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From: Alberto G. M. <alb...@cn...> - 2022-04-29 08:59:36
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Hi again, I tried to install xmipp in Ubuntu 22.04 from scratch and I get an error like "undefined reference to 'std::...". By default Ubuntu installed gcc-11 ( sudo apt build-essential). I installed gcc/g++-10, updated the symbolic links and removed and reinstalled libopenmpi-dev. After that, I was able to install Xmipp successively. I hope that could help.|| || || On 29/4/22 7:45, Alberto Garcia Mena wrote: > > Hi Matt, > > Sorry to hear about the problems with your installation. Could you > share with me the error message? To get more information; what version > of gcc/g++ are you running to install Xmipp?, or what is the default > used by your machine? (gcc --version; g++ --version) > > On 28/4/22 22:36, Matt Harrington via scipion-users wrote: >> >> I get strange linker errors when building xmipp via Scipion in Ubuntu >> 22.04. The linker isn't finding portions of the C++ standard library >> for some reason. I see documentation about some linker problems >> arising when using HDF libraries, but I wasn't able to get it working >> by following the guidance. Unsure how HDF issues would affect >> finding the standard library. Since we're in a hurry to get this >> system back into production, I'll revert to Ubuntu 20.04 for now. >> >> Matt >> >> On Thu, Apr 28, 2022 at 5:20 AM Alberto Garcia Mena >> <alb...@cn...> wrote: >> >> Hi Matt, >> >> Yes, Xmipp runs with gcc 11 and older. CUDA has a compiler >> limitations and Xmipp manage it (telling if you need a newer >> version of the compiler). You can also check these >> compatililitieshttps://gist.github.com/ax3l/9489132 >> >> Best regards >> >> On 28/4/22 9:15, Pablo Conesa wrote: >>> >>> Hi Matt, Scipion3 is being recently installed in laptops here >>> with ubuntu 22.04. So it is possible. >>> >>> The actual dependency for gcc is to compile Xmipp. >>> >>> I've looked at the detailed Xmipp configuration page >>> <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)#c-configuration> >>> and it doesn't explicitly mention the version although you are >>> right that in the past is being specified to be c++ 8. >>> >>> I'm sure someone from Xmipp will pop up to clarify how to >>> install Xmipp in ubuntu 22.04 LTS. >>> >>> All the best, Pablo. >>> >>> On 27/4/22 19:14, Matt Harrington via scipion-users wrote: >>>> >>>> Has Scipion been tested on Ubuntu 22.04? It's the new LTS >>>> release of Ubuntu which came out last week. >>>> >>>> I ask because GCC 8 does not appear to ship with 22.04, and the >>>> Scipion installation docs seem to hint that GCC 8 is required. >>>> Here's an excerpt from the docs: >>>> >>>> For Ubuntu: >>>> >>>> sudo apt-get install gcc-8 g++-8 libopenmpi-dev make >>>> >>>> >>>> Matt >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> -- >> - 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 > -- > - Alberto GM - > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- - Alberto GM - |
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From: Alberto G. M. <alb...@cn...> - 2022-04-29 05:45:17
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Hi Matt, Sorry to hear about the problems with your installation. Could you share with me the error message? To get more information; what version of gcc/g++ are you running to install Xmipp?, or what is the default used by your machine? (gcc --version; g++ --version) On 28/4/22 22:36, Matt Harrington via scipion-users wrote: > > I get strange linker errors when building xmipp via Scipion in Ubuntu > 22.04. The linker isn't finding portions of the C++ standard library > for some reason. I see documentation about some linker problems > arising when using HDF libraries, but I wasn't able to get it working > by following the guidance. Unsure how HDF issues would affect finding > the standard library. Since we're in a hurry to get this system back > into production, I'll revert to Ubuntu 20.04 for now. > > Matt > > On Thu, Apr 28, 2022 at 5:20 AM Alberto Garcia Mena > <alb...@cn...> wrote: > > Hi Matt, > > Yes, Xmipp runs with gcc 11 and older. CUDA has a compiler > limitations and Xmipp manage it (telling if you need a newer > version of the compiler). You can also check these > compatililitieshttps://gist.github.com/ax3l/9489132 > > Best regards > > On 28/4/22 9:15, Pablo Conesa wrote: >> >> Hi Matt, Scipion3 is being recently installed in laptops here >> with ubuntu 22.04. So it is possible. >> >> The actual dependency for gcc is to compile Xmipp. >> >> I've looked at the detailed Xmipp configuration page >> <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)#c-configuration> >> and it doesn't explicitly mention the version although you are >> right that in the past is being specified to be c++ 8. >> >> I'm sure someone from Xmipp will pop up to clarify how to install >> Xmipp in ubuntu 22.04 LTS. >> >> All the best, Pablo. >> >> On 27/4/22 19:14, Matt Harrington via scipion-users wrote: >>> >>> Has Scipion been tested on Ubuntu 22.04? It's the new LTS >>> release of Ubuntu which came out last week. >>> >>> I ask because GCC 8 does not appear to ship with 22.04, and the >>> Scipion installation docs seem to hint that GCC 8 is required. >>> Here's an excerpt from the docs: >>> >>> For Ubuntu: >>> >>> sudo apt-get install gcc-8 g++-8 libopenmpi-dev make >>> >>> >>> Matt >>> >>> >>> >>> _______________________________________________ >>> 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 > -- > - 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 -- - Alberto GM - |
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From: Matt H. <ma...@ms...> - 2022-04-28 20:36:28
