Hi @shneuro, can I ask how much RAM your system has? You can find this out by running free -h in a terminal. It looks to me like one of the installation steps was killed by the OS, which usually means that it ran out of memory.
On an unrelated note, it also looks like there is a bug in the installer script which makes it incompatible with Python 2.7 - do you have a python3 command available on your system?
Hi @paulmccarthy. my logs with python 3:
https://www.dropbox.com/scl/fi/yold1vvhcqk31hefiocuo/fsl_installation_20250121101935.log?rlkey=6g4h6ixleeymfinxf6yb9oitk&st=tb01ofc3&dl=0
$ free -h
total used free shared buff/cache available
Mem: 187Gi 27Gi 6.5Gi 6.6Gi 152Gi 151Gi
Swap: 1.0Gi 1.0Gi 0B
Can I email it to you? I’m unable to upload. Thanks!
@paulmccarthy : I was able to get the installation to run successfully. I thoroughly studied your suggestions and ultimately, using the skip SSL option and throttle downloads option worked. Thank you again for being so helpful. Much appreciated!
Hmm, you have more than enough RAM, so something else is going wrong. What version of Rocky are you using?
In any case, I have made some more changes to the fslinstaller.py script - could you try downloading the latest version (3.16.5) and trying to run it like this?
python fslinstaller.py --miniconda https://anaconda.org/conda-forge/micromamba/2.0.5/download/linux-64/micromamba-2.0.5-0.tar.bz2 --extra truenet
@paulmccarthy, It works now when I run it inside an interactive session with salloc.
It is Rocky Linux release 8.10 (Green Obsidian). Kernel: 4.18.0-553.34.1.el8_10.x86_64. bash 4.4.20
I’m having a similar issue @paulmccarthy . My Mac computer is running Sequoia (15.3) and I noticed on the FSL website Sequoia is not listed as an OS when downloading FSL in the list of OSs.
I ran the following:
python ~/Downloads/fslinstaller.py --miniconda https://anaconda.org/conda-forge/micromamba/2.0.5/download/linux-64/micromamba-2.0.5-0.tar.bz2 --extra truenet
My log file:
12:40:19 fslinstaller.py:4175: /Users/benjaminsilver/Downloads/fslinstaller.py --miniconda https://anaconda.org/conda-forge/micromamba/2.0.5/download/linux-64/micromamba-2.0.5-0.tar.bz2 --extra truenet
12:40:19 fslinstaller.py:4176: Python: /opt/anaconda3/bin/python (3, 12)
12:40:19 fslinstaller.py:4177: Installation log file: /var/folders/y7/4bv2gyxd5hqdxh5t_p607lhh0000gn/T/fslinstaller__si8j82k.log
12:40:19 fslinstaller.py:1327: Downloading FSL installer manifest from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/manifest.json
12:40:19 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/manifest.json ...
12:40:20 fslinstaller.py:3633: Installer is up to date (this version: 3.16.5, latest version: 3.16.5)
12:40:20 fslinstaller.py:2444: Installing FSL implies agreement with the terms of the FSL license - if you do not agree with these terms, you can cancel the installation by pressing CTRL+C. You can view the license at https://fsl.fmrib.ox.ac.uk/fsl/docs/#/license
12:40:20 fslinstaller.py:2445:
12:40:20 fslinstaller.py:4193: During the installation process, please note that some system details will be automatically sent to the FSL development team. These details are extremely basic and cannot be used in any way to identify individual users. If you do not want any information to be sent, please cancel this installation by pressing CTRL+C, and re-run the installer with the --skip_registration option.
12:40:20 fslinstaller.py:2193: FSL 6.0.7.17 selected for installation
12:40:20 fslinstaller.py:2232:
Where do you want to install FSL?
12:40:20 fslinstaller.py:2234: Press enter to install to the default location [/Users/benjaminsilver/fsl]
12:40:21 fslinstaller.py: 689: FSL installation directory [/Users/benjaminsilver/fsl]::
12:40:21 fslinstaller.py:1651: Running nvidia-smi -i 0 [as admin: False]
12:40:21 fslinstaller.py: 889: Unable to interrogate CUDA version: [Errno 2] No such file or directory: 'nvidia-smi'
Traceback (most recent call last):
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 877, in identify_cuda
output = Process.check_output('nvidia-smi -i {}'.format(device))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1703, in check_output
proc = Process(cmd, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1653, in __init__
self.popen = Process.popen(cmd, admin, password,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1885, in popen
proc = sp.Popen(cmd, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/lib/python3.12/subprocess.py", line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/opt/anaconda3/lib/python3.12/subprocess.py", line 1955, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'nvidia-smi'
12:40:21 fslinstaller.py:2756: Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_macos-M1.yml...
12:40:21 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_macos-M1.yml ...
12:40:21 fslinstaller.py:2756: Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_osl-dynamics_macos-M1.yml...
12:40:21 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_osl-dynamics_macos-M1.yml ...
12:40:21 fslinstaller.py:2756: Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_truenet_macos-M1.yml...
12:40:22 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_truenet_macos-M1.yml ...
12:40:22 fslinstaller.py:4226:
Installing FSL in /Users/benjaminsilver/fsl
12:40:22 fslinstaller.py:2877: Downloading miniconda from https://anaconda.org/conda-forge/micromamba/2.0.5/download/linux-64/micromamba-2.0.5-0.tar.bz2...
12:40:22 fslinstaller.py:1241: Downloading https://anaconda.org/conda-forge/micromamba/2.0.5/download/linux-64/micromamba-2.0.5-0.tar.bz2 ...
