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Re: [scipion-users] Antw: Re: Re: Antw: RE: deep consensus pickling error
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From: Pablo C. <pc...@cn...> - 2021-04-22 07:47:35
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Dear Dmitry, there is a inconsistency there. deepLearningToolkit is reported as installed, but in the list of the enviroments it is not. Could you please, remove the "files that flags deepearningtoolkit as installed": scipion3 run rm -rf '$SCIPION_HOME/software/em/deepLearningToolkit*' And try to install deeplearning toolkit again? scipionprod installb deepLearningToolkit On 21/4/21 22:47, Dmitry A. Semchonok wrote: > > Dear Pablo, > > Thank you! > > Please see the result of > > *Scipion3 installb* > > ere** > > Sincerely, > > Dmitry > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > *From: *pc...@cn... <mailto:pc...@cn...> > *Sent: *Wednesday, April 21, 2021 10:19 PM > *To: *Mailing list for Scipion users > <mailto:sci...@li...> > *Subject: *Re: [scipion-users] Antw: Re: Re: Antw: RE: deep consensus > pickling error > > Providing Eman Fonda can handle environments the same way a standard > conda installation does, then, I'd say the deepLearningToolkit > environment is not present. > > What is the output of > > Scipion3 instalb? > > El 21 abr. 2021 20:28, "Dmitry A. Semchonok" <sem...@gm...> > escribió: > > Dear Pablo, > > Thank you ! please have a look below. > > Sincerely, > > Dmitry > > *scipion3 printenv * > > [panos@cryoem01 ~]$ scipion3 printenv > > Scipion v3.0.7 - Eugenius > > export ASCP="~/.aspera/connect/bin/ascp" > > export ASPERA_SCP_PASS="" > > export ATSAS_HOME="/opt/Scipion3/software/em/atsas-3.0.1" > > export BSOFT_HOME="/opt/Scipion3/software/em/bsoft-2.0.7" > > export CCP4_HOME="/opt/Scipion3/software/em/ccp4-7.0.056" > > export CHIMERA_HOME="/opt/Scipion3/software/em/chimerax-1.1" > > export CISTEM_HOME="/opt/Scipion3/software/em/cistem-1.0.0-beta" > > export CONDA_ACTIVATION_CMD="eval > "$(/opt/Scipion3/software/em/eman-2.31/condabin/conda shell.bash > hook)"" > > export CONTINUOUSFLEX_HOME="/opt/Scipion3/software/em/xmipp" > > export CRYOASSESS_ENV_ACTIVATION="conda activate cryoassess-0.1.0" > > export > CRYOASSESS_MODEL_2D="/opt/Scipion3/software/em/cryoassess-models/2dassess_062119.h5" > > export > CRYOASSESS_MODEL_MIC="/opt/Scipion3/software/em/cryoassess-models/micassess_051419.h5" > > export CRYOLO_CUDA_LIB="/usr/local/cuda/lib64" > > export CRYOLO_ENV_ACTIVATION="conda activate cryolo-1.7.6" > > export CRYOLO_ENV_ACTIVATION_CPU="conda activate cryoloCPU-1.7.6" > > export > CRYOLO_GENERIC_DENOISED_MODEL="/opt/Scipion3/software/em/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5" > > export > CRYOLO_GENERIC_MODEL="/opt/Scipion3/software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5" > > export > CRYOLO_NS_GENERIC_MODEL="/opt/Scipion3/software/em/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5" > > export CRYOSPARC_HOME="/home/panos/software/cryosparc" > > export CRYOSPARC_USER="ctueting" > > export > CRYO_PROJECTS_DIR="/data1/ScipionUserData/projects/cryosparc_plugin" > > export CTFFIND4_HOME="/opt/Scipion3/software/em/ctffind4-4.1.14" > > export