| ========================================== |
| Job ID: 5404736 |
| Job Name: ccfm_v2_cached |
| Start: Sun Mar 15 04:58:13 JST 2026 |
| Node: b0021 |
| GPU: NVIDIA H100, 95830 MiB |
| NVIDIA H100, 95830 MiB |
| NVIDIA H100, 95830 MiB |
| NVIDIA H100, 95830 MiB |
| Run: CCFM v2 cached (KV fix + loss fix + EMA + RK4 + logit-normal + warmup + scGPT cache) |
| ========================================== |
| The following values were not passed to `accelerate launch` and had defaults used instead: |
| More than one GPU was found, enabling multi-GPU training. |
| If this was unintended please pass in `--num_processes=1`. |
| `--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`. |
| [W315 04:58:44.021644370 socket.cpp:764] [c10d] The client socket cannot be initialized to connect to [localhost]:29500 (errno: 97 - Address family not supported by protocol). |
| /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") |
| /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") |
| /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") |
| /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") |
| [W315 04:59:02.163293234 socket.cpp:764] [c10d] The client socket cannot be initialized to connect to [localhost]:29500 (errno: 97 - Address family not supported by protocol). |
| [W315 04:59:02.432132628 socket.cpp:764] [c10d] The client socket cannot be initialized to connect to [localhost]:29500 (errno: 97 - Address family not supported by protocol). |
| [W315 04:59:02.432621699 socket.cpp:764] [c10d] The client socket cannot be initialized to connect to [localhost]:29500 (errno: 97 - Address family not supported by protocol). |
| [W315 04:59:02.442458875 socket.cpp:764] [c10d] The client socket cannot be initialized to connect to [localhost]:29500 (errno: 97 - Address family not supported by protocol). |
| 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. |
| 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=10000, mode='predict_y', result_path='./result', 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, ema_decay=0.9999, t_sample_mode='logit_normal', t_expr_mean=0.0, t_expr_std=1.0, t_latent_mean=0.0, t_latent_std=1.0, warmup_steps=2000, 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, ode_method='rk4') |
| Converted var_names to gene symbols, sample: ['RP11-34P13.8', 'RP11-54O7.3', 'SAMD11', 'PERM1', 'HES4'] |
| Warning: ctrl is not in the gene names |
| Warning: ctrl is not in the gene namesWarning: ctrl is not in the gene names |
|
|
| Warning: ctrl is not in the gene names |
| /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/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/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/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/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/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/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: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: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: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/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/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) |
| ##### loading vocab from file ##### |
| ##### loading vocab from file ##### |
| ##### loading vocab from file ##### |
| /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( |
| /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( |
| /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( |
| /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) |
| ##### loading vocab from file ##### |
| /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( |
| Loaded 159/163 pretrained parameters |
| Loaded 159/163 pretrained parameters |
| Loaded 159/163 pretrained parameters |
| Using pre-extracted scGPT cache: scgpt_cache_norman.h5 |
| Cache shape: (91205, 5035, 512), cells: 91205 |
| Loaded 159/163 pretrained parameters |
|
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0%| | 0/200000 [00:00<?, ?it/s][rank0]: Traceback (most recent call last): |
| [rank0]: File "/home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/CCFM/scripts/run_cascaded.py", line 350, in <module> |
| [rank0]: cached_z_target = scgpt_cache.lookup(tgt_cell_names, input_gene_ids, device=device) |
