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Re: [scipion-users] Antw: Re: Re: Antw: RE: deep consensus pickling error
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From: Dmitry A. S. <sem...@gm...> - 2021-04-21 20:48:03
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<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><!--[if !mso]><style>v\:* {behavior:url(#default#VML);} o\:* {behavior:url(#default#VML);} w\:* {behavior:url(#default#VML);} .shape {behavior:url(#default#VML);} </style><![endif]--><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} pre {mso-style-priority:99; mso-style-link:"HTML Preformatted Char"; margin:0in; font-size:10.0pt; font-family:"Courier New";} span.HTMLPreformattedChar {mso-style-name:"HTML Preformatted Char"; mso-style-priority:99; mso-style-link:"HTML Preformatted"; font-family:"Courier New";} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal><span lang=EN-GB>Dear Pablo,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Thank you!<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Please see the result of <o:p></o:p></span></p><p class=MsoNormal><b><span lang=EN-GB>Scipion3 installb<o:p></o:p></span></b></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><img width=458 height=460 style='width:4.7708in;height:4.7864in' id="Picture_x0020_3" src="cid:image003.png@01D73700.5498B2A0"><b><span lang=EN-GB><o:p></o:p></span></b></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sincerely,</p><p class=MsoNormal>Dmitry</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:pc...@cn...">pc...@cn...</a><br><b>Sent: </b>Wednesday, April 21, 2021 10:19 PM<br><b>To: </b><a href="mailto:sci...@li...">Mailing list for Scipion users</a><br><b>Subject: </b>Re: [scipion-users] Antw: Re: Re: Antw: RE: deep consensus pickling error</p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Providing Eman Fonda can handle environments the same way a standard conda installation does, then, I'd say the deepLearningToolkit environment is not present. </p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>What is the output of</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Scipion3 instalb?</p></div></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>El 21 abr. 2021 20:28, "Dmitry A. Semchonok" <sem...@gm...> escribió:</p><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><div><p>Dear Pablo,</p><p>Thank you ! please have a look below.</p><p> </p><p>Sincerely,</p><p>Dmitry</p><p> </p><p><b><span style='color:black;background:yellow'>scipion3 printenv</span> </b></p><p><span style='color:red'>[panos@cryoem01 ~]$ scipion3 printenv</span></p><p><span style='color:red'>Scipion v3.0.7 - Eugenius</span></p><p><span style='color:red'>export ASCP="~/.aspera/connect/bin/ascp"</span></p><p><span style='color:red'>export ASPERA_SCP_PASS=""</span></p><p><span style='color:red'>export ATSAS_HOME="/opt/Scipion3/software/em/atsas-3.0.1"</span></p><p><span style='color:red'>export BSOFT_HOME="/opt/Scipion3/software/em/bsoft-2.0.7"</span></p><p><span style='color:red'>export CCP4_HOME="/opt/Scipion3/software/em/ccp4-7.0.056"</span></p><p><span style='color:red'>export CHIMERA_HOME="/opt/Scipion3/software/em/chimerax-1.1"</span></p><p><span style='color:red'>export CISTEM_HOME="/opt/Scipion3/software/em/cistem-1.0.0-beta"</span></p><p><span style='color:red'>export CONDA_ACTIVATION_CMD="eval "$(/opt/Scipion3/software/em/eman-2.31/condabin/conda shell.bash hook)""</span></p><p><span style='color:red'>export CONTINUOUSFLEX_HOME="/opt/Scipion3/software/em/xmipp"</span></p><p><span style='color:red'>export CRYOASSESS_ENV_ACTIVATION="conda activate cryoassess-0.1.0"</span></p><p><span style='color:red'>export CRYOASSESS_MODEL_2D="/opt/Scipion3/software/em/cryoassess-models/2dassess_062119.h5"</span></p><p><span style='color:red'>export CRYOASSESS_MODEL_MIC="/opt/Scipion3/software/em/cryoassess-models/micassess_051419.h5"</span></p><p><span style='color:red'>export CRYOLO_CUDA_LIB="/usr/local/cuda/lib64"</span></p><p><span style='color:red'>export CRYOLO_ENV_ACTIVATION="conda activate cryolo-1.7.6"</span></p><p><span style='color:red'>export CRYOLO_ENV_ACTIVATION_CPU="conda activate cryoloCPU-1.7.6"</span></p><p><span style='color:red'>export CRYOLO_GENERIC_DENOISED_MODEL="/opt/Scipion3/software/em/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5"</span></p><p><span style='color:red'>export CRYOLO_GENERIC_MODEL="/opt/Scipion3/software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5"</span></p><p><span style='color:red'>export CRYOLO_NS_GENERIC_MODEL="/opt/Scipion3/software/em/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5"</span></p><p><span style='color:red'>export CRYOSPARC_HOME="/home/panos/software/cryosparc"</span></p><p><span style='color:red'>export CRYOSPARC_USER="ctueting"</span></p><p><span style='color:red'>export CRYO_PROJECTS_DIR="/data1/ScipionUserData/projects/cryosparc_plugin"</span></p><p><span style='color:red'>export CTFFIND4_HOME="/opt/Scipion3/software/em/ctffind4-4.1.14"</span></p><p><span style='color:red'>export DOGPICKER_HOME="/opt/Scipion3/software/em/dogpicker-0.2.1.1"</span></p><p><span style='color:red'>export DYNAMO_HOME="/opt/Scipion3/software/em/dynamo-1.146"</span></p><p><span style='color:red'>export EMAN2SCRATCHDIR="/tmp"</span></p><p><span style='color:red'>export EMAN2_HOME="/opt/Scipion3/software/em/eman-2.31"</span></p><p><span