12:40:22 fslinstaller.py:1597: 1 / 5 [ ] 0.0 / 5.7 MB
12:40:22 fslinstaller.py:1597: 1 / 5 [## ] 0.1 / 5.7 MB
12:40:22 fslinstaller.py:1597: 1 / 5 [#### ] 0.2 / 5.7 MB
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12:40:22 fslinstaller.py:1597: 1 / 5 [############## ] 1.0 / 5.7 MB
12:40:22 fslinstaller.py:1597: 1 / 5 [################ ] 1.1 / 5.7 MB
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12:40:22 fslinstaller.py:1597: 1 / 5 [#################### ] 1.4 / 5.7 MB
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12:40:22 fslinstaller.py:1597: 1 / 5 [######################### ] 1.8 / 5.7 MB
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12:40:22 fslinstaller.py:1597: 1 / 5 [############################# ] 2.0 / 5.7 MB
12:40:22 fslinstaller.py:1597: 1 / 5 [############################### ] 2.1 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [################################ ] 2.2 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [################################## ] 2.4 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [#################################### ] 2.5 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [###################################### ] 2.6 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [######################################## ] 2.8 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [########################################## ] 2.9 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [########################################### ] 3.0 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [############################################# ] 3.1 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [############################################### ] 3.2 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [################################################# ] 3.4 / 5.7 MB
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12:40:23 fslinstaller.py:1597: 1 / 5 [#################################################### ] 3.6 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [###################################################### ] 3.8 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [######################################################## ] 3.9 / 5.7 MB
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12:40:23 fslinstaller.py:1597: 1 / 5 [################################################################# ] 4.5 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [################################################################### ] 4.6 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [##################################################################### ] 4.8 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [###################################################################### ] 4.9 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [######################################################################## ] 5.0 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [########################################################################## ] 5.1 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [############################################################################ ] 5.2 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [############################################################################## ] 5.4 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [############################################################################### ] 5.5 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [################################################################################# ] 5.6 / 5.7 MB
12:40:23 fslinstaller.py:1597: 1 / 5 [###################################################################################] 5.7 / 5.7 MB
12:40:23 fslinstaller.py:2926: Installing conda at /Users/benjaminsilver/fsl...
12:40:23 fslinstaller.py:1597: 2 / 5 [####################################################################################] 100 / 100 %
12:40:23 fslinstaller.py:1651: Running find /Users/benjaminsilver/fsl -type f -exec touch {} + [as admin: False]
12:40:23 fslinstaller.py:2976: Creating FSL wrapper management scripts...
12:40:23 fslinstaller.py:1597: 3 / 5 [####################################################################################] 100 / 100 %
12:40:23 fslinstaller.py:1651: Running mkdir -p /Users/benjaminsilver/fsl [as admin: False]
12:40:23 fslinstaller.py:1651: Running cp -f .condarc /Users/benjaminsilver/fsl [as admin: False]
12:40:23 fslinstaller.py:3329: Installing FSL into /Users/benjaminsilver/fsl...
12:40:23 fslinstaller.py:1651: Running /Users/benjaminsilver/fsl/bin/micromamba env update -p /Users/benjaminsilver/fsl -f fsl-6.0.7.17_macos-M1.yml [as admin: False]
12:40:23 fslinstaller.py:4117:
ERROR occurred during installation!
12:40:23 fslinstaller.py:4118: [Errno 8] Exec format error: '/Users/benjaminsilver/fsl/bin/micromamba'
12:40:23 fslinstaller.py:4122: File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 4114, in handle_error
yield
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 4251, in main
func(*funcargs, prefix=prefix)
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 3360, in install_fsl
retry_on_error(ctx.run, ctx.args.num_retries, Process.monitor_progress,
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1037, in retry_on_error
raise e
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1032, in retry_on_error
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 2428, in run
return process_func(admin=self.need_admin,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1801, in monitor_progress
proc = Process(cmd, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1653, in __init__
self.popen = Process.popen(cmd, admin, password,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1885, in popen
proc = sp.Popen(cmd, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/lib/python3.12/subprocess.py", line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/opt/anaconda3/lib/python3.12/subprocess.py", line 1955, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
12:40:23 fslinstaller.py:4125: Environment variables:
12:40:23 fslinstaller.py:4127: CONDA_DEFAULT_ENV=base
12:40:23 fslinstaller.py:4127: CONDA_EXE=/opt/anaconda3/bin/conda
12:40:23 fslinstaller.py:4127: CONDA_PREFIX=/opt/anaconda3
12:40:23 fslinstaller.py:4127: CONDA_PROMPT_MODIFIER=(base)
12:40:23 fslinstaller.py:4127: CONDA_PYTHON_EXE=/opt/anaconda3/bin/python
12:40:23 fslinstaller.py:4127: CONDA_SHLVL=1
12:40:23 fslinstaller.py:4127: GSETTINGS_SCHEMA_DIR=/opt/anaconda3/share/glib-2.0/schemas
12:40:23 fslinstaller.py:4127: GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=
12:40:23 fslinstaller.py:4127: HOME=/Users/benjaminsilver
12:40:23 fslinstaller.py:4127: LANG=en_US.UTF-8
12:40:23 fslinstaller.py:4127: LOGNAME=benjaminsilver
12:40:23 fslinstaller.py:4127: LaunchInstanceID=38EB0FB5-43C9-4745-8729-523460A7C8D7
12:40:23 fslinstaller.py:4127: OLDPWD=/Users/benjaminsilver
12:40:23 fslinstaller.py:4127: PATH=/opt/anaconda3/bin:/opt/anaconda3/condabin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin
12:40:23 fslinstaller.py:4127: PWD=/Users/benjaminsilver
12:40:23 fslinstaller.py:4127: SECURITYSESSIONID=186ab
12:40:23 fslinstaller.py:4127: SHELL=/bin/zsh
12:40:23 fslinstaller.py:4127: SHLVL=1
12:40:23 fslinstaller.py:4127: SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.XKbirO2TQB/Listeners
12:40:23 fslinstaller.py:4127: TERM=xterm-256color
12:40:23 fslinstaller.py:4127: TERM_PROGRAM=Apple_Terminal
12:40:23 fslinstaller.py:4127: TERM_PROGRAM_VERSION=455
12:40:23 fslinstaller.py:4127: TERM_SESSION_ID=375CE363-2603-49D4-A3DF-D490C69ECF29
12:40:23 fslinstaller.py:4127: TMPDIR=/var/folders/y7/4bv2gyxd5hqdxh5t_p607lhh0000gn/T/
12:40:23 fslinstaller.py:4127: USER=benjaminsilver
12:40:23 fslinstaller.py:4127: XPC_FLAGS=0x0
12:40:23 fslinstaller.py:4127: XPC_SERVICE_NAME=0
12:40:23 fslinstaller.py:4127: _=/opt/anaconda3/bin/python
12:40:23 fslinstaller.py:4127: _CE_CONDA=
12:40:23 fslinstaller.py:4127: _CE_M=
12:40:23 fslinstaller.py:4127: __CFBundleIdentifier=com.apple.Terminal
12:40:23 fslinstaller.py:4130: Removing failed installation directory /Users/benjaminsilver/fsl
12:40:23 fslinstaller.py:1651: Running rm -r /Users/benjaminsilver/fsl [as admin: False]
Hi @bms2202, and welcome to neurostars!
