~ julia 1 ✘
Error: The Julia launcher failed to figure out which juliaup channel to use.
Try:
juliaup update
juliaup status
And perhaps
juliaup add 1.10
juliaup default 1.10
if Julia 1.10 is the version you want to use.
There is no information in output.
~ juliaup update ✔
~ juliaup status ✔
Default Channel Version Update
-----------------------------------
If you like i am willing to reinstall everything so i can delete earlier Julia versions. I would like to use latest Julia version.
Try
juliaup add 1.10
juliaup default 1.10
PythonCall uses CondaPkg, which uses micromamba.
1 Like
Why are you using micromamba to install CondaPkg? Use it to install cis.
~ juliaup update ✔
~ juliaup status ✔
Default Channel Version Update
-----------------------------------
~ juliaup add 1.10 ✔
juliaup default 1.10
Installing Julia 1.10.4+0.x64.linux.gnu
Configured the default Julia version to be '1.10'.
(@v1.10) pkg> add CondaPkg
Installing known registries into `~/.julia`
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
Installed MicroMamba ────── v0.1.14
Installed micromamba_jll ── v1.5.8+0
Installed JLLWrappers ───── v1.5.0
Installed Parsers ───────── v2.8.1
Installed Pidfile ───────── v1.3.0
Installed Scratch ───────── v1.2.1
Installed JSON3 ─────────── v1.14.0
Installed Preferences ───── v1.4.3
Installed PrecompileTools ─ v1.2.1
Installed StructTypes ───── v1.10.0
Installed CondaPkg ──────── v0.2.22
Updating `~/.julia/environments/v1.10/Project.toml`
[992eb4ea] + CondaPkg v0.2.22
Updating `~/.julia/environments/v1.10/Manifest.toml`
[992eb4ea] + CondaPkg v0.2.22
[692b3bcd] + JLLWrappers v1.5.0
[0f8b85d8] + JSON3 v1.14.0
[0b3b1443] + MicroMamba v0.1.14
[69de0a69] + Parsers v2.8.1
[fa939f87] + Pidfile v1.3.0
[aea7be01] + PrecompileTools v1.2.1
[21216c6a] + Preferences v1.4.3
[6c6a2e73] + Scratch v1.2.1
[856f2bd8] + StructTypes v1.10.0
[f8abcde7] + micromamba_jll v1.5.8+0
[0dad84c5] + ArgTools v1.1.1
[56f22d72] + Artifacts
[2a0f44e3] + Base64
[ade2ca70] + Dates
[f43a241f] + Downloads v1.6.0
[7b1f6079] + FileWatching
[b77e0a4c] + InteractiveUtils
[4af54fe1] + LazyArtifacts
[b27032c2] + LibCURL v0.6.4
[76f85450] + LibGit2
[8f399da3] + Libdl
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[ca575930] + NetworkOptions v1.2.0
[44cfe95a] + Pkg v1.10.0
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA v0.7.0
[9e88b42a] + Serialization
[6462fe0b] + Sockets
[fa267f1f] + TOML v1.0.3
[a4e569a6] + Tar v1.10.0
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
[deac9b47] + LibCURL_jll v8.4.0+0
[e37daf67] + LibGit2_jll v1.6.4+0
[29816b5a] + LibSSH2_jll v1.11.0+1
[c8ffd9c3] + MbedTLS_jll v2.28.2+1
[14a3606d] + MozillaCACerts_jll v2023.1.10
[83775a58] + Zlib_jll v1.2.13+1
[8e850ede] + nghttp2_jll v1.52.0+1
[3f19e933] + p7zip_jll v17.4.0+2
Precompiling project...
11 dependencies successfully precompiled in 147 seconds. 3 already precompiled.
1 dependency had output during precompilation:
┌ micromamba_jll
│ Downloading artifact: micromamba
│
│ [pid 6261] waiting for IO to finish:
│ Handle type uv_handle_t->data
│ timer 0xe675b0->0x7f1a08d58400
│ This means that a package has started a background task or event source that has not finished running. For precompilation to complete successfully, the event source needs to be closed explicitly. See the developer documentation on fixing precompilation hangs for more help.
│
│ [pid 6261] waiting for IO to finish:
│ Handle type uv_handle_t->data
│ timer 0xe675b0->0x7f1a08d58400
│ This means that a package has started a background task or event source that has not finished running. For precompilation to complete successfully, the event source needs to be closed explicitly. See the developer documentation on fixing precompilation hangs for more help.
└
(@v1.10) pkg>
Looks good to me. This are just warnings you can ignore (I think).
@mkitti I am still getting error. I think i should use micromamba to install cis.
