Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo

[Grigory S. <sha...@gm...>]

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 <+44%201223%20267228>
e-mail: gs...@mr...


On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES <
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.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
> 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"$(/home/impmc/eman2-sphire-sparx/bin/conda
> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c
> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython
> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip
> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed')
>
> ------------------------------
> *From: *"Grigory Sharov" <sha...@gm...>
> *To: *"scipion-users" <sci...@li...>
> *Sent: *Wednesday, September 29, 2021 5:33:09 PM
> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using
> Cryolo
>
> Dear Carlos,
> given the fact that the installation has failed, could you attach all
> output after "scipion3 installp -p scipion-em-sphire" command?
>
> Best regards,
> Grigory
>
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
>
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +44 (0) 1223 267228 <+44%201223%20267228>
> e-mail: gs...@mr...
>
>
> On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES <
> car...@so...> wrote:
>
>> Dear all,
>>
>> I'm facing some problems using cryolo training at Scipion.
>> I found the following error:
>>
>> *Protocol failed: Command ' source
>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate
>> cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10
>> --fine_tune' returned non-zero exit status 127.*
>>
>> I saw some discussion about that at Scipion lists, but I'm still little
>> lost in how to fix it.
>> In my scipion.conf file, I inserted
>> *CONDA_ACTIVATION_CMD = source
>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh *
>> or even
>> CONDA_ACTIVATION_CMD = eval"$(/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...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>
>
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