Looks like you’re using a linux mamba installer when you have MacOS. What if you replace linux-64 with osx-64?
Best,
Steven
Ah, I was confused, I came here because I was having issues and blindly copied someone else’s solution.
In that case, here is my initial command:
python ~/Downloads/fslinstaller.py
And here is the log output:
`12:51:59 fslinstaller.py:4175: /Users/benjaminsilver/Downloads/fslinstaller.py
12:51:59 fslinstaller.py:4176: Python: /opt/anaconda3/bin/python (3, 12)
12:51:59 fslinstaller.py:4177: Installation log file: /var/folders/y7/4bv2gyxd5hqdxh5t_p607lhh0000gn/T/fslinstaller_sr2qqxb1.log
12:51:59 fslinstaller.py:1327: Downloading FSL installer manifest from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/manifest.json
12:51:59 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/manifest.json ...
12:52:00 fslinstaller.py:3633: Installer is up to date (this version: 3.16.5, latest version: 3.16.5)
12:52:00 fslinstaller.py:2444: Installing FSL implies agreement with the terms of the FSL license - if you do not agree with these terms, you can cancel the installation by pressing CTRL+C. You can view the license at https://fsl.fmrib.ox.ac.uk/fsl/docs/#/license
12:52:00 fslinstaller.py:2445:
12:52:00 fslinstaller.py:4193: During the installation process, please note that some system details will be automatically sent to the FSL development team. These details are extremely basic and cannot be used in any way to identify individual users. If you do not want any information to be sent, please cancel this installation by pressing CTRL+C, and re-run the installer with the --skip_registration option.
12:52:00 fslinstaller.py:2193: FSL 6.0.7.17 selected for installation
12:52:00 fslinstaller.py:2232:
Where do you want to install FSL?
12:52:00 fslinstaller.py:2234: Press enter to install to the default location [/Users/benjaminsilver/fsl]
12:52:01 fslinstaller.py: 689: FSL installation directory [/Users/benjaminsilver/fsl]::
12:52:01 fslinstaller.py:1651: Running nvidia-smi -i 0 [as admin: False]
12:52:01 fslinstaller.py: 889: Unable to interrogate CUDA version: [Errno 2] No such file or directory: 'nvidia-smi'
Traceback (most recent call last):
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 877, in identify_cuda
output = Process.check_output('nvidia-smi -i {}'.format(device))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1703, in check_output
proc = Process(cmd, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1653, in __init__
self.popen = Process.popen(cmd, admin, password,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1885, in popen
proc = sp.Popen(cmd, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/lib/python3.12/subprocess.py", line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/opt/anaconda3/lib/python3.12/subprocess.py", line 1955, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'nvidia-smi'
12:52:01 fslinstaller.py:2756: Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_macos-M1.yml...
12:52:01 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_macos-M1.yml ...
12:52:01 fslinstaller.py:2756: Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_osl-dynamics_macos-M1.yml...
12:52:01 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_osl-dynamics_macos-M1.yml ...
12:52:01 fslinstaller.py:2756: Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_truenet_macos-M1.yml...
12:52:01 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_truenet_macos-M1.yml ...
12:52:02 fslinstaller.py:4226:
Installing FSL in /Users/benjaminsilver/fsl
12:52:02 fslinstaller.py:2877: Downloading miniconda from https://anaconda.org/conda-forge/micromamba/2.0.5/download/osx-arm64/micromamba-2.0.5-0.tar.bz2...
12:52:02 fslinstaller.py:1241: Downloading https://anaconda.org/conda-forge/micromamba/2.0.5/download/osx-arm64/micromamba-2.0.5-0.tar.bz2 ...
12:52:02 fslinstaller.py:1597: 1 / 4 [ ] 0.0 / 5.8 MB
12:52:02 fslinstaller.py:1597: 1 / 4 [## ] 0.1 / 5.8 MB
12:52:02 fslinstaller.py:1597: 1 / 4 [#### ] 0.2 / 5.8 MB
12:52:02 fslinstaller.py:1597: 1 / 4 [##### ] 0.4 / 5.8 MB
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12:52:02 fslinstaller.py:1597: 1 / 4 [######### ] 0.6 / 5.8 MB
12:52:02 fslinstaller.py:1597: 1 / 4 [########### ] 0.8 / 5.8 MB
12:52:02 fslinstaller.py:1597: 1 / 4 [############# ] 0.9 / 5.8 MB
12:52:02 fslinstaller.py:1597: 1 / 4 [############## ] 1.0 / 5.8 MB
12:52:02 fslinstaller.py:1597: 1 / 4 [################ ] 1.1 / 5.8 MB
12:52:02 fslinstaller.py:1597: 1 / 4 [################## ] 1.2 / 5.8 MB
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12:52:03 fslinstaller.py:2926: Installing conda at /Users/benjaminsilver/fsl...
12:52:03 fslinstaller.py:1597: 2 / 4 [####################################################################################] 100 / 100 %
12:52:03 fslinstaller.py:1651: Running find /Users/benjaminsilver/fsl -type f -exec touch {} + [as admin: False]
12:52:03 fslinstaller.py:2976: Creating FSL wrapper management scripts...
12:52:03 fslinstaller.py:1597: 3 / 4 [####################################################################################] 100 / 100 %
12:52:03 fslinstaller.py:1651: Running mkdir -p /Users/benjaminsilver/fsl [as admin: False]
12:52:03 fslinstaller.py:1651: Running cp -f .condarc /Users/benjaminsilver/fsl [as admin: False]
12:52:03 fslinstaller.py:3329: Installing FSL into /Users/benjaminsilver/fsl...