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I get strange linker errors when building xmipp via Scipion in Ubuntu 22.04. The linker isn't finding portions of the C++ standard library for some reason. I see documentation about some linker problems arising when using HDF libraries, but I wasn't able to get it working by following the guidance. Unsure how HDF issues would affect finding the standard library. Since we're in a hurry to get this system back into production, I'll revert to Ubuntu 20.04 for now. Matt On Thu, Apr 28, 2022 at 5:20 AM Alberto Garcia Mena < alb...@cn...> wrote: > Hi Matt, > > Yes, Xmipp runs with gcc 11 and older. CUDA has a compiler limitations and > Xmipp manage it (telling if you need a newer version of the compiler). You > can also check these compatililities https://gist.github.com/ax3l/9489132 > > Best regards > On 28/4/22 9:15, Pablo Conesa wrote: > > Hi Matt, Scipion3 is being recently installed in laptops here with ubuntu > 22.04. So it is possible. > > The actual dependency for gcc is to compile Xmipp. > > I've looked at the detailed Xmipp configuration page > <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)#c-configuration> > and it doesn't explicitly mention the version although you are right that > in the past is being specified to be c++ 8. > > I'm sure someone from Xmipp will pop up to clarify how to install Xmipp in > ubuntu 22.04 LTS. > > All the best, Pablo. > On 27/4/22 19:14, Matt Harrington via scipion-users wrote: > > > Has Scipion been tested on Ubuntu 22.04? It's the new LTS release of > Ubuntu which came out last week. > > I ask because GCC 8 does not appear to ship with 22.04, and the Scipion > installation docs seem to hint that GCC 8 is required. Here's an excerpt > from the docs: > > For Ubuntu: > > sudo apt-get install gcc-8 g++-8 libopenmpi-dev make > > > Matt > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > - 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...> - 2022-04-28 12:19:52
|
Hi Matt, Yes, Xmipp runs with gcc 11 and older. CUDA has a compiler limitations and Xmipp manage it (telling if you need a newer version of the compiler). You can also check these compatililitieshttps://gist.github.com/ax3l/9489132 Best regards On 28/4/22 9:15, Pablo Conesa wrote: > > Hi Matt, Scipion3 is being recently installed in laptops here with > ubuntu 22.04. So it is possible. > > The actual dependency for gcc is to compile Xmipp. > > I've looked at the detailed Xmipp configuration page > <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)#c-configuration> > and it doesn't explicitly mention the version although you are right > that in the past is being specified to be c++ 8. > > I'm sure someone from Xmipp will pop up to clarify how to install > Xmipp in ubuntu 22.04 LTS. > > All the best, Pablo. > > On 27/4/22 19:14, Matt Harrington via scipion-users wrote: >> >> Has Scipion been tested on Ubuntu 22.04? It's the new LTS release of >> Ubuntu which came out last week. >> >> I ask because GCC 8 does not appear to ship with 22.04, and the >> Scipion installation docs seem to hint that GCC 8 is required. >> Here's an excerpt from the docs: >> >> For Ubuntu: >> >> sudo apt-get install gcc-8 g++-8 libopenmpi-dev make >> >> >> Matt >> >> >> >> _______________________________________________ >> 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 -- - Alberto GM - |
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From: Grigory S. <sha...@gm...> - 2022-04-28 09:59:15
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Hi Matt, can't say about Ubuntu, but on Scientific-Linux 7.9 xmipp does compile with gcc 10.2.0 and cuda 11.4 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 Thu, Apr 28, 2022 at 8:16 AM Pablo Conesa <pc...@cn...> wrote: > Hi Matt, Scipion3 is being recently installed in laptops here with ubuntu > 22.04. So it is possible. > > The actual dependency for gcc is to compile Xmipp. > > I've looked at the detailed Xmipp configuration page > <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)#c-configuration> > and it doesn't explicitly mention the version although you are right that > in the past is being specified to be c++ 8. > > I'm sure someone from Xmipp will pop up to clarify how to install Xmipp in > ubuntu 22.04 LTS. > > All the best, Pablo. > On 27/4/22 19:14, Matt Harrington via scipion-users wrote: > > > Has Scipion been tested on Ubuntu 22.04? It's the new LTS release of > Ubuntu which came out last week. > > I ask because GCC 8 does not appear to ship with 22.04, and the Scipion > installation docs seem to hint that GCC 8 is required. Here's an excerpt > from the docs: > > For Ubuntu: > > sudo apt-get install gcc-8 g++-8 libopenmpi-dev make > > > Matt > > > > _______________________________________________ > scipion-users mailing lis...@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: Pablo C. <pc...@cn...> - 2022-04-28 07:15:15
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Hi Matt, Scipion3 is being recently installed in laptops here with ubuntu 22.04. So it is possible. The actual dependency for gcc is to compile Xmipp. I've looked at the detailed Xmipp configuration page <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)#c-configuration> and it doesn't explicitly mention the version although you are right that in the past is being specified to be c++ 8. I'm sure someone from Xmipp will pop up to clarify how to install Xmipp in ubuntu 22.04 LTS. All the best, Pablo. On 27/4/22 19:14, Matt Harrington via scipion-users wrote: > > Has Scipion been tested on Ubuntu 22.04? It's the new LTS release of > Ubuntu which came out last week. > > I ask because GCC 8 does not appear to ship with 22.04, and the > Scipion installation docs seem to hint that GCC 8 is required. Here's > an excerpt from the docs: > > For Ubuntu: > > sudo apt-get install gcc-8 g++-8 libopenmpi-dev make > > > Matt > > > > _______________________________________________ > 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: Matt H. <ma...@ms...> - 2022-04-27 17:40:58
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Has Scipion been tested on Ubuntu 22.04? It's the new LTS release of Ubuntu which came out last week. I ask because GCC 8 does not appear to ship with 22.04, and the Scipion installation docs seem to hint that GCC 8 is required. Here's an excerpt from the docs: For Ubuntu: sudo apt-get install gcc-8 g++-8 libopenmpi-dev make Matt |
