Dear arm porters, I was trying to port bolt-lmm package, which currently builds only on amd64, i386 and ppc to more archs - particularly arm. I am trying to workaround amd64-specific SIMD intrinsics with the libsimde-dev (SIMDEverywhere package) - debian wiki here[1]
I've committed the patch I used here[2]. Along with this, I had added in "-DSIMDE_ENABLE_OPENMP -fopenmp-simd" to CFLAGS and CXXFLAGS in the box I built this in. I am able to get it building on arm64 box, but it does not seem to run the right way. It seems to trigger the bolt command again while trying to make initial guess - don't know why. I used the same command as used in autopkgtest to test it out. You can find the sample correct output for this here[3] Log pasted at the end of the e-mail. I'd appreciate any help. [1]: https://wiki.debian.org/SIMDEverywhere [2]: https://salsa.debian.org/med-team/bolt-lmm/-/commit/50badf3338741e739b2bb591a8930d177fa6de6c [3]: https://ci.debian.net/data/autopkgtest/unstable/amd64/b/bolt-lmm/24156452/log.gz -- Best, Nilesh On arm64 box:- $ ./bolt \ --bfile=EUR_subset \ --phenoFile=EUR_subset.pheno2.covars \ --exclude=EUR_subset.exclude2 \ --phenoCol=PHENO \ --phenoCol=QCOV1 \ --modelSnps=EUR_subset.modelSnps2 \ --reml \ --numThreads=2 +-----------------------------+ | ___ | | BOLT-LMM, v2.3.6 /_ / | | October 29, 2021 /_/ | | Po-Ru Loh // | | / | +-----------------------------+ Copyright (C) 2014-2021 Harvard University. Distributed under the GNU GPLv3 open source license. Boost version: 1_74 Command line options: ./bolt \ --bfile=EUR_subset \ --phenoFile=EUR_subset.pheno2.covars \ --exclude=EUR_subset.exclude2 \ --phenoCol=PHENO \ --phenoCol=QCOV1 \ --modelSnps=EUR_subset.modelSnps2 \ --reml \ --numThreads=2 Setting number of threads to 2 fam: EUR_subset.fam bim(s): EUR_subset.bim bed(s): EUR_subset.bed === Reading genotype data === Total indivs in PLINK data: Nbed = 379 Total indivs stored in memory: N = 379 Reading bim file #1: EUR_subset.bim Read 54051 snps Total snps in PLINK data: Mbed = 54051 Reading exclude file (SNPs to exclude): EUR_subset.exclude2 Excluded 47959 SNP(s) Reading list of SNPs to include in model (i.e., GRM): EUR_subset.modelSnps2 WARNING: SNP has been excluded: rs2176153 WARNING: SNP has been excluded: rs77036651 WARNING: SNP has been excluded: rs189917831 WARNING: SNP has been excluded: rs76452819 WARNING: SNP has been excluded: rs77203822 Included 1331 SNP(s) in model in 2 variance component(s) WARNING: 10420 SNP(s) had been excluded Breakdown of SNP pre-filtering results: 1331 SNPs to include in model (i.e., GRM) 0 additional non-GRM SNPs loaded 52720 excluded SNPs Allocating 1331 x 380/4 bytes to store genotypes Reading genotypes and performing QC filtering on snps and indivs... Reading bed file #1: EUR_subset.bed Expecting 5134845 (+3) bytes for 379 indivs, 54051 snps Total indivs after QC: 379 Total post-QC SNPs: M = 1331 Variance component 1: 660 post-QC SNPs (name: 'chr21') Variance component 2: 671 post-QC SNPs (name: 'chr22') Time for SnpData setup = 0.630153 sec === Reading phenotype and covariate data === Read data for 373 indivs (ignored 0 without genotypes) from: EUR_subset.pheno2.covars Number of indivs with no missing phenotype(s) to use: 369 NOTE: Using all-1s vector (constant term) in addition to specified covariates Using quantitative covariate: CONST_ALL_ONES Number of individuals used in analysis: Nused = 369 Singular values of covariate matrix: S[0] = 19.2094 Total covariate vectors: C = 1 Total independent covariate vectors: Cindep = 1 === Initializing Bolt object: projecting and normalizing SNPs === Number of chroms with >= 1 good SNP: 2 Average norm of projected SNPs: 368.000000 Dimension of all-1s proj space (Nused-1): 368 Time for covariate data setup + Bolt initialization = 0.0125201 sec Phenotype 1: N = 369 mean = -0.000706532 std = 1.02606 Phenotype 2: N = 369 mean = 1.53117 std = 0.499705 === Estimating variance parameters === === Making initial guesses for phenotype 1 === Using 3 random trials +-----------------------------+ | ___ | | BOLT-LMM, v2.3.6 /_ / | | October 29, 2021 /_/ | | Po-Ru Loh // | | / | +-----------------------------+ Copyright (C) 2014-2021 Harvard University. Distributed under the GNU GPLv3 open source license. Boost version: 1_74 Command line options: (null) ERROR: Use exactly one of the --bfile, --bfilegz, or --fam,bim,bed input formats Aborting due to error processing command line arguments For list of arguments, run with -h (--help) option
