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Error undefined symbol cublasGetSmCountTarget from libcublas.so.11 #69

Closed dithiii closed 9 months ago

dithiii commented 1 year ago

Running dorado 0.1.1 with any model on a fresh install of ubuntu 22.04 gives the following error. However, the base calling still appears to be working despite this error. Any fix? [2022-12-30 09:46:27.264] [info] > Creating basecall pipeline Could not load symbol cublasGetSmCountTarget from libcublas.so.11. Error: /home/cfaulk/Desktop/dorado-0.1.1+eb48766-Linux/bin/../lib/libcublas.so.11: undefined symbol: cublasGetSmCountTarget

dithiii commented 1 year ago

Update. This error only appears when --modified-bases is used.

Also, when run with --modified-bases, the process eventually crashes non-deterministically, at about 22 Gb of output. I've tried using various inputs, fast5s, monolithic pod5s, and individually converted pod5s. Same result. Looks like something is going wrong with modified base calling.

dithiii commented 1 year ago

Different issue, but maybe related? I'm trying to compile from the github and cannot complete due to the following error. [ 31%] Completed 'streamvbyte' [ 31%] Built target streamvbyte gmake: *** [Makefile:166: all] Error 2

dithiii commented 1 year ago

On the build problem, I installed h5py and autoconf (version 2.6.9 is needed), and a few other undocumented dependencies, but now I'm stuck at the following error. I did install htslib with libdeflate (both compiled and with apt).

[100%] Linking CXX executable bin/dorado /usr/bin/ld: 3rdparty/htslib/lib/libhts.a(cram_io.o): in function libdeflate_deflate': /home/cfaulk/Desktop/monkeymeth/dorado/dorado/3rdparty/htslib/cram/cram_io.c:1118: undefined reference to libdeflate_alloc_compressor' /usr/bin/ld: /home/cfaulk/Desktop/monkeymeth/dorado/dorado/3rdparty/htslib/cram/cram_io.c:1133: undefined reference to libdeflate_gzip_compress' /usr/bin/ld: /home/cfaulk/Desktop/monkeymeth/dorado/dorado/3rdparty/htslib/cram/cram_io.c:1134: undefined reference to libdeflate_free_compressor' /usr/bin/ld: /home/cfaulk/Desktop/monkeymeth/dorado/dorado/3rdparty/htslib/cram/cram_io.c:1129: undefined reference to libdeflate_free_compressor' /usr/bin/ld: 3rdparty/htslib/lib/libhts.a(cram_io.o): in function uint7_decode_crc64':

maximum411 commented 1 year ago

I have this same issue on Windows. I do get partial basecalling output, which seems to include mod information, but it exits after about 100k reads. Has anyone found a solution? I am also getting:

Could not load symbol cublasGetSmCountTarget from cublas64_11.dll. Error code 127

rainwala commented 1 year ago

Hi @dithiii, I have this same issue on the epi2me human variation workflow, using Ubuntu 20.04. DId you ever solve this?

faulk-lab commented 1 year ago

Hi ranwala, I was never able to solve compiling with ubuntu, however the latest dorado binary builds have worked successfully on several of my Ubuntu systems running both 20.04 and 22.04. Sorry that's all the information I have.