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Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
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From: Pablo C. <pc...@cn...> - 2021-09-30 08:29:30
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I agree with Grigory, using eman2 conda is not a good practice. Probably he did not decided that but Scipion installer used the available one, and probably that one was eman2 one. If you want to undo this you will need to install miniconda, and have it available instead of eman2 one. "which conda" will tell you the available one. On 29/9/21 18:54, Grigory Sharov wrote: > Thanks! In run.stderr you can see the reason it has failed: > > 2021-09-30 02:14:42.492074: W > tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could > not load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: > cannot open shared object file: No such file or directory; > LD_LIBRARY_PATH: /usr/local/cuda/lib64::/home/impmc/scipion/software/lib > > For some reason it's looking for libcudnn.so.8 but the cryolo package > should have installed libcudnn.so.7.1.2 for you. Can you check that > a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I > dont know where is your env is installed. You can activate conda and > "check conda list env" > b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct > path for cryolo env. The previous command should tell you where it > should be > > In general, my advice would be to not use eman2 conda for anything > except eman. You'd be better off using a separate miniconda3 > installation. Which conda did you use for cryolo 1.8? From eman? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> wrote: > > Dear Grigory, > > The files that you requested are attached. > Thanks so much again > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" <sci...@li... > <mailto:sci...@li...>> > *Sent: *Wednesday, September 29, 2021 6:18:12 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD > using Cryolo > > Hi, > The config files look ok. Could you attach run.stderr and > run.stdout for the failed protocol? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> wrote: > > Dear Grigory, > > Thank you so much, fixing this space solved the problem with > cryolo_1.7.6_installing (shame on me for this). > However, I tried to run the cryolo training and I obtained the > same previous error: > > eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash > hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && > cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 > --fine_tune > 00022: Protocol failed: Command ' eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py > -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned > non-zero exit status 1. > 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 > 02:14:42.822982 > > Bellow, it is my current scipion.conf file > [PYWORKFLOW] > SCIPION_DOMAIN = pwem > SCIPION_FONT_NAME = Helvetica > SCIPION_GUI_REFRESH_IN_THREAD = False > SCIPION_LOG = ~/ScipionUserData/logs/scipion.log > SCIPION_LOGO = scipion_logo.gif > SCIPION_LOGS = ~/ScipionUserData/logs > SCIPION_NOTES_FILE = notes.txt > SCIPION_NOTIFY = True > SCIPION_PLUGIN_REPO_URL = http://scipion.i2pc.es/getplugins/ > <http://scipion.i2pc.es/getplugins/> > SCIPION_SOFTWARE = ${SCIPION_HOME}/software > SCIPION_SUPPORT_EMAIL = sc...@cn... > <mailto:sc...@cn...> > SCIPION_TESTS = ${SCIPION_HOME}/data/tests > SCIPION_TESTS_CMD = scipion3 tests > SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests > SCIPION_TMP = ~/ScipionUserData/tmp > SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion > <http://scipion.cnb.csic.es/downloads/scipion> > SCIPION_URL_SOFTWARE = > http://scipion.cnb.csic.es/downloads/scipion/software > <http://scipion.cnb.csic.es/downloads/scipion/software> > SCIPION_URL_TESTDATA = > http://scipion.cnb.csic.es/downloads/scipion/data/tests > <http://scipion.cnb.csic.es/downloads/scipion/data/tests> > SCIPION_USER_DATA = ~/ScipionUserData > WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] > CONDA_ACTIVATION_CMD = eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)" > > [PLUGINS] > CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 > CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 > CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta > CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 > CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 > CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 > CRYOLO_GENERIC_DENOISED_MODEL = > %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 > CRYOLO_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 > CRYOLO_NS_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 > CRYOSPARC_HOME = /home/impmc/ > CRYO_PROJECTS_DIR = scipion_projects > CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 > EMAN2SCRATCHDIR = /tmp > EMAN2_HOME = %(EM_ROOT)s/eman-2.91 > EM_ROOT = software/em > JANNI_GENERIC_MODEL = > %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 > MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 > MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 > MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 > MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 > PHENIX_HOME = %(EM_ROOT)s/phenix- > RELION_CUDA_LIB = /usr/local/cuda/lib64 > RELION_HOME = %(EM_ROOT)s/relion-3.1.2 > XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src > XMIPP_HOME = %(EM_ROOT)s/xmipp > > > Thanks again. > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" <sci...