I think the
PYTHONPATH needs to be different, hmm..
Maybe the
numpy-base-1.20.3-py37h74d4b33_0 part will be different
well, it found the package
PyError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.
We have compiled some common reasons and troubleshooting tips at:
https://numpy.org/devdocs/user/troubleshooting-importerror.html
Please note and check the following:
* The Python version is: Python3.8 from "/home/assrivat/miniconda3/bin/python3"
* The NumPy version is: "1.21.0"
and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.
Original error was: No module named 'numpy.core._multiarray_umath'
Raised from: pyobj.exc_check
Sry that's my one
Replace with your home dir
What about
conda install numpy?
That did work though
That's what I just did
would I have to port it under that dir
What path do you get?
I think you can just set
PYTHONPATH to that..
I think everything is good now, thanks
seqc run on v0.10.1 thru v0.10.3 works just fine on any source file. seqc build works on v0.10.1 but not .2 or.3. I haven't quite been able to sort out the issue. I've tried on both Ubuntu 20.04 on WSL on Windows and Ubuntu 21.04 on Linux. Typical output:mhenders@DESKTOP-3B448LI:~/seq-code$ seqc build hello.seq
/usr/bin/ld: /home/mhenders/.seq/lib/seq/libseqrt.so: undefined reference to `BZ2_bzBuffToBuffCompress'
/usr/bin/ld: /home/mhenders/.seq/lib/seq/libseqrt.so: undefined reference to `BZ2_bzBuffToBuffDecompress'
/usr/bin/ld: /home/mhenders/.seq/lib/seq/libseqrt.so: undefined reference to `lzma_code'
/usr/bin/ld: /home/mhenders/.seq/lib/seq/libseqrt.so: undefined reference to `lzma_stream_buffer_bound'
/usr/bin/ld: /home/mhenders/.seq/lib/seq/libseqrt.so: undefined reference to `lzma_easy_decoder_memusage'
/usr/bin/ld: /home/mhenders/.seq/lib/seq/libseqrt.so: undefined reference to `lzma_easy_buffer_encode'
/usr/bin/ld: /home/mhenders/.seq/lib/seq/libseqrt.so: undefined reference to `lzma_stream_decoder'
/usr/bin/ld: /home/mhenders/.seq/lib/seq/libseqrt.so: undefined reference to `lzma_end'
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: process for 'clang' exited with status 1
was a static linking issue
Hey, is there a way to sample from a list over some probability distribution list. I see random.choices, but i guess that requires me to multiply through the distribution by a fixed integer. That would probably keep the sampling properties I am looking for but I'm not sure
Hey @arjunsrivatsa -- yes
random.choices is probably the right thing to use for that. We should actually allow float weights there, but for now you can do exactly what you said by multiplying my an integer (e.g. 1000000) and then convert the entries to int. This'll be the same as if you had used float (only difference would be the 6th decimal and beyond if multiplying by a million)
Is there any way to check the memory usage at a certain point in the program? i.e. a print call to check the memory
It looks like my memory is blowing up in the cluster when I didn't expect it to
e.g. you should be able to do this:
from C import GC_get_heap_size() -> int
print(GC_get_heap_size())
There's also
GC_get_total_bytes to get total allocated bytes up to that point (i.e. that value will never decrease)
Otherwise we can just add a libdeflate dependency and statically link it
I remember htslib's libdeflate detection to be very fragile though