12:52:03 fslinstaller.py:1651: Running /Users/benjaminsilver/fsl/bin/micromamba env update -p /Users/benjaminsilver/fsl -f fsl-6.0.7.17_macos-M1.yml [as admin: False]
12:52:03 fslinstaller.py:1597: 4 / 4 [ ] 0 / 100 %
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
12:52:03 fslinstaller.py:1842: [stderr]:
12:52:03 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
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12:52:27 fslinstaller.py:1842: [stderr]: critical libmamba Could not solve for environment specs
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12:52:27 fslinstaller.py:4117:
ERROR occurred during installation!
12:52:27 fslinstaller.py:4118: This command returned an error: /Users/benjaminsilver/fsl/bin/micromamba env update -p /Users/benjaminsilver/fsl -f fsl-6.0.7.17_macos-M1.yml
12:52:27 fslinstaller.py:4122: File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 4114, in handle_error
yield
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 4251, in main
func(*funcargs, prefix=prefix)
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 3360, in install_fsl
retry_on_error(ctx.run, ctx.args.num_retries, Process.monitor_progress,
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1037, in retry_on_error
raise e
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1032, in retry_on_error
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 2428, in run
return process_func(admin=self.need_admin,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1814, in monitor_progress
raise RuntimeError('This command returned '
12:52:27 fslinstaller.py:4125: Environment variables:
12:52:27 fslinstaller.py:4127: CONDA_DEFAULT_ENV=base
12:52:27 fslinstaller.py:4127: CONDA_EXE=/opt/anaconda3/bin/conda
12:52:27 fslinstaller.py:4127: CONDA_PREFIX=/opt/anaconda3
12:52:27 fslinstaller.py:4127: CONDA_PROMPT_MODIFIER=(base)
12:52:27 fslinstaller.py:4127: CONDA_PYTHON_EXE=/opt/anaconda3/bin/python
12:52:27 fslinstaller.py:4127: CONDA_SHLVL=1
12:52:27 fslinstaller.py:4127: GSETTINGS_SCHEMA_DIR=/opt/anaconda3/share/glib-2.0/schemas
12:52:27 fslinstaller.py:4127: GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=
12:52:27 fslinstaller.py:4127: HOME=/Users/benjaminsilver
12:52:27 fslinstaller.py:4127: LANG=en_US.UTF-8
12:52:27 fslinstaller.py:4127: LOGNAME=benjaminsilver
12:52:27 fslinstaller.py:4127: LaunchInstanceID=38EB0FB5-43C9-4745-8729-523460A7C8D7
12:52:27 fslinstaller.py:4127: OLDPWD=/Users/benjaminsilver
12:52:27 fslinstaller.py:4127: PATH=/opt/anaconda3/bin:/opt/anaconda3/condabin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin
12:52:27 fslinstaller.py:4127: PWD=/Users/benjaminsilver
12:52:27 fslinstaller.py:4127: SECURITYSESSIONID=186ab
12:52:27 fslinstaller.py:4127: SHELL=/bin/zsh
12:52:27 fslinstaller.py:4127: SHLVL=1
12:52:27 fslinstaller.py:4127: SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.XKbirO2TQB/Listeners
12:52:27 fslinstaller.py:4127: TERM=xterm-256color
12:52:27 fslinstaller.py:4127: TERM_PROGRAM=Apple_Terminal
12:52:27 fslinstaller.py:4127: TERM_PROGRAM_VERSION=455
12:52:27 fslinstaller.py:4127: TERM_SESSION_ID=375CE363-2603-49D4-A3DF-D490C69ECF29
12:52:27 fslinstaller.py:4127: TMPDIR=/var/folders/y7/4bv2gyxd5hqdxh5t_p607lhh0000gn/T/
12:52:27 fslinstaller.py:4127: USER=benjaminsilver
12:52:27 fslinstaller.py:4127: XPC_FLAGS=0x0
12:52:27 fslinstaller.py:4127: XPC_SERVICE_NAME=0
12:52:27 fslinstaller.py:4127: _=/opt/anaconda3/bin/python
12:52:27 fslinstaller.py:4127: _CE_CONDA=
12:52:27 fslinstaller.py:4127: _CE_M=
12:52:27 fslinstaller.py:4127: __CFBundleIdentifier=com.apple.Terminal
12:52:27 fslinstaller.py:4130: Removing failed installation directory /Users/benjaminsilver/fsl
12:52:27 fslinstaller.py:1651: Running rm -r /Users/benjaminsilver/fsl [as admin: False]'
Hi @bms2202,
I wouldn’t worry about the nividia-smi error. It looks like the real error happens at
Can you try python fslinstaller.py --miniconda https://anaconda.org/conda-forge/micromamba/2.0.5/download/osx-64/micromamba-2.0.5-0.tar.bz2?
Best,
Steven
Hi Steven,
Thanks for your help thus far. I tried that command, and got the following error:
(This line
13:47:14 fslinstaller.py:1597: 4 / 4 [ ] 0 / 100 %
repeated way more times but I had to delete a bunch so that my post wasn’t too long.)
13:47:03 fslinstaller.py:4175: /Users/benjaminsilver/Downloads/fslinstaller.py --miniconda https://anaconda.org/conda-forge/micromamba/2.0.5/download/osx-64/micromamba-2.0.5-0.tar.bz2
13:47:03 fslinstaller.py:4176: Python: /opt/anaconda3/bin/python (3, 12)
13:47:03 fslinstaller.py:4177: Installation log file: /var/folders/y7/4bv2gyxd5hqdxh5t_p607lhh0000gn/T/fslinstaller_0dh_13hv.log
13:47:03 fslinstaller.py:1327: Downloading FSL installer manifest from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/manifest.json
13:47:03 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/manifest.json ...