@li... > <mailto:sci...@li...>> > *Sent: *Wednesday, September 29, 2021 5:51:06 PM > *Subject: *Re: [scipion-users] Problems with > CONDA_ACTIVATION_CMD using Cryolo > > Hello Carlos, > > to start, you are missing a space between eval and the rest in: > CONDA_ACTIVATION_CMD = eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> wrote: > > Dear Grigory, > > Thanks for the message. The all output is bellow: > > Scipion v3.0.9 - Eugenius > Building scipion-em-sphire ... > /home/impmc/scipion/.scipion3/bin/python -m pip install > scipion-em-sphire==3.0.7 > Looking in indexes: https://pypi.org/simple > <https://pypi.org/simple>, https://pypi.ngc.nvidia.com > <https://pypi.ngc.nvidia.com> > Requirement already satisfied: scipion-em-sphire==3.0.7 in > ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) > Requirement already satisfied: scipion-em in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em-sphire==3.0.7) (3.0.13) > Requirement already satisfied: biopython==1.76 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-sphire==3.0.7) (1.76) > Requirement already satisfied: tifffile in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) > Requirement already satisfied: scipion-pyworkflow>=3.0.15 > in ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-sphire==3.0.7) (3.0.17) > Requirement already satisfied: numpy in > ./scipion/.scipion3/lib/python3.8/site-packages (from > biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) > (1.18.4) > Requirement already satisfied: mpi4py<=3.0.3 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (3.0.3) > Requirement already satisfied: configparser<=5.0.2 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (5.0.0) > Requirement already satisfied: psutil<=5.8.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (5.7.0) > Requirement already satisfied: pillow<=8.2.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (7.1.2) > Requirement already satisfied: bibtexparser<=1.2.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.2.0) > Requirement already satisfied: requests<=2.25.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.25.1) > Requirement already satisfied: matplotlib==3.2.2 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (3.2.2) > Requirement already satisfied: tkcolorpicker<=2.1.3 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.1.3) > Requirement already satisfied: cycler>=0.10 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (0.10.0) > Requirement already satisfied: python-dateutil>=2.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.8.1) > Requirement already satisfied: > pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.4.7) > Requirement already satisfied: kiwisolver>=1.0.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.3.1) > Requirement already satisfied: future>=0.16.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (0.18.2) > Requirement already satisfied: six in > ./scipion/.scipion3/lib/python3.8/site-packages (from > cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.16.0) > Requirement already satisfied: certifi>=2017.4.17 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2020.12.5) > Requirement already satisfied: urllib3<1.27,>=1.21.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.26.4) > Requirement already satisfied: chardet<5,>=3.0.2 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (4.0.0) > Requirement already satisfied: idna<3,>=2.5 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.10) > Done (0.84 seconds) > Building cryolo-1.7.6 ... > Skipping command: wget -nv -c -O > /home/impmc/scipion/software/em/void.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz > <http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz> > mv -v /home/impmc/scipion/software/em/void.tgz.part > /home/impmc/scipion/software/em/void.tgz > All targets exist. > Skipping command: mkdir > /home/impmc/scipion/software/em/cryolo-1.7.6 > All targets exist. > Skipping command: tar -xf void.tgz -C cryolo-1.7.6 > All targets exist. > cd /home/impmc/scipion/software/em/cryolo-1.7.6 > eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash > hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c > conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 > numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 > &&conda activate cryolo-1.7.6 &&pip install > cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed > /bin/sh: 1: evalexport > CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' > export _CE_M='' > export _CE_CONDA='' > export > CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' > > # Copyright (C) 2012 Anaconda, Inc > # SPDX-License-Identifier: BSD-3-Clause > > __add_sys_prefix_to_path() { > # In dev-mode CONDA_EXE is python.exe and on Windows > # it is in a different relative location to condabin. > if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then > SYSP=$(\dirname "${CONDA_EXE}") > else > SYSP=$(\dirname "${CONDA_EXE}") > SYSP=$(\dirname "${SYSP}") > fi > > if [ -n "${WINDIR+x}" ]; then > PATH="${SYSP}/bin:${PATH}" > PATH="${SYSP}/Scripts:${PATH}" > PATH="${SYSP}/Library/bin:${PATH}" > PATH="${SYSP}/Library/usr/bin:${PATH}" > PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" > PATH="${SYSP}:${PATH}" > else > PATH="${SYSP}/bin:${PATH}" > fi > \export PATH > } > > __conda_exe() ( > __add_sys_prefix_to_path > "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" > ) > > __conda_hashr() { > if [ -n "${ZSH_VERSION:+x}" ]; then > \rehash > elif [ -n "${POSH_VERSION:+x}" ]; then > : # pass > else > \hash -r > fi > } > > __conda_activate() { > if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then > # Handle transition from shell activated with > conda <= 4.3 to a subsequent activation > # after conda updated to >= 4.4. See issue #6173. > PS1="$CONDA_PS1_BACKUP" > \unset CONDA_PS1_BACKUP > fi > \local ask_conda > ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix > "$@")" || \return > \eval "$ask_conda" > __conda_hashr > } > > __conda_reactivate() { > \local ask_conda > ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix > reactivate)" || \return > \eval "$ask_conda" > __conda_hashr > } > > conda() { > \local cmd="${1-__missing__}" > case "$cmd" in > activate|deactivate) > __conda_activate "$@" > ;; > install|update|upgrade|remove|uninstall) > __conda_exe "$@" || \return > __conda_reactivate > ;; > *) > __conda_exe "$@" > ;; > esac > } > > if [ -z "${CONDA_SHLVL+x}" ]; then > \export CONDA_SHLVL=0 > # In dev-mode CONDA_EXE is python.exe and on Windows > # it is in a different relative location to condabin. > if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then > PATH="$(\dirname > "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" > else > PATH="$(\dirname "$(\dirname > "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" > fi > \export PATH > > # We're not allowing PS1 to be unbound. It must at > least be set. > # However, we're not exporting it, which can cause > problems when starting a second shell > # via a first shell (i.e. starting zsh from bash). > if [ -z "${PS1+x}" ]; then > PS1= > fi > fi > > conda activate base: not found > Traceback (most recent call last): > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 470, in <module> > main() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 293, in main > installPluginMethods() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 232, in installPluginMethods > plugin.installBin({'args': ['-j', numberProcessor]}) > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' > not built (after running > 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)"&&conda create -y -n > cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 > cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 > intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') > Error at main: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' > not built (after running > 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)"&&conda create -y -n > cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 > cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 > intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" <sci...@li... > <mailto:sci...@li...>> > *Sent: *Wednesday, September 29, 2021 5:33:09 PM > *Subject: *Re: [scipion-users] Problems with > CONDA_ACTIVATION_CMD using Cryolo > > Dear Carlos, > given the fact that the installation has failed, could you > attach all output after "scipion3 installp -p > scipion-em-sphire" command? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> > wrote: > > Dear all, > > I'm facing some problems using cryolo training at Scipion. > I found the following error: > *Protocol failed: Command ' source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& > conda activate cryolo-1.7.6 && cryolo_train.py -c > config.json -w 5 -g 0 -nc 4 -e 10 --fine_tune' > returned non-zero exit status 127. > * > * > * > I saw some discussion about that at Scipion lists, but > I'm still little lost in how to fix it. > In my scipion.conf file, I inserted > /CONDA_ACTIVATION_CMD = source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh /// > or even > CONDA_ACTIVATION_CMD = > eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook)"// > (I saw these pathways in my bash.rc) > > Moreover, when I try to install cryolo using command > line (scipion3 installp -p scipion-em-sphire), the > following error apears: > *AssertionError: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' > not built (after running 'source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda > create -y -n cryolo-1.7.6 -c conda-forge -c anaconda > python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython > wxPython==4.0.4 intel-openmp==2019.4 &&conda activate > cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch > cryolo_1.7.6_installed')* > > I am not sure if these errors are related and hinder > performing cryolo in Scipion. > I have conda installed in the computer and I'm able to > use cryolo 1.8 outside from Scipion in the same > computer (using /source activate cryolo /command). > > Anyone know what I'm doing wrong? Thanks in advance, > Carlos. > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