| [rank0]: File "/home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/CCFM/src/data/scgpt_cache.py", line 55, in lookup |
| [rank0]: raw = self.features[row_indices] # (B, G_full, D) as numpy |
| [rank0]: ~~~~~~~~~~~~~^^^^^^^^^^^^^ |
| [rank0]: File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper |
| [rank0]: File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper |
| [rank0]: File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/h5py/_hl/dataset.py", line 945, in __getitem__ |
| [rank0]: selection = sel.select(self.shape, args, dataset=self) |
| [rank0]: File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/h5py/_hl/selections.py", line 85, in select |
| [rank0]: return selector.make_selection(args) |
| [rank0]: ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^ |
| [rank0]: File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper |
| [rank0]: File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper |
| [rank0]: File "h5py/_selector.pyx", line 297, in h5py._selector.Selector.make_selection |
| [rank0]: File "h5py/_selector.pyx", line 216, in h5py._selector.Selector.apply_args |
| [rank0]: TypeError: Indexing elements must be in increasing order |
| [rank2]: Traceback (most recent call last): |
| [rank2]: File "/home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/CCFM/scripts/run_cascaded.py", line 350, in <module> |
| [rank2]: cached_z_target = scgpt_cache.lookup(tgt_cell_names, input_gene_ids, device=device) |
| [rank2]: File "/home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/CCFM/src/data/scgpt_cache.py", line 55, in lookup |
| [rank2]: raw = self.features[row_indices] # (B, G_full, D) as numpy |
| [rank2]: ~~~~~~~~~~~~~^^^^^^^^^^^^^ |
| [rank2]: File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper |
| [rank2]: File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper |
| [rank2]: File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/h5py/_hl/dataset.py", line 945, in __getitem__ |
| [rank2]: selection = sel.select(self.shape, args, dataset=self) |
| [rank2]: File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/h5py/_hl/selections.py", line 85, in select |
| [rank2]: return selector.make_selection(args) |
| [rank2]: ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^ |
| [rank2]: File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper |
| [rank2]: File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper |
| [rank2]: File "h5py/_selector.pyx", line 297, in h5py._selector.Selector.make_selection |
| [rank2]: File "h5py/_selector.pyx", line 216, in h5py._selector.Selector.apply_args |
| [rank2]: TypeError: Indexing elements must be in increasing order |
| [rank1]: Traceback (most recent call last): |
| [rank1]: File "/home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/CCFM/scripts/run_cascaded.py", line 350, in <module> |
| [rank1]: cached_z_target = scgpt_cache.lookup(tgt_cell_names, input_gene_ids, device=device) |
| [rank1]: File "/home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/CCFM/src/data/scgpt_cache.py", line 55, in lookup |
| [rank1]: raw = self.features[row_indices] # (B, G_full, D) as numpy |
| [rank1]: ~~~~~~~~~~~~~^^^^^^^^^^^^^ |
| [rank1]: File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper |
| [rank1]: File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper |
| [rank1]: File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/h5py/_hl/dataset.py", line 945, in __getitem__ |
| [rank1]: selection = sel.select(self.shape, args, dataset=self) |
| [rank1]: File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/h5py/_hl/selections.py", line 85, in select |
| [rank1]: return selector.make_selection(args) |
| [rank1]: ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^ |
| [rank1]: File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper |
| [rank1]: File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper |
| [rank1]: File "h5py/_selector.pyx", line 297, in h5py._selector.Selector.make_selection |
| [rank1]: File "h5py/_selector.pyx", line 216, in h5py._selector.Selector.apply_args |
| [rank1]: TypeError: Indexing elements must be in increasing order |
| [rank3]: Traceback (most recent call last): |
| [rank3]: File "/home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/CCFM/scripts/run_cascaded.py", line 350, in <module> |
