To: Thu Nguyen [ mailto: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. [ https://github.com/I2PC/xmipp/wiki/Installing-Xmipp-on-CentOS-7-9.2009 | We have a installation guide for Centos ] . 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. BQ_END -- - Alberto GM - BQ_END -- - Alberto GM - _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END BQ_END _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2022-03-16 10:10:29
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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 <+44%201223%20267228> 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 <+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 >> > |
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From: Grigory S. <sha...@gm...> - 2022-03-16 09:51:17
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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 > |
|
From: Thu N. <t.n...@un...> - 2022-03-15 11:16:08
|
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 -
--
- Alberto GM -
|
|
From: Alberto G. M. <alb...@cn...> - 2022-03-15 10:36:18
|
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 - |
|
From: Grigory S. <sha...@gm...> - 2022-03-15 10:25:19
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Hi Thu, I think the actual problem is before that. I see that you are compiling apps, while I believe the xmippCore compiled before that has problems finding 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 Tue, Mar 15, 2022 at 10:17 AM Thu Nguyen <t.n...@un...> 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...> > <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 - > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Thu N. <t.n...@un...> - 2022-03-15 10:17:01
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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 - |
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From: Alberto G. M. <alb...@cn...> - 2022-03-15 06:50:50
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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...> > *Sent:* Monday, 14 March 2022 6:49 PM > *To:* Thu Nguyen <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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From: Thu N. <t.n...@un...> - 2022-03-14 22:59:42
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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...> Sent: Monday, 14 March 2022 6:49 PM To: Thu Nguyen <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. |
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From: Alberto G. M. <alb...@cn...> - 2022-03-14 14:02:09
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Hello Thu Nguyen again (best to respond to the list so that everyone can follow up, sorry) 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. On 14/3/22 14:52, Grigory Sharov wrote: > Hi Thu, > > Have you tried adding correct hdf5 paths to INCDIRFLAGS and > LIBDIRFLAGS in xmipp.conf? > > 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 <tel:+44%201223%20267228> > e-mail: gs...@mr... > > > On Mon, Mar 14, 2022 at 1:47 AM Thu Nguyen <t.n...@un...> > wrote: > > Thank you Pablo for your help, > > With your hints, I went ahead and install hdf5 and hdf5-dev > version 1.10.4 from a 3^rd party repo (Springdale computational, > Princeton), having to remove the centos’ 1.8.12 in the process. I > did try conda install hdf5 with the same version as well, but this > alone is not enough as it seems to need hdf5-dev > > The build could not find the new package at first, even after my > attempt to add PATH and LD_LIBRARY_PATH; however I was able to add > its include and the lib64 manually into xmipp.conf, then rerun > (after export XMIPP_NOCONFIG=True). > > The compiling seems to go further on, but then failed again with > the same error. > > /opt/gnu/gcc/bin/g++ -o bin/xmipp_micrograph_automatic_picking > -flto > applications/programs/micrograph_automatic_picking/micrograph_automatic_picking_main.o > -L/share/apps/scipion3/software/em/xmippSrc-v3.22.01.0/src/xmippCore/lib > -Llib -Llib -L/usr/local/hdf5/gcc/1.10.4/lib64 > -L/share/apps/anaconda3/envs/scipion3/lib > -L/usr/local/hdf5/gcc/1.10.4/lib64 -L/opt/cuda_10.2.89/lib64 > -L/opt/gnu/gcc/lib64 -L/opt/gnu/gmp/lib -L/opt/gnu/mpfr/lib > -L/opt/gnu/mpc/lib -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' > > I am a bit lost here, hoping for more hints. > > PS Scipion seems to be able to install other plugins with little > problem, it’s just xmipp3 that is the pain. > > *----------------------------------------------------------------------------------------------------------------* > > *Thu D. Nguyen* > > Bio21 Institute > > The University of Melbourne, Victoria 3010 Australia > > *From:*Pablo Conesa <pc...@cn...> > *Sent:* Saturday, 12 March 2022 2:12 AM > *To:* Mailing list for Scipion users > <sci...@li...>; Thu Nguyen > <t.n...@un...> > *Subject:* [EXT] Re: [scipion-users] Problem compiling xmipp in > Scipion3 on Centos 7 cluster > > *External email: *Please exercise caution > > ------------------------------------------------------------------------ > > Dear Thu! > > I soon (I hope) some Xmipp developer will give a better answer. > > All I can say is that in my case it is linked to a system hdf5 > lib, seems to be happy with v 10.3: > > pablo@youyou:~/software/scipion/software/lib$ ldd libXmippCore.so > linux-vdso.so.1 (0x00007ffe5a1e9000) > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 > (0x00007f6be37c7000) > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6be3678000) > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6be3486000) > libfftw3.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3.so.3 > (0x00007f6be3280000) > libfftw3_threads.so.3 => > /usr/lib/x86_64-linux-gnu/libfftw3_threads.so.3 (0x00007f6be3276000) > libhdf5_serial.so.103 => > /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103 (0x00007f6be2ef9000) > libhdf5_cpp.so.103 => > /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103 (0x00007f6be2e7a000) > libtiff.so.5 => /usr/lib/x86_64-linux-gnu/libtiff.so.5 > (0x00007f6be2df9000) > libjpeg.so.8 => /usr/lib/x86_64-linux-gnu/libjpeg.so.8 > (0x00007f6be2d74000) > libsqlite3.so.0 => /usr/lib/x86_64-linux-gnu/libsqlite3.so.0 > (0x00007f6be2c4b000) > libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 > (0x00007f6be2a69000) > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 > (0x00007f6be2a4e000) > /lib64/ld-linux-x86-64.so.2 (0x00007f6be4046000) > libsz.so.2 => /usr/lib/x86_64-linux-gnu/libsz.so.2 > (0x00007f6be2a47000) > libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f6be2a2b000) > libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 > (0x00007f6be2a25000) > libwebp.so.6 => /usr/lib/x86_64-linux-gnu/libwebp.so.6 > (0x00007f6be29bb000) > libzstd.so.1 => /usr/lib/x86_64-linux-gnu/libzstd.so.1 > (0x00007f6be2912000) > liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 > (0x00007f6be28e9000) > libjbig.so.0 => /usr/lib/x86_64-linux-gnu/libjbig.so.0 > (0x00007f6be26d9000) > libaec.so.0 => /usr/lib/x86_64-linux-gnu/libaec.so.0 > (0x00007f6be26d0000) > > Based on the xmipp doc > <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> > : > "In addition, if hdf5 is not found there, Xmipp will look for it > in /usr/lib and /usr/include/hdf5/serial. If found it, the paths > are appended to the INCDIRFLAGS and LIBDIRFLAGS. If not found and > a specific conda environ is present, Xmipp will try to install > hdf5 through conda under the current conda-environ." > > Not sure if conda hdf5 version can be fixed? > > On 11/3/22 1:49, Thu Nguyen wrote: > > Hi Scipion experts ! > > I administer a cluster built with Centos 7. The cluster has > scipion2 and users want to have scipion3 installed, mainly to > use the topography plugins. > > I followed the instructions and have Scipion3 core installed > fine, but when it comes to building xmipp, I always have this > error: > > libXmipp.so: undefined reference to `non-virtual > thunk to H5::H5File::throwException … > > I guess it relates to hdf5. I do have hdf5 and hdf5-devel > install via yum, and make sure than ‘conda list’ does not have > any hdf5 installed, but it makes no differences. > > As centos 7 has them up to version 1.8.12 only, I wonder if > this is the cause of the problem. I seem to have read > somewhere that xmipp requires at least hdf5 1.10.4 but could > not confirm it. > > I hope anyone has a solution for this. Being a cluster, I do > not have the freedom as stand-alone servers: whatever changes > has to be implemented on all the nodes. > > FYI, I have tried gcc 7.2.0 and 8.5.0, cuda 10,11 , they made > no differences. Installing hdf5 in conda (different versions) > also made no difference as well. > > Thank you all in advance > > *----------------------------------------------------------------------------------------------------------------* > > *Thu D. Nguyen* > > Bio21 Institute > > The University of Melbourne, Victoria 3010 Australia > > > > > _______________________________________________ > > scipion-users mailing list > > sci...@li... > > https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- - Alberto GM - |
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From: Grigory S. <sha...@gm...> - 2022-03-14 13:53:13
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Hi Thu, Have you tried adding correct hdf5 paths to INCDIRFLAGS and LIBDIRFLAGS in xmipp.conf? 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 Mon, Mar 14, 2022 at 1:47 AM Thu Nguyen <t.n...@un...> wrote: > Thank you Pablo for your help, > > > > With your hints, I went ahead and install hdf5 and hdf5-dev version 1.10.4 > from a 3rd party repo (Springdale computational, Princeton), having to > remove the centos’ 1.8.12 in the process. I did try conda install hdf5 > with the same version as well, but this alone is not enough as it seems to > need hdf5-dev > > > > The build could not find the new package at first, even after my attempt > to add PATH and LD_LIBRARY_PATH; however I was able to add its include and > the lib64 manually into xmipp.conf, then rerun (after export > XMIPP_NOCONFIG=True). > > > > The compiling seems to go further on, but then failed again with the same > error. > > > > /opt/gnu/gcc/bin/g++ -o bin/xmipp_micrograph_automatic_picking -flto > applications/programs/micrograph_automatic_picking/micrograph_automatic_picking_main.o > -L/share/apps/scipion3/software/em/xmippSrc-v3.22.01.0/src/xmippCore/lib > -Llib -Llib -L/usr/local/hdf5/gcc/1.10.4/lib64 > -L/share/apps/anaconda3/envs/scipion3/lib > -L/usr/local/hdf5/gcc/1.10.4/lib64 -L/opt/cuda_10.2.89/lib64 > -L/opt/gnu/gcc/lib64 -L/opt/gnu/gmp/lib -L/opt/gnu/mpfr/lib > -L/opt/gnu/mpc/lib -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' > > > > I am a bit lost here, hoping for more hints. > > > > PS Scipion seems to be able to install other plugins with little problem, > it’s just xmipp3 that is the pain. > > > > > > > *----------------------------------------------------------------------------------------------------------------* > > *Thu D. Nguyen* > > > > Bio21 Institute > > The University of Melbourne, Victoria 3010 Australia > > > > > > *From:* Pablo Conesa <pc...@cn...> > *Sent:* Saturday, 12 March 2022 2:12 AM > *To:* Mailing list for Scipion users <sci...@li...>; > Thu Nguyen <t.n...@un...> > *Subject:* [EXT] Re: [scipion-users] Problem compiling xmipp in Scipion3 > on Centos 7 cluster > > > > *External email: *Please exercise caution > > > ------------------------------ > > Dear Thu! > > I soon (I hope) some Xmipp developer will give a better answer. > > All I can say is that in my case it is linked to a system hdf5 lib, seems > to be happy with v 10.3: > > pablo@youyou:~/software/scipion/software/lib$ ldd libXmippCore.so > linux-vdso.so.1 (0x00007ffe5a1e9000) > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 > (0x00007f6be37c7000) > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6be3678000) > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6be3486000) > libfftw3.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3.so.3 > (0x00007f6be3280000) > libfftw3_threads.so.3 => > /usr/lib/x86_64-linux-gnu/libfftw3_threads.so.3 (0x00007f6be3276000) > libhdf5_serial.so.103 => > /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103 (0x00007f6be2ef9000) > libhdf5_cpp.