| ========================================== |
| Job ID: 5404526 |
| Job Name: ccfm_1gpu_cached |
| Start: Sun Mar 15 01:17:06 JST 2026 |
| Node: b0027 |
| GPU: NVIDIA H100, 95830 MiB |
| Run: CCFM 1GPU cached scGPT |
| ========================================== |
| The following values were not passed to `accelerate launch` and had defaults used instead: |
| `--num_machines` was set to a value of `1` |
| `--mixed_precision` was set to a value of `'no'` |
| `--dynamo_backend` was set to a value of `'no'` |
| To avoid this warning pass in values for each of the problematic parameters or run `accelerate config`. |
| /home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/scGPT/scgpt/model/model.py:21: UserWarning: flash_attn is not installed |
| warnings.warn("flash_attn is not installed") |
| WARNING:accelerate.utils.other:[RANK 0] Detected kernel version 4.18.0, which is below the recommended minimum of 5.5.0; this can cause the process to hang. It is recommended to upgrade the kernel to the minimum version or higher. |
| /home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/scDFM/src/data_process/data.py:185: ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual. |
| self.adata.obs['condition'] = self.adata.obs['condition'].str.replace('ctrl', 'control') |
| /home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/scanpy/preprocessing/_highly_variable_genes.py:806: ImplicitModificationWarning: Trying to modify attribute `._uns` of view, initializing view as actual. |
| adata.uns["hvg"] = {"flavor": flavor} |
| /home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/scDFM/src/data_process/data.py:277: ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual. |
| self.adata.obs['perturbation_covariates'] = self.adata.obs[perturbation_covariates].apply(lambda x: '+'.join(x), axis=1) |
| /home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/scDFM/src/data_process/data.py:329: ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual. |
| self.adata.obs['perturbation_covariates'] = self.adata.obs[perturbation_covariates].apply(lambda x: '+'.join(x), axis=1) |
| /home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/CCFM/src/data/scgpt_extractor.py:109: UserWarning: FrozenScGPTExtractor: 498/5035 HVG genes not found in scGPT vocab, will use zero vectors. |
| warnings.warn( |
| CascadedFlowConfig(model_type='cascaded', batch_size=48, ntoken=512, d_model=128, nhead=8, nlayers=4, lr=5e-05, steps=200000, eta_min=1e-06, devices='1', test_only=False, data_name='norman', perturbation_function='crisper', noise_type='Gaussian', poisson_alpha=0.8, poisson_target_sum=-1, print_every=5000, mode='predict_y', result_path='./result_scgpt', fusion_method='differential_perceiver', infer_top_gene=1000, n_top_genes=5000, checkpoint_path='', gamma=0.5, split_method='additive', use_mmd_loss=True, fold=1, use_negative_edge=True, topk=30, scgpt_dim=512, bottleneck_dim=128, latent_weight=1.0, choose_latent_p=0.4, target_std=1.0, dh_depth=2, warmup_batches=200, scgpt_model_dir='transfer/data/scGPT_pretrained', scgpt_max_seq_len=1200, scgpt_cache_path='scgpt_cache_norman.h5', latent_steps=20, expr_steps=20) |
| Converted var_names to gene symbols, sample: ['RP11-34P13.8', 'RP11-54O7.3', 'SAMD11', 'PERM1', 'HES4'] |
| Warning: ctrl is not in the gene names |
| ##### loading vocab from file ##### |
| Loaded 159/163 pretrained parameters |
| Using pre-extracted scGPT cache: scgpt_cache_norman.h5 |
| Cache shape: (91205, 5035, 512), cells: 91205 |
|
0%| | 0/200000 [00:00<?, ?it/s]Traceback (most recent call last): |
| File "/home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/CCFM/scripts/run_cascaded.py", line 325, in <module> |
| cached_z_target = scgpt_cache.lookup(tgt_cell_names, input_gene_ids, device=device) |
| File "/home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/CCFM/src/data/scgpt_cache.py", line 55, in lookup |
| raw = self.features[row_indices] # (B, G_full, D) as numpy |
| ~~~~~~~~~~~~~^^^^^^^^^^^^^ |
| File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper |
| File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper |
| File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/h5py/_hl/dataset.py", line 945, in __getitem__ |
| selection = sel.select(self.shape, args, dataset=self) |
| File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/h5py/_hl/selections.py", line 85, in select |
| return selector.make_selection(args) |
| ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^ |
| File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper |
| File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper |
| File "h5py/_selector.pyx", line 297, in h5py._selector.Selector.make_selection |
| File "h5py/_selector.pyx", line 216, in h5py._selector.Selector.apply_args |
| TypeError: Indexing elements must be in increasing order |
|
0%| | 0/200000 [00:42<?, ?it/s] |
| Traceback (most recent call last): |
| File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/bin/accelerate", line 8, in <module> |
| sys.exit(main()) |
| ~~~~^^ |
| File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/accelerate/commands/accelerate_cli.py", line 50, in main |
| args.func(args) |
| ~~~~~~~~~^^^^^^ |
| File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/accelerate/commands/launch.py", line 1405, in launch_command |
| simple_launcher(args) |
| ~~~~~~~~~~~~~~~^^^^^^ |
| File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/accelerate/commands/launch.py", line 993, in simple_launcher |
| raise subprocess.CalledProcessError(returncode=process.returncode, cmd=cmd) |
| subprocess.CalledProcessError: Command '['/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/bin/python', 'scripts/run_cascaded.py', '--data-name', 'norman', '--d-model', '128', '--nhead', '8', '--nlayers', '4', '--batch-size', '48', '--lr', '5e-5', '--steps', '200000', '--fusion-method', 'differential_perceiver', '--perturbation-function', 'crisper', '--noise-type', 'Gaussian', '--infer-top-gene', '1000', '--n-top-genes', '5000', '--use-mmd-loss', '--gamma', '0.5', '--split-method', 'additive', '--fold', '1', '--scgpt-dim', '512', '--bottleneck-dim', '128', '--latent-weight', '1.0', '--choose-latent-p', '0.4', '--dh-depth', '2', '--print-every', '5000', '--topk', '30', '--use-negative-edge', '--scgpt-cache-path', 'scgpt_cache_norman.h5', '--result-path', './result_scgpt']' returned non-zero exit status 1. |
| ========================================== |
| Finished: Sun Mar 15 01:19:22 JST 2026 |
| ========================================== |
| |
