Issue about installing Miniconda (conda: command not found)

Wesley

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May 7, 2020, 12:19:51 PM5/7/20

to moose-users

I am using Mint 18 in VMware workstation, the Mint 18 was downloaded from old moose website.

Now I am trying to reinstall MOOSE because of the python version update. I cannot activate moose after installing Miniconda.

1. I removed the moose-environment, then copy+paste all the instructions in the home directory (the home directory is /home/moose using pwd). I have done this several times so some files already exist.

moose@moose ~ $ curl -L -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 81.1M 100 81.1M 0 0 2716k 0 0:00:30 0:00:30 --:--:-- 1486k
moose@moose ~ $ bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/miniconda3
ERROR: File or directory already exists: '/home/moose/miniconda3'
If you want to update an existing installation, use the -u option.
moose@moose ~ $ export PATH=$HOME/miniconda3/bin:$PATH
moose@moose ~ $ conda config --add channels conda-forge
Warning: 'conda-forge' already in 'channels' list, moving to the top
moose@moose ~ $ conda config --add channels https://mooseframework.org/conda/moose
Warning: 'https://mooseframework.org/conda/moose' already in 'channels' list, moving to the top
moose@moose ~ $ conda create --name moose moose-libmesh moose-tools
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.2
latest version: 4.8.3
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/moose/miniconda3/envs/moose
added / updated specs:
- moose-libmesh
- moose-tools
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_llvm
beautifulsoup4 conda-forge/linux-64::beautifulsoup4-4.9.0-py37hc8dfbb8_0
binutils_impl_lin~ pkgs/main/linux-64::binutils_impl_linux-64-2.33.1-he6710b0_7
binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.33.1-h9595d00_16
bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_2
ca-certificates conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0
certifi conda-forge/linux-64::certifi-2020.4.5.1-py37hc8dfbb8_0
cloudpickle conda-forge/noarch::cloudpickle-1.4.1-py_0
cmake conda-forge/linux-64::cmake-3.17.0-h28c56e5_0
curl conda-forge/linux-64::curl-7.69.1-h33f0ec9_0
cycler conda-forge/noarch::cycler-0.10.0-py_2
cytoolz conda-forge/linux-64::cytoolz-0.10.1-py37h516909a_0
dask-core conda-forge/noarch::dask-core-2.15.0-py_0
dbus conda-forge/linux-64::dbus-1.13.6-he372182_0
decorator conda-forge/noarch::decorator-4.4.2-py_0
expat conda-forge/linux-64::expat-2.2.9-he1b5a44_2
fontconfig conda-forge/linux-64::fontconfig-2.13.1-h86ecdb6_1001
freetype conda-forge/linux-64::freetype-2.10.1-he06d7ca_0
future conda-forge/linux-64::future-0.18.2-py37hc8dfbb8_1
gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-7.3.0-hd420e75_5
gcc_linux-64 conda-forge/linux-64::gcc_linux-64-7.3.0-h553295d_16
gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002
gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_5
gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-7.3.0-h553295d_16
glib conda-forge/linux-64::glib-2.64.2-h6f030ca_0
gst-plugins-base conda-forge/linux-64::gst-plugins-base-1.14.5-h0935bb2_2
gstreamer conda-forge/linux-64::gstreamer-1.14.5-h36ae1b5_2
gxx_impl_linux-64 conda-forge/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_5
gxx_linux-64 conda-forge/linux-64::gxx_linux-64-7.3.0-h553295d_16
hdf4 conda-forge/linux-64::hdf4-4.2.13-hf30be14_1003
hdf5 conda-forge/linux-64::hdf5-1.10.5-nompi_h3c11f04_1104
