Fsl installation fails on HCP

km345 · February 26, 2024, 10:06am

Hi NeuroStars,

I’m trying to install fsl on a HPC but it fails few minutes into the installation. Could you advise which version to choose and if there’s any specific flags to use to compensate for no root privileges?

Command used

python fslinstaller.py # installed into scratch
# also tried with python2 and --conda

Part of the log file (with 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: [stderr]: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: 09:23:56 fslinstaller.py:1084: 09:23:58 fslinstaller.py:1084: [stderr]: error 09:23:58 fslinstaller.py:1084: 09:23:58 fslinstaller.py:1084: [stderr]: 09:24:00 fslinstaller.py: 206:
ERROR occurred during installation!
09:24:00 fslinstaller.py: 206: the error):
[stderr]: # >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
[stderr]:
Traceback (most recent call last):
File “/mnt/shared/scratch/kmarians/apps/fsl/lib/python3.10/site-packages/conda/exception_handler.py”, line 17, in call
return func(*args, **kwargs)
File “/mnt/shared/scratch/kmarians/apps/fsl/lib/python3.10/site-packages/conda_env/cli/main.py”, line 56, in do_call
exit_code = getattr(module, func_name)(arguments, parser)
File “/mnt/shared/scratch/kmarians/apps/fsl/lib/python3.10/site-packages/conda/notices/core.py”, line 124, in wrapper
return func(*args, **kwargs)
File “/mnt/shared/scratch/kmarians/apps/fsl/lib/python3.10/site-packages/conda_env/cli/main_update.py”, line 143, in execute
result[installer_type] = installer.install(prefix, specs, args, env)
File “/mnt/shared/scratch/kmarians/apps/fsl/lib/python3.10/site-packages/mamba/mamba_env.py”, line 155, in mamba_install
transaction.fetch_extract_packages()
RuntimeError: Resource temporarily unavailable
[stderr]:
[stderr]: $ /home/kmarians/scratch/apps/fsl/bin/mamba update -p /home/kmarians/scratch/apps/fsl -f /tmp/tmpypxrahjp/fsl-6.0.7.7_linux-64.yml
[stderr]:
environment variables:
CIO_TEST=
CONDA_AUTO_UPDATE_CONDA=false
CONDA_ROOT=/mnt/shared/scratch/kmarians/apps/fsl
CURL_CA_BUNDLE=
LD_LIBRARY_PATH=/opt/slurm/latest/lib64
LD_PRELOAD=
MANPATH=/opt/slurm/latest/share/man/:/opt/slurm/latest/share/man/:/opt/slurm/l
atest/share/man/::
MODULEPATH=/etc/scl/modulefiles:/etc/scl/modulefiles:/etc/scl/modulefiles:/usr/sh
are/Modules/modulefiles:/etc/modulefiles:/usr/share/modulefiles
PATH=/opt/openmpi/latest/bin:/opt/slurm/latest/bin:/mnt/shared/apps/guppy/4
.2.2:/mnt/shared/apps/aspera/3.9.2/bin:/mnt/cluster/scripts:/mnt/share
d/scratch/kmarians/apps/conda/bin:/opt/openmpi/latest/bin:/opt/slurm/l
atest/bin:/mnt/shared/apps/guppy/4.2.2:/mnt/shared/apps/aspera/3.9.2/b
in:/mnt/cluster/scripts:/mnt/shared/scratch/kmarians/apps/conda/bin:/h
ome/kmarians/.local/bin:/home/kmarians/bin:/opt/openmpi/latest/bin:/op
t/slurm/latest/bin:/usr/share/Modules/bin:/mnt/shared/apps/guppy/4.2.2
:/mnt/shared/apps/aspera/3.9.2/bin:/mnt/cluster/scripts:/mnt/shared/sc
ratch/kmarians/apps/conda/condabin:/mnt/shared/scratch/kmarians/apps/c
onda/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
[stderr]:
active environment : None
user config file : /home/kmarians/.condarc
populated config files : /mnt/shared/scratch/kmarians/apps/fsl/.condarc
/home/kmarians/.condarc
/home/kmarians/scratch/apps/fsl/.condarc
conda version : 23.11.0
conda-build version : not installed
python version : 3.10.13.final.0
solver : libmamba (default)
virtual packages : __archspec=1=skylake_avx512
__conda=23.11.0=0
__glibc=2.28=0
__linux=4.18.0=0
__unix=0=0
base environment : /mnt/shared/scratch/kmarians/apps/fsl (writable)
conda av data dir : /mnt/shared/scratch/kmarians/apps/fsl/etc/conda
conda av metadata url : None
channel URLs : public/linux-64
public/noarch
conda-forge/linux-64
conda-forge/noarch
package cache : /home/kmarians/scratch/apps/fsl/pkgs
envs directories : /mnt/shared/scratch/kmarians/apps/fsl/envs
/home/kmarians/.conda/envs
platform : linux-64
user-agent : conda/23.11.0 requests/2.31.0 CPython/3.10.13 Linux/4.18.0-513.11.1.el8_9.0.1.x86_64 rocky/8.9 glibc/2.28 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.5
UID:GID : 896600222:896600222
netrc file : None
offline mode : False
[stderr]:
[stderr]:
[stderr]: An unexpected error has occurred. Conda has prepared the above report.
[stderr]: If you suspect this error is being caused by a malfunctioning plugin,
[stderr]: consider using the --no-plugins option to turn off plugins.
[stderr]:
[stderr]: Example: conda --no-plugins install
[stderr]:
[stderr]: Alternatively, you can set the CONDA_NO_PLUGINS environment variable on
[stderr]: the command line to run the command without plugins enabled.
[stderr]:
[stderr]: Example: CONDA_NO_PLUGINS=true conda install
[stderr]:
libmamba Error when extracting package: std::bad_alloc
[stderr]: terminate called after throwing an instance of ‘std::bad_alloc’
what(): std::bad_alloc
This command returned an error: /home/kmarians/scratch/apps/fsl/bin/mamba env update -p /home/kmarians/scratch/apps/fsl -f /tmp/tmpypxrahjp/fsl-6.0.7.7_linux-64.yml

09:24:00 fslinstaller.py:2768: File “/mnt/shared/scratch/kmarians/apps/FSL/fslinstaller.py”, line 2760, in handle_error
yield
File “/mnt/shared/scratch/kmarians/apps/FSL/fslinstaller.py”, line 2875, in main
install_fsl(ctx)
File “/mnt/shared/scratch/kmarians/apps/FSL/fslinstaller.py”, line 2138, in install_fsl
ctx.run(Process.monitor_progress, cmd,
File “/mnt/shared/scratch/kmarians/apps/FSL/fslinstaller.py”, line 1586, in run
return process_func(admin=self.need_admin,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/mnt/shared/scratch/kmarians/apps/FSL/fslinstaller.py”, line 1056, in monitor_progress
raise RuntimeError('This command returned ’ …

(happy to include the entire log file if that helps)

Steven · February 26, 2024, 1:09pm

A post was merged into an existing topic: Problems installing FSL

Steven · February 26, 2024, 1:09pm