style='color:red'>export EMFACILITIES_HOME="/opt/Scipion3/software/em/"</span></p><p><span style='color:red'>export EMPIAR_TOKEN=""</span></p><p><span style='color:red'>export EMXLIB_HOME="/opt/Scipion3/software/em/emx_export-1.0.0"</span></p><p><span style='color:red'>export EM_ROOT="software/em"</span></p><p><span style='color:red'>export ETHAN_HOME="/opt/Scipion3/software/em/ethan-1.2"</span></p><p><span style='color:red'>export FSC3D_ACTIVATION_CMD="conda activate 3DFSC"</span></p><p><span style='color:red'>export FSC3D_HOME="/opt/Scipion3/software/em/fsc3D-3.0"</span></p><p><span style='color:red'>export GAUTOMATCH="Gautomatch_v0.56_sm30-75_cu10.1"</span></p><p><span style='color:red'>export GAUTOMATCH_CUDA_LIB="/usr/local/cuda/lib64"</span></p><p><span style='color:red'>export GAUTOMATCH_HOME="/opt/Scipion3/software/em/gautomatch-0.56"</span></p><p><span style='color:red'>export GCTF="Gctf-v1.06_sm_30_cu8.0_x86_64"</span></p><p><span style='color:red'>export GCTF_CUDA_LIB="/usr/local/cuda-8.0/lib64"</span></p><p><span style='color:red'>export GCTF_HOME="/opt/Scipion3/software/em/Gctf_v1.06"</span></p><p><span style='color:red'>export IMAGIC_HOME="/opt/Scipion3/software/em/imagic-190830"</span></p><p><span style='color:red'>export IMOD_HOME="/opt/Scipion3/software/em/imod-4.10.42/IMOD"</span></p><p><span style='color:red'>export JANNI_GENERIC_MODEL="/opt/Scipion3/software/em/janni_model-20190703/gmodel_janni_20190703.h5"</span></p><p><span style='color:red'>export JAVA_MAX_MEMORY="12"</span></p><p><span style='color:red'>export LOCSCALE_HOME="/opt/Scipion3/software/em/locscale-0.1"</span></p><p><span style='color:red'>export MAXIT_HOME="/opt/Scipion3/software/em/maxit-10.1"</span></p><p><span style='color:red'>export MOTIONCOR2_BIN="MotionCor2_1.3.2-Cuda100"</span></p><p><span style='color:red'>export MOTIONCOR2_CUDA_LIB="/usr/local/cuda/lib64"</span></p><p><span style='color:red'>export MOTIONCOR2_HOME="/opt/Scipion3/software/em/motioncor2-1.3.2"</span></p><p><span style='color:red'>export NMA_HOME="/opt/Scipion3/software/em/nma"</span></p><p><span style='color:red'>export NOVACTF_HOME="/opt/Scipion3/software/em/novactf-master"</span></p><p><span style='color:red'>export PHENIX_HOME="/opt/Scipion3/software/em/phenix-"</span></p><p><span style='color:red'>export RELION_CUDA_BIN="/usr/local/cuda/bin"</span></p><p><span style='color:red'>export RELION_CUDA_LIB="/usr/local/cuda/lib64"</span></p><p><span style='color:red'>export RELION_HOME="/opt/Scipion3/software/em/relion-3.1.0"</span></p><p><span style='color:red'>export RESMAP="ResMap-1.95-cuda-Centos7x64"</span></p><p><span style='color:red'>export RESMAP_GPU_LIB="ResMap_krnl-cuda-V8.0.61-sm60_gpu.so"</span></p><p><span style='color:red'>export RESMAP_HOME="/opt/Scipion3/software/em/resmap-1.95"</span></p><p><span style='color:red'>export SCIPION_CONFIG="/opt/Scipion3/config/scipion.conf"</span></p><p><span style='color:red'>export SCIPION_CWD="/home/panos"</span></p><p><span style='color:red'>export SCIPION_DOMAIN="pwem"</span></p><p><span style='color:red'>export SCIPION_FONT_NAME="Helvetica"</span></p><p><span style='color:red'>export SCIPION_HOME="/opt/Scipion3"</span></p><p><span style='color:red'>export SCIPION_HOSTS="/opt/Scipion3/config/hosts.conf"</span></p><p><span style='color:red'>export SCIPION_LOCAL_CONFIG="/home/panos/.config/scipion/scipion.conf"</span></p><p><span style='color:red'>export SCIPION_LOG="/home/panos/ScipionUserData/logs/scipion.log"</span></p><p><span style='color:red'>export SCIPION_LOGO="scipion_logo.gif"</span></p><p><span style='color:red'>export SCIPION_LOGS="/home/panos/ScipionUserData/logs"</span></p><p><span style='color:red'>export SCIPION_NOTES_FILE="notes.txt"</span></p><p><span style='color:red'>export SCIPION_NOTIFY="True"</span></p><p><span style='color:red'>export SCIPION_PLUGIN_REPO_URL="http://scipion.i2pc.es/getplugins/"</span></p><p><span style='color:red'>export SCIPION_PROTOCOLS="/opt/Scipion3/config/protocols.conf"</span></p><p><span style='color:red'>export SCIPION_SOFTWARE="/opt/Scipion3/software"</span></p><p><span style='color:red'>export SCIPION_SUPPORT_EMAIL="sc...@cn..."</span></p><p><span style='color:red'>export SCIPION_TESTS="/opt/Scipion3/data/tests"</span></p><p><span style='color:red'>export SCIPION_TESTS_CMD="scipion3 tests"</span></p><p><span style='color:red'>export SCIPION_TESTS_OUTPUT="/home/panos/ScipionUserData/Tests"</span></p><p><span style='color:red'>export SCIPION_TMP="/home/panos/ScipionUserData/tmp"</span></p><p><span style='color:red'>export SCIPION_URL="http://scipion.cnb.csic.es/downloads/scipion"</span></p><p><span style='color:red'>export SCIPION_URL_SOFTWARE="http://scipion.cnb.csic.es/downloads/scipion/software"</span></p><p><span style='color:red'>export SCIPION_URL_TESTDATA="http://scipion.cnb.csic.es/downloads/scipion/data/tests"</span></p><p><span style='color:red'>export SCIPION_USER_DATA="/data1/ScipionUserData"</span></p><p><span style='color:red'>export SCIPION_VERSION="v3.0.7 - Eugenius"</span></p><p><span style='color:red'>export SIDESPLITTER_HOME="/opt/Scipion3/software/em/sidesplitter-1.2"</span></p><p><span style='color:red'>export SPIDER="spider_linux_mp_intel64"</span></p><p><span style='color:red'>export SPIDER_HOME="/opt/Scipion3/software/em/spider-26.06"</span></p><p><span style='color:red'>export SPIDER_MPI="spider_linux_mpi_opt64"</span></p><p><span