icu conda-forge/linux-64::icu-64.2-he1b5a44_1
imageio conda-forge/noarch::imageio-2.8.0-py_0
jinja2 conda-forge/noarch::jinja2-2.11.2-pyh9f0ad1d_0
jpeg conda-forge/linux-64::jpeg-9c-h14c3975_1001
jsoncpp conda-forge/linux-64::jsoncpp-1.8.4-hc9558a2_1002
kiwisolver conda-forge/linux-64::kiwisolver-1.2.0-py37h99015e2_0
krb5 conda-forge/linux-64::krb5-1.17.1-h2fd8d38_0
latexcodec conda-forge/noarch::latexcodec-2.0.0-py_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
libblas conda-forge/linux-64::libblas-3.8.0-16_openblas
libcblas conda-forge/linux-64::libcblas-3.8.0-16_openblas
libclang conda-forge/linux-64::libclang-9.0.1-default_hde54327_0
libcurl conda-forge/linux-64::libcurl-7.69.1-hf7181ac_0
libdrm-cos6-x86_64 pkgs/main/noarch::libdrm-cos6-x86_64-2.4.65-hd39d64f_0
libedit conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001
libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2
libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5
libglu conda-forge/linux-64::libglu-9.0.0-hf484d3e_1000
libgomp conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2
libice-cos6-x86_64 pkgs/main/noarch::libice-cos6-x86_64-1.0.6-hc649955_0
libice-devel-cos6~ pkgs/main/noarch::libice-devel-cos6-x86_64-1.0.6-h94b5eae_0
libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1006
liblapack conda-forge/linux-64::liblapack-3.8.0-16_openblas
libllvm9 conda-forge/linux-64::libllvm9-9.0.1-he513fc3_1
libnetcdf conda-forge/linux-64::libnetcdf-4.6.2-h303dfb8_1003
libopenblas conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0
libpng conda-forge/linux-64::libpng-1.6.37-hed695b0_0
libsm-cos6-x86_64 pkgs/main/noarch::libsm-cos6-x86_64-1.2.1-h5e9240c_0
libsm-devel-cos6-~ pkgs/main/noarch::libsm-devel-cos6-x86_64-1.2.1-h6ebe058_0
libssh2 conda-forge/linux-64::libssh2-1.8.2-h22169c7_2
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2
libtiff conda-forge/linux-64::libtiff-4.1.0-hc7e4089_6
libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000
libuv conda-forge/linux-64::libuv-1.34.0-h516909a_0
libwebp-base conda-forge/linux-64::libwebp-base-1.1.0-h516909a_3
libx11-common-cos~ pkgs/main/noarch::libx11-common-cos6-x86_64-1.6.4-h023ea50_0
libx11-cos6-x86_64 pkgs/main/noarch::libx11-cos6-x86_64-1.6.4-h64a1553_0
libx11-devel-cos6~ pkgs/main/noarch::libx11-devel-cos6-x86_64-1.6.4-hb9851ce_0
libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002
libxext-cos6-x86_~ pkgs/main/noarch::libxext-cos6-x86_64-1.3.3-hc47956f_0
libxext-devel-cos~ pkgs/main/noarch::libxext-devel-cos6-x86_64-1.3.3-hf6a4bb0_0
libxkbcommon conda-forge/linux-64::libxkbcommon-0.10.0-he1b5a44_0
libxml2 conda-forge/linux-64::libxml2-2.9.10-hee79883_0
libxslt conda-forge/linux-64::libxslt-1.1.33-h31b3aaa_0
libxt-cos6-x86_64 pkgs/main/noarch::libxt-cos6-x86_64-1.1.4-hc01df4b_0
libxt-devel-cos6-~ pkgs/main/noarch::libxt-devel-cos6-x86_64-1.1.4-hd4125e4_0
livereload conda-forge/noarch::livereload-2.6.1-py_0
llvm-openmp conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0
lxml conda-forge/linux-64::lxml-4.5.0-py37he3881c9_1
lz4-c conda-forge/linux-64::lz4-c-1.8.3-he1b5a44_1001
mako conda-forge/noarch::mako-1.1.0-py_0
markupsafe conda-forge/linux-64::markupsafe-1.1.1-py37h8f50634_1
matplotlib conda-forge/linux-64::matplotlib-3.2.1-0
matplotlib-base conda-forge/linux-64::matplotlib-base-3.2.1-py37h30547a4_0
mesa-libgl-cos6-x~ pkgs/main/noarch::mesa-libgl-cos6-x86_64-11.0.7-h045e36e_0