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103 > (0x00007f6be2e7a000) > libtiff.so.5 => /usr/lib/x86_64-linux-gnu/libtiff.so.5 > (0x00007f6be2df9000) > libjpeg.so.8 => /usr/lib/x86_64-linux-gnu/libjpeg.so.8 > (0x00007f6be2d74000) > libsqlite3.so.0 => /usr/lib/x86_64-linux-gnu/libsqlite3.so.0 > (0x00007f6be2c4b000) > libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 > (0x00007f6be2a69000) > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 > (0x00007f6be2a4e000) > /lib64/ld-linux-x86-64.so.2 (0x00007f6be4046000) > libsz.so.2 => /usr/lib/x86_64-linux-gnu/libsz.so.2 (0x00007f6be2a47000) > libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f6be2a2b000) > libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f6be2a25000) > libwebp.so.6 => /usr/lib/x86_64-linux-gnu/libwebp.so.6 > (0x00007f6be29bb000) > libzstd.so.1 => /usr/lib/x86_64-linux-gnu/libzstd.so.1 > (0x00007f6be2912000) > liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007f6be28e9000) > libjbig.so.0 => /usr/lib/x86_64-linux-gnu/libjbig.so.0 > (0x00007f6be26d9000) > libaec.so.0 => /usr/lib/x86_64-linux-gnu/libaec.so.0 > (0x00007f6be26d0000) > > > > Based on the xmipp doc > <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> : > "In addition, if hdf5 is not found there, Xmipp will look for it in > /usr/lib and /usr/include/hdf5/serial. If found it, the paths are appended > to the INCDIRFLAGS and LIBDIRFLAGS. If not found and a specific conda > environ is present, Xmipp will try to install hdf5 through conda under the > current conda-environ." > > Not sure if conda hdf5 version can be fixed? > > On 11/3/22 1:49, Thu Nguyen wrote: > > > > Hi Scipion experts ! > > > > I administer a cluster built with Centos 7. The cluster has scipion2 and > users want to have scipion3 installed, mainly to use the topography plugins. > > > > I followed the instructions and have Scipion3 core installed fine, but > when it comes to building xmipp, I always have this error: > > > > libXmipp.so: undefined reference to `non-virtual thunk to > H5::H5File::throwException … > > > > I guess it relates to hdf5. I do have hdf5 and hdf5-devel install via > yum, and make sure than ‘conda list’ does not have any hdf5 installed, but > it makes no differences. > > > > As centos 7 has them up to version 1.8.12 only, I wonder if this is the > cause of the problem. I seem to have read somewhere that xmipp requires at > least hdf5 1.10.4 but could not confirm it. > > > > I hope anyone has a solution for this. Being a cluster, I do not have the > freedom as stand-alone servers: whatever changes has to be implemented on > all the nodes. > > > > FYI, I have tried gcc 7.2.0 and 8.5.0, cuda 10,11 , they made no > differences. Installing hdf5 in conda (different versions) also made no > difference as well. > > > > Thank you all in advance > > > > > > > *----------------------------------------------------------------------------------------------------------------* > > *Thu D. Nguyen* > > > > Bio21 Institute > > The University of Melbourne, Victoria 3010 Australia > > > > > > > > > > > _______________________________________________ > > scipion-users mailing list > > sci...@li... > > https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Thu N. <t.n...@un...> - 2022-03-14 01:46:58
|
Thank you Pablo for your help,
With your hints, I went ahead and install hdf5 and hdf5-dev version 1.10.4 from a 3rd party repo (Springdale computational, Princeton), having to remove the centos’ 1.8.12 in the process. I did try conda install hdf5 with the same version as well, but this alone is not enough as it seems to need hdf5-dev
The build could not find the new package at first, even after my attempt to add PATH and LD_LIBRARY_PATH; however I was able to add its include and the lib64 manually into xmipp.conf, then rerun (after export XMIPP_NOCONFIG=True).
The compiling seems to go further on, but then failed again with the same error.