13:47:04 fslinstaller.py:3633: Installer is up to date (this version: 3.16.5, latest version: 3.16.5)
13:47:04 fslinstaller.py:2444: Installing FSL implies agreement with the terms of the FSL license - if you do not agree with these terms, you can cancel the installation by pressing CTRL+C. You can view the license at https://fsl.fmrib.ox.ac.uk/fsl/docs/#/license
13:47:04 fslinstaller.py:2445:
13:47:04 fslinstaller.py:4193: During the installation process, please note that some system details will be automatically sent to the FSL development team. These details are extremely basic and cannot be used in any way to identify individual users. If you do not want any information to be sent, please cancel this installation by pressing CTRL+C, and re-run the installer with the --skip_registration option.
13:47:04 fslinstaller.py:2193: FSL 6.0.7.17 selected for installation
13:47:04 fslinstaller.py:2232:
Where do you want to install FSL?
13:47:04 fslinstaller.py:2234: Press enter to install to the default location [/Users/benjaminsilver/fsl]
13:47:05 fslinstaller.py: 689: FSL installation directory [/Users/benjaminsilver/fsl]::
13:47:05 fslinstaller.py:3684:
Destination directory [/Users/benjaminsilver/fsl] already exists!
13:47:08 fslinstaller.py: 689: Do you want to overwrite it [y/N]?: y
13:47:08 fslinstaller.py:3703: Deleting directory /Users/benjaminsilver/fsl
13:47:08 fslinstaller.py:1651: Running mv /Users/benjaminsilver/fsl /private/var/folders/y7/4bv2gyxd5hqdxh5t_p607lhh0000gn/T/tmpz9akvsuj/old_destdir0 [as admin: False]
13:47:08 fslinstaller.py:1651: Running nvidia-smi -i 0 [as admin: False]
13:47:08 fslinstaller.py: 889: Unable to interrogate CUDA version: [Errno 2] No such file or directory: 'nvidia-smi'
Traceback (most recent call last):
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 877, in identify_cuda
output = Process.check_output('nvidia-smi -i {}'.format(device))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1703, in check_output
proc = Process(cmd, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1653, in __init__
self.popen = Process.popen(cmd, admin, password,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1885, in popen
proc = sp.Popen(cmd, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/lib/python3.12/subprocess.py", line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/opt/anaconda3/lib/python3.12/subprocess.py", line 1955, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'nvidia-smi'
13:47:08 fslinstaller.py:2756: Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_macos-M1.yml...
13:47:08 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_macos-M1.yml ...
13:47:09 fslinstaller.py:2756: Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_osl-dynamics_macos-M1.yml...
13:47:09 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_osl-dynamics_macos-M1.yml ...
13:47:09 fslinstaller.py:2756: Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_truenet_macos-M1.yml...
13:47:09 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_truenet_macos-M1.yml ...
13:47:09 fslinstaller.py:4226:
Installing FSL in /Users/benjaminsilver/fsl
13:47:09 fslinstaller.py:2877: Downloading miniconda from https://anaconda.org/conda-forge/micromamba/2.0.5/download/osx-64/micromamba-2.0.5-0.tar.bz2...
13:47:09 fslinstaller.py:1241: Downloading https://anaconda.org/conda-forge/micromamba/2.0.5/download/osx-64/micromamba-2.0.5-0.tar.bz2 ...
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13:47:10 fslinstaller.py:1597: 1 / 4 [###################################################################################] 5.8 / 5.8 MB
13:47:10 fslinstaller.py:2926: Installing conda at /Users/benjaminsilver/fsl...
13:47:10 fslinstaller.py:1597: 2 / 4 [####################################################################################] 100 / 100 %
13:47:10 fslinstaller.py:1651: Running find /Users/benjaminsilver/fsl -type f -exec touch {} + [as admin: False]
13:47:10 fslinstaller.py:2976: Creating FSL wrapper management scripts...
13:47:10 fslinstaller.py:1597: 3 / 4 [####################################################################################] 100 / 100 %
13:47:10 fslinstaller.py:1651: Running mkdir -p /Users/benjaminsilver/fsl [as admin: False]
13:47:10 fslinstaller.py:1651: Running cp -f .condarc /Users/benjaminsilver/fsl [as admin: False]
13:47:10 fslinstaller.py:3329: Installing FSL into /Users/benjaminsilver/fsl...
13:47:10 fslinstaller.py:1651: Running /Users/benjaminsilver/fsl/bin/micromamba env update -p /Users/benjaminsilver/fsl -f fsl-6.0.7.17_macos-M1.yml [as admin: False]
13:47:10 fslinstaller.py:1597: 4 / 4 [ ] 0 / 100 %
13:47:12 fslinstaller.py:1597: 4 / 4 [ ] 0 / 100 %
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba Please make sure you understand Anaconda Terms of Services.
13:47:13 fslinstaller.py:1842: [stderr]:
13:47:13 fslinstaller.py:1842: [stderr]: warning libmamba See: https://legal.anaconda.com/policies/en/
13:47:14 fslinstaller.py:1597: 4 / 4 [ ] 0 / 100 %
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13:47:25 fslinstaller.py:1842: [stdout]:
13:47:26 fslinstaller.py:1597: 4 / 4 [ ] 0 / 100 %
13:54:02 fslinstaller.py:1842: [stderr]: critical libmamba Could not solve for environment specs
13:54:03 fslinstaller.py:1597: 4 / 4 [ ] 0 / 100 %
13:54:03 fslinstaller.py:4117:
ERROR occurred during installation!
