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Re: [scipion-users] DeepLearning toolkit installation issue
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From: Carlos O. S. <co...@cn...> - 2021-04-16 06:28:30
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It does now. It is in the development branch, you may have access to it if you install Xmipp from sources. Cheers, Carlos Oscar El 16/04/2021 a las 8:00, David Maluenda escribió: > Yes, that's the problem. Xmipp is not installed since it is not > supporting cuda11. > > To install cuda10, please check nvidia webpage. Then localize where > cuda10 is installed (usually in |/usr/local/cuda10|). > > You can leave cuda11 as default on the system, while setting cuda10 > just for xmipp. There are two possibilities to do that: > > 1. If <SCIPION_HOME>/config/scipion.conf exists, edit it to add > > |XMIPP_CUDA_BIN=/usr/local/cuda10/bin > XMIPP_CUDA_LIB=/usr/local/cuda10/lib | > > and try again. If it does not exist, you can create it with just these > two lines. > > 2. Alternatively, without editing the config file, you can run the > following > > |export XMIPP_CUDA_BIN=/usr/local/cuda10/bin export > XMIPP_CUDA_LIB=/usr/local/cuda10/lib scipion3 installb xmippSrc | > > check your cuda-bin and cuda-lib paths. > > > > *_____ > Dr. David Maluenda Niubó* > dma...@ub... <mailto:dma...@ub...> - (+34) 619 029 310 > Wavefront Engineering Group > <https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA> > Applied Physics - UB <https://www.ub.edu/portal/web/dp-fisica-aplicada> > > This email message and any documents attached to it may contain > confidential or legally protected material and are intended solely for > the use of the individual or organization to whom they are addressed. > We remind you that if you are not the intended recipient of this email > message or the person responsible for processing it, then you are not > authorized to read, save, modify, send, copy or disclose any of its > contents. If you have received this email message by mistake, we > kindly ask you to inform the sender of this and to eliminate both the > message and any attachments it carries from your account. Thank you > for your collaboration. > > > > On Thu, Apr 15, 2021 at 11:18 PM Grigory Sharov > <sha...@gm... <mailto:sha...@gm...>> wrote: > > Hi Dmitry, > > xmipp does not support cuda 11 yet. You need to use cuda 10 or older. > > 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... <mailto:gs...@mr...> > > > On Thu, Apr 15, 2021 at 3:46 PM Dmitry Semchonok > <Sem...@gm... <mailto:Sem...@gm...>> wrote: > > Dear David, > > I did the steps and got the following error: > > > [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 > installb xmippSrc -j 8 > Scipion v3.0.7 - Eugenius > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in > Scipion plugin manager window) > > > Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' > Building xmippSrc-3.20.07 ... > Skipping command: wget -nv -c -O > /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz > <http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz> > mv -v > /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz.part > /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07.tgz > All targets exist. > Skipping command: tar -xf xmippSrc-v3.20.07.tgz > All targets exist. > cd /home/user/Data/Software/Scipion3/software/em/xmippSrc-v3.20.07 > cd . && ./xmipp config noAsk && ./xmipp check_config && > ./xmipp compileAndInstall N=8 && ln -srfn build > /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && > touch installation_finished && rm bindings_linked 2> /dev/null > Configuring ----------------------------------------- > gcc detected > g++ -c -w -mtune=native -march=native -std=c++11 -O3 > xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ > -I/home/user/.conda/envs/.scipion3env/include > g++ -w -mtune=native -march=native -std=c++11 -O3 > xmipp_test_opencv.cpp -o xmipp_test_opencv -I../ > -I/home/user/.conda/envs/.scipion3env/include > ./xmipp_test_opencv > g++ -c -w -mtune=native -march=native -std=c++11 -O3 > xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ > -I/home/user/.conda/envs/.scipion3env/include > OPENCV-2 detected without CUDA support > rm -v xmipp_test_opencv* > 'mpirun' detected. > 'mpicc' detected. > 'mpicxx' detected. > Java detected at: > /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.282.b08-1.el7_9.x86_64 > Traceback (most recent call last): > File "./xmipp", line 1794, in <module> > configDict = config() > File "./xmipp", line 1151, in config > configCuda(new_config_dict) > File "./xmipp", line 942, in configCuda > nvccVersion, nvccFullVersion = getCudaVersion(nvcc) > File "./xmipp", line 1655, in getCudaVersion > nvccVersion = float(str(tokens[0] + '.' + tokens[1])) > ValueError: could not convert string to float: 'Build > cuda_11.0_bu' > Traceback (most recent call last): > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", > line 457, in <module> > main() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", > line 297, in main > installPluginMethods() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 259, in installPluginMethods > pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && > ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln > -srfn build > /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && > touch installation_finished && rm bindings_linked 2> /dev/null') > Error at main: target > '/home/user/Data/Software/Scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && > ./xmipp check_config && ./xmipp compileAndInstall N=8 && ln > -srfn build > /home/user/Data/Software/Scipion3/software/em/xmipp && cd - && > touch installation_finished && rm bindings_linked 2> /dev/null') > > [user@dataanalysisserver1 xmippSrc-v3.20.07]$rm -rf > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit > [user@dataanalysisserver1 xmippSrc-v3.20.07]$ scipion3 > installb deepLearningToolkit > Scipion v3.0.7 - Eugenius > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in > Scipion plugin manager window) > > > Error retrieving plugin locscale binaries: 'SCIPION_MPI_FLAGS' > Building deepLearningToolkit-0.2 ... > Skipping command: wget -nv -c -O > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.parthttp://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz > <http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz> > mv -v > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz > All targets exist. > cd /home/user/Data/Software/Scipion3/software/em > tar -xf deepLearningToolkit.tgz > cd > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit > if ls > /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > > /dev/null ; then touch xmippLibToken; echo ' > CUDA support > find. Driver version: 460' ; else echo ; echo ' > Xmipp > installation not found, please install it first (xmippSrc or > xmippBin*).';echo; fi > ls: cannot access > /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so: > No such file or directory > > > Xmipp installation not found, please install it first > (xmippSrc or xmippBin*). > > Traceback (most recent call last): > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", > line 457, in <module> > main() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", > line 297, in main > installPluginMethods() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 259, in installPluginMethods > pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' > not built (after running 'if ls > /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > > /dev/null ; then touch xmippLibToken; echo ' > CUDA support > find. Driver version: 460' ; else echo ; echo ' > Xmipp > installation not found, please install it first (xmippSrc or > xmippBin*).';echo; fi') > Error at main: target > '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmippLibToken' > not built (after running 'if ls > /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > > /dev/null ; then touch xmippLibToken; echo ' > CUDA support > find. Driver version: 460' ; else echo ; echo ' > Xmipp > installation not found, please install it first (xmippSrc or > xmippBin*).';echo; fi') > > > Am I doing something wrong? > > Thank you > > Sincerely, > Dmitry > > > > >> On 15. Apr 2021, at 16:02, David Maluenda <dma...@ub... >> <mailto:dma...@ub...>> wrote: >> >> Hi Dimitry, >> >> It seems like Xmipp is not installed yet. >> >> I recommend you the following: >> >> scipion3 installb xmippSrc -j 8 >> rm >> -rf /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >> scipion3 installb deepLearningToolkit >> >> >> Hope it helps, >> >> *_____* >> *Dr. David Maluenda Niubó* >> dma...@ub... <mailto:dma...@ub...> - (+34) 619 029 310 >> Wavefront Engineering Group >> <https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA> >> Applied Physics - UB >> <https://www.ub.edu/portal/web/dp-fisica-aplicada> >> >> This email message and any documents attached to it may >> contain confidential or legally protected material and are >> intended solely for the use of the individual or organization >> to whom they are addressed. We remind you that if you are not >> the intended recipient of this email message or the person >> responsible for processing it, then you are not authorized to >> read, save, modify, send, copy or disclose any of its >> contents. If you have received this email message by mistake, >> we kindly ask you to inform the sender of this and to >> eliminate both the message and any attachments it carries >> from your account. Thank you for your collaboration. >> >> >> >> >> >> On Thu, Apr 15, 2021 at 1:41 PM Dmitry Semchonok >> <Sem...@gm... <mailto:Sem...@gm...