Linking setuptools-70.0.0-pyhd8ed1ab_0
critical libmamba filesystem error: cannot copy: No space left on device [/home/raman/micromamba/pkgs/setuptools-70.0.0-pyhd8ed1ab_0/site-packages/setuptools/_distutils/dist.py] [/tmp/jl_sH1Okd/.CondaPkg/env/lib/python3.11/site-packages/setuptools/_distutils/dist.py]
What should i type to install cis using micromamba? micromamba install cis gives error.
see error
~ micromamba install cis ✔
info libmamba ****************** Backtrace Start ******************
debug libmamba Loading configuration
trace libmamba Compute configurable 'create_base'
trace libmamba Compute configurable 'no_env'
trace libmamba Compute configurable 'no_rc'
trace libmamba Compute configurable 'rc_files'
trace libmamba Compute configurable 'root_prefix'
trace libmamba Get RC files configuration from locations up to HomeDir
trace libmamba Configuration not found at '/home/raman/.mambarc'
trace libmamba Configuration not found at '/home/raman/.mamba/mambarc.d'
trace libmamba Configuration not found at '/home/raman/.mamba/mambarc'
trace libmamba Configuration not found at '/home/raman/.mamba/.mambarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/mambarc.d'
trace libmamba Configuration not found at '/home/raman/.config/mamba/mambarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/.mambarc'
trace libmamba Configuration found at '/home/raman/.condarc'
trace libmamba Configuration not found at '/home/raman/.conda/condarc.d'
trace libmamba Configuration not found at '/home/raman/.conda/condarc'
trace libmamba Configuration not found at '/home/raman/.conda/.condarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/../conda/condarc.d'
trace libmamba Configuration not found at '/home/raman/.config/mamba/../conda/condarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/../conda/.condarc'
trace libmamba Configuration not found at '/home/raman/micromamba/.mambarc'
trace libmamba Configuration not found at '/home/raman/micromamba/condarc.d'
trace libmamba Configuration not found at '/home/raman/micromamba/condarc'
trace libmamba Configuration not found at '/home/raman/micromamba/.condarc'
trace libmamba Configuration not found at '/var/lib/conda/.mambarc'
trace libmamba Configuration not found at '/var/lib/conda/condarc.d/'
trace libmamba Configuration not found at '/var/lib/conda/condarc'
trace libmamba Configuration not found at '/var/lib/conda/.condarc'
trace libmamba Configuration not found at '/etc/conda/.mambarc'
trace libmamba Configuration not found at '/etc/conda/condarc.d/'
trace libmamba Configuration not found at '/etc/conda/condarc'
trace libmamba Configuration not found at '/etc/conda/.condarc'
trace libmamba Update configurable 'no_env'
trace libmamba Compute configurable 'envs_dirs'
trace libmamba Compute configurable 'file_specs'
trace libmamba Compute configurable 'spec_file_env_name'
trace libmamba Compute configurable 'env_name'
trace libmamba Compute configurable 'use_target_prefix_fallback'
trace libmamba Compute configurable 'target_prefix'
trace libmamba Get RC files configuration from locations up to TargetPrefix
trace libmamba Configuration not found at '/home/raman/.mambarc'
trace libmamba Configuration not found at '/home/raman/.mamba/mambarc.d'
trace libmamba Configuration not found at '/home/raman/.mamba/mambarc'
trace libmamba Configuration not found at '/home/raman/.mamba/.mambarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/mambarc.d'
trace libmamba Configuration not found at '/home/raman/.config/mamba/mambarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/.mambarc'
trace libmamba Configuration found at '/home/raman/.condarc'
trace libmamba Configuration not found at '/home/raman/.conda/condarc.d'
trace libmamba Configuration not found at '/home/raman/.conda/condarc'
trace libmamba Configuration not found at '/home/raman/.conda/.condarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/../conda/condarc.d'
trace libmamba Configuration not found at '/home/raman/.config/mamba/../conda/condarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/../conda/.condarc'
trace libmamba Configuration not found at '/home/raman/micromamba/.mambarc'
trace libmamba Configuration not found at '/home/raman/micromamba/condarc.d'
trace libmamba Configuration not found at '/home/raman/micromamba/condarc'
trace libmamba Configuration not found at '/home/raman/micromamba/.condarc'
trace libmamba Configuration not found at '/var/lib/conda/.mambarc'
trace libmamba Configuration not found at '/var/lib/conda/condarc.d/'
trace libmamba Configuration not found at '/var/lib/conda/condarc'
trace libmamba Configuration not found at '/var/lib/conda/.condarc'
trace libmamba Configuration not found at '/etc/conda/.mambarc'
trace libmamba Configuration not found at '/etc/conda/condarc.d/'
trace libmamba Configuration not found at '/etc/conda/condarc'
trace libmamba Configuration not found at '/etc/conda/.condarc'
trace libmamba Update configurable 'no_env'
trace libmamba Compute configurable 'relocate_prefix'
trace libmamba Compute configurable 'target_prefix_checks'
error libmamba No target prefix specified
critical libmamba Aborting.
info libmamba ****************** Backtrace End ********************
What is your output of:
df -h /home/raman
and
df -h /tmp
?