mesa-libgl-devel-~ pkgs/main/noarch::mesa-libgl-devel-cos6-x86_64-11.0.7-h5a2c0ac_0
mesalib conda-forge/linux-64::mesalib-18.3.1-h590aaf7_0
mock conda-forge/linux-64::mock-4.0.2-py37hc8dfbb8_0
moose-libmesh moose/linux-64::moose-libmesh-2020.04.13-build_0
moose-libmesh-vtk moose/linux-64::moose-libmesh-vtk-6.3.0-build_3
moose-mpich moose/linux-64::moose-mpich-3.3.2-build_3
moose-petsc moose/linux-64::moose-petsc-3.12.5-build_1
moose-tools moose/linux-64::moose-tools-2020.04.13-py37h734910c_0
mpi conda-forge/linux-64::mpi-1.0-mpich
ncurses conda-forge/linux-64::ncurses-6.1-hf484d3e_1002
networkx conda-forge/noarch::networkx-2.4-py_1
nspr conda-forge/linux-64::nspr-4.25-he1b5a44_0
nss conda-forge/linux-64::nss-3.47-he751ad9_0
numpy conda-forge/linux-64::numpy-1.18.4-py37h8960a57_0
olefile conda-forge/noarch::olefile-0.46-py_0
openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_0
pandas conda-forge/linux-64::pandas-1.0.3-py37h0da4684_1
pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0
pillow conda-forge/linux-64::pillow-7.1.2-py37h718be6c_0
pip conda-forge/noarch::pip-20.1-pyh9f0ad1d_0
pkg-config conda-forge/linux-64::pkg-config-0.29.2-h516909a_1006
pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001
pybtex conda-forge/linux-64::pybtex-0.22.2-py37hc8dfbb8_1
pylatexenc conda-forge/noarch::pylatexenc-2.3-pyh9f0ad1d_0
pyparsing conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
pyqt conda-forge/linux-64::pyqt-5.12.3-py37h8685d9f_3
python conda-forge/linux-64::python-3.7.6-h8356626_5_cpython
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
python_abi conda-forge/linux-64::python_abi-3.7-1_cp37m
pytz conda-forge/noarch::pytz-2020.1-pyh9f0ad1d_0
pywavelets conda-forge/linux-64::pywavelets-1.1.1-py37h03ebfcd_1
pyyaml conda-forge/linux-64::pyyaml-5.3.1-py37h8f50634_0
qt conda-forge/linux-64::qt-5.12.5-hd8c4c69_1
readline conda-forge/linux-64::readline-8.0-hf8c457e_0
rhash conda-forge/linux-64::rhash-1.3.6-h14c3975_1001
scikit-image conda-forge/linux-64::scikit-image-0.16.2-py37hb3f55d8_0
scipy conda-forge/linux-64::scipy-1.4.1-py37ha3d9a3c_3
setuptools conda-forge/linux-64::setuptools-46.1.3-py37hc8dfbb8_0
six conda-forge/noarch::six-1.14.0-py_1
soupsieve conda-forge/linux-64::soupsieve-1.9.4-py37hc8dfbb8_1
sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0
tbb conda-forge/linux-64::tbb-2020.1-hc9558a2_0
tk conda-forge/linux-64::tk-8.6.10-hed695b0_0
toolz conda-forge/noarch::toolz-0.10.0-py_0
tornado conda-forge/linux-64::tornado-6.0.4-py37h8f50634_1
vtk conda-forge/linux-64::vtk-8.2.0-py37hfdee58b_203
wheel conda-forge/noarch::wheel-0.34.2-py_1
xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002
xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0
xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000
xorg-libx11 conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0
xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0
xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0
xorg-libxt conda-forge/linux-64::xorg-libxt-1.2.0-h516909a_0
xorg-x11-proto-de~ pkgs/main/noarch::xorg-x11-proto-devel-cos6-x86_64-7.7-h8d4a98b_0
xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007
xz conda-forge/linux-64::xz-5.2.5-h516909a_0
yaml conda-forge/linux-64::yaml-0.2.4-h516909a_0
zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1006
zstd conda-forge/linux-64::zstd-1.4.4-h3b9ef0a_2
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate moose
#
# To deactivate an active environment, use
#
# $ conda deactivate