style='color:red'>export TOPAZ_ENV_ACTIVATION="conda activate topaz-0.2.3"</span></p><p><span style='color:red'>export VMD_HOME="/usr/local/lib/vmd"</span></p><p><span style='color:red'>export WIZARD_MASK_COLOR="[0.125, 0.909, 0.972]"</span></p><p><span style='color:red'>export XMIPP2_HOME="/opt/Scipion3/software/em/Xmipp-2.4-src"</span></p><p><span style='color:red'>export XMIPP_HOME="/opt/Scipion3/software/em/xmipp"</span></p><p><span style='color:red'>[panos@cryoem01 ~]$</span></p><p><b><span style='color:black;background:yellow'>scipion3 run printenv</span></b></p><p> </p><p><span style='color:red'>[panos@cryoem01 ~]$ scipion3 run printenv</span></p><p><span style='color:red'>Scipion v3.0.7 - Eugenius</span></p><p><span style='color:red'>** Running command: printenv </span></p><p><span style='color:red'>SCIPION_VERSION=v3.0.7 - Eugenius</span></p><p><span style='color:red'>SCIPION_LOGO=scipion_logo.gif</span></p><p><span style='color:red'>GAUTOMATCH_CUDA_LIB=/usr/local/cuda/lib64</span></p><p><span style='color:red'>MAXIT_HOME=software/em/maxit-10.1</span></p><p><span style='color:red'>XDG_SESSION_ID=c3</span></p><p><span style='color:red'>SSH_AGENT_PID=2160</span></p><p><span style='color:red'>IMOD_DIR=/usr/local/IMOD</span></p><p><span style='color:red'>HOSTNAME=cryoem01</span></p><p><span style='color:red'>SCIPION_FONT_NAME=Helvetica</span></p><p><span style='color:red'>RELION_CUDA_BIN=/usr/local/cuda/bin</span></p><p><span style='color:red'>IMSETTINGS_INTEGRATE_DESKTOP=yes</span></p><p><span style='color:red'>XRDP_SOCKET_PATH=/run/xrdp</span></p><p><span style='color:red'>CRYOLO_GENERIC_DENOISED_MODEL=software/em/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5</span></p><p><span style='color:red'>SCIPION_TESTS_CMD=scipion3 tests</span></p><p><span style='color:red'>VTE_VERSION=5204</span></p><p><span style='color:red'>XDG_MENU_PREFIX=gnome-</span></p><p><span style='color:red'>SHELL=/bin/bash</span></p><p><span style='color:red'>TERM=xterm-256color</span></p><p><span style='color:red'>SIDESPLITTER_HOME=software/em/sidesplitter-1.2</span></p><p><span style='color:red'>HISTSIZE=1000</span></p><p><span style='color:red'>IMOD_QTLIBDIR=/usr/local/IMOD/qtlib</span></p><p><span style='color:red'>SCIPION_NOTIFY=True</span></p><p><span style='color:red'>SCIPION_URL=http://scipion.cnb.csic.es/downloads/scipion</span></p><p><span style='color:red'>CISTEM_HOME=software/em/cistem-1.0.0-beta</span></p><p><span style='color:red'>SPIDER_HOME=software/em/spider-26.06</span></p><p><span style='color:red'>SCIPION_DOMAIN=pwem</span></p><p><span style='color:red'>SCIPION_USER_DATA=/data1/ScipionUserData</span></p><p><span style='color:red'>CRYOLO_GENERIC_MODEL=software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5</span></p><p><span style='color:red'>SCIPION_TESTS_OUTPUT=/home/panos/ScipionUserData/Tests</span></p><p><span style='color:red'>GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/409e3dd0_2aca_48db_a92c_2905ab5689a1</span></p><p><span style='color:red'>GJS_DEBUG_OUTPUT=stderr</span></p><p><span style='color:red'>DOGPICKER_HOME=software/em/dogpicker-0.2.1.1</span></p><p><span style='color:red'>SCIPION_PROTOCOLS=/opt/Scipion3/config/protocols.conf</span></p><p><span style='color:red'>CCP4_HOME=software/em/ccp4-7.0.056</span></p><p><span style='color:red'>CRYOASSESS_ENV_ACTIVATION=conda activate cryoassess-0.1.0</span></p><p><span style='color:red'>DYNAMO_HOME=software/em/dynamo-1.146</span></p><p><span style='color:red'>PHENIX_HOME=software/em/phenix-</span></p><p><span style='color:red'>GJS_DEBUG_TOPICS=JS ERROR;JS LOG</span></p><p><span style='color:red'>SCIPION_HOSTS=/opt/Scipion3/config/hosts.conf</span></p><p><span style='color:red'>GAUTOMATCH_HOME=software/em/gautomatch-0.56</span></p><p><span style='color:red'>SCIPION_PLUGIN_REPO_URL=http://scipion.i2pc.es/getplugins/</span></p><p><span style='color:red'>CRYOLO_NS_GENERIC_MODEL=software/em/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5</span></p><p><span style='color:red'>GCTF_HOME=software/em/Gctf_v1.06</span></p><p><span style='color:red'>LC_ALL=en_US.UTF-8</span></p><p><span style='color:red'>CRYOASSESS_MODEL_MIC=software/em/cryoassess-models/micassess_051419.h5</span></p><p><span style='color:red'>IMSETTINGS_MODULE=none</span></p><p><span style='color:red'>CUDA_HOME=/usr/local/cuda</span></p><p><span style='color:red'>USER=panos</span></p><p><span style='color:red'>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:</span></p><p><span style='color:red'>LD_LIBRARY_PATH=/usr/local/cuda-10.0/lib64:/opt/Scipion3/software/lib</span></p><p><span style='color:red'>SCIPION_URL_TESTDATA=http://scipion.cnb.csic.es/downloads/scipion/data/tests</span></p><p><span style='color:red'>MOTIONCOR2_BIN=MotionCor2_1.3.2-Cuda100</span></p><p><span style='color:red'>GNOME_TERMINAL_SERVICE=:1.103</span></p><p><span style='color:red'>SCIPION_SUPPORT_EMAIL=sc...@cn...