From 2853fd10c1de29221d87b101e49c0fee7d61f520 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 12 Mar 2022 14:39:18 +0100
Subject: issue: gemma: is decent for running the LMM

---
 issues/gemma/HS-Rat-crashes-gemma.gmi | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'issues')

diff --git a/issues/gemma/HS-Rat-crashes-gemma.gmi b/issues/gemma/HS-Rat-crashes-gemma.gmi
index 6d8f5c8..5d0171a 100644
--- a/issues/gemma/HS-Rat-crashes-gemma.gmi
+++ b/issues/gemma/HS-Rat-crashes-gemma.gmi
@@ -93,6 +93,31 @@ Next run lmm with
 
 ```
 /usr/bin/time -v gemma -loco 1 -lmm 9 -g HSNIH-Palmer_true_geno.txt -p PHENO_2+FcfQiTVSC7FmmbsatUPg.txt -a HSNIH-Palmer_true_snps.txt -k output/result.cXX.txt
+
+GEMMA 0.98.5-pre1 (2021-08-14) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021
+Reading Files ...
+## number of total individuals = 6147
+## number of analyzed individuals = 1306
+## number of covariates = 1
+## number of phenotypes = 1
+## leave one chromosome out (LOCO) =        1
+## number of total SNPs/var        =   134918
+## number of SNPS for K            =   121094
+## number of SNPS for GWAS         =    13824
+## number of analyzed SNPs         =   132628
+Start Eigen-Decomposition...
+pve estimate =0.161934
+se(pve) =0.0355033
+================================================== 100%
+**** INFO: Done.
+        Command being timed: "gemma -loco 1 -lmm 9 -g HSNIH-Palmer_true_geno.txt -p PHENO_2+FcfQiTVSC7FmmbsatUPg.txt -a HSNIH-Palmer_true_snps.txt -k output/result.cXX.txt"
+        User time (seconds): 225.04
+        System time (seconds): 110.63
+        Percent of CPU this job got: 214%
+        Elapsed (wall clock) time (h:mm:ss or m:ss): 2:36.55
+        Maximum resident set size (kbytes): 523876
 ```
 
+Running the LMM takes only 2.5 minutes and uses less than 1GB RAM.
+
 Now the goal is to try and crash the server before setting overcommit.
-- 
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