2. Then I close the terminal and re-open a new terminal, trying to activate moose

moose@moose ~ $ conda activate moose

conda: command not found

My question is:

In the instruction it says the "Miniconda installed to your home directory", however, in my Mint 18, when I goes into the home directory and using pwd command, it gives me /home/moose

Is this the problem?

When I goes in the actual /home directory, I have the Permission denied, see below:

moose@moose /home $ pwd
/home
moose@moose /home $ curl -L -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Warning: Failed to create the file Miniconda3-latest-Linux-x86_64.sh:
Warning: Permission denied
0 81.1M 0 467 0 0 4411 0 5:21:22 --:--:-- 5:21:22 4405
curl: (23) Failed writing body (0 != 467)
moose@moose /home $ bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/miniconda3
bash: Miniconda3-latest-Linux-x86_64.sh: No such file or director

Any suggestions?

Thanks

Jason Miller

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May 7, 2020, 1:17:19 PM5/7/20

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On Thu, May 7, 2020 at 10:19 AM Wesley <zuzup...@gmail.com> wrote:

I am using Mint 18 in VMware workstation, the Mint 18 was downloaded from old moose website.

I can not remember when we last had a VMWare image available for download on mooseframework.org. Ever since Windows Subsystem for Linux (WSL) was introduced, that image was removed. You should try to use something more modern (Or use WSL). I do not think you will run into issues, but I only mention it, since you are starting fresh.

You should not have closed your terminal before attempting to activate moose. By doing this, you undid the earlier PATH exporting instructions, which was making the 'conda' command available. I am curious, was it this line that made you think to close and reopen your terminal? : Activate the moose environment (do this for any new terminal opened): If so, I think I need to remove that line from the instructions. And perhaps mention it later on instead.

In order to pick up where you left off, re-export PATH:

export PATH=$HOME/mininconda3/bin:$PATH

...and then try and activate moose again, follow the on-screen instructions. Which should be explaining how to initialize conda. You are probably going to need to do this:

conda init bash

Once you do that:

conda activate moose

...should work.

Each time you open a new terminal window, you will need to perform:

conda activate moose

moose@moose ~ $ conda activate moose
conda: command not found

My question is:

In the instruction it says the "Miniconda installed to your home directory", however, in my Mint 18, when I goes into the home directory and using pwd command, it gives me /home/moose

Correct!

The instructions imply that miniconda is installed in your home directory. Or 'home directory'/miniconda3. In your case '/home/moose/miniconda3'

Is this the problem?

When I goes in the actual /home directory, I have the Permission denied, see below:

moose@moose /home $ pwd
/home
moose@moose /home $ curl -L -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Warning: Failed to create the file Miniconda3-latest-Linux-x86_64.sh:
Warning: Permission denied
0 81.1M 0 467 0 0 4411 0 5:21:22 --:--:-- 5:21:22 4405
curl: (23) Failed writing body (0 != 467)
moose@moose /home $ bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/miniconda3
bash: Miniconda3-latest-Linux-x86_64.sh: No such file or director

Any suggestions?

Thanks

Home directory, is a common term, meaning, the place where all your files reside. A place where you have write access. Your home on the machine in which you are using. The literal location '/home' is a directory where everyone's home directories are located (most operating systems are multi-user friendly). And because one user should never have access to all users, you are supposed to get a 'permission denied when trying to modify this location.

/home/moose is MOOSE's home directory on Linux machines. /Users/moose is MOOSE's home directory on Macintosh machines (note that the literal word 'home' is not being used), C:\Users\MOOSE is MOOSE's home directory on Windows machines (same absence of the word 'home'). Yet in all cases, this location would be considered MOOSE's Home Directory.

I hope that clears up some things! Cheers!

Jason

Wesley

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May 7, 2020, 2:05:51 PM5/7/20

to moose-users

Hi Jason, thanks for your explanation. I can understand most of them. Unfortunately, I get stuck here as below

I fail here. I keep have the "conda: command not found" issue. In the image below, the red circle is the case without opening a new terminal, the blue circle is the case that opening a new terminal. Neither of them works. The black circle is just to show I have mininconda3 installed.