/opt/gnu/gcc/bin/g++ -o bin/xmipp_micrograph_automatic_picking -flto applications/programs/micrograph_automatic_picking/micrograph_automatic_picking_main.o -L/share/apps/scipion3/software/em/xmippSrc-v3.22.01.0/src/xmippCore/lib -Llib -Llib -L/usr/local/hdf5/gcc/1.10.4/lib64 -L/share/apps/anaconda3/envs/scipion3/lib -L/usr/local/hdf5/gcc/1.10.4/lib64 -L/opt/cuda_10.2.89/lib64 -L/opt/gnu/gcc/lib64 -L/opt/gnu/gmp/lib -L/opt/gnu/mpfr/lib -L/opt/gnu/mpc/lib -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'
I am a bit lost here, hoping for more hints.
PS Scipion seems to be able to install other plugins with little problem, it’s just xmipp3 that is the pain.
----------------------------------------------------------------------------------------------------------------
Thu D. Nguyen
Bio21 Institute
The University of Melbourne, Victoria 3010 Australia
From: Pablo Conesa <pc...@cn...>
Sent: Saturday, 12 March 2022 2:12 AM
To: Mailing list for Scipion users <sci...@li...>; Thu Nguyen <t.n...@un...>
Subject: [EXT] Re: [scipion-users] Problem compiling xmipp in Scipion3 on Centos 7 cluster
External email: Please exercise caution
________________________________
Dear Thu!
I soon (I hope) some Xmipp developer will give a better answer.
All I can say is that in my case it is linked to a system hdf5 lib, seems to be happy with v 10.3:
pablo@youyou:~/software/scipion/software/lib$ ldd libXmippCore.so
linux-vdso.so.1 (0x00007ffe5a1e9000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f6be37c7000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6be3678000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6be3486000)
libfftw3.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3.so.3 (0x00007f6be3280000)
libfftw3_threads.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3_threads.so.3 (0x00007f6be3276000)
libhdf5_serial.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103 (0x00007f6be2ef9000)
libhdf5_cpp.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103 (0x00007f6be2e7a000)
libtiff.so.5 => /usr/lib/x86_64-linux-gnu/libtiff.so.5 (0x00007f6be2df9000)
libjpeg.so.8 => /usr/lib/x86_64-linux-gnu/libjpeg.so.8 (0x00007f6be2d74000)
libsqlite3.so.0 => /usr/lib/x86_64-linux-gnu/libsqlite3.so.0 (0x00007f6be2c4b000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f6be2a69000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f6be2a4e000)
/lib64/ld-linux-x86-64.so.2 (0x00007f6be4046000)
libsz.so.2 => /usr/lib/x86_64-linux-gnu/libsz.so.2 (0x00007f6be2a47000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f6be2a2b000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f6be2a25000)
libwebp.so.6 => /usr/lib/x86_64-linux-gnu/libwebp.so.6 (0x00007f6be29bb000)
libzstd.so.1 => /usr/lib/x86_64-linux-gnu/libzstd.so.1 (0x00007f6be2912000)
liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007f6be28e9000)
libjbig.so.0 => /usr/lib/x86_64-linux-gnu/libjbig.so.0 (0x00007f6be26d9000)
libaec.so.0 => /usr/lib/x86_64-linux-gnu/libaec.so.0 (0x00007f6be26d0000)
Based on the xmipp doc<https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> :
"In addition, if hdf5 is not found there, Xmipp will look for it in /usr/lib and /usr/include/hdf5/serial. If found it, the paths are appended to the INCDIRFLAGS and LIBDIRFLAGS. If not found and a specific conda environ is present, Xmipp will try to install hdf5 through conda under the current conda-environ."
Not sure if conda hdf5 version can be fixed?
On 11/3/22 1:49, Thu Nguyen wrote:
Hi Scipion experts !
I administer a cluster built with Centos 7. The cluster has scipion2 and users want to have scipion3 installed, mainly to use the topography plugins.
I followed the instructions and have Scipion3 core installed fine, but when it comes to building xmipp, I always have this error:
libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException …
I guess it relates to hdf5. I do have hdf5 and hdf5-devel install via yum, and make sure than ‘conda list’ does not have any hdf5 installed, but it makes no differences.