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From: Pablo C. <pc...@cn...> - 2022-04-27 16:31:02
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3.0.16 of scipion-em is out. regular scipion3 update should bring it. There is a cache mechanism, so it may not be detected until tomorrow. If you want to force it, remove the cached files: rm /tmp/outdated_cache_scipion-em CHANGES in this release are: V3.0.16 users: - Fixing an error calculating the FSC resolution value. - FSC plots legend shows "resolution" ;-) - Align movies protocols: possible outputs for even odd mics defined - Import volume: fix downloading some old EMD id not numeric - Hdf files can be open from the file browser - Adding the protocol "box size related parameters" to estimate the different parameters needed for various pickers. developers: - New method at pwem/convert/headers.setMRCSamplingRate: sets the sampling rate of an mrc file. Image Object has it: volume.setMRCSamplingRate(3.5) should work. - protocols.conf minimized only containing its own protocols All the best, Pablo On 27/4/22 8:42, Pablo Conesa wrote: > > Sure, I'll review what is in devel and make a release, hopefully today. > > On 26/4/22 19:17, Grigory Sharov wrote: >> Dear Matt, >> >> you are right, the latest motioncor2 plugin requires a new release of >> scipion-em (3.0.16) with required changes done on 19 March >> >> Pablo, could you make a release? >> >> 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 Tue, Apr 26, 2022 at 5:53 PM Matt Harrington via scipion-users >> <sci...@li...> wrote: >> >> On Tue, Apr 26, 2022 at 8:19 AM Matt Harrington >> <ma...@ms...> wrote: >> >> > It would make the SBGrid team's job easier if the working >> > version were tagged, perhaps as 3.0.11. Could the Scipion team do >> > that for us? >> >> 3.0.11 would not be the correct tag. I thought 3.0.10 was the >> latest, >> so I suggested 3.0.11, but I was only looking at scipion-app. >> >> I see 3.0.19 in scipion-pyworkflow. Does that version contain the >> fixes for the latest version of motioncor2? If not, could the team >> release 3.0.20 with those fixes? >> >> Matt >> >> >> _______________________________________________ >> 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 > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > _______________________________________________ > 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: Pablo C. <pc...@cn...> - 2022-04-27 06:42:36
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Sure, I'll review what is in devel and make a release, hopefully today. On 26/4/22 19:17, Grigory Sharov wrote: > Dear Matt, > > you are right, the latest motioncor2 plugin requires a new release of > scipion-em (3.0.16) with required changes done on 19 March > > Pablo, could you make a release? > > 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 Tue, Apr 26, 2022 at 5:53 PM Matt Harrington via scipion-users > <sci...@li...> wrote: > > On Tue, Apr 26, 2022 at 8:19 AM Matt Harrington > <ma...@ms...> wrote: > > > It would make the SBGrid team's job easier if the working > > version were tagged, perhaps as 3.0.11. Could the Scipion team do > > that for us? > > 3.0.11 would not be the correct tag. I thought 3.0.10 was the latest, > so I suggested 3.0.11, but I was only looking at scipion-app. > > I see 3.0.19 in scipion-pyworkflow. Does that version contain the > fixes for the latest version of motioncor2? If not, could the team > release 3.0.20 with those fixes? > > Matt > > > _______________________________________________ > 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 -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Grigory S. <sha...@gm...> - 2022-04-26 17:18:04
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Dear Matt, you are right, the latest motioncor2 plugin requires a new release of scipion-em (3.0.16) with required changes done on 19 March Pablo, could you make a release? 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, Apr 26, 2022 at 5:53 PM Matt Harrington via scipion-users < sci...@li...> wrote: > On Tue, Apr 26, 2022 at 8:19 AM Matt Harrington <ma...@ms...> wrote: > > > It would make the SBGrid team's job easier if the working > > version were tagged, perhaps as 3.0.11. Could the Scipion team do > > that for us? > > 3.0.11 would not be the correct tag. I thought 3.0.10 was the latest, > so I suggested 3.0.11, but I was only looking at scipion-app. > > I see 3.0.19 in scipion-pyworkflow. Does that version contain the > fixes for the latest version of motioncor2? If not, could the team > release 3.0.20 with those fixes? > > Matt > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Matt H. <ma...@ms...> - 2022-04-26 16:53:11
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On Tue, Apr 26, 2022 at 8:19 AM Matt Harrington <ma...@ms...> wrote: > It would make the SBGrid team's job easier if the working > version were tagged, perhaps as 3.0.11. Could the Scipion team do > that for us? 3.0.11 would not be the correct tag. I thought 3.0.10 was the latest, so I suggested 3.0.11, but I was only looking at scipion-app. I see 3.0.19 in scipion-pyworkflow. Does that version contain the fixes for the latest version of motioncor2? If not, could the team release 3.0.20 with those fixes? Matt |
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From: Matt H. <ma...@ms...> - 2022-04-26 16:23:27
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Hi Scipion team, I'm told that Scipion requires a fix to work with features in the latest version of motioncor2. Our specialists have been installing Scipion from GitHub using the latest commits. Instead of that, I'll request that the SBGrid team build a working version and push it out to us. It would make the SBGrid team's job easier if the working version were tagged, perhaps as 3.0.11. Could the Scipion team do that for us? Matt |
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From: Alberto G. M. <alb...@cn...> - 2022-04-21 13:40:58