DOGPICKER_HOME="/opt/Scipion3/software/em/dogpicker-0.2.1.1" > > export DYNAMO_HOME="/opt/Scipion3/software/em/dynamo-1.146" > > export EMAN2SCRATCHDIR="/tmp" > > export EMAN2_HOME="/opt/Scipion3/software/em/eman-2.31" > > export EMFACILITIES_HOME="/opt/Scipion3/software/em/" > > export EMPIAR_TOKEN="" > > export EMXLIB_HOME="/opt/Scipion3/software/em/emx_export-1.0.0" > > export EM_ROOT="software/em" > > export ETHAN_HOME="/opt/Scipion3/software/em/ethan-1.2" > > export FSC3D_ACTIVATION_CMD="conda activate 3DFSC" > > export FSC3D_HOME="/opt/Scipion3/software/em/fsc3D-3.0" > > export GAUTOMATCH="Gautomatch_v0.56_sm30-75_cu10.1" > > export GAUTOMATCH_CUDA_LIB="/usr/local/cuda/lib64" > > export GAUTOMATCH_HOME="/opt/Scipion3/software/em/gautomatch-0.56" > > export GCTF="Gctf-v1.06_sm_30_cu8.0_x86_64" > > export GCTF_CUDA_LIB="/usr/local/cuda-8.0/lib64" > > export GCTF_HOME="/opt/Scipion3/software/em/Gctf_v1.06" > > export IMAGIC_HOME="/opt/Scipion3/software/em/imagic-190830" > > export IMOD_HOME="/opt/Scipion3/software/em/imod-4.10.42/IMOD" > > export > JANNI_GENERIC_MODEL="/opt/Scipion3/software/em/janni_model-20190703/gmodel_janni_20190703.h5" > > export JAVA_MAX_MEMORY="12" > > export LOCSCALE_HOME="/opt/Scipion3/software/em/locscale-0.1" > > export MAXIT_HOME="/opt/Scipion3/software/em/maxit-10.1" > > export MOTIONCOR2_BIN="MotionCor2_1.3.2-Cuda100" > > export MOTIONCOR2_CUDA_LIB="/usr/local/cuda/lib64" > > export MOTIONCOR2_HOME="/opt/Scipion3/software/em/motioncor2-1.3.2" > > export NMA_HOME="/opt/Scipion3/software/em/nma" > > export NOVACTF_HOME="/opt/Scipion3/software/em/novactf-master" > > export PHENIX_HOME="/opt/Scipion3/software/em/phenix-" > > export RELION_CUDA_BIN="/usr/local/cuda/bin" > > export RELION_CUDA_LIB="/usr/local/cuda/lib64" > > export RELION_HOME="/opt/Scipion3/software/em/relion-3.1.0" > > export RESMAP="ResMap-1.95-cuda-Centos7x64" > > export RESMAP_GPU_LIB="ResMap_krnl-cuda-V8.0.61-sm60_gpu.so" > > export RESMAP_HOME="/opt/Scipion3/software/em/resmap-1.95" > > export SCIPION_CONFIG="/opt/Scipion3/config/scipion.conf" > > export SCIPION_CWD="/home/panos" > > export SCIPION_DOMAIN="pwem" > > export SCIPION_FONT_NAME="Helvetica" > > export SCIPION_HOME="/opt/Scipion3" > > export SCIPION_HOSTS="/opt/Scipion3/config/hosts.conf" > > export SCIPION_LOCAL_CONFIG="/home/panos/.config/scipion/scipion.conf" > > export SCIPION_LOG="/home/panos/ScipionUserData/logs/scipion.log" > > export SCIPION_LOGO="scipion_logo.gif" > > export SCIPION_LOGS="/home/panos/ScipionUserData/logs" > > export SCIPION_NOTES_FILE="notes.txt" > > export SCIPION_NOTIFY="True" > > export SCIPION_PLUGIN_REPO_URL="http://scipion.i2pc.es/getplugins/" > > export SCIPION_PROTOCOLS="/opt/Scipion3/config/protocols.conf" > > export SCIPION_SOFTWARE="/opt/Scipion3/software" > > export SCIPION_SUPPORT_EMAIL="sc...