As centos 7 has them up to version 1.8.12 only, I wonder if this is the cause of the problem. I seem to have read somewhere that xmipp requires at least hdf5 1.10.4 but could not confirm it.
I hope anyone has a solution for this. Being a cluster, I do not have the freedom as stand-alone servers: whatever changes has to be implemented on all the nodes.
FYI, I have tried gcc 7.2.0 and 8.5.0, cuda 10,11 , they made no differences. Installing hdf5 in conda (different versions) also made no difference as well.
Thank you all in advance
----------------------------------------------------------------------------------------------------------------
Thu D. Nguyen
Bio21 Institute
The University of Melbourne, Victoria 3010 Australia
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users<https://lists.sourceforge.net/lists/listinfo/scipion-users>
--
Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team
|
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From: Pablo C. <pc...@cn...> - 2022-03-11 15:12:30
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Dear Thu! I soon (I hope) some Xmipp developer will give a better answer. All I can say is that in my case it is linked to a system hdf5 lib, seems to be happy with v 10.3: pablo@youyou:~/software/scipion/software/lib$ ldd libXmippCore.so linux-vdso.so.1 (0x00007ffe5a1e9000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f6be37c7000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6be3678000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6be3486000) libfftw3.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3.so.3 (0x00007f6be3280000) libfftw3_threads.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3_threads.so.3 (0x00007f6be3276000) libhdf5_serial.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103 (0x00007f6be2ef9000) libhdf5_cpp.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103 (0x00007f6be2e7a000) libtiff.so.5 => /usr/lib/x86_64-linux-gnu/libtiff.so.5 (0x00007f6be2df9000) libjpeg.so.8 => /usr/lib/x86_64-linux-gnu/libjpeg.so.8 (0x00007f6be2d74000) libsqlite3.so.0 => /usr/lib/x86_64-linux-gnu/libsqlite3.so.0 (0x00007f6be2c4b000) libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f6be2a69000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f6be2a4e000) /lib64/ld-linux-x86-64.so.2 (0x00007f6be4046000) libsz.so.2 => /usr/lib/x86_64-linux-gnu/libsz.so.2 (0x00007f6be2a47000) libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f6be2a2b000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f6be2a25000) libwebp.so.6 => /usr/lib/x86_64-linux-gnu/libwebp.so.6 (0x00007f6be29bb000) libzstd.so.1 => /usr/lib/x86_64-linux-gnu/libzstd.so.1 (0x00007f6be2912000) liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007f6be28e9000) libjbig.so.0 => /usr/lib/x86_64-linux-gnu/libjbig.so.0 (0x00007f6be26d9000) libaec.so.0 => /usr/lib/x86_64-linux-gnu/libaec.so.0 (0x00007f6be26d0000) Based on the xmipp doc <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> : "In addition, if hdf5 is not found there, Xmipp will look for it in /usr/lib and /usr/include/hdf5/serial. If found it, the paths are appended to the INCDIRFLAGS and LIBDIRFLAGS. If not found and a specific conda environ is present, Xmipp will try to install hdf5 through conda under the current conda-environ." Not sure if conda hdf5 version can be fixed? On 11/3/22 1:49, Thu Nguyen wrote: > > Hi Scipion experts ! > > I administer a cluster built with Centos 7. The cluster has scipion2 > and users want to have scipion3 installed, mainly to use the > topography plugins. > > I followed the instructions and have Scipion3 core installed fine, but > when it comes to building xmipp, I always have this error: > > libXmipp.so: undefined reference to `non-virtual thunk to > H5::H5File::throwException … > > I guess it relates to hdf5. I do have hdf5 and hdf5-devel install via > yum, and make sure than ‘conda list’ does not have any hdf5 installed, > but it makes no differences. > > As centos 7 has them up to version 1.8.12 only, I wonder if this is > the cause of the problem. I seem to have read somewhere that xmipp > requires at least hdf5 1.10.4 but could not confirm it. > > I hope anyone has a solution for this. Being a cluster, I do not have > the freedom as stand-alone servers: whatever changes has to be > implemented on all the nodes. > > FYI, I have tried gcc 7.2.0 and 8.5.0, cuda 10,11 , they made no > differences. Installing hdf5 in conda (different versions) also made > no difference as well. > > Thank you all in advance > > *----------------------------------------------------------------------------------------------------------------* > > *Thu D. Nguyen* > > Bio21 Institute > > The University of Melbourne, Victoria 3010 Australia > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Thu N. <t.n...@un...> - 2022-03-11 00:49:43
|
Hi Scipion experts !