</span></p><p><span style='color:red'>GCTF=Gctf-v1.06_sm_30_cu8.0_x86_64</span></p><p><span style='color:red'>XMIPP_HOME=software/em/xmipp</span></p><p><span style='color:red'>FSC3D_HOME=software/em/fsc3D-3.0</span></p><p><span style='color:red'>SSH_AUTH_SOCK=/tmp/ssh-ZJq5X9BOWO6G/agent.1847</span></p><p><span style='color:red'>SPIDER_MPI=spider_linux_mpi_opt64</span></p><p><span style='color:red'>SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/1847,unix/unix:/tmp/.ICE-unix/1847</span></p><p><span style='color:red'>CRYOLO_ENV_ACTIVATION_CPU=conda activate cryoloCPU-1.7.6</span></p><p><span style='color:red'>EMPIAR_TOKEN=</span></p><p><span style='color:red'>VIRTUAL_ENV=/opt/Scipion3/.scipion3env</span></p><p><span style='color:red'>XRDP_PULSE_SINK_SOCKET=xrdp_chansrv_audio_out_socket_10</span></p><p><span style='color:red'>SCIPION_CWD=/home/panos</span></p><p><span style='color:red'>PULSE_SCRIPT=/etc/xrdp/pulse/default.pa</span></p><p><span style='color:red'>SCIPION_TESTS=/opt/Scipion3/data/tests</span></p><p><span style='color:red'>SPIDER=spider_linux_mp_intel64</span></p><p><span style='color:red'>GNOME_SHELL_SESSION_MODE=classic</span></p><p><span style='color:red'>CRYOSPARC_USER=ctueting</span></p><p><span style='color:red'>MAIL=/var/spool/mail/panos</span></p><p><span style='color:red'>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</span></p><p><span style='color:red'>SCIPION_LOGS=/home/panos/ScipionUserData/logs</span></p><p><span style='color:red'>SCIPION_CONFIG=/opt/Scipion3/config/scipion.conf</span></p><p><span style='color:red'>IMOD_PLUGIN_DIR=/usr/local/IMOD/lib/imodplug</span></p><p><span style='color:red'>QT_IM_MODULE=ibus</span></p><p><span style='color:red'>_=/bin/printenv</span></p><p><span style='color:red'>CRYOLO_ENV_ACTIVATION=conda activate cryolo-1.7.6</span></p><p><span style='color:red'>WIZARD_MASK_COLOR=[0.125, 0.909, 0.972]</span></p><p><span style='color:red'>ATSAS_HOME=software/em/atsas-3.0.1</span></p><p><span style='color:red'>JANNI_GENERIC_MODEL=software/em/janni_model-20190703/gmodel_janni_20190703.h5</span></p><p><span style='color:red'>PWD=/home/panos</span></p><p><span style='color:red'>XMODIFIERS=@im=ibus</span></p><p><span style='color:red'>CRYOLO_CUDA_LIB=/usr/local/cuda/lib64</span></p><p><span style='color:red'>ETHAN_HOME=software/em/ethan-1.2</span></p><p><span style='color:red'>GCTF_CUDA_LIB=/usr/local/cuda-8.0/lib64</span></p><p><span style='color:red'>MOTIONCOR2_HOME=software/em/motioncor2-1.3.2</span></p><p><span style='color:red'>XMIPP2_HOME=software/em/Xmipp-2.4-src</span></p><p><span style='color:red'>pkgdir=/usr/local/I-TASSER5.1</span></p><p><span style='color:red'>XRDP_SESSION=1</span></p><p><span style='color:red'>IMOD_JAVADIR=/usr/local/java</span></p><p><span style='color:red'>SCIPION_SOFTWARE=/opt/Scipion3/software</span></p><p><span style='color:red'>LANG=en_US.UTF-8</span></p><p><span style='color:red'>XRDP_PULSE_SOURCE_SOCKET=xrdp_chansrv_audio_in_socket_10</span></p><p><span style='color:red'>SCIPION_NOTES_FILE=notes.txt</span></p><p><span style='color:red'>CRYOASSESS_MODEL_2D=software/em/cryoassess-models/2dassess_062119.h5</span></p><p><span style='color:red'>CRYOSPARC_HOME=/home/panos/software/cryosparc</span></p><p><span style='color:red'>MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles</span></p><p><span style='color:red'>SCIPION_URL_SOFTWARE=http://scipion.cnb.csic.es/downloads/scipion/software</span></p><p><span style='color:red'>GAUTOMATCH=Gautomatch_v0.56_sm30-75_cu10.1</span></p><p><span style='color:red'>RELION_CUDA_LIB=/usr/local/cuda/lib64</span></p><p><span style='color:red'>LOADEDMODULES=</span></p><p><span style='color:red'>LOCSCALE_HOME=software/em/locscale-0.1</span></p><p><span style='color:red'>FOR_DISABLE_STACK_TRACE=1</span></p><p><span style='color:red'>EMFACILITIES_HOME=software/em/</span></p><p><span style='color:red'>ASCP=~/.aspera/connect/bin/ascp</span></p><p><span style='color:red'>RESMAP_HOME=software/em/resmap-1.95</span></p><p><span style='color:red'>SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass</span></p><p><span style='color:red'>HISTCONTROL=ignoredups</span></p><p><span style='color:red'>ASPERA_SCP_PASS=</span></p><p><span style='color:red'>SHLVL=5</span></p><p><span style='color:red'>HOME=/home/panos</span></p><p><span style='color:red'>CONDA_ACTIVATION_CMD=eval "$(/opt/Scipion3/software/em/eman-2.31/condabin/conda shell.bash hook)"</span></p><p><span style='color:red'>CTFFIND4_HOME=software/em/ctffind4-4.1.14</span></p><p><span style='color:red'>MOTIONCOR2_CUDA_LIB=/usr/local/cuda/lib64</span></p><p><span style='color:red'>SCIPION_TMP=/home/panos/ScipionUserData/tmp</span></p><p><span style='color:red'>EMAN2_HOME=software/em/eman-2.31</span></p><p><span style='color:red'>GNOME_DESKTOP_SESSION_ID=this-is-deprecated</span></p><p><span style='color:red'>CRYO_PROJECTS_DIR=/data1/ScipionUserData/projects/cryosparc_plugin</span></p><p><span style='color:red'>IMAGIC_HOME=software/em/imagic-190830</span></p><p><span style='color:red'>SCIPION_LOCAL_CONFIG=/home/panos/.config/scipion/scipion.conf</span></p><p><span style='color:red'>PYTHONPATH=:/opt/Scipion3/software/bindings</span></p><p><span style='color:red'>LOGNAME=panos</span></p><p><span style='color:red'>NOVACTF_HOME=software/em/novactf-master</span></p><p><span style='color:red'>BSOFT_HOME=software/em/bsoft-2.0.7</span></p><p><span style='color:red'>DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-FKQakXHYCC,guid=649474707764c616b7441e9f60802f4a</span></p><p><span style='color:red'>XDG_DATA_DIRS=/home/panos/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share</span></p><p><span style='color:red'>MODULESHOME=/usr/share/Modules</span></p><p><span style='color:red'>MPI_HOME=/usr/local/mpich-3.2.1</span></p><p><span style='color:red'>UID=1000</span></p><p><span