@cn..." > > export SCIPION_TESTS="/opt/Scipion3/data/tests" > > export SCIPION_TESTS_CMD="scipion3 tests" > > export SCIPION_TESTS_OUTPUT="/home/panos/ScipionUserData/Tests" > > export SCIPION_TMP="/home/panos/ScipionUserData/tmp" > > export SCIPION_URL="http://scipion.cnb.csic.es/downloads/scipion" > > export > SCIPION_URL_SOFTWARE="http://scipion.cnb.csic.es/downloads/scipion/software" > > export > SCIPION_URL_TESTDATA="http://scipion.cnb.csic.es/downloads/scipion/data/tests" > > export SCIPION_USER_DATA="/data1/ScipionUserData" > > export SCIPION_VERSION="v3.0.7 - Eugenius" > > export SIDESPLITTER_HOME="/opt/Scipion3/software/em/sidesplitter-1.2" > > export SPIDER="spider_linux_mp_intel64" > > export SPIDER_HOME="/opt/Scipion3/software/em/spider-26.06" > > export SPIDER_MPI="spider_linux_mpi_opt64" > > export TOPAZ_ENV_ACTIVATION="conda activate topaz-0.2.3" > > export VMD_HOME="/usr/local/lib/vmd" > > export WIZARD_MASK_COLOR="[0.125, 0.909, 0.972]" > > export XMIPP2_HOME="/opt/Scipion3/software/em/Xmipp-2.4-src" > > export XMIPP_HOME="/opt/Scipion3/software/em/xmipp" > > [panos@cryoem01 ~]$ > > *scipion3 run printenv* > > [panos@cryoem01 ~]$ scipion3 run printenv > > Scipion v3.0.7 - Eugenius > > ** Running command: printenv > > SCIPION_VERSION=v3.0.7 - Eugenius > > SCIPION_LOGO=scipion_logo.gif > > GAUTOMATCH_CUDA_LIB=/usr/local/cuda/lib64 > > MAXIT_HOME=software/em/maxit-10.1 > > XDG_SESSION_ID=c3 > > SSH_AGENT_PID=2160 > > IMOD_DIR=/usr/local/IMOD > > HOSTNAME=cryoem01 > > SCIPION_FONT_NAME=Helvetica > > RELION_CUDA_BIN=/usr/local/cuda/bin > > IMSETTINGS_INTEGRATE_DESKTOP=yes > > XRDP_SOCKET_PATH=/run/xrdp > > CRYOLO_GENERIC_DENOISED_MODEL=software/em/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 > > SCIPION_TESTS_CMD=scipion3 tests > > VTE_VERSION=5204 > > XDG_MENU_PREFIX=gnome- > > SHELL=/bin/bash > > TERM=xterm-256color > > SIDESPLITTER_HOME=software/em/sidesplitter-1.2 > > HISTSIZE=1000 > > IMOD_QTLIBDIR=/usr/local/IMOD/qtlib > > SCIPION_NOTIFY=True > > SCIPION_URL=http://scipion.cnb.csic.es/downloads/scipion > > CISTEM_HOME=software/em/cistem-1.0.0-beta > > SPIDER_HOME=software/em/spider-26.06 > > SCIPION_DOMAIN=pwem > > SCIPION_USER_DATA=/data1/ScipionUserData > > CRYOLO_GENERIC_MODEL=software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 > > SCIPION_TESTS_OUTPUT=/home/panos/ScipionUserData/Tests > > GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/409e3dd0_2aca_48db_a92c_2905ab5689a1 > > GJS_DEBUG_OUTPUT=stderr > > DOGPICKER_HOME=software/em/dogpicker-0.2.1.1 > > SCIPION_PROTOCOLS=/opt/Scipion3/config/protocols.conf > > CCP4_HOME=software/em/ccp4-7.0.056 > > CRYOASSESS_ENV_ACTIVATION=conda activate cryoassess-0.1.0 > > DYNAMO_HOME=software/em/dynamo-1.146 > > PHENIX_HOME=software/em/phenix- > > GJS_DEBUG_TOPICS=JS ERROR;JS LOG > > SCIPION_HOSTS=/opt/Scipion3/config/hosts.conf > > GAUTOMATCH_HOME=software/em/gautomatch-0.56 > > SCIPION_PLUGIN_REPO_URL=http://scipion.i2pc.es/getplugins/ > > CRYOLO_NS_GENERIC_MODEL=software/em/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 > > GCTF_HOME=software/em/Gctf_v1.06 > > LC_ALL=en_US.UTF-8 > > CRYOASSESS_MODEL_MIC=software/em/cryoassess-models/micassess_051419.h5 > > IMSETTINGS_MODULE=none > > CUDA_HOME=/usr/local/cuda > > USER=panos > > LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45: > > LD_LIBRARY_PATH=/usr/local/cuda-10.0/lib64:/opt/Scipion3/software/lib > > SCIPION_URL_TESTDATA=http://scipion.cnb.csic.es/downloads/scipion/data/tests > > MOTIONCOR2_BIN=MotionCor2_1.3.2-Cuda100 > > GNOME_TERMINAL_SERVICE=:1.103 > > SCIPION_SUPPORT_EMAIL=sc...