RJPenic
commented
6 months ago Hello, thank you for using RiNALMo! 😄
- Can you provide us with the script
/projects/p32327/RNAFOLD/RiNALMo-main/try.pyyou are using to get RiNALMo's embeddings? Is it the same inference example code from README file? - Have you encountered any errors/warnings when you were installing flash attention (
pip install flash-attn==2.3.2)? - What CUDA version do you have installed on your machine? Does your GPU support newer versions of CUDA (>= 11.8)?
WeiminWu2000
ylzdmm
/tmp/tmp5oe3edsd/main.c: In function ‘list_to_cuuint64_array’: /tmp/tmp5oe3edsd/main.c:354:3: error: ‘for’ loop initial declarations are only allowed in C99 mode for (Py_ssize_t i = 0; i < len; i++) { ^ /tmp/tmp5oe3edsd/main.c:354:3: note: use option -std=c99 or -std=gnu99 to compile your code /tmp/tmp5oe3edsd/main.c: In function ‘list_to_cuuint32_array’: /tmp/tmp5oe3edsd/main.c:365:3: error: ‘for’ loop initial declarations are only allowed in C99 mode for (Py_ssize_t i = 0; i < len; i++) { ^ Traceback (most recent call last): File "/projects/p32327/RNAFOLD/RiNALMo-main/try.py", line 13, in
outputs = model(tokens)
^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl
return self._call_impl(*args, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl
return forward_call(*args, *kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/projects/p32327/RNAFOLD/RiNALMo-main/rinalmo/model/model.py", line 26, in forward
representation, attn_weights = self.transformer(
^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl
return self._call_impl(args, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl
return forward_call(*args, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/projects/p32327/RNAFOLD/RiNALMo-main/rinalmo/model/modules.py", line 58, in forward
x, attn = checkpoint.checkpoint(
^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/torch/_compile.py", line 24, in inner
return torch._dynamo.disable(fn, recursive)(*args, *kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/torch/_dynamo/eval_frame.py", line 489, in _fn
return fn(args, kwargs)
^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/torch/_dynamo/external_utils.py", line 17, in inner
return fn(*args, kwargs)
^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/torch/utils/checkpoint.py", line 489, in checkpoint
ret = function(*args, *kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl
return self._call_impl(args, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl
return forward_call(*args, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/projects/p32327/RNAFOLD/RiNALMo-main/rinalmo/model/modules.py", line 125, in forward
mh_out, attn = self.mh_attn(x, key_padding_mask=key_padding_mask, return_attn_probs=need_attn_weights)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl
return self._call_impl(*args, *kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl
return forward_call(args, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/projects/p32327/RNAFOLD/RiNALMo-main/rinalmo/model/attention.py", line 193, in forward
qkv = self.rotary_emb(qkv, seqlen_offset=0)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl
return self._call_impl(*args, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl
return forward_call(*args, *kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/flash_attn/layers/rotary.py", line 438, in forward
return apply_rotary_embqkv(
^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/flash_attn/layers/rotary.py", line 233, in apply_rotary_embqkv
return ApplyRotaryEmbQKV_.apply(qkv, cos, sin, cos_k, sin_k, interleaved, seqlen_offsets)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/torch/autograd/function.py", line 553, in apply
return super().apply(args, kwargs) # type: ignore[misc]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/flash_attn/layers/rotary.py", line 151, in forward
apply_rotary(
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/flash_attn/ops/triton/rotary.py", line 213, in apply_rotary
rotary_kernel[grid](
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/triton/runtime/jit.py", line 550, in run
bin.c_wrapper(
^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/triton/compiler/compiler.py", line 692, in getattribute
self._init_handles()
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/triton/compiler/compiler.py", line 670, in _init_handles
bin_path = {driver.HIP: "hsaco_path", driver.CUDA: "cubin"}[driver.backend]
^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/triton/runtime/driver.py", line 157, in getattr
self._initialize_obj()
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/triton/runtime/driver.py", line 154, in _initialize_obj
self._obj = self._init_fn()
^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/triton/runtime/driver.py", line 187, in initialize_driver
return CudaDriver()
^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/triton/runtime/driver.py", line 77, in init
self.utils = CudaUtils()
^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/triton/runtime/driver.py", line 47, in init
so = _build("cuda_utils", src_path, tmpdir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/triton/common/build.py", line 106, in _build
ret = subprocess.check_call(cc_cmd)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vqc8153/miniconda3/envs/rna/lib/python3.11/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/usr/bin/gcc', '/tmp/tmp5oe3edsd/main.c', '-O3', '-I/home/vqc8153/miniconda3/envs/rna/lib/python3.11/site-packages/triton/common/../third_party/cuda/include', '-I/home/vqc8153/miniconda3/envs/rna/include/python3.11', '-I/tmp/tmp5oe3edsd', '-shared', '-fPIC', '-lcuda', '-o', '/tmp/tmp5oe3edsd/cuda_utils.cpython-311-x86_64-linux-gnu.so', '-L/.singularity.d/libs']' returned non-zero exit status 1.