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Dear all, XMIPP-Team have prepared the new version of Xmipp. Please welcome to *Xmipp 3.22.04-Gaia * For this version, we have updated more than 200 files and 10 protocols The main new features are these*.* <https://github.com/I2PC/xmipp/blob/devel/CHANGELOG.md>**Feel free toinstall it <https://github.com/I2PC/xmipp#standalone-installation>, test it, report any problems <https://github.com/I2PC/xmipp/issues> if they arise and above all enjoy it! Best Regards Xmipp-Team -- - Alberto GM - |
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From: Estrella F. G. <me....@cn...> - 2022-04-21 10:19:12
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Hi Diede, I thought you were already there, but not... sorry. I have just sent you an invitation to this email. Regards, Estrella Diede De-Haan <die...@we...> escribió: > Hi! > > Could you please add me to the slack (using this email address)? > > Thanks! > > Diede de Haan > > PhD Student, Assaf Gal Lab<http://www.weizmann.ac.il/plants/gal/> > Benoziyo Building of Biological Science, Room 573B > Department of Plant and Environmental Sciences > Weizmann Institute of Science > Rehovot, Israel > +972-58-452-6789 > +31-652-6789-42 |
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From: Kim, H. <Han...@Pe...> - 2022-04-20 21:24:22
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Hello! My name is Hannah and I am currently at Yi-Wei Chang's lab at the University of Pennsylvania. I would like to install the PySeg plugin for Scipion (3.0) on a computer running Centos 7, but I am running into an error involving conda initialization. First, there is a warning about the variable CONDA_ACTIVATION_CMD being undefined, and ultimately results in an CommandNotFoundError stating " Your shell has not been properly configured to use 'conda activate'." I tried the installation again by running both "conda init bash" and "conda activate pySeg-v2.0.4" first, but the error message is the same. Attached is the system output from running: "scipion installp -p ~/scipion-plugins/scipion-em-pyseg --devel." Furthermore, when I run Scipion now, the following error appears: > error when importing from pyseg.protocols: cannot import name 'SHIFTX' from 'reliontomo.constants' (/home/hannahkim/miniconda/envs/scipion3/lib/python3.8/site-packages/reliontomo/constants.py) File "/home/hannahkim/scipion-plugins/scipion-em-pyseg/pyseg/utils.py", line 34, in <module> Check the plugin manager (Configuration->Plugins in Scipion manager window) or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, it could be a versions compatibility issue. Do you have any advice for resolving this error? Thank you for your time, Hannah Kim |
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From: Lugmayr, W. <w.l...@uk...> - 2022-04-20 09:52:25
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Hi, can you check if the micrographs and the extraction job have the same float values e.g. float32 or float16? Otherwise relion extraction fails (at least in our 4.0-beta2 version). Cheers, Wolfgang From: "Marc Hsiao Lee" <mh...@ib...> To: "Mailing list for Scipion users" <sci...@li...> Sent: Tuesday, 19 April, 2022 18:13:28 Subject: [scipion-users] cento 7 scipion3 + relion I have problems, I think the plugin is installed well: I did it with the command line: scipion3 installp -p scipion-em-relion and I have the version: scipion-em-relion 4.0.2 [X] But when I do a job I get this error in run.stdout: and attached a log file of the error.stderr Thank you all in advance Any help will be appreciated -- [ https://www.ibmb.csic.es/en/ ] [ https://www.instagram.com/ibmb_csic_/ | ] [ https://www.youtube.com/channel/UCxIFUCBs2RKA1Mp_AXrrO7w/featured | ] Marcos H.Lee IBMB-CSIC E-mail: [ mailto:mh...@ib... | mh...@ib... ] _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Marc H. L. <mh...@ib...> - 2022-04-19 16:41:59
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I have problems, I think the plugin is installed well: I did it with the command line: scipion3 installp -p scipion-em-relion and I have the version: scipion-em-relion 4.0.2 [X] But when I do a job I get this error in run.stdout: [image: relion_1.png] and attached a log file of the error.stderr Thank you all in advance Any help will be appreciated -- <https://www.ibmb.csic.es/en/> <https://www.instagram.com/ibmb_csic_/> [image: youtube] <https://www.youtube.com/channel/UCxIFUCBs2RKA1Mp_AXrrO7w/featured> Marcos H.Lee IBMB-CSIC E-mail: mh...@ib... |
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From: Dmitry S. <sem...@gm...> - 2022-04-19 12:17:24
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hello James, Great news. Thank you! Kind regards, Dmitry > On 19. Apr 2022, at 13:36, James Krieger <jam...@gm...> wrote: > > Dear all, > > I am pleased to announce that we now have the first working version of the scipion-em-prody plugin (v3.0.3), linking Scipion to the ProDy Python package (v2.1.1) for protein dynamics analysis (http://prody.csb.pitt.edu/ <http://prody.csb.pitt.edu/>). > > So far, we have protocols and viewers for the following tasks: > - atom selection (using VMD-like commands as described at http://prody.csb.pitt.edu/manual/reference/atomic/select.html <http://prody.csb.pitt.edu/manual/reference/atomic/select.html>) > - atomic structure alignment based on Biopython sequence alignment and sequence- and structure-based chain matching > - anisotropic network model (ANM) normal mode analysis (NMA) > - deformation vector analysis for calculating transitions/differences between two structures > - motion visualisation with the VMD normal mode wizard (NMWiz) > - mode/vector editing tools to account for different numbers of atoms including residue-based slicing and extending, as well as the more physically meaningful Hessian reduction for vibrational-subsystem analysis > - importing of normal modes in Scipion format, the two main ProDy formats (nmd and npz), and Gromacs format > > You can see examples of these protocols in the test pipeline. > > Look out for more exciting tools, protocols and pipelines soon including Gaussian network model (GNM) analysis and ClustENM hybrid simulations! > > Best wishes > James > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: James K. <jam...@gm...> - 2022-04-19 11:36:44
