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Author SHA1 Message Date
Olamide Isreal
9ffba5cb2c Production config: disable MSA, 1 sample, errorStrategy ignore 
- Disable MSA to reduce GPU memory for large complexes
- Default to 1 diffusion sample to fit within GPU VRAM
- Add errorStrategy 'ignore' so pipeline completes even if
  individual tasks fail (standard bioinformatics pattern)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
 2026-03-16 20:29:24 +01:00
Olamide Isreal
fdbd7bf863 Use dedicated input subdirectory to avoid stale files 
Previous runs left rcsb_pdb_1QGS.fasta in the work dir.
Using s3://omic/eureka/chai1/input/ ensures only our files are picked up.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
 2026-03-16 19:54:59 +01:00
Olamide Isreal
64a323a486 Use v3 image with transformers 4.44.2 (EsmModel compatible) 
Pin transformers<4.45 and use v3 tag to ensure K8s pulls
the corrected image with working EsmModel imports.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
 2026-03-16 18:21:46 +01:00
Olamide Isreal
a191b6e192 Pin transformers<4.45 to fix EsmModel import at runtime 
Chai-1 requires EsmModel from transformers top-level import.
Versions 4.45+ moved it, causing ImportError at runtime.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
 2026-03-16 17:54:19 +01:00
3 changed files with 8 additions and 7 deletions
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4
Dockerfile
View File

@@ -15,7 +15,7 @@ WORKDIR /workspace
# Install chai_lab and compatible transformers in a single layer # Install chai_lab and compatible transformers in a single layer
RUN pip install --no-cache-dir \ RUN pip install --no-cache-dir \
chai_lab==0.5.2 \ chai_lab==0.5.2 \
"transformers>=4.30.0,<5.0.0" "transformers>=4.30.0,<4.45.0"
# Make package dirs writable for any user (K8s may run as non-root) # Make package dirs writable for any user (K8s may run as non-root)
RUN chmod -R a+rw /opt/conda/lib/python3.11/site-packages/chai_lab/ && \ RUN chmod -R a+rw /opt/conda/lib/python3.11/site-packages/chai_lab/ && \
@@ -26,7 +26,7 @@ RUN chmod -R a+rw /opt/conda/lib/python3.11/site-packages/chai_lab/ && \
# Verify installations # Verify installations
RUN python -c "import torch; print(f'PyTorch: {torch.__version__}')" && \ RUN python -c "import torch; print(f'PyTorch: {torch.__version__}')" && \
python -c "import transformers; print(f'transformers: {transformers.__version__}')" && \ python -c "from transformers import EsmModel; print('EsmModel: OK')" && \
python -c "import chai_lab; print('chai_lab: OK')" && \ python -c "import chai_lab; print('chai_lab: OK')" && \
chai --help chai --help

9
main.nf
View File

@@ -1,17 +1,18 @@
#!/usr/bin/env nextflow #!/usr/bin/env nextflow
nextflow.enable.dsl=2 nextflow.enable.dsl=2
params.input_dir = 's3://omic/eureka/chai1' params.input_dir = 's3://omic/eureka/chai1/input'
params.outdir = 's3://omic/eureka/chai1/output' params.outdir = 's3://omic/eureka/chai1/output'
params.use_msa = true params.use_msa = false
params.msa_server = 'https://api.colabfold.com' params.msa_server = 'https://api.colabfold.com'
params.num_samples = 5 params.num_samples = 1
process CHAI1 { process CHAI1 {
container 'harbor.cluster.omic.ai/omic/chai1:v2' container 'harbor.cluster.omic.ai/omic/chai1:v3'
publishDir params.outdir, mode: 'copy' publishDir params.outdir, mode: 'copy'
stageInMode 'copy' stageInMode 'copy'
maxForks 1 maxForks 1
errorStrategy 'ignore'
input: input:
path fasta path fasta

2
nextflow.config
View File

@@ -3,7 +3,7 @@ docker {
} }
process { process {
container = 'harbor.cluster.omic.ai/omic/chai1:v2' container = 'harbor.cluster.omic.ai/omic/chai1:v3'
memory = '32 GB' memory = '32 GB'
cpus = 4 cpus = 4
} }