I administer a cluster built with Centos 7. The cluster has scipion2 and users want to have scipion3 installed, mainly to use the topography plugins.
I followed the instructions and have Scipion3 core installed fine, but when it comes to building xmipp, I always have this error:
libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException ...
I guess it relates to hdf5. I do have hdf5 and hdf5-devel install via yum, and make sure than 'conda list' does not have any hdf5 installed, but it makes no differences.
As centos 7 has them up to version 1.8.12 only, I wonder if this is the cause of the problem. I seem to have read somewhere that xmipp requires at least hdf5 1.10.4 but could not confirm it.
I hope anyone has a solution for this. Being a cluster, I do not have the freedom as stand-alone servers: whatever changes has to be implemented on all the nodes.
FYI, I have tried gcc 7.2.0 and 8.5.0, cuda 10,11 , they made no differences. Installing hdf5 in conda (different versions) also made no difference as well.
Thank you all in advance
----------------------------------------------------------------------------------------------------------------
Thu D. Nguyen
Bio21 Institute
The University of Melbourne, Victoria 3010 Australia
|
|
From: Thu N. <t.n...@un...> - 2022-03-11 00:25:28
|
Hi Scipion experts !
I administer a cluster built with Centos 7. The cluster has scipion2 and users want to have scipion3 installed, mainly to use the topography plugins.
I followed the instructions and have Scipion3 core installed fine, but when it comes to building xmipp, I always have this error:
libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException ...
I guess it relates to hdf5. I do have hdf5 and hdf5-devel install via yum, and make sure than 'conda list' does not have any hdf5 installed, but it makes no differences.
As centos 7 has them up to version 1.8.12 only, I wonder if this is the cause of the problem. I seem to have read somewhere that xmipp requires at least hdf5 1.10.4 but could not confirm it.
I hope anyone has a solution for this. Being a cluster, I do not have the freedom as stand-alone servers: whatever changes has to be implemented on all the nodes.
FYI, I have tried gcc 7.2.0 and 8.5.0, cuda 10,11 , they made no differences
Thank you all in advance
----------------------------------------------------------------------------------------------------------------
Thu D. Nguyen
Bio21 Institute
The University of Melbourne, Victoria 3010 Australia
|
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From: 范宏成 <187...@16...> - 2022-03-08 09:20:58
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Thank you Pablo! The problem has been fixed according to your advice | | 范宏成 | | m18...@16... | 签名由网易邮箱大师定制 On 3/8/2022 16:22，Pablo Conesa<pc...@cn...> wrote： hi! I'd say you have some problems reaching the eman's download url. If this is the case, this may fail too: wget https://cryoem.bcm.edu/cryoem/static/software/release-2.31/eman2.31_sphire1.3.linux64.sh Does this work for you?: https://cryoem.bcm.edu/cryoem/static/software/release-2.31/eman2.31_sphire1.3.linux64.sh --no-check-certificate You can always install eman outside Scipion and let scipion know where it is -->https://scipion-em.github.io/docs/docs/scipion-modes/linking-existing-software.html On 8/3/22 9:10, 范宏成 wrote: Hi all, I recently intalled the eman2 into scipion3. I faced the followting these problems. How to fix it? Thank you! 00001: wget: /Customer/fanhc/eman2-sphire-sparx/lib/libuuid.so.1: no version information available (required by wget) 00002: --2022-03-08 03:06:11-- https://cryoem.bcm.edu/cryoem/static/software/release-2.31/eman2.31_sphire1.3.linux64.sh 00003: Resolving cryoem.bcm.edu (cryoem.bcm.edu)... 