>> wrote: >> >> Dear colleagues, >> >> >> I received an error while trying to install DeepLearning >> toolkit on our server PC from the commandline >> >> >> >> scipion3 installb deepLearningToolkit >> >> Scipion v3.0.7 - Eugenius >> >> >> >>> WARNING: Image library not found! >> >> > Please install Xmipp to get full functionality. >> >> (Configuration->Plugins->scipion-em-xmipp -> expand, in >> Scipion plugin manager window) >> >> >> Error retrieving plugin locscale binaries:'SCIPION_MPI_FLAGS' >> >> Building deepLearningToolkit-0.2 ... >> >> Skipping command: wget -nv -c -O >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.parthttp://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz >> <http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz> >> >> mv -v >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz >> >> All targets exist. >> >> Skipping command: tar -xf deepLearningToolkit.tgz >> >> All targets exist. >> >> Skipping command: if ls >> /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so >> > /dev/null ; then touch xmippLibToken; echo ' > CUDA >> support find. Driver version: 460' ; else echo ; echo ' > >> Xmipp installation not found, please install it first >> (xmippSrc or xmippBin*).';echo; fi >> >> All targets exist. >> >> cd >> /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit >> >> echo "Some error occurred when importing xmipp_base (from >> Xmipp binding): No module named 'xmipp_base'" >> >> Some error occurred when importing xmipp_base (from Xmipp >> binding): No module named 'xmipp_base' >> >> Traceback (most recent call last): >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >> line 457, in <module> >> >> main() >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", >> line 297, in main >> >> installPluginMethods() >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", >> line 259, in installPluginMethods >> >> pinfo.installBin({'args': [binTarget, '-j', >> numberProcessor]}) >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >> line 166, in installBin >> >> environment.execute() >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 748, in execute >> >> self._executeTargets(targetList) >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 690, in _executeTargets >> >> tgt.execute() >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 221, in execute >> >> command.execute() >> >> File >> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 161, in execute >> >> assert glob(t), ("target '%s' not built (after " >> >> AssertionError: target >> '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' >> not built (after running 'echo "Some error occurred when >> importing xmipp_base (from Xmipp binding): No module >> named 'xmipp_base'"') >> >> Error at main: target >> '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/void.target.yml' >> not built (after running 'echo "Some error occurred when >> importing xmipp_base (from Xmipp binding): No module >> named 'xmipp_base'"') >> >> >> Any options? >> >> >> Thank you! >> >> >> Sincerely, >> >> Dmitry >> >> >> >> >> Aquest missatge, i els fitxers adjunts que hi pugui >> haver, pot contenir informació confidencial o protegida >> legalment i s’adreça exclusivament a la persona o entitat >> destinatària. Si no consteu com a destinatari final o no >> teniu l’encàrrec de rebre’l, no esteu autoritzat a >> llegir-lo, retenir-lo, modificar-lo, distribuir-lo, >> copiar-lo ni a revelar-ne el contingut. Si l’heu rebut >> per error, informeu-ne el remitent i elimineu del sistema >> tant el missatge com els fitxers adjunts que hi pugui haver. >> >> Este mensaje, y los ficheros adjuntos que pueda incluir, >> puede contener información confidencial o legalmente >> protegida y está exclusivamente dirigido a la persona o >> entidad destinataria. Si usted no consta como >> destinatario final ni es la persona encargada de >> recibirlo, no está autorizado a leerlo, retenerlo, >> modificarlo, distribuirlo o copiarlo, ni a revelar su >> contenido. Si lo ha recibido por error, informe de ello >> al remitente y elimine del sistema tanto el mensaje como >> los ficheros adjuntos que pueda contener. >> >> This email message and any attachments it carries may >> contain confidential or legally protected material and >> are intended solely for the individual or organization to >> whom they are addressed. If you are not the intended >> recipient of this message or the person responsible for >> processing it, then you are not authorized to read, save, >> modify, send, copy or disclose any part of it. If you >> have received the message by mistake, please inform the >> sender of this and eliminate the message and any >> attachments it carries from your account. >> >> _______________________________________________ >> 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> >> >> >> >> Aquest missatge, i els fitxers adjunts que hi pugui haver, >> pot contenir informació confidencial o protegida legalment i >> s’adreça exclusivament a la persona o entitat destinatària. >> Si no consteu com a destinatari final o no teniu l’encàrrec >> de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, >> modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el >> contingut. Si l’heu rebut per error, informeu-ne el remitent >> i elimineu del sistema tant el missatge com els fitxers >> adjunts que hi pugui haver. >> >> Este mensaje, y los ficheros adjuntos que pueda incluir, >> puede contener información confidencial o legalmente >> protegida y está exclusivamente dirigido a la persona o >> entidad destinataria. Si usted no consta como destinatario >> final ni es la persona encargada de recibirlo, no está >> autorizado a leerlo, retenerlo, modificarlo, distribuirlo o >> copiarlo, ni a revelar su contenido. Si lo ha recibido por >> error, informe de ello al remitente y elimine del sistema >> tanto el mensaje como los ficheros adjuntos que pueda contener. >> >> This email message and any attachments it carries may contain >> confidential or legally protected material and are intended >> solely for the individual or organization to whom they are >> addressed. If you are not the intended recipient of this >> message or the person responsible for processing it, then you >> are not authorized to read, save, modify, send, copy or >> disclose any part of it. If you have received the message by >> mistake, please inform the sender of this and eliminate the >> message and any attachments it carries from your account. >> >> _______________________________________________ >> 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> > > _______________________________________________ > 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> > > > > Aquest missatge, i els fitxers adjunts que hi pugui haver, pot > contenir informació confidencial o protegida legalment i s’adreça > exclusivament a la persona o entitat destinatària. Si no consteu > com a destinatari final o no teniu l’encàrrec de rebre’l, no esteu > autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, > copiar-lo ni a revelar-ne el contingut. Si l’heu rebut per error, > informeu-ne el remitent i elimineu del sistema tant el missatge > com els fitxers adjunts que hi pugui haver. > > Este mensaje, y los ficheros adjuntos que pueda incluir, puede > contener información confidencial o legalmente protegida y está > exclusivamente dirigido a la persona o entidad destinataria. Si > usted no consta como destinatario final ni es la persona encargada > de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, > distribuirlo o copiarlo, ni a revelar su contenido. Si lo ha > recibido por error, informe de ello al remitente y elimine del > sistema tanto el mensaje como los ficheros adjuntos que pueda > contener. > > This email message and any attachments it carries may contain > confidential or legally protected material and are intended solely > for the individual or organization to whom they are addressed. If > you are not the intended recipient of this message or the person > responsible for processing it, then you are not authorized to > read, save, modify, send, copy or disclose any part of it. If you > have received the message by mistake, please inform the sender of > this and eliminate the message and any attachments it carries from > your account. > _______________________________________________ > 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> > > > > Aquest missatge, i els fitxers adjunts que hi pugui haver, pot > contenir informació confidencial o protegida legalment i s’adreça > exclusivament a la persona o entitat destinatària. Si no consteu com a > destinatari final o no teniu l’encàrrec de rebre’l, no esteu > autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, > copiar-lo ni a revelar-ne el contingut. Si l’heu rebut per error, > informeu-ne el remitent i elimineu del sistema tant el missatge com > els fitxers adjunts que hi pugui haver. > > Este mensaje, y los ficheros adjuntos que pueda incluir, puede > contener información confidencial o legalmente protegida y está > exclusivamente dirigido a la persona o entidad destinataria. Si usted > no consta como destinatario final ni es la persona encargada de > recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, > distribuirlo o copiarlo, ni a revelar su contenido. Si lo ha recibido > por error, informe de ello al remitente y elimine del sistema tanto el > mensaje como los ficheros adjuntos que pueda contener. > > This email message and any attachments it carries may contain > confidential or legally protected material and are intended solely for > the individual or organization to whom they are addressed. If you are > not the intended recipient of this message or the person responsible > for processing it, then you are not authorized to read, save, modify, > send, copy or disclose any part of it. If you have received the > message by mistake, please inform the sender of this and eliminate the > message and any attachments it carries from your account. > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