| [rank3]: cached_z_target = scgpt_cache.lookup(tgt_cell_names, input_gene_ids, device=device) |
| [rank3]: File "/home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/CCFM/src/data/scgpt_cache.py", line 55, in lookup |
| [rank3]: raw = self.features[row_indices] # (B, G_full, D) as numpy |
| [rank3]: ~~~~~~~~~~~~~^^^^^^^^^^^^^ |
| [rank3]: File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper |
| [rank3]: File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper |
| [rank3]: File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/h5py/_hl/dataset.py", line 945, in __getitem__ |
| [rank3]: selection = sel.select(self.shape, args, dataset=self) |
| [rank3]: File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/h5py/_hl/selections.py", line 85, in select |
| [rank3]: return selector.make_selection(args) |
| [rank3]: ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^ |
| [rank3]: File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper |
| [rank3]: File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper |
| [rank3]: File "h5py/_selector.pyx", line 297, in h5py._selector.Selector.make_selection |
| [rank3]: File "h5py/_selector.pyx", line 216, in h5py._selector.Selector.apply_args |
| [rank3]: TypeError: Indexing elements must be in increasing order |
| [rank0]:[W315 05:00:15.940375045 ProcessGroupNCCL.cpp:1553] Warning: WARNING: destroy_process_group() was not called before program exit, which can leak resources. For more info, please see https: |
|
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| W0315 05:00:19.854000 128 torch/distributed/elastic/multiprocessing/api.py:1010] Sending process 200 closing signal SIGTERM |
| W0315 05:00:19.856000 128 torch/distributed/elastic/multiprocessing/api.py:1010] Sending process 201 closing signal SIGTERM |
| W0315 05:00:19.856000 128 torch/distributed/elastic/multiprocessing/api.py:1010] Sending process 203 closing signal SIGTERM |
| E0315 05:00:20.071000 128 torch/distributed/elastic/multiprocessing/api.py:984] failed (exitcode: 1) local_rank: 2 (pid: 202) of binary: /home/hp250092/ku50001222/qian/aivc/lfj/stack_env/bin/python |
| 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 1396, in launch_command |
| multi_gpu_launcher(args) |
| ~~~~~~~~~~~~~~~~~~^^^^^^ |
| File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/accelerate/commands/launch.py", line 1023, in multi_gpu_launcher |
| distrib_run.run(args) |
| ~~~~~~~~~~~~~~~^^^^^^ |
| File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/torch/distributed/run.py", line 982, in run |
| elastic_launch( |
| ~~~~~~~~~~~~~~~ |
| config=config, |
| ~~~~~~~~~~~~~~ |
| entrypoint=cmd, |
| ~~~~~~~~~~~~~~~ |
| )(*cmd_args) |
| ~^^^^^^^^^^^ |
| File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/torch/distributed/launcher/api.py", line 170, in __call__ |
| return launch_agent(self._config, self._entrypoint, list(args)) |
| File "/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/torch/distributed/launcher/api.py", line 317, in launch_agent |
| raise ChildFailedError( |
| ...<2 lines>... |
| ) |
| torch.distributed.elastic.multiprocessing.errors.ChildFailedError: |
| ============================================================ |
| scripts/run_cascaded.py FAILED |
| ------------------------------------------------------------ |
| Failures: |
| [1]: |
| time : 2026-03-15_05:00:20 |
| host : b0021 |
| rank : 0 (local_rank: 0) |
| exitcode : 1 (pid: 200) |
| error_file: <N/A> |
| traceback : To enable traceback see: https: |
| [2]: |
| time : 2026-03-15_05:00:20 |
| host : b0021 |
| rank : 1 (local_rank: 1) |
| exitcode : 1 (pid: 201) |
| error_file: <N/A> |
| traceback : To enable traceback see: https: |
| [3]: |
| time : 2026-03-15_05:00:20 |
| host : b0021 |
| rank : 3 (local_rank: 3) |
| exitcode : 1 (pid: 203) |
| error_file: <N/A> |
| traceback : To enable traceback see: https: |
| ------------------------------------------------------------ |
| Root Cause (first observed failure): |
| [0]: |
| time : 2026-03-15_05:00:19 |
| host : b0021 |
| rank : 2 (local_rank: 2) |
| exitcode : 1 (pid: 202) |
| error_file: <N/A> |
| traceback : To enable traceback see: https: |
| ============================================================ |
| ========================================== |
| Finished: Sun Mar 15 05:00:21 JST 2026 |
| ========================================== |
|
|