13:54:03 fslinstaller.py:4118: This command returned an error: /Users/benjaminsilver/fsl/bin/micromamba env update -p /Users/benjaminsilver/fsl -f fsl-6.0.7.17_macos-M1.yml
13:54:03 fslinstaller.py:4122: File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 4114, in handle_error
yield
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 4251, in main
func(*funcargs, prefix=prefix)
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 3360, in install_fsl
retry_on_error(ctx.run, ctx.args.num_retries, Process.monitor_progress,
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1037, in retry_on_error
raise e
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1032, in retry_on_error
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 2428, in run
return process_func(admin=self.need_admin,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/benjaminsilver/Downloads/fslinstaller.py", line 1814, in monitor_progress
raise RuntimeError('This command returned '
13:54:03 fslinstaller.py:4125: Environment variables:
13:54:03 fslinstaller.py:4127: CONDA_DEFAULT_ENV=base
13:54:03 fslinstaller.py:4127: CONDA_EXE=/opt/anaconda3/bin/conda
13:54:03 fslinstaller.py:4127: CONDA_PREFIX=/opt/anaconda3
13:54:03 fslinstaller.py:4127: CONDA_PROMPT_MODIFIER=(base)
13:54:03 fslinstaller.py:4127: CONDA_PYTHON_EXE=/opt/anaconda3/bin/python
13:54:03 fslinstaller.py:4127: CONDA_SHLVL=1
13:54:03 fslinstaller.py:4127: GSETTINGS_SCHEMA_DIR=/opt/anaconda3/share/glib-2.0/schemas
13:54:03 fslinstaller.py:4127: GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=
13:54:03 fslinstaller.py:4127: HOME=/Users/benjaminsilver
13:54:03 fslinstaller.py:4127: LANG=en_US.UTF-8
13:54:03 fslinstaller.py:4127: LOGNAME=benjaminsilver
13:54:03 fslinstaller.py:4127: LaunchInstanceID=38EB0FB5-43C9-4745-8729-523460A7C8D7
13:54:03 fslinstaller.py:4127: OLDPWD=/Users/benjaminsilver
13:54:03 fslinstaller.py:4127: PATH=/opt/anaconda3/bin:/opt/anaconda3/condabin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin
13:54:03 fslinstaller.py:4127: PWD=/Users/benjaminsilver
13:54:03 fslinstaller.py:4127: SECURITYSESSIONID=186ab
13:54:03 fslinstaller.py:4127: SHELL=/bin/zsh
13:54:03 fslinstaller.py:4127: SHLVL=1
13:54:03 fslinstaller.py:4127: SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.XKbirO2TQB/Listeners
13:54:03 fslinstaller.py:4127: TERM=xterm-256color
13:54:03 fslinstaller.py:4127: TERM_PROGRAM=Apple_Terminal
13:54:03 fslinstaller.py:4127: TERM_PROGRAM_VERSION=455
13:54:03 fslinstaller.py:4127: TERM_SESSION_ID=375CE363-2603-49D4-A3DF-D490C69ECF29
13:54:03 fslinstaller.py:4127: TMPDIR=/var/folders/y7/4bv2gyxd5hqdxh5t_p607lhh0000gn/T/
13:54:03 fslinstaller.py:4127: USER=benjaminsilver
13:54:03 fslinstaller.py:4127: XPC_FLAGS=0x0
13:54:03 fslinstaller.py:4127: XPC_SERVICE_NAME=0
13:54:03 fslinstaller.py:4127: _=/opt/anaconda3/bin/python
13:54:03 fslinstaller.py:4127: _CE_CONDA=
13:54:03 fslinstaller.py:4127: _CE_M=
13:54:03 fslinstaller.py:4127: __CFBundleIdentifier=com.apple.Terminal
13:54:03 fslinstaller.py:4130: Removing failed installation directory /Users/benjaminsilver/fsl
13:54:03 fslinstaller.py:1651: Running rm -r /Users/benjaminsilver/fsl [as admin: False]
13:54:04 fslinstaller.py:4138: Restoring contents of /Users/benjaminsilver/fsl
13:54:04 fslinstaller.py:1651: Running mv /private/var/folders/y7/4bv2gyxd5hqdxh5t_p607lhh0000gn/T/tmpz9akvsuj/old_destdir0 /Users/benjaminsilver/fsl [as admin: False]
Hi @bms2202, unfortunately there is an outstanding bug in micromamba which we hadn’t caught during testing. I’ve patched the fslinstaller.py script to try and work around it - could you re-download it from here and try again?
That worked! Thanks so much for the help.
Hey @paulmccarthy, I’m also having trouble with installation. The script tries to tar an sh file and raises an error.
Here is the log output:
16:26:31 fslinstaller.py:4198: /mnt/c/Users/itayh/Downloads/fslinstaller.py
16:26:31 fslinstaller.py:4199: Python: /usr/bin/python3 (3, 12)
16:26:31 fslinstaller.py:4200: Installation log file: /tmp/fslinstaller_f7v8xwol.log
16:26:31 fslinstaller.py:1327: Downloading FSL installer manifest from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/manifest.json
16:26:31 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/manifest.json ...
16:26:32 fslinstaller.py:3656: Installer is up to date (this version: 3.16.7, latest version: 3.16.7)
16:26:32 fslinstaller.py:2444: Installing FSL implies agreement with the terms of the FSL license - if you do not agree with these terms, you can cancel the installation by pressing CTRL+C. You can view the license at https://fsl.fmrib.ox.ac.uk/fsl/docs/#/license
16:26:32 fslinstaller.py:2445:
16:26:32 fslinstaller.py:4216: During the installation process, please note that some system details will be automatically sent to the FSL development team. These details are extremely basic and cannot be used in any way to identify individual users. If you do not want any information to be sent, please cancel this installation by pressing CTRL+C, and re-run the installer with the --skip_registration option.
16:26:32 fslinstaller.py:2193: FSL 6.0.7.17 selected for installation
16:26:32 fslinstaller.py:2232:
Where do you want to install FSL?
