Comments (4)
Hi,
It seems a similar error as the one here:
#39 (comment)
Can you try changing the permissions before launching docker and providing the working directory to docker. The example of command is given in the comment of the previous issue.
from instagraal.
Oh, thank you very much, I missed this post.
It worked but I encountered a second error after some steps:
...
INFO :: import reference genome
INFO :: loading data from level = 3
INFO :: mean frag area = 611.1701049804688
INFO :: N frag duplicated = 0
INFO :: MAX ID CONTIG = 11021
INFO :: total mem used by sparse data = 11.676732
Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/pycuda-2021.1-py3.6-linux-x86_64.egg/pycuda/tools.py", line 470, in wrapper
return ctx_dict[cur_ctx][cache_key]
KeyError: <pycuda._driver.Context object at 0x7f044abf8710>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/bin/instagraal", line 11, in
load_entry_point('instagraal', 'console_scripts', 'instagraal')()
File "/src/instagraal/instagraal/instagraal.py", line 1178, in main
output_folder=output_folder,
File "/src/instagraal/instagraal/instagraal.py", line 160, in init
output_folder=output_folder,
File "/src/instagraal/instagraal/simu_single.py", line 168, in init
self.pos,
File "/src/instagraal/instagraal/cuda_lib_gl_single.py", line 251, in init
self.setup_all_gpu_struct()
File "/src/instagraal/instagraal/cuda_lib_gl_single.py", line 371, in setup_all_gpu_struct
self.gpu_counter_select = ga.zeros(1, dtype=np.int32)
File "/usr/local/lib/python3.6/dist-packages/pycuda-2021.1-py3.6-linux-x86_64.egg/pycuda/gpuarray.py", line 1244, in zeros
result.fill(zero)
File "/usr/local/lib/python3.6/dist-packages/pycuda-2021.1-py3.6-linux-x86_64.egg/pycuda/gpuarray.py", line 659, in fill
func = elementwise.get_fill_kernel(self.dtype)
File "/usr/local/lib/python3.6/dist-packages/pycuda-2021.1-py3.6-linux-x86_64.egg/pycuda/tools.py", line 474, in wrapper
result = func(*args, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/pycuda-2021.1-py3.6-linux-x86_64.egg/pycuda/elementwise.py", line 566, in get_fill_kernel
"fill",
File "/usr/local/lib/python3.6/dist-packages/pycuda-2021.1-py3.6-linux-x86_64.egg/pycuda/elementwise.py", line 193, in get_elwise_kernel
arguments, operation, name, keep, options, **kwargs
File "/usr/local/lib/python3.6/dist-packages/pycuda-2021.1-py3.6-linux-x86_64.egg/pycuda/elementwise.py", line 178, in get_elwise_kernel_and_types
mod = module_builder(arguments, operation, name, keep, options, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/pycuda-2021.1-py3.6-linux-x86_64.egg/pycuda/elementwise.py", line 82, in get_elwise_module
no_extern_c=True,
File "/usr/local/lib/python3.6/dist-packages/pycuda-2021.1-py3.6-linux-x86_64.egg/pycuda/compiler.py", line 358, in init
include_dirs,
File "/usr/local/lib/python3.6/dist-packages/pycuda-2021.1-py3.6-linux-x86_64.egg/pycuda/compiler.py", line 298, in compile
return compile_plain(source, options, keep, nvcc, cache_dir, target)
File "/usr/local/lib/python3.6/dist-packages/pycuda-2021.1-py3.6-linux-x86_64.egg/pycuda/compiler.py", line 87, in compile_plain
checksum.update(preprocess_source(source, options, nvcc).encode("utf-8"))
File "/usr/local/lib/python3.6/dist-packages/pycuda-2021.1-py3.6-linux-x86_64.egg/pycuda/compiler.py", line 59, in preprocess_source
"nvcc preprocessing of %s failed" % source_path, cmdline, stderr=stderr
pycuda.driver.CompileError: nvcc preprocessing of /tmp/tmpqlcffcwz.cu failed
[command: nvcc --preprocess -arch sm_86 -I/usr/local/lib/python3.6/dist-packages/pycuda-2021.1-py3.6-linux-x86_64.egg/pycuda/cuda /tmp/tmpqlcffcwz.cu --compiler-options -P]
[stderr:
b"nvcc fatal : Value 'sm_86' is not defined for option 'gpu-architecture'\n"]
which also looks like issue 24, but not completely.
