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prehensilecode
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alphafold_singularity
Singularity recipe for AlphaFold
GNU General Public License v3.0
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Dependencies outdated in container definition
#39
atb1r21
opened
1 week ago
0
ERROR: No matching distribution found for numpy==1.21.6
#38
johnnytam100
opened
7 months ago
6
Relaxation step error CUDA_ERROR_ILLEGAL_ADDRESS
#37
sarah872
closed
1 year ago
1
conda version and python version "conflict"
#36
hermannschwaerzlerUIBK
closed
1 year ago
6
RuntimeError: HHSearch failed: stdout: stderr:
#35
erdaqorri
closed
1 year ago
3
singularity process stalls during binidng databases
#34
Comp-era
closed
1 year ago
8
alphafold 2.3.2 could not locate params directory
#33
artcmd
closed
1 year ago
2
Correctly handle --output_dir argument to run_singularity.py
#32
prehensilecode
closed
1 year ago
0
singularity image mounting output directory to /tmp
#31
nfbourg
closed
1 year ago
0
Update for AlphaFold 2.3.2. Reset author email.
#30
prehensilecode
closed
1 year ago
0
Update for AlphaFold 2.3.2
#29
prehensilecode
closed
1 year ago
0
run_singularity.py doesn't use output_dir flag
#28
mokca
closed
1 year ago
2
Update for AlphaFold 2.3.1
#27
prehensilecode
closed
1 year ago
0
run_singularity.py does not terminate even if >1 GPU is requested
#26
prehensilecode
closed
1 year ago
2
amber_minimize.py - Minimizing protein failed - No compatible CUDA device is available
#25
prehensilecode
closed
1 year ago
10
stockholm msa write failed - system error: No space left on device
#24
prehensilecode
closed
1 year ago
3
sample Slurm batch file and Python command fails with Error for command "run": unknown flag: --env
#23
SomePersonSomeWhereInTheWorld
closed
1 year ago
3
/.post.script: 75: /.post.script: cannot open /app/alphafold/docker/openmm.patch: No such file
#22
SomePersonSomeWhereInTheWorld
closed
1 year ago
16
prebuilt image missing
#21
GentleInfant
closed
1 year ago
4
Updating calls to uniclust30 with new UniRef30
#20
GentleInfant
closed
1 year ago
0
Missing `uniclust30/uniclust30_2018_08`
#19
GentleInfant
closed
1 year ago
4
Error while running Alphafold in singularity
#18
Comp-era
closed
1 year ago
6
jaxlib.xla_extension.XlaRuntimeError: RESOURCE_EXHAUSTED
#17
infinity01
closed
1 year ago
9
Error for command "run": unknown flag: --env
#16
infinity01
closed
1 year ago
3
Update for AlphaFold 2.3.0
#15
prehensilecode
closed
1 year ago
2
Maybe update the requirements
#14
prehensilecode
closed
1 year ago
2
`IsADirectoryError` when building image
#13
multimeric
closed
1 year ago
1
openmm.patch file missing referenced by Singularity.def
#12
amichaleas
closed
2 years ago
2
Patch fails to find file to patch when building
#11
terrycojones
closed
2 years ago
3
Discussion: recommended to build sandbox first?
#10
jonathanking
closed
2 years ago
1
Update for AlphaFold 2.2.4
#9
prehensilecode
closed
2 years ago
0
2.2.2 2
#8
prehensilecode
closed
2 years ago
0
Fail during singularity build
#7
cb4github
closed
2 years ago
19
update to 2.2.3?
#6
ckywong
closed
2 years ago
4
Add CUDA utilities path
#5
prehensilecode
closed
2 years ago
0
apptainer (singualrity) container fails: Can't find ptxas binary
#4
hseara
closed
2 years ago
10
Update for 2.2.2
#3
prehensilecode
closed
2 years ago
0
Test run fails - ldconfig errors, unknown command line flag errors
#2
prehensilecode
closed
2 years ago
2
Broken for AlphaFold 2.1.1 and 2.2.0
#1
prehensilecode
closed
2 years ago
1