@cn... > > GCTF=Gctf-v1.06_sm_30_cu8.0_x86_64 > > XMIPP_HOME=software/em/xmipp > > FSC3D_HOME=software/em/fsc3D-3.0 > > SSH_AUTH_SOCK=/tmp/ssh-ZJq5X9BOWO6G/agent.1847 > > SPIDER_MPI=spider_linux_mpi_opt64 > > SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/1847,unix/unix:/tmp/.ICE-unix/1847 > > CRYOLO_ENV_ACTIVATION_CPU=conda activate cryoloCPU-1.7.6 > > EMPIAR_TOKEN= > > VIRTUAL_ENV=/opt/Scipion3/.scipion3env > > XRDP_PULSE_SINK_SOCKET=xrdp_chansrv_audio_out_socket_10 > > SCIPION_CWD=/home/panos > > PULSE_SCRIPT=/etc/xrdp/pulse/default.pa > > SCIPION_TESTS=/opt/Scipion3/data/tests > > SPIDER=spider_linux_mp_intel64 > > GNOME_SHELL_SESSION_MODE=classic > > CRYOSPARC_USER=ctueting > > MAIL=/var/spool/mail/panos > > PATH=/opt/Scipion3/.scipion3env/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/home/panos/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/local/IMOD/bin:/sbin:/bin:/usr/bin:/usr/local/bin:/usr/local/sbin:/usr/sbin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/panos/.local/bin:/home/panos/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/panos/.local/bin:/home/panos/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/panos/.local/bin:/home/panos/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap/:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin > > SCIPION_LOGS=/home/panos/ScipionUserData/logs > > SCIPION_CONFIG=/opt/Scipion3/config/scipion.conf > > IMOD_PLUGIN_DIR=/usr/local/IMOD/lib/imodplug > > QT_IM_MODULE=ibus > > _=/bin/printenv > > CRYOLO_ENV_ACTIVATION=conda activate cryolo-1.7.6 > > WIZARD_MASK_COLOR=[0.125, 0.909, 0.972] > > ATSAS_HOME=software/em/atsas-3.0.1 > > JANNI_GENERIC_MODEL=software/em/janni_model-20190703/gmodel_janni_20190703.h5 > > PWD=/home/panos > > XMODIFIERS=@im=ibus > > CRYOLO_CUDA_LIB=/usr/local/cuda/lib64 > > ETHAN_HOME=software/em/ethan-1.2 > > GCTF_CUDA_LIB=/usr/local/cuda-8.0/lib64 > > MOTIONCOR2_HOME=software/em/motioncor2-1.3.2 > > XMIPP2_HOME=software/em/Xmipp-2.4-src > > pkgdir=/usr/local/I-TASSER5.1 > > XRDP_SESSION=1 > > IMOD_JAVADIR=/usr/local/java > > SCIPION_SOFTWARE=/opt/Scipion3/software > > LANG=en_US.UTF-8 > > XRDP_PULSE_SOURCE_SOCKET=xrdp_chansrv_audio_in_socket_10 > > SCIPION_NOTES_FILE=notes.txt > > CRYOASSESS_MODEL_2D=software/em/cryoassess-models/2dassess_062119.h5 > > CRYOSPARC_HOME=/home/panos/software/cryosparc > > MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles > > SCIPION_URL_SOFTWARE=http://scipion.cnb.csic.es/downloads/scipion/software > > GAUTOMATCH=Gautomatch_v0.56_sm30-75_cu10.1 > > RELION_CUDA_LIB=/usr/local/cuda/lib64 > > LOADEDMODULES= > > LOCSCALE_HOME=software/em/locscale-0.1 > > FOR_DISABLE_STACK_TRACE=1 > > EMFACILITIES_HOME=software/em/ > > ASCP=~/.aspera/connect/bin/ascp > > RESMAP_HOME=software/em/resmap-1.95 > > SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass > > HISTCONTROL=ignoredups > > ASPERA_SCP_PASS= > > SHLVL=5 > > HOME=/home/panos > > CONDA_ACTIVATION_CMD=eval > "$(/opt/Scipion3/software/em/eman-2.31/condabin/conda shell.bash > hook)" > > CTFFIND4_HOME=software/em/ctffind4-4.1.14 > > MOTIONCOR2_CUDA_LIB=/usr/local/cuda/lib64 > > SCIPION_TMP=/home/panos/ScipionUserData/tmp > > EMAN2_HOME=software/em/eman-2.31 > > GNOME_DESKTOP_SESSION_ID=this-is-deprecated > > CRYO_PROJECTS_DIR=/data1/ScipionUserData/projects/cryosparc_plugin > > IMAGIC_HOME=software/em/imagic-190830 > > SCIPION_LOCAL_CONFIG=/home/panos/.config/scipion/scipion.conf > > PYTHONPATH=:/opt/Scipion3/software/bindings > > LOGNAME=panos > > NOVACTF_HOME=software/em/novactf-master > > BSOFT_HOME=software/em/bsoft-2.0.7 > > DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-FKQakXHYCC,guid=649474707764c616b7441e9f60802f4a > > XDG_DATA_DIRS=/home/panos/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share > > MODULESHOME=/usr/share/Modules > > MPI_HOME=/usr/local/mpich-3.2.1 > > UID=1000 > > CONTINUOUSFLEX_HOME=software/em/xmipp > > LESSOPEN=||/usr/bin/lesspipe.sh %s > > IMOD_CALIB_DIR=/usr/local/ImodCalib > > JAVA_MAX_MEMORY=12 > > RESMAP=ResMap-1.95-cuda-Centos7x64 > > EMAN2SCRATCHDIR=/tmp > > SCIPION_HOME=/opt/Scipion3 > > FSC3D_ACTIVATION_CMD=conda activate 3DFSC > > RELION_HOME=software/em/relion-3.1.0 > > VMD_HOME=/usr/local/lib/vmd > > VIEWERS={"Volume":["pwem.viewers.DataViewer"], > "VolumeMask":["pwem.viewers.DataViewer"]} > > DISPLAY=:10.0 > > XDG_RUNTIME_DIR=/run/user/1000 > > SCIPION_LOG=/home/panos/ScipionUserData/logs/scipion.log > > XDG_CURRENT_DESKTOP=GNOME > > EM_ROOT=software/em > > NMA_HOME=software/em/nma > > COLORTERM=truecolor > > CHIMERA_HOME=software/em/chimerax-1.1 > > EMXLIB_HOME=software/em/emx_export-1.0.0 > > IMOD_HOME=software/em/imod-4.10.42/IMOD > > RESMAP_GPU_LIB=ResMap_krnl-cuda-V8.0.61-sm60_gpu.so > > TOPAZ_ENV_ACTIVATION=conda activate topaz-0.2.3 > > BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*` > > } > > [panos@cryoem01 ~]$ > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> > for Windows 10 > > *From: *Pablo Conesa <mailto:pc...@cn...> > *Sent: *Wednesday, April 21, 2021 7:06 PM > *To: *sci...@li... > <mailto:sci...@li...> > *Subject: *Re: [scipion-users] Antw: Re: Re: Antw: RE: deep > consensus pickling error > > You have eman2 acting as a conda manager, that is a problem. > > At least the environment is not listed there. > > Does the other plugins work? e.g. cryolo? > > Can you send the output of: > > scipion3 printenv > > and > > scipion3 run printenv > > ? > > On 21/4/21 17:06, Dmitry Semchonok wrote: > > Dear colleagues, > > Just to add our current error from the xmipp deep learning > installation. > > Interestingly we almost fun to an end of this step but conda > issue appeared. > > Any suggestions? > > currentDir: > /data1/ScipionUserData/projects/Image_processing_cn_10688 > > 00890: workingDir: Runs/007643_XmippProtScreenDeepLearning > > 00891: runMode: Continue > > 00892: MPI: 1 > > 00893: threads: 4 > > 00894: Starting at step: 3 > > 00895: Running steps > > 00896: STARTED: predict, step 3, time 2021-04-20 11:08:26.633086 > > 00897: > > 00898: $ /usr/local/EMAN_2.21/bin/conda info --env > > 00899: # conda environments: > > 00900: # > > 00901: 3DFSC /home/panos/.conda/envs/3DFSC > > 00902: cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0 > > 00903: cryolo /home/panos/.conda/envs/cryolo > > 00904: cryolo /usr/local/EMAN_2.21/envs/cryolo > > 00905: cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4 > > 00906: fsc /usr/local/EMAN_2.21/envs/fsc > > 00907: topaz /usr/local/EMAN_2.21/envs/topaz > > 00908: root * /usr/local/EMAN_2.21 > > 00909: > > 00910: > > 00911: >>> 'xmipp_DLTK_v0.3' conda environment not found... > (check list above) > > 00912: Traceback (most recent call last): > > 00913: File > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", > line 189, in run > > 00914: self._run() > > 00915: File > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", > line 240, in _run > > 00916: resultFiles = self._runFunc() > > 00917: File > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", > line 236, in _runFunc > > 00918: return self._func(*self._args) > > 00919: File > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/protocols/protocol_screen_deeplearning.py", > line 319, in predict > > 00920: env=self.getCondaEnv()) > > 00921: File > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py", > line 204, in getCondaEnv > > 00922: return CondaEnvManager.getCondaEnv(env, envName) > > 00923: File > "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in > getCondaEnv > > 00924: envBin = os.path.join(environDir, "bin") > > 00925: File "/usr/lib64/python3.6/posixpath.py", line 80, > in join > > 00926: a = os.fspath(a) > > 00927: TypeError: expected str, bytes or os.PathLike object, > not NoneType > > 00928: Protocol failed: expected str, bytes or os.PathLike > object, not NoneType > > 00929: FAILED: predict, step 3, time 2021-04-20 11:08:27.020467 > > 00930: *** Last status is failed > > 00931: ------------------- PROTOCOL FAILED (DONE 3/4) > > Thank you! > > Sincerely, > > Dmitry > > On 20. Apr 2021, at 11:25, Christian Tüting > <chr...@bi... > <mailto:chr...@bi...>> wrote: > > Hi, > > thank you for your response. I tried this twice. The first > time, the > "_BACKUP2" folder was popping up again under .conda/envs, > so I followed > your steps again, deleting the folder under software and > removed the > conda enviroment, and now, no enviroment is generated at > all. Logically, > running a job gives this error: ">>> 'xmipp_DLTK_v0.3' > conda environment > not found... (check list above)". > > Another long-term job is currently running, after this is > done, we will > restart everything to have a clean system. But do you have any > additional tips? > > Thanks in advance > Christian > > > > David Maluenda <dma...@ub... > <mailto:dma...@ub...>> 20.04.21 10.02 Uhr >>> > > Hi Christian, > > If it already works, I would leave it as it is. > > To make a clear installation, you don't need to reinstall > the whole > xmipp. You can just reinstall the deepLearningToolkit by > > rm -rf /opt/Scipion3/software/em/deepLearningToolkit > conda env remove --name xmipp_DLTK_v0.3_BACKUP2 > scipion3 installb deepLearningToolkit > > > Cheers, > > <http://ucm.es/ <http://ucm.es/>> > _____ > Dr. David Maluenda Niubó > dma...@ub... > <mailto:dma...@ub...><mailto:dma...@ub... > <mailto:dma...@ub...>> - (+34) 619 029 310 > Wavefront Engineering > Group<https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA > <https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA>> > Applied Physics - > UB<https://www.ub.edu/portal/web/dp-fisica-aplicada > <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 Tue, Apr 20, 2021 at 9:53 AM Christian Tüting > <chr...