David Lecomber

Read index in blocks rather than pairs for efficiency

7

This patch freads multiple pairs from the index file rather in single pairs for efficiency. On my tests, this reduced run time during index load of a short read index...

This patch changes Makefile.simde such that it compiles on aarch64 Linux using SIMDe. GCC will error on aarch64 with the "-msse4.1" flag - so this is removed for aarch64. However...

dill fails to compile on aarch64: requires update from upstream

1

Arm Compiler for Linux (ACfL 23.10) and recent LLVM compilers now error on implicit function declaration whilst building for aarch64. With 2.9.2 and 2.10.0-rc1: ``` 494 cd /tmp/ec2-user/spack-stage/spack-stage-adios2-2.9.2-iph22u4sk64qkbjcepsmqvr3myouweuj/spack-build-iph22u4/thirdparty/enet/enet && /home/ec2-user/spack/lib/spack/env/arm/armclang...

### Steps to reproduce the issue ```console $ spack spec -I gromacs +sve ==> Error: Spack concretizer internal error. Please submit a bug report and include the command, environment if...

Fixes #966 This fix resolves performance issue where Boost::math unnecessarily promotes doubles to long double, which is not fully supported by hardware leading to slow-downs. The change is to set...

Performance issue in use of boost::math::digamma on aarch64 Linux

2

Due to a current default in the boost library (https://github.com/boostorg/math/issues/1211) in boost::math::digamma, there is a performance hit on aarch64. This happens on v1.10.3 of Salmon, with GNU compiler 13 on...

With GCC and Rocky-9 Linux, and cmake 3.26.5, the path for building pufferfish on Arm is not being followed. Adding a 'message' to dump out the CMAKE_SYSTEM_PROCESSOR shows it to...

### Steps to reproduce the issue ```console $ spack spec --fresh openfoam%[email protected] ^openmpi%[email protected] Input spec -------------------------------- - openfoam%[email protected] - ^openmpi%[email protected] Concretized -------------------------------- [+] openfoam@2312%[email protected]~int64~kahip~knl~metis~mgridgen~paraview+scotch+source~vtk~zoltan build_system=generic precision=dp arch=linux-debian12-neoverse_v2 [+] ^[email protected]%[email protected]~aws+blosc2+bzip2~campaign~cuda~dataspaces~fortran~hdf5~ipo~kokkos+libcatalyst~libpressio+mgard+mpi~pic+png~python~rocm+sst~sycl+sz+zfp build_system=cmake...

Compilation failure on aarch64 with Arm Compiler for Linux's flang

5

Using Spack to set up config and compile, the following error occurs: 5 errors found in build log. It makes no difference if I disable the non-standard float16 - using...

Enable python3

1

This PR updates the python sources to work with Python3. The changes are quite small - and have been tested by the limitedt of the bioconda recipe.