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

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

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.
>
>
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