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kalis: High Performance Li & Stephens Local Ancestry Inference

Home Page: https://kalis.louisaslett.com/

R 10.99% C 80.82% HTML 8.20%
genomics genetics hpc-applications r

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eriqande

kalis's Issues

No special instruction sets targeted during compilation despite avx2 support on cpu

Hi, really look forward to using kalis! I am working on a remote cluster with avx2 support:

lscpu

Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                80
On-line CPU(s) list:   0-79
Thread(s) per core:    2
Core(s) per socket:    20
Socket(s):             2
NUMA node(s):          2
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 79
Model name:            Intel(R) Xeon(R) CPU E5-2698 v4 @ 2.20GHz
Stepping:              1
CPU MHz:               1199.902
CPU max MHz:           3600.0000
CPU min MHz:           1200.0000
BogoMIPS:              4399.95
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              51200K
NUMA node0 CPU(s):     0,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78
NUMA node1 CPU(s):     1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79
Flags:                 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 invpcid_single ssbd rsb_ctxsw ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap intel_pt xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts md_clear spec_ctrl intel_stibp flush_l1d

And installed kalis like:

> remotes::install_github("louisaslett/kalis",
...   configure.vars = c(kalis = "PKG_CFLAGS='-march=native -mtune=native -O3'"), force=T)
Downloading GitHub repo louisaslett/kalis@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: vctrs (0.5.1  -> 0.5.2) [CRAN]
5: utf8  (1.2.2  -> 1.2.3) [CRAN]
6: fansi (1.0.3  -> 1.0.4) [CRAN]
7: dplyr (1.0.10 -> 1.1.0) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/tmp/RtmpKsGm65/remotes114585e6cc772/louisaslett-kalis-ed0d60e/DESCRIPTION’ ...
─  preparing ‘kalis’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘kalis_0.91.1.tar.gz’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘kalis/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘kalis/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘kalis/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘kalis/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘kalis/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘kalis/docs/deps/bootstrap-5.2.2/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘kalis/docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘kalis/docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff’
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     ‘kalis/docs/deps/bootstrap-5.2.2/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff’
   Warning: invalid uid value replaced by that for user 'nobody'
   Warning: invalid gid value replaced by that for user 'nobody'

n*** Successfully loaded .Rprofile ***n
* installing *source* package ‘kalis’ ...
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=  -march=native -mtune=native -O3
Using PKG_LIBS=-lz   -lz
No special assembly instruction set extentions will by used (auto-detected).
Loop unrolling at default value
** libs
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactBackward.c -o ExactBackward.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactBackwardScalarMu.c -o ExactBackwardScalarMu.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactBackwardScalarMuPi.c -o ExactBackwardScalarMuPi.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactBackwardScalarMuPiSpeidel.c -o ExactBackwardScalarMuPiSpeidel.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactBackwardScalarMuSpeidel.c -o ExactBackwardScalarMuSpeidel.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactBackwardScalarPi.c -o ExactBackwardScalarPi.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactBackwardScalarPiSpeidel.c -o ExactBackwardScalarPiSpeidel.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactBackwardSpeidel.c -o ExactBackwardSpeidel.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactBackwardStencil.c -o ExactBackwardStencil.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactForward.c -o ExactForward.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactForward1stepScalarMuPi.c -o ExactForward1stepScalarMuPi.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactForward1stepScalarMuPiSpeidel.c -o ExactForward1stepScalarMuPiSpeidel.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactForwardScalarMu.c -o ExactForwardScalarMu.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactForwardScalarMuPi.c -o ExactForwardScalarMuPi.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactForwardScalarMuPiSpeidel.c -o ExactForwardScalarMuPiSpeidel.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactForwardScalarMuSpeidel.c -o ExactForwardScalarMuSpeidel.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactForwardScalarPi.c -o ExactForwardScalarPi.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactForwardScalarPiSpeidel.c -o ExactForwardScalarPiSpeidel.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactForwardSpeidel.c -o ExactForwardSpeidel.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c ExactForwardStencil.c -o ExactForwardStencil.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c R_Backward.c -o R_Backward.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c R_Cache.c -o R_Cache.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c R_ComputeStatus.c -o R_ComputeStatus.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c R_Forward.c -o R_Forward.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c R_MatAndMul.c -o R_MatAndMul.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c R_MatAndMulBtwVar.c -o R_MatAndMulBtwVar.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c R_Registrations.c -o R_Registrations.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c R_TableCache.c -o R_TableCache.o
x86_64-conda-linux-gnu-cc -I"/home/samm/miniconda3/envs/R-env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/samm/miniconda3/envs/R-env/include -I/home/samm/miniconda3/envs/R-env/include -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib  -march=native -mtune=native -O3 -DKALIS_ISA_NOASM -pthread -DKALIS_AFFINITY -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/samm/miniconda3/envs/R-env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1667676773505/work=/usr/local/src/conda/r-base-4.2.2 -fdebug-prefix-map=/home/samm/miniconda3/envs/R-env=/usr/local/src/conda-prefix  -c R_TableMaker.c -o R_TableMaker.o
x86_64-conda-linux-gnu-cc -shared -L/home/samm/miniconda3/envs/R-env/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/samm/miniconda3/envs/R-env/lib -Wl,-rpath-link,/home/samm/miniconda3/envs/R-env/lib -L/home/samm/miniconda3/envs/R-env/lib -o kalis.so ExactBackward.o ExactBackwardScalarMu.o ExactBackwardScalarMuPi.o ExactBackwardScalarMuPiSpeidel.o ExactBackwardScalarMuSpeidel.o ExactBackwardScalarPi.o ExactBackwardScalarPiSpeidel.o ExactBackwardSpeidel.o ExactBackwardStencil.o ExactForward.o ExactForward1stepScalarMuPi.o ExactForward1stepScalarMuPiSpeidel.o ExactForwardScalarMu.o ExactForwardScalarMuPi.o ExactForwardScalarMuPiSpeidel.o ExactForwardScalarMuSpeidel.o ExactForwardScalarPi.o ExactForwardScalarPiSpeidel.o ExactForwardSpeidel.o ExactForwardStencil.o R_Backward.o R_Cache.o R_ComputeStatus.o R_Forward.o R_MatAndMul.o R_MatAndMulBtwVar.o R_Registrations.o R_TableCache.o R_TableMaker.o -lz -lz -lpthread -pthread -L/home/samm/miniconda3/envs/R-env/lib/R/lib -lR
installing to /home/samm/miniconda3/envs/R-env/lib/R/library/00LOCK-kalis/00new/kalis/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
n*** Successfully loaded .Rprofile ***n
** help
*** installing help indices
** building package indices
n*** Successfully loaded .Rprofile ***n
** installing vignettes
** testing if installed package can be loaded from temporary location
n*** Successfully loaded .Rprofile ***n
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
n*** Successfully loaded .Rprofile ***n
** testing if installed package keeps a record of temporary installation path
* DONE (kalis)
*

But when I load the library, it seems like avx2 support hasn't been targeted during the compilation step. Is this expected or am I doing something wrong?

> library(kalis)

Running in 64-bit mode using x86-64 architecture.
Loops unrolled to depth 4.

Currently not using any special instruction sets (WARNING: poor performance likely).
If this is unexpected (e.g. your CPU is Intel Haswell or newer architecture, or ARMv7+ with NEON support), then ensure that you are targeting the native architecture in compilation.  The easiest method is to add/change the following line in ~/.R/Makevars
CFLAGS=-march=native -mtune=native -O3

R version:

R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.

Thanks.

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