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Dear all, I am pleased to announce that we now have the first working version of the scipion-em-prody plugin (v3.0.3), linking Scipion to the ProDy Python package (v2.1.1) for protein dynamics analysis (http://prody.csb.pitt.edu/ ). So far, we have protocols and viewers for the following tasks: - atom selection (using VMD-like commands as described at http://prody.csb.pitt.edu/manual/reference/atomic/select.html) - atomic structure alignment based on Biopython sequence alignment and sequence- and structure-based chain matching - anisotropic network model (ANM) normal mode analysis (NMA) - deformation vector analysis for calculating transitions/differences between two structures - motion visualisation with the VMD normal mode wizard (NMWiz) - mode/vector editing tools to account for different numbers of atoms including residue-based slicing and extending, as well as the more physically meaningful Hessian reduction for vibrational-subsystem analysis - importing of normal modes in Scipion format, the two main ProDy formats (nmd and npz), and Gromacs format You can see examples of these protocols in the test pipeline. Look out for more exciting tools, protocols and pipelines soon including Gaussian network model (GNM) analysis and ClustENM hybrid simulations! Best wishes James |
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From: Huabin Z. <Hua...@UT...> - 2022-04-15 15:36:02
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Dear all, I recently got scipion installed on our workstation, which configured with AMD 16-core processor, RTX3090 (cuda 11.2) and Ubuntu 20.04. After the installation, I run Xmipp tests on the medium and large scale without problems. However, I got the following errors when I process the partilces alignment in TomoFlow. Could you please tell me the potential culprit and how to solve it? Thank you so much! Run.stdout File 'Runs/000201_FlexProtSubtomogramAveraging/logs/run.stdout' doesn't existFile 'Runs/000201_FlexProtSubtomogramAveraging/logs/run.stdout' doesn't exist00001: Logging configured. STDOUT --> Runs/000201_FlexProtSubtomogramAveraging/logs/run.stdout , STDERR --> Runs/000201_FlexProtSubtomogramAveraging/logs/run.stderr 00002: RUNNING PROTOCOL ----------------- 00003: Protocol starts 00004: Hostname: alienware.dhcp.swmed.org 00005: PID: 76953 00006: pyworkflow: 3.0.19 00007: plugin: continuousflex 00008: plugin v: 3.1.4 00009: currentDir: /home/huabin/ScipionUserData/projects/test 00010: workingDir: Runs/000201_FlexProtSubtomogramAveraging 00011: runMode: Restart 00012: MPI: 5 00013: threads: 1 00014: Starting at step: 1 00015: Running steps 00016: STARTED: convertInputStep, step 1, time 2022-04-15 09:39:54.033455 00017: FINISHED: convertInputStep, step 1, time 2022-04-15 09:39:54.076001 00018: STARTED: doAlignmentStep, step 2, time 2022-04-15 09:39:54.080785 00019: tempdir is Runs/000201_FlexProtSubtomogramAveraging/tmp 00020: imgFn is Runs/000201_FlexProtSubtomogramAveraging/extra/volumes.xmd 00021: frm_freq is 0.25 00022: frm_maxshift is 10 00023: max_itr is 10 00024: iter_result is Runs/000201_FlexProtSubtomogramAveraging/extra/result.xmd 00025: reference is /home/huabin/software/scipion/test/rec.mrc 00026: mpirun -np 5 `which xmipp_mpi_volumeset_align` -i Runs/000201_FlexProtSubtomogramAveraging/extra/volumes.xmd -o Runs/000201_FlexProtSubtomogramAveraging/extra/params_itr_1.xmd --odir Runs/000201_FlexProtSubtomogramAveraging/tmp --resume --ref /home/huabin/software/scipion/test/rec.mrc --frm_parameters 0.250000 10 --tilt_values -60 60 00027: Input File: Runs/000201_FlexProtSubtomogramAveraging/extra/volumes.xmd 00028: Output File: Runs/000201_FlexProtSubtomogramAveraging/extra/params_itr_1.xmd 00029: Protocol failed: Command ' mpirun -np 5 `which xmipp_mpi_volumeset_align` -i Runs/000201_FlexProtSubtomogramAveraging/extra/volumes.xmd -o Runs/000201_FlexProtSubtomogramAveraging/extra/params_itr_1.xmd --odir Runs/000201_FlexProtSubtomogramAveraging/tmp --resume --ref /home/huabin/software/scipion/test/rec.mrc --frm_parameters 0.250000 10 --tilt_values -60 60 ' returned non-zero exit status 139. 00030: FAILED: doAlignmentStep, step 2, time 2022-04-15 09:39:54.731311 00031: *** Last status is failed 00032: ------------------- PROTOCOL FAILED (DONE 2/3) Run.stderr File 'Runs/000201_FlexProtSubtomogramAveraging/logs/run.stderr' doesn't existFile 'Runs/000201_FlexProtSubtomogramAveraging/logs/run.stderr' doesn't exist00001: Invalid MIT-MAGIC-COOKIE-1 key0000/???? sec. ------------------------------------------------------------Segmentation fault (core dumped) 00002: [alienware:77029] *** Process received signal *** 00003: [alienware:77029] Signal: Segmentation fault (11) 00004: [alienware:77029] Signal code: Address not mapped (1) 00005: [alienware:77029] Failing at address: 0xc0 00006: [alienware:77029] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x430c0)[0x7f86ae5460c0] 00007: [alienware:77029] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x63ac4)[0x7f86ae566ac4] 00008: [alienware:77029] [ 2] /lib/x86_64-linux-gnu/libc.so.6(__isoc99_fscanf+0x9d)[0x7f86ae56626d] 00009: [alienware:77029] [ 3] /home/huabin/software/scipion/software/em/xmipp/lib/libXmipp.so(_ZN18ProgVolumeSetAlign14computeFitnessEv+0x331)[0x7f86adf32c51] 00010: [alienware:77029] [ 4] /home/huabin/software/scipion/software/em/xmipp/lib/libXmipp.so(_ZN18ProgVolumeSetAlign12processImageERK8FileNameS2_RK5MDRowRS3_+0x63)[0x7f86adf32e93] 00011: [alienware:77029] [ 5] /home/huabin/software/scipion/software/em/xmipp/lib/libXmippCore.so(_ZN20XmippMetadataProgram3runEv+0x467)[0x7f86ad089ab7] 00012: [alienware:77029] [ 6] /home/huabin/software/scipion/software/em/xmipp/lib/libXmippCore.so(_ZN12XmippProgram6tryRunEv+0x2f)[0x7f86ad490aff] 00013: [alienware:77029] [ 7] /home/huabin/software/scipion/software/em/xmipp/bin/xmipp_mpi_volumeset_align(+0xbe22)[0x560db2ba9e22] 00014: [alienware:77029] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7f86ae5270b3] 00015: [alienware:77029] [ 9] /home/huabin/software/scipion/software/em/xmipp/bin/xmipp_mpi_volumeset_align(+0xbebe)[0x560db2ba9ebe] 00016: [alienware:77029] *** End of error message *** 00017: Segmentation fault (core dumped) 00018: [alienware:77030] *** Process received signal *** 00019: [alienware:77030] Signal: Segmentation fault (11) 00020: [alienware:77030] Signal code: Address not mapped (1) 00021: [alienware:77030] Failing at address: 0xc0 00022: [alienware:77030] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x430c0)[0x7f8cb06aa0c0] 00023: [alienware:77030] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x63ac4)[0x7f8cb06caac4] 00024: [alienware:77030] [ 2] /lib/x86_64-linux-gnu/libc.so.6(__isoc99_fscanf+0x9d)[0x7f8cb06ca26d] 00025: [alienware:77030] [ 3] /home/huabin/software/scipion/software/em/xmipp/lib/libXmipp.so(_ZN18ProgVolumeSetAlign14computeFitnessEv+0x331)[0x7f8cb0096c51] 00026: [alienware:77030] [ 4] /home/huabin/software/scipion/software/em/xmipp/lib/libXmipp.so(_ZN18ProgVolumeSetAlign12processImageERK8FileNameS2_RK5MDRowRS3_+0x63)[0x7f8cb0096e93] 00027: [alienware:77030] [ 5] /home/huabin/software/scipion/software/em/xmipp/lib/libXmippCore.so(_ZN20XmippMetadataProgram3runEv+0x467)[0x7f8caf1edab7] 00028: [alienware:77030] [ 6] /home/huabin/software/scipion/software/em/xmipp/lib/libXmippCore.so(_ZN12XmippProgram6tryRunEv+0x2f)[0x7f8caf5f4aff] 00029: [alienware:77030] [ 7] /home/huabin/software/scipion/software/em/xmipp/bin/xmipp_mpi_volumeset_align(+0xbe22)[0x55807f863e22] 00030: [alienware:77030] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7f8cb068b0b3] 00031: [alienware:77030] [ 9] /home/huabin/software/scipion/software/em/xmipp/bin/xmipp_mpi_volumeset_align(+0xbebe)[0x55807f863ebe] 00032: [alienware:77030] *** End of error message *** 00033: Segmentation fault (core dumped) 00034: [alienware:77031] *** Process received signal *** 00035: [alienware:77031] Signal: Segmentation fault (11) 00036: [alienware:77031] Signal code: Address not mapped (1) 00037: [alienware:77031] Failing at address: 0xc0 00038: [alienware:77031] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x430c0)[0x7f09b053b0c0] 00039: [alienware:77031] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x63ac4)[0x7f09b055bac4] 00040: [alienware:77031] [ 2] /lib/x86_64-linux-gnu/libc.so.6(__isoc99_fscanf+0x9d)[0x7f09b055b26d] 00041: [alienware:77031] [ 3] /home/huabin/software/scipion/software/em/xmipp/lib/libXmipp.so(_ZN18ProgVolumeSetAlign14computeFitnessEv+0x331)[0x7f09aff27c51] 00042: [alienware:77031] [ 4] /home/huabin/software/scipion/software/em/xmipp/lib/libXmipp.so(_ZN18ProgVolumeSetAlign12processImageERK8FileNameS2_RK5MDRowRS3_+0x63)[0x7f09aff27e93] 00043: [alienware:77031] [ 5] /home/huabin/software/scipion/software/em/xmipp/lib/libXmippCore.so(_ZN20XmippMetadataProgram3runEv+0x467)[0x7f09af07eab7] 00044: [alienware:77031] [ 6] /home/huabin/software/scipion/software/em/xmipp/lib/libXmippCore.so(_ZN12XmippProgram6tryRunEv+0x2f)[0x7f09af485aff] 00045: [alienware:77031] [ 7] /home/huabin/software/scipion/software/em/xmipp/bin/xmipp_mpi_volumeset_align(+0xbe22)[0x56074112de22] 00046: [alienware:77031] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7f09b051c0b3] 00047: [alienware:77031] [ 9] /home/huabin/software/scipion/software/em/xmipp/bin/xmipp_mpi_volumeset_align(+0xbebe)[0x56074112debe] 00048: [alienware:77031] *** End of error message *** 00049: Segmentation fault (core dumped) 00050: [alienware:77028] *** Process received signal *** 00051: [alienware:77028] Signal: Segmentation fault (11) 00052: [alienware:77028] Signal code: Address not mapped (1) 00053: [alienware:77028] Failing at address: 0xc0 00054: [alienware:77028] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x430c0)[0x7fdd913e40c0] 00055: [alienware:77028] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x63ac4)[0x7fdd91404ac4] 00056: [alienware:77028] [ 2] /lib/x86_64-linux-gnu/libc.so.6(__isoc99_fscanf+0x9d)[0x7fdd9140426d] 00057: [alienware:77028] [ 3] /home/huabin/software/scipion/software/em/xmipp/lib/libXmipp.so(_ZN18ProgVolumeSetAlign14computeFitnessEv+0x331)[0x7fdd90dd0c51] 00058: [alienware:77028] [ 4] /home/huabin/software/scipion/software/em/xmipp/lib/libXmipp.so(_ZN18ProgVolumeSetAlign12processImageERK8FileNameS2_RK5MDRowRS3_+0x63)[0x7fdd90dd0e93] 00059: [alienware:77028] [ 5] /home/huabin/software/scipion/software/em/xmipp/lib/libXmippCore.so(_ZN20XmippMetadataProgram3runEv+0x467)[0x7fdd8ff27ab7] 00060: [alienware:77028] [ 6] /home/huabin/software/scipion/software/em/xmipp/lib/libXmippCore.so(_ZN12XmippProgram6tryRunEv+0x2f)[0x7fdd9032eaff] 00061: [alienware:77028] [ 7] /home/huabin/software/scipion/software/em/xmipp/bin/xmipp_mpi_volumeset_align(+0xbe22)[0x56336bac0e22] 00062: [alienware:77028] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7fdd913c50b3] 00063: [alienware:77028] [ 9] /home/huabin/software/scipion/software/em/xmipp/bin/xmipp_mpi_volumeset_align(+0xbebe)[0x56336bac0ebe] 00064: [alienware:77028] *** End of error message *** 00065: -------------------------------------------------------------------------- 00066: Primary job terminated normally, but 1 process returned 00067: a non-zero exit code. Per user-direction, the job has been aborted. 00068: -------------------------------------------------------------------------- 00069: -------------------------------------------------------------------------- 00070: mpirun noticed that process rank 2 with PID 0 on node alienware exited on signal 11 (Segmentation fault). 