128.249.13.2 00004: Connecting to cryoem.bcm.edu (cryoem.bcm.edu)|128.249.13.2|:443... connected. 00005: ERROR: cannot verify cryoem.bcm.edu's certificate, issued by ‘/C=US/O=Let's Encrypt/CN=R3’: 00006: Issued certificate has expired. 00007: To connect to cryoem.bcm.edu insecurely, use `--no-check-certificate'. Hongcheng Fan _______________________________________________ scipion-users mailing list sci...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - Madrid Scipion team |
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From: Pablo C. <pc...@cn...> - 2022-03-08 08:22:40
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hi! I'd say you have some problems reaching the eman's download url. If this is the case, this may fail too: wget https://cryoem.bcm.edu/cryoem/static/software/release-2.31/eman2.31_sphire1.3.linux64.sh Does this work for you?: https://cryoem.bcm.edu/cryoem/static/software/release-2.31/eman2.31_sphire1.3.linux64.sh --no-check-certificate You can always install eman outside Scipion and let scipion know where it is -->https://scipion-em.github.io/docs/docs/scipion-modes/linking-existing-software.html On 8/3/22 9:10, 范宏成 wrote: > Hi all, > I recently intalled the eman2 into scipion3. I faced the followting > these problems. How to fix it? Thank you! > > > 00001: wget: /Customer/fanhc/eman2-sphire-sparx/lib/libuuid.so.1: no > version information available (required by wget) > 00002: --2022-03-08 03:06:11-- > https://cryoem.bcm.edu/cryoem/static/software/release-2.31/eman2.31_sphire1.3.linux64.sh > 00003: Resolving cryoem.bcm.edu (cryoem.bcm.edu)... 128.249.13.2 > 00004: Connecting to cryoem.bcm.edu > (cryoem.bcm.edu)|128.249.13.2|:443... connected. > 00005: ERROR: cannot verify cryoem.bcm.edu's certificate, issued by > ‘/C=US/O=Let's Encrypt/CN=R3’: > 00006: Issued certificate has expired. > 00007: To connect to cryoem.bcm.edu insecurely, use > `--no-check-certificate'. > > > Hongcheng Fan > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: 范宏成 <187...@16...> - 2022-03-08 08:11:03
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Hi all, I recently intalled the eman2 into scipion3. I faced the followting these problems. How to fix it? Thank you! 00001: wget: /Customer/fanhc/eman2-sphire-sparx/lib/libuuid.so.1: no version information available (required by wget) 00002: --2022-03-08 03:06:11-- https://cryoem.bcm.edu/cryoem/static/software/release-2.31/eman2.31_sphire1.3.linux64.sh 00003: Resolving cryoem.bcm.edu (cryoem.bcm.edu)... 128.249.13.2 00004: Connecting to cryoem.bcm.edu (cryoem.bcm.edu)|128.249.13.2|:443... connected. 00005: ERROR: cannot verify cryoem.bcm.edu's certificate, issued by ‘/C=US/O=Let's Encrypt/CN=R3’: 00006: Issued certificate has expired. 00007: To connect to cryoem.bcm.edu insecurely, use `--no-check-certificate'. Hongcheng Fan |
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From: Alberto G. M. <alb...@cn...> - 2022-02-21 13:20:03
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Good afternoon, From Scipion for facility we are updating the list of facilities using Scipion. Would you be so kind to check if your facility are included in this map <https://www.google.com/maps/d/viewer?mid=1MHEnnhBsUarOGJnlo0BapQrrGtA&ll=18.22935121090646%2C73.30078125&z=2> and is good clasiffied?. Please let us know through this list any update. Thank you very much -- - Alberto GM - |
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