@bi... > <mailto:chr...@bi...><mailto:chr...@bi... > <mailto:chr...@bi...>>> > wrote: > Hi Pablo, > > I will take an eye on this. I have a question regarding > dependencies: > tensorflow 1.15 requires keras-application>=1.0.8 and > keras-preprocessing>=1.0.5, but keras 2.2 requieres older > versions > (1.0.2 and 1.0.1, respectivly). > > Should we try to uninstall and a clean reinstall of xmipp, > to resolve > all dependency issues? > > Thank you for your support. > > Best > Christian > > > Pablo Conesa <pc...@cn... > <mailto:pc...@cn...><mailto:pc...@cn... > <mailto:pc...@cn...>>> > > 20.04.21 9.16 Uhr >>> > Thanks Christian. > > In theory, xmipp defines dependencies strictly > (https://github.com/I2PC/xmipp/blob/devel/src/xmipp/bindings/python/xmipp_conda_envs.py > <https://github.com/I2PC/xmipp/blob/devel/src/xmipp/bindings/python/xmipp_conda_envs.py>) > > I do not know how it ended up with higher versions, but > something to > keep an eye on. > > On 20/4/21 7:00, Christian Tüting wrote: > > Hi all, > > first the conda path looks actually very strange, and > I fixed this > direclty. We had some other issues, which were > tensorflow-related, but > this is fixed. > > > Just to comment on that, there were first an issue > with the tensorflow > module. Installing the latest release (2.x) gives an > error on "module > 'tensorflow' has no attribute 'Session'". After fixing > that by > downgrading, keras was giving an error, that the > module does not have > > no > > attribute "tf", which was also fixed by downgrading. > > > > TL;DR Eventually, downgrading tensorflow to 1.15.0 and > downgrading > > keras > > to 2.2.4 (from 2.2.5) solved the issue > > > Best > Christian > > > "Dmitry A. Semchonok" > > <sem...@gm... > <mailto:sem...@gm...><mailto:sem...@gm... > <mailto:sem...@gm...>>> 19.04.21 16.24 Uhr >>> > > Dear Carlos Oscar, Pablo, David, Ruben, > > > Thank you very much for your fast response. > > > Currently, deep learning is running. > A colleague of mine, Christian, kindly looked at the > problem. > > > Let me, please post the errors we had and where we are > now. > May be Christian can comment more on this issue. > > > Please see the errors here. > https://yadi.sk/d/KlTeKv1O9UCTQg > <https://yadi.sk/d/KlTeKv1O9UCTQg> > > > Since> Sent: Monday, April 19, 2021 12:57 PM > To: Mailing list for Scipion users; Pablo Conesa; > Rubén Sánchez; David > Maluenda > Subject: Re: [scipion-users] deep consensus pickling error > > > Dear Dmitry, > let us see if David or Rubén knows where this > environment is coming > from. > Kind regards, Carlos Oscar > El 19/04/2021 a las 9:37, Pablo Conesa escribió: > > Hi Dmitry... you have no environment for xmipp_DLTK_v0.3. > You have a "weird" xmipp_DLTK_v0.3_BACKUP2 > /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2 > > On 17/4/21 8:56, Dmitry A. Semchonok wrote: > > Dear colleagues, > > During deep consensus pickling I received the > following error > > Any ideas? > > Thank you > > Sincerely, > Dmitry > > > > [Parallel(n_jobs=12)]: Done 176 tasks | elapsed: > 1.8min > [Parallel(n_jobs=12)]: Done 426 tasks | elapsed: > 4.3min > [Parallel(n_jobs=12)]: Done 776 