style='color:red'>CONTINUOUSFLEX_HOME=software/em/xmipp</span></p><p><span style='color:red'>LESSOPEN=||/usr/bin/lesspipe.sh %s</span></p><p><span style='color:red'>IMOD_CALIB_DIR=/usr/local/ImodCalib</span></p><p><span style='color:red'>JAVA_MAX_MEMORY=12</span></p><p><span style='color:red'>RESMAP=ResMap-1.95-cuda-Centos7x64</span></p><p><span style='color:red'>EMAN2SCRATCHDIR=/tmp</span></p><p><span style='color:red'>SCIPION_HOME=/opt/Scipion3</span></p><p><span style='color:red'>FSC3D_ACTIVATION_CMD=conda activate 3DFSC</span></p><p><span style='color:red'>RELION_HOME=software/em/relion-3.1.0</span></p><p><span style='color:red'>VMD_HOME=/usr/local/lib/vmd</span></p><p><span style='color:red'>VIEWERS={"Volume":["pwem.viewers.DataViewer"], "VolumeMask":["pwem.viewers.DataViewer"]}</span></p><p><span style='color:red'>DISPLAY=:10.0</span></p><p><span style='color:red'>XDG_RUNTIME_DIR=/run/user/1000</span></p><p><span style='color:red'>SCIPION_LOG=/home/panos/ScipionUserData/logs/scipion.log</span></p><p><span style='color:red'>XDG_CURRENT_DESKTOP=GNOME</span></p><p><span style='color:red'>EM_ROOT=software/em</span></p><p><span style='color:red'>NMA_HOME=software/em/nma</span></p><p><span style='color:red'>COLORTERM=truecolor</span></p><p><span style='color:red'>CHIMERA_HOME=software/em/chimerax-1.1</span></p><p><span style='color:red'>EMXLIB_HOME=software/em/emx_export-1.0.0</span></p><p><span style='color:red'>IMOD_HOME=software/em/imod-4.10.42/IMOD</span></p><p><span style='color:red'>RESMAP_GPU_LIB=ResMap_krnl-cuda-V8.0.61-sm60_gpu.so</span></p><p><span style='color:red'>TOPAZ_ENV_ACTIVATION=conda activate topaz-0.2.3</span></p><p><span style='color:red'>BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*`</span></p><p><span style='color:red'>}</span></p><p><span style='color:red'>[panos@cryoem01 ~]$</span></p><p><span style='color:red'> </span></p><p> </p><p>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p> </p><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p><b>From: </b><a href="mailto:pc...@cn...">Pablo Conesa</a><br><b>Sent: </b>Wednesday, April 21, 2021 7:06 PM<br><b>To: </b><a href="mailto:sci...@li...">sci...@li...</a><br><b>Subject: </b>Re: [scipion-users] Antw: Re: Re: Antw: RE: deep consensus pickling error</p></div><p> </p><p>You have eman2 acting as a conda manager, that is a problem.</p><p>At least the environment is not listed there. </p><p>Does the other plugins work? e.g. cryolo?</p><p>Can you send the output of:</p><p>scipion3 printenv </p><p>and </p><p>scipion3 run printenv</p><p>?</p><div><p>On 21/4/21 17:06, Dmitry Semchonok wrote:</p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>Dear colleagues, </p><div><p>Just to add our current error from the xmipp deep learning installation.</p></div><div><p> </p></div><div><p>Interestingly we almost fun to an end of this step but conda issue appeared.</p></div><div><p> </p></div><div><p>Any suggestions?</p></div><div><p> </p></div><div><p> </p></div><div><p> </p></div><div><p><span style='color:#0433FF'>currentDir: /data1/ScipionUserData/projects/Image_processing_cn_10688</span></p></div><div><p><span style='color:#0433FF'>00890: workingDir: Runs/007643_XmippProtScreenDeepLearning</span></p></div><div><p><span style='color:#0433FF'>00891: runMode: Continue</span></p></div><div><p><span style='color:#0433FF'>00892: MPI: 1</span></p></div><div><p><span style='color:#0433FF'>00893: threads: 4</span></p></div><div><p><span style='color:#0433FF'>00894: Starting at step: 3</span></p></div><div><p><span style='color:#0433FF'>00895: Running steps</span></p></div><div><p><span style='color:#0433FF'>00896: STARTED: predict, step 3, time 2021-04-20 11:08:26.633086</span></p></div><div><p><span style='color:#0433FF'>00897: </span></p></div><div><p><span style='color:#0433FF'>00898: $ /usr/local/EMAN_2.21/bin/conda info --env</span></p></div><div><p><span style='color:#0433FF'>00899: # conda environments:</span></p></div><div><p><span style='color:#0433FF'>00900: #</span></p></div><div><p><span style='color:#0433FF'>00901: 3DFSC /home/panos/.conda/envs/3DFSC</span></p></div><div><p><span style='color:#0433FF'>00902: cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0</span></p></div><div><p><span style='color:#0433FF'>00903: cryolo /home/panos/.conda/envs/cryolo</span></p></div><div><p><span style='color:#0433FF'>00904: cryolo /usr/local/EMAN_2.21/envs/cryolo</span></p></div><div><p><span style='color:#0433FF'>00905: cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4</span></p></div><div><p><span style='color:#0433FF'>00906: fsc /usr/local/EMAN_2.21/envs/fsc</span></p></div><div><p><span style='color:#0433FF'>00907: topaz /usr/local/EMAN_2.21/envs/topaz</span></p></div><div><p><span style='color:#0433FF'>00908: root * /usr/local/EMAN_2.21</span></p></div><div><p><span style='color:#0433FF'>00909: </span></p></div><div><p><span style='color:#0433FF'>00910: </span></p></div><div><p><span style='color:#0433FF'>00911: >>> 'xmipp_DLTK_v0.3' conda environment not found... (check list above)</span></p></div><div><p><span style='color:#0433FF'>00912: Traceback (most recent call last):</span></p></div><div><p><span style='color:#0433FF'>00913: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 189, in run</span></p></div><div><p><span style='color:#0433FF'>00914: self._run()</span></p></div><div><p><span