16:26:32 fslinstaller.py:2234: Press enter to install to the default location [/home/itayh/fsl]
16:26:33 fslinstaller.py: 689: FSL installation directory [/home/itayh/fsl]::
16:26:33 fslinstaller.py:1651: Running nvidia-smi -i 0 [as admin: False]
16:26:33 fslinstaller.py:1842: [stdout]: Tue Mar 11 16:26:33 2025
16:26:33 fslinstaller.py:1842: [stdout]: +-----------------------------------------------------------------------------------------+
16:26:33 fslinstaller.py:1842: [stdout]: | NVIDIA-SMI 555.61 Driver Version: 556.18 CUDA Version: 12.5 |
16:26:33 fslinstaller.py:1842: [stdout]: |-----------------------------------------+------------------------+----------------------+
16:26:33 fslinstaller.py:1842: [stdout]: | GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC |
16:26:33 fslinstaller.py:1842: [stdout]: | Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |
16:26:33 fslinstaller.py:1842: [stdout]: | | | MIG M. |
16:26:33 fslinstaller.py:1842: [stdout]: |=========================================+========================+======================|
16:26:33 fslinstaller.py:1842: [stdout]: | 0 NVIDIA RTX A4000 On | 00000000:01:00.0 Off | Off |
16:26:33 fslinstaller.py:1842: [stdout]: | 41% 31C P8 8W / 140W | 653MiB / 16376MiB | 1% Default |
16:26:33 fslinstaller.py:1842: [stdout]: | | | N/A |
16:26:33 fslinstaller.py:1842: [stdout]: +-----------------------------------------+------------------------+----------------------+
16:26:33 fslinstaller.py:1842: [stdout]:
16:26:33 fslinstaller.py:1842: [stdout]: +-----------------------------------------------------------------------------------------+
16:26:33 fslinstaller.py:1842: [stdout]: | Processes: |
16:26:33 fslinstaller.py:1842: [stdout]: | GPU GI CI PID Type Process name GPU Memory |
16:26:33 fslinstaller.py:1842: [stdout]: | ID ID Usage |
16:26:33 fslinstaller.py:1842: [stdout]: |=========================================================================================|
16:26:33 fslinstaller.py:1842: [stdout]: | No running processes found |
16:26:33 fslinstaller.py:1842: [stdout]: +-----------------------------------------------------------------------------------------+
16:26:33 fslinstaller.py:2591:
By downloading and using the CUDA Toolkit conda packages, you accept the terms and conditions of the CUDA End User License Agreement (EULA): https://docs.nvidia.com/cuda/eula/index.html
16:26:33 fslinstaller.py:2756: Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_linux-64.yml...
16:26:33 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_linux-64.yml ...
16:26:33 fslinstaller.py:2756: Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_osl-dynamics_linux-64.yml...
16:26:33 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_osl-dynamics_linux-64.yml ...
16:26:33 fslinstaller.py:2756: Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_truenet_linux-64.yml...
16:26:33 fslinstaller.py:1241: Downloading https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.17_truenet_linux-64.yml ...
16:26:34 fslinstaller.py:4249:
Installing FSL in /home/itayh/fsl
16:26:34 fslinstaller.py:2877: Downloading miniconda from https://anaconda.org/conda-forge/micromamba/2.0.5/download/linux-64/micromamba-2.0.5-0.tar.bz2...
16:26:34 fslinstaller.py:1241: Downloading https://anaconda.org/conda-forge/micromamba/2.0.5/download/linux-64/micromamba-2.0.5-0.tar.bz2 ...
16:26:35 fslinstaller.py:1597: 1 / 4 [ ] 0.0 / 5.7 MB
16:26:35 fslinstaller.py:1597: 1 / 4 [## ] 0.1 / 5.7 MB
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16:26:42 fslinstaller.py:1597: 1 / 4 [################################################################################################] 5.7 / 5.7 MB
16:26:42 fslinstaller.py:2926: Installing conda at /home/itayh/fsl...
16:26:42 fslinstaller.py:1651: Running mkdir /home/itayh/fsl [as admin: False]
16:26:42 fslinstaller.py:1597: 2 / 4 [################################################# ] 50 / 100 %
16:26:42 fslinstaller.py:1651: Running tar -x -f miniconda.sh -C /home/itayh/fsl [as admin: False]
16:26:42 fslinstaller.py:1842: [stderr]: tar (child): lbzip2: Cannot exec: No such file or directory
16:26:42 fslinstaller.py:1842: [stderr]: tar (child): Error is not recoverable: exiting now
16:26:42 fslinstaller.py:1842: [stderr]: tar: Child returned status 2
16:26:42 fslinstaller.py:1842: [stderr]: tar: Error is not recoverable: exiting now
16:26:42 fslinstaller.py:4140:
ERROR occurred during installation!
16:26:42 fslinstaller.py:4141: This command returned an error: tar -x -f miniconda.sh -C /home/itayh/fsl
16:26:42 fslinstaller.py:4145: File "/mnt/c/Users/itayh/Downloads/fslinstaller.py", line 4137, in handle_error
yield
File "/mnt/c/Users/itayh/Downloads/fslinstaller.py", line 4274, in main
func(*funcargs, prefix=prefix)
File "/mnt/c/Users/itayh/Downloads/fslinstaller.py", line 2942, in install_miniconda
ctx.run(Process.check_call, cmd)
File "/mnt/c/Users/itayh/Downloads/fslinstaller.py", line 2428, in run
return process_func(admin=self.need_admin,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/c/Users/itayh/Downloads/fslinstaller.py", line 1736, in check_call
raise RuntimeError('This command returned an error: ' + cmd)
16:26:42 fslinstaller.py:4148: Environment variables:
16:26:42 fslinstaller.py:4150: DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus
16:26:42 fslinstaller.py:4150: DISPLAY=:0
16:26:42 fslinstaller.py:4150: HOME=/home/itayh
16:26:42 fslinstaller.py:4150: HOSTTYPE=x86_64
16:26:42 fslinstaller.py:4150: LANG=C.UTF-8
16:26:42 fslinstaller.py:4150: LESSCLOSE=/usr/bin/lesspipe %s %s
16:26:42 fslinstaller.py:4150: LESSOPEN=| /usr/bin/lesspipe %s
16:26:42 fslinstaller.py:4150: LOGNAME=itayh
16:26:42 fslinstaller.py:4150: LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=00:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.avif=01;35:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.webp=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:*~=00;90:*#=00;90:*.bak=00;90:*.crdownload=00;90:*.dpkg-dist=00;90:*.dpkg-new=00;90:*.dpkg-old=00;90:*.dpkg-tmp=00;90:*.old=00;90:*.orig=00;90:*.part=00;90:*.rej=00;90:*.rpmnew=00;90:*.rpmorig=00;90:*.rpmsave=00;90:*.swp=00;90:*.tmp=00;90:*.ucf-dist=00;90:*.ucf-new=00;90:*.ucf-old=00;90:
16:26:42 fslinstaller.py:4150: NAME=MAROM-LAB6
16:26:42 fslinstaller.py:4150: PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/SIMULIA/Commands:/mnt/c/Program Files/Microsoft MPI/Bin/:/mnt/c/Windows/system32:/mnt/c/Windows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowerShell/v1.0/:/mnt/c/Windows/System32/OpenSSH/:/mnt/c/Program Files/MATLAB/R2022a/runtime/win64:/mnt/c/Program Files/MATLAB/R2022a/bin:/mnt/c/Users/itayh/AppData/Local/Microsoft/WindowsApps:/snap/bin
16:26:42 fslinstaller.py:4150: PULSE_SERVER=unix:/mnt/wslg/PulseServer
16:26:42 fslinstaller.py:4150: PWD=/mnt/c/Users/itayh
16:26:42 fslinstaller.py:4150: SHELL=/bin/bash
16:26:42 fslinstaller.py:4150: SHLVL=1
16:26:42 fslinstaller.py:4150: TERM=xterm-256color
16:26:42 fslinstaller.py:4150: USER=itayh
16:26:42 fslinstaller.py:4150: WAYLAND_DISPLAY=wayland-0
16:26:42 fslinstaller.py:4150: WSL2_GUI_APPS_ENABLED=1
16:26:42 fslinstaller.py:4150: WSLENV=
16:26:42 fslinstaller.py:4150: WSL_DISTRO_NAME=Ubuntu
16:26:42 fslinstaller.py:4150: WSL_INTEROP=/run/WSL/358_interop
16:26:42 fslinstaller.py:4150: XDG_DATA_DIRS=/usr/local/share:/usr/share:/var/lib/snapd/desktop
16:26:42 fslinstaller.py:4150: XDG_RUNTIME_DIR=/run/user/1000/
16:26:42 fslinstaller.py:4150: _=/usr/bin/python3
16:26:42 fslinstaller.py:4153: Removing failed installation directory /home/itayh/fsl
16:26:42 fslinstaller.py:1651: Running rm -r /home/itayh/fsl [as admin: False]
I tried using all the solutions suggested here, none of them helped the issue.