tasks | elapsed: > 7.5min > [Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: > 11.5min > [Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: > 16.7min > [Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: > 23.7min > [Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: > 32.1min > [Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: > 41.4min > [Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: > 51.8min > [Parallel(n_jobs=12)]: Done 5285 out of 5285 | > elapsed: 55.1min > > finished > > [35mFINISHED[0m: extractParticles, step 12, time > 2021-04-17 > 04:05:07.093613 > [35mSTARTED[0m: joinSetOfParticlesStep, step 13, time > 2021-04-17 > 04:05:07.574152 > [35mFINISHED[0m: joinSetOfParticlesStep, step 13, time > 2021-04-17 > 04:26:59.879548 > [35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 > 04:26:59.920444 > None None None None > > $ /usr/local/EMAN_2.21/bin/conda info --env > # conda environments: > # > 3DFSC /home/panos/.conda/envs/3DFSC > cryoassess-0.1.0 > /home/panos/.conda/envs/cryoassess-0.1.0 > cryolo > /home/panos/.conda/envs/cryolo> cryolo > > /usr/local/EMAN_2.21/envs/cryolo > > cryolo-1.5.4 > /usr/local/EMAN_2.21/envs/cryolo-1.5.4 > fsc /usr/local/EMAN_2.21/envs/fsc > topaz /usr/local/EMAN_2.21/envs/topaz > root * /usr/local/EMAN_2.21 > > > 'xmipp_DLTK_v0.3' conda environment not > found... (check list above) > > Traceback (most recent call last): > File > > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", > > line 189, in run > self._run() > File > > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", > > line 240, in _run > resultFiles = self._runFunc() > File > > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", > > line 236, in _runFunc > return self._func(*self._args) > File > "/opt/Scipion env=self.getCondaEnv()) > File > > "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py", > > line 204, in getCondaEnv > return CondaEnvManager.getCondaEnv(env, envName) > File > "/opt/Scipion3/software/bindings/xmipp_base.py", line > 245, in > getCondaEnv > envBin = os.path.join(environDir, "bin") > File "/usr/lib64/python3.6/posixpath.py", line 80, > in join > a = os.fspath(a) > TypeError: expected str, bytes or os.PathLike object, > not NoneType > [31mProtocol failed: expected str, bytes or > os.PathLike object, not > NoneType[0m > [35mFAILED[0m: trainCNN, step 14, time 2021-04-17 > 04:27:00.607417 > *** Last status is failed > Sent from Mail for Windows 10 > > > > > > _______________________________________________scipion-users > mailing > > lis...@li...https > <mailto:lis...@li...https>://lists.sourceforge.net/lists/listinfo/scipion-users--<http://lists.sourceforge.net/lists/listinfo/scipion-users--> > <http://lists.sourceforge.net/lists/listinfo/scipion-users--> > > > Pablo Conesa - Madrid Scipion team > > > > > > _______________________________________________scipion-users > mailing > > lis...@li...https > <mailto:lis...@li...https>:/> > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es > <http://scipion.i2pc.es>> team* > > > > 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. > > > 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> > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