style='color:#0433FF'>00915: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run</span></p></div><div><p><span style='color:#0433FF'>00916: resultFiles = self._runFunc()</span></p></div><div><p><span style='color:#0433FF'>00917: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc</span></p></div><div><p><span style='color:#0433FF'>00918: return self._func(*self._args)</span></p></div><div><p><span style='color:#0433FF'>00919: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/protocols/protocol_screen_deeplearning.py", line 319, in predict</span></p></div><div><p><span style='color:#0433FF'>00920: env=self.getCondaEnv())</span></p></div><div><p><span style='color:#0433FF'>00921: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py", line 204, in getCondaEnv</span></p></div><div><p><span style='color:#0433FF'>00922: return CondaEnvManager.getCondaEnv(env, envName)</span></p></div><div><p><span style='color:#0433FF'>00923: File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in getCondaEnv</span></p></div><div><p><span style='color:#0433FF'>00924: envBin = os.path.join(environDir, "bin")</span></p></div><div><p><span style='color:#0433FF'>00925: File "/usr/lib64/python3.6/posixpath.py", line 80, in join</span></p></div><div><p><span style='color:#0433FF'>00926: a = os.fspath(a)</span></p></div><div><p><span style='color:#0433FF'>00927: TypeError: expected str, bytes or os.PathLike object, not NoneType</span></p></div><div><p><span style='color:#0433FF'>00928: Protocol failed: expected str, bytes or os.PathLike object, not NoneType</span></p></div><div><p><span style='color:#0433FF'>00929: FAILED: predict, step 3, time 2021-04-20 11:08:27.020467</span></p></div><div><p><span style='color:#0433FF'>00930: *** Last status is failed </span></p></div><div><p><span style='color:#0433FF'>00931: ------------------- PROTOCOL FAILED (DONE 3/4)</span></p></div><div><p> </p></div><div><p> </p></div><div><p>Thank you!</p></div><div><p> </p></div><div><p> </p></div><div><p>Sincerely,</p></div><div><p>Dmitry</p></div><div><p> </p></div><div><p> </p><div><p style='margin-bottom:12.0pt'><o:p> </o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p>On 20. Apr 2021, at 11:25, Christian Tüting <<a href="mailto:chr...@bi...">chr...@bi...</a>> wrote:</p></div><p> </p><div><div><p style='margin-bottom:12.0pt'>Hi,<br><br>thank you for your response. I tried this twice. The first time, the<br>"_BACKUP2" folder was popping up again under .conda/envs, so I followed<br>your steps again, deleting the folder under software and removed the<br>conda enviroment, and now, no enviroment is generated at all. Logically,<br>running a job gives this error: ">>> 'xmipp_DLTK_v0.3' conda environment<br>not found... (check list above)". <br><br>Another long-term job is currently running, after this is done, we will<br>restart everything to have a clean system. But do you have any<br>additional tips?<br><br>Thanks in advance<br>Christian<br><br><br><br></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>David Maluenda <<a href="mailto:dma...@ub...">dma...@ub...</a>> 20.04.21 10.02 Uhr >>></p></blockquote></blockquote></blockquote><p style='margin-bottom:12.0pt'>Hi Christian,<br><br>If it already works, I would leave it as it is.<br><br>To make a clear installation, you don't need to reinstall the whole<br>xmipp. You can just reinstall the deepLearningToolkit by<br><br>rm -rf /opt/Scipion3/software/em/deepLearningToolkit<br>conda env remove --name xmipp_DLTK_v0.3_BACKUP2<br>scipion3 installb deepLearningToolkit<br><br><br>Cheers,<br><br><<a href="http://ucm.es/">http://ucm.es/</a>><br>_____<br>Dr. David Maluenda Niubó<br><a href="mailto:dma...@ub...">dma...@ub...</a><<a href="mailto:dma...@ub...">mailto:dma...@ub...</a>> - (+34) 619 029 310<br>Wavefront Engineering<br>Group<<a href="https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA">https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA</a>><br>Applied Physics - UB<<a href="https://www.ub.edu/portal/web/dp-fisica-aplicada">https://www.ub.edu/portal/web/dp-fisica-aplicada</a>><br><br>This email message and any documents attached to it may contain<br>confidential or legally protected material and are intended solely for<br>the use of the individual or organization to whom they are addressed. We<br>remind you that if you are not the intended recipient of this email<br>message or the person responsible for processing it, then you are not<br>authorized to read, save, modify, send, copy or disclose any of its<br>contents. If you have received this email message by mistake, we kindly<br>ask you to inform the sender of this and to eliminate both the message<br>and any attachments it carries from your account. Thank you for your<br>collaboration.<br><br><br><br>On Tue, Apr 20, 2021 at 9:53 AM Christian Tüting<br><<a href="mailto:chr...@bi...">chr...@bi...</a><<a href="mailto:chr...@bi...">mailto:chr...@bi...</a>>><br>wrote:<br>Hi Pablo,<br><br>I will take an eye on this. I have a question regarding dependencies:<br>tensorflow 1.15 requires keras-application>=1.0.8 and<br>keras-preprocessing>=1.0.5, but keras 2.2 requieres older versions<br>(1.0.2 and 1.0.1, respectivly).<br><br>Should we try to uninstall and a clean reinstall of xmipp, to resolve<br>all dependency issues?<br><br>Thank you for your support.<br><br>Best<br>Christian<br><br><br></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>Pablo Conesa <<a href="mailto:pc...