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| -rw-r--r-- | topics/lmms/GSL_ERROR_function_value_is_not_finite_in_brent.c-issue210.gmi | 93 |
1 files changed, 93 insertions, 0 deletions
diff --git a/topics/lmms/GSL_ERROR_function_value_is_not_finite_in_brent.c-issue210.gmi b/topics/lmms/GSL_ERROR_function_value_is_not_finite_in_brent.c-issue210.gmi new file mode 100644 index 0000000..23ad3e5 --- /dev/null +++ b/topics/lmms/GSL_ERROR_function_value_is_not_finite_in_brent.c-issue210.gmi @@ -0,0 +1,93 @@ +# GEMMA GSL ERROR: function value is not finite in brent.c + +In github issue 210 this comes up. @hrwang was kind enough to send me a dataset that brings up this error. Now we stand a chance of doing something about it! As in + +``` +napoli:~/iwrk/opensource/code/genetics/gemma/tmp/issue210$ ../../bin/gemma -bfile 20 -k BS_kinship.sXX.txt -lmm 1 -c Covariate_PC3.txt -n 1 -o outname +GEMMA 0.99.0-pre1 (2021-08-11) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 +Reading Files ... +## number of total individuals = 727 +## number of analyzed individuals = 57 +## number of covariates = 4 +## number of phenotypes = 1 +## number of total SNPs/var = 215451 +## number of analyzed SNPs = 72731 +Start Eigen-Decomposition... +pve estimate =0.956403 +se(pve) =0.255427 +GSL ERROR: function value is not finite in newton.c at line 88 errno 9 +``` + +Next I ran with the debug switch and it stops with the slightly more informative + +``` +../../bin/gemma -bfile 20 -k BS_kinship.sXX.txt -lmm 1 -c Covariate_PC3.txt -n 1 -o outname -debug +GEMMA 0.99.0-pre1 (2021-08-11) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 +GSL random generator type: mt19937; seed = 25479 (option -1); first value = 191757793 +Reading Files ... +## number of total individuals = 727 +## number of analyzed individuals = 57 +## number of covariates = 4 +## number of phenotypes = 1 +## number of total SNPs/var = 215451 +## number of analyzed SNPs = 72731 +Start Eigen-Decomposition... +pve estimate =0.956403 +se(pve) =0.255427 +ERROR: Enforce failed for Trying to take the log of 0.000000 in src/mathfunc.cpp at line 118 in safe_log +``` + +Next step is rebuilding gemma with debug info `make debug` and rerun in the debugger. A backtrace of + +``` +gdb --args ../../bin/gemma -bfile 20 -k BS_kinship.sXX.txt -lmm 1 -c Covariate_PC3.txt -n 1 -o outname -debug +``` + +shows + +``` +#2 0x000000000047dcb0 in safe_log (d=d@entry=0) at src/mathfunc.cpp:118 +#3 0x00000000004707ea in LogRL_f (l=l@entry=1.0000000000000001e-05, params=params@entry=0x7fffffffcc20) + at src/lmm.cpp:851 +#4 0x0000000000471b05 in CalcLambda (func_name=func_name@entry=82 'R', params=..., + l_min=l_min@entry=1.0000000000000001e-05, l_max=100000, n_region=10, + lambda=@0x7fffffffccc8: 3.2054654756518093, logf=@0x7fffffffcca0: 0.83040722111380116) + at src/lmm.cpp:1970 +#5 0x0000000000475cac in LMM::AnalyzePlink (this=this@entry=0x7fffffffd1a0, U=U@entry=0x4fcc80, + eval=eval@entry=0x52dff0, UtW=UtW@entry=0x4fccc0, Uty=Uty@entry=0x7fffffffd140, W=W@entry=0x4fe140, + y=<optimized out>, gwasnps=...) at src/lmm.cpp:1860 +#6 0x00000000004359f5 in GEMMA::BatchRun (this=this@entry=0x7fffffffe720, cPar=...) + at src/gemma.cpp:2798 +#7 0x000000000047bed0 in main (argc=14, argv=0x7fffffffe888) at src/main.cpp:86 +``` + +In this case a SNP for some reason balks. Another run, after disabling the log check renders + +``` +#0 0x00007ffff5e1deca in raise () + from /gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib/libpthread.so.0 +#1 0x00000000004245ba in gemma_gsl_error_handler (reason=<optimized out>, file=<optimized out>, + line=88, gsl_errno=<optimized out>) at src/gemma.cpp:75 +#2 0x00007ffff7e59f6d in newton_iterate () + from /gnu/store/qsr7pw4cbka4qhxm3h0bkwwl7h08qfmw-profile/lib/libgsl.so.25 +#3 0x0000000000471cba in CalcLambda (func_name=func_name@entry=82 'R', params=..., + l_min=l_min@entry=1.0000000000000001e-05, l_max=100000, n_region=<optimized out>, + lambda=@0x7fffffffccc8: 1.0000000000000001e-05, logf=@0x7fffffffcca0: 507.88508012472289) + at src/lmm.cpp:2040 +``` + +points out that in line 2040 `gsl_root_fdfsolver_iterate` is not happy executing a Newton root solver. What is interesting is that, in this case, the gemma_gsl_error_handler is called and stops processing. We now have three ways to stop GEMMA from the same error! + +The original version bails out inside GSL: + +``` +GSL ERROR: function value is not finite in newton.c at line 88 errno 9 + +#0 0x00007ffff5e1deca in raise () + from /gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib/libpthread.so.0 +#1 0x00007ffff7e59f6d in newton_iterate () + from /gnu/store/qsr7pw4cbka4qhxm3h0bkwwl7h08qfmw-profile/lib/libgsl.so.25 +#2 0x000000000047a9c5 in CalcLambda(char, FUNC_PARAM&, double, double, unsigned long, double&, double&) [clone .constprop.671] () +``` + +@hrwang had a good suggestion to make sure that the output for the SNP is made invalid and to continue processing. Disabling the error handler let GEMMA continue. I added a check for the status flag to make sure output was set to invalid (nan). In the test set 178 out of 72732 SNPs failed. |