Jason Miller

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May 7, 2020, 2:43:44 PM5/7/20

to moose...@googlegroups.com

moose@moose ~ $ bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/miniconda3
ERROR: File or directory already exists: '/home/moose/miniconda3'

Hmmm, perhaps the very first time you attempted to install miniconda it failed in some way and did not complete. Odd considering it continued forward to installing packages. I assumed otherwise. I am curious, what is in miniconda3?

ls /home/moose/minicoinda3

and then:

ls $HOME/miniconda3

And one last test:

ls /home/moose/miniconda3/bin

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Wesley

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May 7, 2020, 3:45:56 PM5/7/20

to moose-users

Thanks for the hits, they are attached here. Does that mean something to you?

moose@moose ~/Desktop $ ls /home/moose/miniconda3

bin conda-meta include pkgs ssl

compiler_compat envs lib share x86_64-conda_cos6-linux-gnu

condabin etc LICENSE.txt shell

moose@moose ~/Desktop $ ls $HOME/miniconda3

bin conda-meta include pkgs ssl

compiler_compat envs lib share x86_64-conda_cos6-linux-gnu

condabin etc LICENSE.txt shell

moose@moose ~/Desktop $ ls /home/moose/miniconda3/bin

2to3 lzma tclsh

2to3-3.7 lzmadec tclsh8.6

activate lzmainfo tic

captoinfo lzmore toe

chardetect ncursesw6-config tput

clear openssl tqdm

conda pip tset

conda-env pydoc unlzma

cph pydoc3 unxz

c_rehash pydoc3.7 wheel

deactivate python wish

easy_install python3 wish8.6

idle3 python3.7 x86_64-conda_cos6-linux-gnu-ld

idle3.7 python3.7-config xz

infocmp python3.7m xzcat

infotocap python3.7m-config xzcmp

lzcat python3-config xzdec

lzcmp pyvenv xzdiff

lzdiff pyvenv-3.7 xzegrep

lzegrep reset xzfgrep

lzfgrep sqlite3 xzgrep

lzgrep sqlite3_analyzer xzless

lzless tabs xzmore

Jason Miller

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May 7, 2020, 4:02:32 PM5/7/20

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Ah... would you look at my mistake... I misspelled miniconda.

In order to pick up where you left off, re-export PATH:

export PATH=$HOME/mininconda3/bin:$PATH

----------------------^

...and then try and activate moose again, follow the on-screen instructions. Which should be explaining how to initialize conda. You are probably going to need to do this:

conda init bash

Once you do that:

conda activate moose

...should work.

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Wesley

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May 7, 2020, 4:42:45 PM5/7/20

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Hi Jason, yes it works now. I am moving forward to the "Compile and Test MOOSE" step. Thanks for your help. For the problem I post here, I think it is due to the "close and re-open" step, as you mentioned above, it will undid the earlier PATH exporting. To answer this question:

I am curious, was it this line that made you think to close and reopen your terminal? : Activate the moose environment (do this for any new terminal opened): If so, I think I need to remove that line from the instructions. And perhaps mention it later on instead.

This is because in the earlier version, I remember when I installed MOOSE environment, it required to close the terminal and re-open. So I misunderstood here, there is nothing wrong with your description on the website.

Two more questions here:

1.
I also notice this:

If you close, and re-open this terminal window, know that you will need to conda activate moose again. You will need to do this for each terminal you open. If you wish to make this automatic, you may append conda activate moose to your bash or zsh profiles.

I wish to let it happen automatic, Is it just put conda activate moose into .bashrc file?

2. I also remember we have to update_and_rebuild_libmesh using the following, it is not required now?

cd ~/projects/moose

scripts/update_and_rebuild_libmesh.sh

Thanks for your time.

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Jason Miller

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May 7, 2020, 5:13:59 PM5/7/20

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1. The graphical login prompt is treated a bit differently once you are logged into the graphical environment. ~/.bashrc file is correct. But know with Mint, you might actually need to log all the way out, and back again for those changes to take effect (not just close and reopen the gnome terminal).

2. That is also correct. No need to build libMesh with installing the moose-libmesh conda package.

Cheers!

Jason

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Wesley

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May 7, 2020, 5:39:04 PM5/7/20

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Thank you Jason. I have passed the tests, and have several examples running good. I am glad everything is back to me.

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Benjamin W. Spencer

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Sep 18, 2020, 12:39:50 PM9/18/20

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I’m working with someone (cc’d) who seems to be having this same problem with WSL. Did this ever get resolved?

-Ben

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Jason Miller

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Sep 18, 2020, 2:43:13 PM9/18/20

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What is the contents of /home/moose/miniconda3/bin ?

Is $HOME set?

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