@cn...">pc...@cn...</a><<a href="mailto:pc...@cn...">mailto:pc...@cn...</a>>></p></blockquote></blockquote></blockquote><p style='margin-bottom:12.0pt'>20.04.21 9.16 Uhr >>><br>Thanks Christian.<br><br>In theory, xmipp defines dependencies strictly<br>(<a href="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</a>)<br><br>I do not know how it ended up with higher versions, but something to<br>keep an eye on.<br><br>On 20/4/21 7:00, Christian Tüting wrote:</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>Hi all,<br><br>first the conda path looks actually very strange, and I fixed this<br>direclty. We had some other issues, which were tensorflow-related, but<br>this is fixed.<br><br><br>Just to comment on that, there were first an issue with the tensorflow<br>module. Installing the latest release (2.x) gives an error on "module<br>'tensorflow' has no attribute 'Session'". After fixing that by<br>downgrading, keras was giving an error, that the module does not have</p></blockquote><p style='margin-bottom:12.0pt'>no</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>attribute "tf", which was also fixed by downgrading.<br><br><br><br>TL;DR Eventually, downgrading tensorflow to 1.15.0 and downgrading</p></blockquote><p style='margin-bottom:12.0pt'>keras</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'>to 2.2.4 (from 2.2.5) solved the issue<br><br><br>Best<br>Christian<br><br><br></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>"Dmitry A. Semchonok"</p></blockquote></blockquote></blockquote></blockquote><p style='margin-bottom:12.0pt'><<a href="mailto:sem...@gm...">sem...@gm...</a><<a href="mailto:sem...@gm...">mailto:sem...@gm...</a>>> 19.04.21 16.24 Uhr >>></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>Dear Carlos Oscar, Pablo, David, Ruben,<br><br><br>Thank you very much for your fast response.<br><br><br>Currently, deep learning is running.<br>A colleague of mine, Christian, kindly looked at the problem.<br><br><br>Let me, please post the errors we had and where we are now.<br>May be Christian can comment more on this issue.<br><br><br>Please see the errors here.<br><a href="https://yadi.sk/d/KlTeKv1O9UCTQg">https://yadi.sk/d/KlTeKv1O9UCTQg</a><br><br><br>Since> Sent: Monday, April 19, 2021 12:57 PM<br>To: Mailing list for Scipion users; Pablo Conesa; Rubén Sánchez; David<br>Maluenda<br>Subject: Re: [scipion-users] deep consensus pickling error<br><br><br>Dear Dmitry,<br>let us see if David or Rubén knows where this environment is coming<br>from.<br>Kind regards, Carlos Oscar<br>El 19/04/2021 a las 9:37, Pablo Conesa escribió:<br><br>Hi Dmitry... you have no environment for xmipp_DLTK_v0.3.<br>You have a "weird" xmipp_DLTK_v0.3_BACKUP2<br>/home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2<br><br>On 17/4/21 8:56, Dmitry A. Semchonok wrote:<br><br>Dear colleagues,<br><br>During deep consensus pickling I received the following error<br><br>Any ideas?<br><br>Thank you<br><br>Sincerely,<br>Dmitry<br><br><br><br>[Parallel(n_jobs=12)]: Done 176 tasks | elapsed: 1.8min<br>[Parallel(n_jobs=12)]: Done 426 tasks | elapsed: 4.3min<br>[Parallel(n_jobs=12)]: Done 776 tasks | elapsed: 7.5min<br>[Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: 11.5min<br>[Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: 16.7min<br>[Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: 23.7min<br>[Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: 32.1min<br>[Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: 41.4min<br>[Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: 51.8min<br>[Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min</p></blockquote><p style='margin-bottom:12.0pt'>finished</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>[35mFINISHED[0m: extractParticles, step 12, time 2021-04-17<br>04:05:07.093613<br>[35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17<br>04:05:07.574152<br>[35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17<br>04:26:59.879548<br>[35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444<br>None None None None<br><br>$ /usr/local/EMAN_2.21/bin/conda info --env<br># conda environments:<br>#<br>3DFSC /home/panos/.conda/envs/3DFSC<br>cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0<br>cryolo /home/panos/.conda/envs/cryolo> cryolo </p></blockquote><p style='margin-bottom:12.0pt'> /usr/local/EMAN_2.21/envs/cryolo</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'>cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4<br>fsc /usr/local/EMAN_2.21/envs/fsc<br>topaz /usr/local/EMAN_2.21/envs/topaz<br>root * /usr/local/EMAN_2.21<br><br><br></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>'xmipp_DLTK_v0.3' conda environment not found... (check list above)</p></blockquote></blockquote></blockquote><p style='margin-bottom:12.0pt'>Traceback (most recent call last):<br> File</p></blockquote><p style='margin-bottom:12.0pt'>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'>line 189, in run<br> self._run()<br> File</p></blockquote><p style='margin-bottom:12.0pt'>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'>line 240, in _run<br> resultFiles = self._runFunc()<br> File</p></blockquote><p style='margin-bottom:12.0pt'>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py",</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'>line 236, in _runFunc<br> return self._func(*self._args)<br> File<br>"/opt/Scipion