Both commands executed on the command line, not at the Julia prompt.
No space left on device is a very clear error message, I think.
~ df -h /home/raman ✔
Filesystem Size Used Avail Use% Mounted on
/dev/sda2 117G 69G 42G 63% /
~ df -h /tmp ✔
Filesystem Size Used Avail Use% Mounted on
tmpfs 906M 0 906M 0% /tmp
On my machine:
ufechner@ufryzen:~$ df -h /tmp
Filesystem Size Used Avail Use% Mounted on
/dev/mapper/vgubuntu-root 1,8T 1,5T 253G 86% /
There should be no need to use micromamba directly to install cis.
The micromamba error is also clear, it is not configured yet.
trace libmamba Configuration not found at '/etc/conda/.condarc'
trace libmamba Update configurable 'no_env'
trace libmamba Compute configurable 'relocate_prefix'
trace libmamba Compute configurable 'target_prefix_checks'
error libmamba No target prefix specified
critical libmamba Aborting.
For me the question is if 906M space on /tmp are enough. Can you try to extend the size of tmpfs ?
And to use conda from within Julia you must enter the package manager mode first by pressing the ] key.
When I start julia, add CondaPkg, then enter the package manager mode and then type
conda add cis
all gets installed fine. The last lines of the output are:
Linking iris-3.9.0-pyha770c72_0
Linking cis-1.7.9-py311h38be061_0
Transaction finished
To activate this environment, use:
micromamba activate /home/ufechner/repos/tmp/.CondaPkg/env
Or to execute a single command in this environment, use:
micromamba run -p /home/ufechner/repos/tmp/.CondaPkg/env mycommand
(tmp) pkg>
Launching Julia with
julia --project
and then using CondaPkg and switching to package manager mode gives me:
julia> using CondaPkg
(tmp) pkg> conda status
CondaPkg Status /home/ufechner/repos/tmp/CondaPkg.toml
Environment
/home/ufechner/repos/tmp/.CondaPkg/env
Packages
cis v1.7.9
(tmp) pkg>
Typing help in package manager mode lists all available commands including the conda commands.
@ufechner7 Ignore it all. What should i do to overcome my error?
What is your output of:
cat /etc/fstab
A line like
tmpfs /tmp tmpfs defaults,size=2G,mode=1777 0 0
at the end, followed by a reboot might help.
Or executing
sudo mount -o remount,size=2G /tmp
without reboot, but that would only temporarily increase the size of the /tmp folder.
1 Like
You need to fix ths file system error:
Linking setuptools-70.0.0-pyhd8ed1ab_0
critical libmamba filesystem error: cannot copy: No space left on device [/home/raman/micromamba/pkgs/setuptools-70.0.0-pyhd8ed1ab_0/site-packages/setuptools/_distutils/dist.py] [/tmp/jl_sH1Okd/.CondaPkg/env/lib/python3.11/site-packages/setuptools/_distutils/dist.py]
There are a few possibilities:
- Your /tmp is full, has too many files, or is not accessible to you. We figure out how to clear /tmp
- libmamba is wrong, and this is a mamba bug
- We ask @cjdoris for help
- We set the environment variable
TMPDIRto something else.
julia> mkdir("mytemp")
julia> ENV["TMPDIR"] = abspath("mytemp")
3 Likes
~ cat /etc/fstab ✔
# /etc/fstab: static file system information.
#
# Use 'blkid' to print the universally unique identifier for a device; this may
# be used with UUID= as a more robust way to name devices that works even if
# disks are added and removed. See fstab(5).
#
# <file system> <mount point> <type> <options> <dump> <pass>
UUID=CAFB-B9A0 /boot/efi vfat umask=0077 0 2
UUID=3aae5405-92e6-4f9f-b5f8-206f00df12e0 / ext4 defaults,noatime 0 1
tmpfs /tmp tmpfs defaults,noatime,mode=1777 0 0
/swapfile none swap defaults 0 0
~ sudo mount -o remount,size=2G /tmp ✔
[sudo] password for raman:
~ ✔
and now i think it is fine 
But i am getting error in lines below.
1 Like
Why are you passing a HDF5.jl File to cis.read_data? It requires two strings.