Hi @itay_Hadar and welcome to neurostars!
That appears to be the root of the problem. You will need to install this library so the tar function can work. Without knowing more about your operating system it is hard to give you precise steps. But it can be installed in a conda/mamba environment with conda/mamba install -c conda-forge bzip2.
Best,
Steven
Hi @itay_Hadar, @Steven is correct - it looks like your system is missing the bzip2 command. FWIW, the downloaded file is always saved as miniconda.sh, but it may be either a shell script (e.g. miniconda/miniforge installer), or a tar.bz2 file (micromamba).
Hi all, I met a problem when install FSL. I attached the screenshot. I am using macOS 10.13 High Sierra. I also tried to add “-- conda”, but still failed. Could you please help with this? Thank you!
Here are the last several lines in log:
13:39:57 fslinstaller.py: 675:
ERROR occurred during installation!
13:39:57 fslinstaller.py: 675: This command returned an error: /Users/zhangtiying/fsl/bin/conda env update -p /Users/zhangtiying/fsl -f fsl-6.0.7.17_macos-64.yml
13:39:57 fslinstaller.py:4145: File "/Users/zhangtiying/Downloads/fslinstaller.py", line 4137, in handle_error
yield
File "/Users/zhangtiying/Downloads/fslinstaller.py", line 4274, in main
func(*funcargs, prefix=prefix)
File "/Users/zhangtiying/Downloads/fslinstaller.py", line 3378, in install_fsl
retry_condition=retry_install, **kwargs)
File "/Users/zhangtiying/Downloads/fslinstaller.py", line 1037, in retry_on_error
raise e
13:39:57 fslinstaller.py:4148: Environment variables:
13:39:57 fslinstaller.py:4150: Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.3vaRkXixox/Render
13:39:57 fslinstaller.py:4150: HOME=/Users/zhangtiying
13:39:57 fslinstaller.py:4150: LC_CTYPE=UTF-8
13:39:57 fslinstaller.py:4150: LOGNAME=zhangtiying
13:39:57 fslinstaller.py:4150: PATH=/Library/Frameworks/Python.framework/Versions/3.13/bin:/Library/Frameworks/Python.framework/Versions/3.13/bin:/Library/Frameworks/Python.framework/Versions/3.12/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
13:39:57 fslinstaller.py:4150: PWD=/Users/zhangtiying
13:39:57 fslinstaller.py:4150: SHELL=/bin/bash
13:39:57 fslinstaller.py:4150: SHLVL=1
13:39:57 fslinstaller.py:4150: SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.pFUoW6gydH/Listeners
13:39:57 fslinstaller.py:4150: TERM=xterm-256color
13:39:57 fslinstaller.py:4150: TERM_PROGRAM=Apple_Terminal
13:39:57 fslinstaller.py:4150: TERM_PROGRAM_VERSION=404.1
13:39:57 fslinstaller.py:4150: TERM_SESSION_ID=4D8672F8-1DB9-467E-875A-491F2F1296D2
13:39:57 fslinstaller.py:4150: TMPDIR=/var/folders/r2/3tcmrl1n5qx3yv6dl3hstx8h0000gn/T/
13:39:57 fslinstaller.py:4150: USER=zhangtiying
13:39:57 fslinstaller.py:4150: VERSIONER_PYTHON_PREFER_32_BIT=no
13:39:57 fslinstaller.py:4150: VERSIONER_PYTHON_VERSION=2.7
13:39:57 fslinstaller.py:4150: XPC_FLAGS=0x0
13:39:57 fslinstaller.py:4150: XPC_SERVICE_NAME=0
13:39:57 fslinstaller.py:4150: _=/usr/bin/python
13:39:57 fslinstaller.py:4150: __CF_USER_TEXT_ENCODING=0x1F5:0x19:0x34
13:39:57 fslinstaller.py: 675: Removing failed installation directory /Users/zhangtiying/fsl
13:39:57 fslinstaller.py:1651: Running rm -r /Users/zhangtiying/fsl [as admin: False]
Hi @Tiying, can you upload the full log file from your attempt to run the fslinstaller.py script without any additional options? If you can’t attach the file here, you can use one of dropbox, google drive, etc etc.
Thanks Paul, I attached the Google Drive link below, hope this helps.
Hi @paulmccarthy , I haven’t solved this problem, can you please help? Thanks.
The log link: fsl_installation_20250317134000.log - Google Drive
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