env=self.getCondaEnv())<br> File</p></blockquote><p style='margin-bottom:12.0pt'>"/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py",</p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'>line 204, in getCondaEnv<br> return CondaEnvManager.getCondaEnv(env, envName)<br> File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in<br>getCondaEnv<br> envBin = os.path.join(environDir, "bin")<br> File "/usr/lib64/python3.6/posixpath.py", line 80, in join<br> a = os.fspath(a)<br>TypeError: expected str, bytes or os.PathLike object, not NoneType<br>[31mProtocol failed: expected str, bytes or os.PathLike object, not<br>NoneType[0m<br>[35mFAILED[0m: trainCNN, step 14, time 2021-04-17 04:27:00.607417<br>*** Last status is failed<br>Sent from Mail for Windows 10<br><br><br><br><br><br>_______________________________________________scipion-users mailing</p></blockquote><p style='margin-bottom:12.0pt'><a href="mailto:lis...@li...https">lis...@li...https</a>://lists.sourceforge.net/lists/listinfo/scipion-users--<a href="http://lists.sourceforge.net/lists/listinfo/scipion-users--"><http://lists.sourceforge.net/lists/listinfo/scipion-users--></a></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'><br>Pablo Conesa - Madrid Scipion team<br><br><br><br><br><br>_______________________________________________scipion-users mailing</p></blockquote><p style='margin-bottom:12.0pt'><a href="mailto:lis...@li...https">lis...@li...https</a>:/></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p style='margin-bottom:12.0pt'><o:p> </o:p></p></blockquote><p style='margin-bottom:12.0pt'>--<br>Pablo Conesa - *Madrid Scipion <<a href="http://scipion.i2pc.es">http://scipion.i2pc.es</a>> team*<br><br><br><br>Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir<br>informació confidencial o protegida legalment i s’adreça exclusivament a<br>la persona o entitat destinatària. Si no consteu com a destinatari final<br>o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo,<br>retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el<br>contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu<br>del sistema tant el missatge com els fitxers adjunts que hi pugui haver.<br><br>Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener<br>información confidencial o legalmente protegida y está exclusivamente<br>dirigido a la persona o entidad destinataria. Si usted no consta como<br>destinatario final ni es la persona encargada de recibirlo, no está<br>autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni<br>a revelar su contenido. Si lo ha recibido por error, informe de ello al<br>remitente y elimine del sistema tanto el mensaje como los ficheros<br>adjuntos que pueda contener.<br><br>This email message and any attachments it carries may contain<br>confidential or legally protected material and are intended solely for<br>the individual or organization to whom they are addressed. If you are<br>not the intended recipient of this message or the person responsible for<br>processing it, then you are not authorized to read, save, modify, send,<br>copy or disclose any part of it. If you have received the message by<br>mistake, please inform the sender of this and eliminate the message and<br>any attachments it carries from your account.<br><br><br>Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir<br>informació confidencial o protegida legalment i s’adreça exclusivament a<br>la persona o entitat destinatària. Si no consteu com a destinatari final<br>o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo,<br>retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el<br>contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu<br>del sistema tant el missatge com els fitxers adjunts que hi pugui haver.<br><br>Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener<br>información confidencial o legalmente protegida y está exclusivamente<br>dirigido a la persona o entidad destinataria. Si usted no consta como<br>destinatario final ni es la persona encargada de recibirlo, no está<br>autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni<br>a revelar su contenido. Si lo ha recibido por error, informe de ello al<br>remitente y elimine del sistema tanto el mensaje como los ficheros<br>adjuntos que pueda contener.<br><br>This email message and any attachments it carries may contain<br>confidential or legally protected material and are intended solely for<br>the individual or organization to whom they are addressed. If you are<br>not the intended recipient of this message or the person responsible for<br>processing it, then you are not authorized to read, save, modify, send,<br>copy or disclose any part of it. If you have received the message by<br>mistake, please inform the sender of this and eliminate the message and<br>any attachments it carries from your account.</p></div></div></blockquote></div><p> </p></div><p style='margin-bottom:12.0pt'><br><br></p><pre>_______________________________________________</pre><pre>scipion-users mailing list</pre><pre><a href="mailto:sci...@li...">sci...@li...</a></pre><pre><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></pre></blockquote><p>-- <br>Pablo Conesa - <strong><span style='font-family:"Calibri",sans-serif'>Madrid <a href="http://scipion.i2pc.es">Scipion</a> team</span></strong></p><p> </p></div></div></blockquote></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
