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chanzuckerberg / shasta

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
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CMake not using FindBLAS #268

Closed ocaisa closed 2 years ago

ocaisa commented 2 years ago

In https://github.com/chanzuckerberg/shasta/commit/b42f82d2369caad4a2dab1856783a2da39a197dc , BLAS and Lapack libraries are being linked in, but there are actually quite a few implementations that can provide these (for example, OpenBLAS can provide both blas and lapack in the single library openblas). The FindBLAS Cmake module handles all these, it would be good to leverage this rather than link to explicit libraries (that cannot be overridden).

paoloczi commented 2 years ago

This is a good suggestion and I will implement it as soon as I have a chance. Alternatively, if you are willing to make this change in a PR, I will be happy to merge it.

paoloczi commented 2 years ago

I was able to do this for the dynamic library and the dynamic executable, but not for the static executable. I tried adding the following to staticExecutable/CMakeLists.txt:

set(BLA_STATIC ON)
find_package(BLAS REQUIRED)
find_package(LAPACK REQUIRED)

But when running cmake I get the following error messages:

-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.a  
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
CMake Error at /usr/share/cmake-3.16/Modules/FindLAPACK.cmake:423 (message):
  A required library with LAPACK API not found.  Please specify library
  location.
Call Stack (most recent call first):
  staticExecutable/CMakeLists.txt:74 (find_package)

-- Configuring incomplete, errors occurred!

All of this is on Ubuntu 20.04, the currently supported platform for Shasta Linux builds. Blas and Lapack are both installed and the existing cmake files, which don't use find_package, work without problems.

Any suggestions from @ocaisa or others would be welcome. And a tested PR would be very welcome!

paoloczi commented 2 years ago

I found on the Internet several mentions of this problem with static linking. I will close this for now given that there is no known solution (not known to me, at least). If @ocaisa or others find a way to do it, please post that information here and reopen the issue and I will make the change.

ocaisa commented 2 years ago

Sorry for being non-responsive on this, I'm transitioning job at the moment. I wouldn't be much help anyway, I have a lot of experience installing software but not a lot of specific CMake experience.

paoloczi commented 2 years ago

Thank you - this is a good suggestion anyway. Perhaps I can revive it at some point in the future if/when this Cmake problem gets fixed.