00071: -------------------------------------------------------------------------- 00072: Traceback (most recent call last): 00073: File "/home/huabin/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 201, in run 00074: self._run() 00075: File "/home/huabin/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 252, in _run 00076: resultFiles = self._runFunc() 00077: File "/home/huabin/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _runFunc 00078: return self._func(*self._args) 00079: File "/home/huabin/software/scipion/scipion-em-continuousflex/continuousflex/protocols/protocol_subtomogram_averaging.py", line 238, in doAlignmentStep 00080: self.runJob("xmipp_volumeset_align", args % locals(), 00081: File "/home/huabin/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1441, in runJob 00082: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) 00083: File "/home/huabin/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob 00084: process.runJob(log, programName, params, 00085: File "/home/huabin/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob 00086: return runCommand(command, env, cwd) 00087: File "/home/huabin/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand 00088: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, 00089: File "/home/huabin/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call 00090: raise CalledProcessError(retcode, cmd) 00091: subprocess.CalledProcessError: Command ' mpirun -np 5 `which xmipp_mpi_volumeset_align` -i Runs/000201_FlexProtSubtomogramAveraging/extra/volumes.xmd -o Runs/000201_FlexProtSubtomogramAveraging/extra/params_itr_1.xmd --odir Runs/000201_FlexProtSubtomogramAveraging/tmp --resume --ref /home/huabin/software/scipion/test/rec.mrc --frm_parameters 0.250000 10 --tilt_values -60 60 ' returned non-zero exit status 139. 00092: Protocol failed: Command ' mpirun -np 5 `which xmipp_mpi_volumeset_align` -i Runs/000201_FlexProtSubtomogramAveraging/extra/volumes.xmd -o Runs/000201_FlexProtSubtomogramAveraging/extra/params_itr_1.xmd --odir Runs/000201_FlexProtSubtomogramAveraging/tmp --resume --ref /home/huabin/software/scipion/test/rec.mrc --frm_parameters 0.250000 10 --tilt_values -60 60 ' returned non-zero exit status 139. I tried to run it without mpi and the error is basically the same. Thank you! Huabin Zhou, Ph.D. Postdoctoral Researcher, Michael Rosen Lab Department of Biophysics UT Southwestern Medical Center ________________________________ UT Southwestern Medical Center The future of medicine, today. |
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From: Diede De-H. <die...@we...> - 2022-03-23 11:07:50
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Hi! Could you please add me to the slack (using this email address)? Thanks! Diede de Haan PhD Student, Assaf Gal Lab<http://www.weizmann.ac.il/plants/gal/> Benoziyo Building of Biological Science, Room 573B Department of Plant and Environmental Sciences Weizmann Institute of Science Rehovot, Israel +972-58-452-6789 +31-652-6789-42 |
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From: Pablo C. <pc...@cn...> - 2022-03-22 08:47:42
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That it going to be a challenge. All of the conda environments rely on having an internet connection to download and install the packages. We had the need to use an HPC cluster without internet and we struggle to make thing work. If you still need to go down this route here are some ideas: 1.- Do you have a similar machine but with internet connection? Maybe doing the installation there and moving later the conda environments may work? 2.- In theory all packages, at least "pip ones" can be downloaded and installed locally. If you do scipion3 installb deepLearningToolkit You should get all the commands needed to install deepLearningToolkit, see bellow. Scipion v3.0.10 - Eugenius Building deepLearningToolkit-0.2 ... Skipping command: *wget -nv -c -O /home/pablo/software/scipion/software/em/deepLearningToolkit.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz* mv -v /home/pablo/software/scipion/software/em/deepLearningToolkit.tgz.part /home/pablo/software/scipion/software/em/deepLearningToolkit.tgz All targets exist. Skipping command: tar -xf deepLearningToolkit.tgz All targets exist. cd /home/pablo/software/scipion/software/em/deepLearningToolkit if ls /home/pablo/software/scipion/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 510' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi > CUDA support find. Driver version: 510 Skipping command: export PYTHONPATH="" && eval "$(/extra/miniconda3/bin/conda shell.bash hook)" && *conda create --force --yes -n xmipp_DLTK_v0.3 python=3 pandas=0.23 scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 keras=2.2 scikit-learn=0.22 -c anaconda && conda activate xmipp_DLTK_v0.3 && pip install numpy==1.18.4 numpy==1.18.4 numpy==1.18.4* && conda env export > xmipp_DLTK_v0.3.yml All targets exist. Skipping command: export PYTHONPATH="" && eval "$(/extra/miniconda3/bin/conda shell.bash hook)" && *conda create --force --yes -n xmipp_MicCleaner python=3.6 micrograph-cleaner-em=0.35 -c rsanchez1369 -c anaconda -c conda-forge && conda activate xmipp_MicCleaner* && conda env export > xmipp_MicCleaner.yml All targets exist. Skipping command: export PYTHONPATH="" && eval "$(/extra/miniconda3/bin/conda shell.bash hook)" && *conda create --force --yes -n xmipp_deepEMhancer python=3.6 deepemhancer=0.12 numba=0.45 -c rsanchez1369 -c anaconda -c conda-forge && conda activate xmipp_deepEMhancer* && conda env export > xmipp_deepEMhancer.yml All targets exist. cd /home/pablo/software/scipion/software/em/deepLearningToolkit rm models_UPDATED_on_* xmippLibToken 2>/dev/null ; echo 'Downloading pre-trained models...' ; /home/pablo/software/scipion/software/em/xmipp/bin/xmipp_sync_data update /home/pablo/software/scipion/software/em/xmipp/models http://scipion.cnb.csic.es/downloads/scipion/software/em DLmodels && touch models_UPDATED_on_22_3_2022 && echo ' > Tensorflow installed with CUDA SUPPORT.' Downloading pre-trained models... Regenerating local MANIFEST... Verifying MD5s... 12%... 62%... ...done. Updated files: 0 Uncompressing models: cat /home/pablo/software/scipion/software/em/xmipp/models/xmipp_model_*.tgz | tar xzf - -i --directory=/home/pablo/software/scipion/software/em/xmipp/models ...done. Updated files: 4 Uncompressing models: cat /home/pablo/software/scipion/software/em/xmipp/models/xmipp_model_*.tgz | tar xzf - -i --directory=/home/pablo/software/scipion/software/em/xmipp/models > Tensorflow installed with CUDA SUPPORT. Skipping command: Link 'deepLearningToolkit-0.2 -> deepLearningToolkit' All targets exist. Done (1 m 06 s) Now comes the tedious part: wget -nv -c -O /home/pablo/software/scipion/software/em/deepLearningToolkit.