Can this correspond to a cuda version issue? How should I check that?
Thank you very much again for your help!
Best regards
from instagraal.
Sorry, I forgot to answer you.
Have you check, that is not due to incompatible version of pycuda. Instagraal is not working with the last versions of pycuda. You can see this issue: #42.
Best regards,
from instagraal.
Hi, I thank you again for your answer!
I struggle a little with the versions of the programs and I think that somehow I made a mess with the nvidia driver, because now gives this error:
sudo docker run --gpus all --workdir $WORKDIR --mount "type=bind,src=$WORKDIR,dst=$WORKDIR" koszullab/instagraal instagraal ~/PATH/matrice ~/PATH/assembly.fasta ~/PATH/instagraal_out/
docker: Error response from daemon: could not select device driver "" with capabilities: [[gpu]].
ERRO[0000] error waiting for container:
Here are informations on the nvidia driver and cuda installations:
nvidia-smi
Tue Aug 22 19:52:56 2023
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 470.199.02 Driver Version: 470.199.02 CUDA Version: 11.4 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|===============================+======================+======================|
| 0 NVIDIA GeForce ... Off | 00000000:0B:00.0 Off | N/A |
| 0% 37C P8 10W / 350W | 35MiB / 24260MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================|
| 0 N/A N/A 1106 G /usr/lib/xorg/Xorg 33MiB |
+-----------------------------------------------------------------------------+
nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2019 NVIDIA Corporation
Built on Sun_Jul_28_19:07:16_PDT_2019
Cuda compilation tools, release 10.1, V10.1.243
Do you know what I did wrong here?
Also, while the docker wasn't working, I managed to install the program locally but also got an error:
instagraal ~/PATH/matrice ~/PATH/assembly.fasta ~/PATH/instagraal_out/
INFO :: Selected_device: NVIDIA GeForce RTX 3090
Traceback (most recent call last):
File "/usr/local/bin/instagraal", line 8, in <module>
sys.exit(main())
File "/usr/local/lib/python3.8/dist-packages/instagraal/instagraal.py", line 2146, in main
p2 = window(
File "/usr/local/lib/python3.8/dist-packages/instagraal/instagraal.py", line 208, in __init__
self.cuda_gl_init()
File "/usr/local/lib/python3.8/dist-packages/instagraal/instagraal.py", line 1447, in cuda_gl_init
self.ctx_gl = cudagl.make_context(
pycuda._driver.Error: cuGLCtxCreate failed: unknown error
I noticed this error is reported elsewhere #34, #12
and from the little I understood, it might still be a pycuda version issue, but how do I chose the right version, check which one is running and change it?
I used these commands to install pycuda:
git clone --recurse-submodules https://github.com/inducer/pycuda.git
cd pycuda
python3 configure.py --cuda-enable-gl --no-use-shipped-boost
sudo python3 setup.py install
Thanks again and sorry for my lack of understanding of the answers on previous posts!
Best regards
from instagraal.
Related Issues (20)
- Should the initial reference assembly and final polished genome have equal sequence lengths? HOT 1
- How to use genetic linkage data?
- What does "--bomb" do? HOT 1
- Description of new_info_frags.txt file HOT 1
- instagraal-polish: problem with -j option HOT 1
- OSError: [Errno 28] No space left on device HOT 2
- module.cpp:1:10: fatal error: boost/python.hpp: No such file or directory HOT 3
- Instagraal docker run gives error about pyramid directory HOT 2
- KeyError on import reference genome HOT 3
- tools option not showing HOT 41
- Instagraal polish - KeyError HOT 2
- instagraal-polish HOT 8
- How to separate "merged" chromosomes? HOT 2
- Module 'numpy' has no attribute 'asscalar'
- pycuda issue with CUDA toolkit 12.0 HOT 8
- Error with --simple HOT 2
- pycuda installation HOT 2
- pycuda version 2022 not supported HOT 1
- usage of __shfl_down is deprecated HOT 2
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from instagraal.