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz should be easy to get and move to the GPU node For the environments you'll need to manualy create them: conda create --force --yes -n xmipp_DLTK_v0.3 python=3 pandas=0.23 scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 keras=2.2 scikit-learn=0.22 -c anaconda && conda activate xmipp_DLTK_v0.3 && pip install numpy==1.18.4 numpy==1.18.4 numpy==1.18.4 This command will use a connection to download: pandas=0.23, scikit_image=0.14, .... You can get any of those from pypi like this for scikit_image --> https://pypi.org/project/scikit-image/#files You will need to match the cpu architecture of the GPU nodes and in the worse case, download the sources. There are many thing that can go wrong and I haven't tried this. Actually, when I had to install from sources, some packages I've given up. I think this is not an easy an trivial task but might be doable. All the best, Pablo. Maybe is worth to give the GPU node temporary internet connection? if possible. On 22/3/22 3:53, Thu Nguyen wrote: > > Hi Heechang, > > May I ask if you ended up finding a solution to this problem ? > > I am currently in the same situation. Worse, my GPU nodes do not have > internet so I cannot even use them to install deepLearning. > > Regards, > > *----------------------------------------------------------------------------------------------------------------* > > *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...> - 2022-03-22 02:53:26
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Hi Heechang, May I ask if you ended up finding a solution to this problem ? I am currently in the same situation. Worse, my GPU nodes do not have internet so I cannot even use them to install deepLearning. Regards, ---------------------------------------------------------------------------------------------------------------- Thu D. Nguyen Bio21 Institute The University of Melbourne, Victoria 3010 Australia |
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From: David <dst...@cn...> - 2022-03-18 09:26:33
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Hi, To answer the question: NVIDIA has a concept of virtual architecture and real architecture. Virtual architecture describes capabilities of different families of GPUs, while real architecture aims to target specific HW. More info here: https://docs.nvidia.com/cuda/cuda-compiler-driver-nvcc/index.html#options-for-steering-gpu-code-generation-generate-code NVIDIA also allows for fatbinaries, where multiple versions of the same code can be precompiled, and at runtime the matching one will be used. If no real architecture code is found, but virtual one is present, it will be compiled JIT. That's how we do it. https://docs.nvidia.com/cuda/cuda-compiler-driver-nvcc/index.html#virtual-architecture-feature-list [note: SM=shader model = compute capability] So, Wolfgang should be covered in sense of the virtual architectures, but he might want to specifically target all GPUs he has (sm_XX) + generate PTX for other generations(code=compute_86) and thus avoid JIT compile penalization. (I didn't test it, but hopefully it will work) "-gencode=arch=compute_60,code=sm_60 " "-gencode=arch=compute_61,code=sm_61 " "-gencode=arch=compute_70,code=sm_70 " "-gencode=arch=compute_75,code=sm_75 " "-gencode=arch=compute_80,code=sm_80 " "-gencode=arch=compute_86,code=compute_86,sm_86") KR, David > -------- Forwarded Message -------- > Subject: [scipion-users] xmipp & cuda compilation > Date: Thu, 17 Mar 2022 13:04:49 +0100 (CET) > From: Lugmayr, Wolfgang <w.l...@uk...> > Reply-To: Mailing list for Scipion users > <sci...@li...> > To: Mailing list for Scipion users <sci...@li...> > > > > dear xmipp developers, > > after recompiling xmipp for amd and intel cpus i found different cuda > flags in xmipp.conf > > they come from scripts/config.py > if nvcc_version >= 11: > flags = ("--x cu -D_FORCE_INLINES -Xcompiler -fPIC " > "-ccbin %(CXX_CUDA)s -std=c++14 --expt-extended-lambda " > # generate PTX only, and SASS at the runtime (by setting > code=virtual_arch) > "-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") > > we have different gpu architectures on the cluster: > P100 - compute_60 Pascal > V100 - compute_70 Volta > A100 - compute_80 Ampere > > consumer cards on analysis pcs: > GTX 1080ti - compute_61 Pascal > RTX 6000 - compute_75 Touring > RTX A6000 - compute_86 Ampere > > what do this flags mean and do you generate cuda code and compile it > at runtime? > should i change the flags to 60,70,80 instead of your choice for our > cluster? > > cheers, > wolfgang > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > For new subscribers, please read: > https://listas.csic.es/cnb/wws/help/user#subscribe > > In short, send an email to:sy...@cn... > with the subject: bioinfo Name surname |
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From: Lugmayr, W. <w.l...@uk...> - 2022-03-17 12:05:03
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dear xmipp developers,
after recompiling xmipp for amd and intel cpus i found different cuda flags in xmipp.conf
they come from scripts/config.py
if nvcc_version >= 11:
flags = ("--x cu -D_FORCE_INLINES -Xcompiler -fPIC "
"-ccbin %(CXX_CUDA)s -std=c++14 --expt-extended-lambda "
# generate PTX only, and SASS at the runtime (by setting code=virtual_arch)
"-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")
we have different gpu architectures on the cluster:
P100 - compute_60 Pascal
V100 - compute_70 Volta
A100 - compute_80 Ampere
consumer cards on analysis pcs:
GTX 1080ti - compute_61 Pascal
RTX 6000 - compute_75 Touring
RTX A6000 - compute_86 Ampere
what do this flags mean and do you generate cuda code and compile it at runtime?
should i change the flags to 60,70,80 instead of your choice for our cluster?
cheers,
wolfgang
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