Illegal instruction

[bamorim-bio]

Hello, I have been trying to run smartpca and I keep getting this error:

/home/bamorim/EIG/bin/smartpca -p smartpca.params.txt

THE INPUT PARAMETERS

PARAMETER NAME: VALUE

genotypename: /home/bamorim/DEMI/PCA/DEMI_HumanOrigins.Khwe.ped snpname: /home/bamorim/DEMI/PCA/DEMI_HumanOrigins.Khwe.map indivname: /home/bamorim/DEMI/PCA/DEMI_HumanOrigins.Khwe.ped evecoutname: /home/bamorim/DEMI/PCA/DEMI_HumanOrigins.Khwe.pca.evec.txt evaloutname: /home/bamorim/DEMI/PCA/DEMI_HumanOrigins.Khwe.pca.eval.txt lsqproject: YES

smartpca version: 18140

norm used

lsqproject used genetic distance set from physical distance genotype file processed snps deleted (nodata): 0. deletesnpoutname: for detailsnumber of samples used: 85 number of snps used: 478950 number of pops for axes: 1 Using 23 threads, and partial sum lookup algorithm. snp AX-50064432 ignored . allelecnt: 0 missing: 1 snp AX-50069775 ignored . allelecnt: 0 missing: 0 snp AX-50070472 ignored . allelecnt: 0 missing: 0 snp AX-50071782 ignored . allelecnt: 0 missing: 0 snp AX-50074365 ignored . allelecnt: 0 missing: 0 snp AX-50075476 ignored . allelecnt: 0 missing: 4 snp AX-50120905 ignored . allelecnt: 0 missing: 0 snp AX-50142355 ignored . allelecnt: 0 missing: 0 snp AX-50149625 ignored . allelecnt: 0 missing: 0 snp AX-50201779 ignored . allelecnt: 0 missing: 0 total number of snps killed in pass: 3942 used: 475008 Illegal instruction

I have tried running this analysis with both .ped/.map and eigenstrat that I converted using convertf and I keep getting the same illegal instruction error. I also get this error if I use all my dataset (853 individuals) and when I specify poplistname. Do you know what I could be doing wrong?

[bumblenick]

This looks like a problem at my end, but I have failed to reproduce the problem at Harvard. I assume you have recompiled -- try again with all optimzing flags turned off.

Two other things to try 1) numoutliter: 0 [I most always run this way] 2) run with valgrind

Nick

On Mon, Oct 18, 2021 at 12:34 PM xsupernaturalx @.***> wrote:

Hello, I have been trying to run smartpca and I keep getting this error:

/home/bamorim/EIG/bin/smartpca -p smartpca.params.txt

THE INPUT PARAMETERS

PARAMETER NAME: VALUE

genotypename: /home/bamorim/DEMI/PCA/DEMI_HumanOrigins.Khwe.ped snpname: /home/bamorim/DEMI/PCA/DEMI_HumanOrigins.Khwe.map indivname: /home/bamorim/DEMI/PCA/DEMI_HumanOrigins.Khwe.ped evecoutname: /home/bamorim/DEMI/PCA/DEMI_HumanOrigins.Khwe.pca.evec.txt evaloutname: /home/bamorim/DEMI/PCA/DEMI_HumanOrigins.Khwe.pca.eval.txt lsqproject: YES smartpca version: 18140

norm used

lsqproject used genetic distance set from physical distance genotype file processed snps deleted (nodata): 0. deletesnpoutname: for detailsnumber of samples used: 85 number of snps used: 478950 number of pops for axes: 1 Using 23 threads, and partial sum lookup algorithm. snp AX-50064432 ignored . allelecnt: 0 missing: 1 snp AX-50069775 ignored . allelecnt: 0 missing: 0 snp AX-50070472 ignored . allelecnt: 0 missing: 0 snp AX-50071782 ignored . allelecnt: 0 missing: 0 snp AX-50074365 ignored . allelecnt: 0 missing: 0 snp AX-50075476 ignored . allelecnt: 0 missing: 4 snp AX-50120905 ignored . allelecnt: 0 missing: 0 snp AX-50142355 ignored . allelecnt: 0 missing: 0 snp AX-50149625 ignored . allelecnt: 0 missing: 0 snp AX-50201779 ignored . allelecnt: 0 missing: 0 total number of snps killed in pass: 3942 used: 475008 Illegal instruction

I have tried running this analysis with both .ped/.map and eigenstrat that I converted using convertf and I keep getting the same illegal instruction error. I also get this error if I use all my dataset (853 individuals) and when I specify poplistname. Do you know what I could be doing wrong?

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[bamorim-bio]

Hi nick, thanks for answering! Sorry for the question but how do I do this?

I assume you have recompiled -- try again with all optimzing flags turned off.

[bumblenick]

It looks as if the default is no optimize I assume you compiled the code locally. Do NOT use a released binary If you compile (make smartpca) and see "O2" in the logfile then you should edit the Makefile

Nick

On Mon, Oct 18, 2021 at 3:49 PM Beatriz Amorim @.***> wrote:

Hi nick, thanks for answering! Sorry for the question but how do I recompile with the optimizing flags turned off?

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[bamorim-bio]

So I decided to try to install on my mac to use valgrind (i was on a remote server and I do not have sudo permissions) and I keep getting this error:

(base) beatrizamorim@Beatrizs-MacBook-Pro-2021 src % make cc -I../include -I/usr/include/openblas -c -o baseprog.o baseprog.c cc -I../include -I/usr/include/openblas -c -o mcio.o mcio.c mcio.c:110:16: warning: result of '10 ^ 8' is 2; did you mean '1e8'? [-Wxor-used-as-pow] base[1] = 10 ^ 8;

            1e8
mcio.c:110:16: note: replace expression with '0xA ^ 8' to silence this warning
mcio.c:111:16: warning: result of '10 ^ 9' is 3; did you mean '1e9'? [-Wxor-used-as-pow]
  base[2] = 10 ^ 9;
            ~~~^~~
            1e9
mcio.c:111:16: note: replace expression with '0xA ^ 9' to silence this warning
mcio.c:871:15: warning: comparison of array 'sdpt->alleles' not equal to a null pointer is always true [-Wtautological-pointer-compare]
    if (sdpt->alleles != NULL) {
        ~~~~~~^~~~~~~    ~~~~
3 warnings generated.
cc -I../include -I/usr/include/openblas   -c -o egsubs.o egsubs.c
cc -I../include -I/usr/include/openblas   -c -o admutils.o admutils.c
admutils.c:540:10: error: implicitly declaring library function 'finite' with type 'int (double)' [-Werror,-Wimplicit-function-declaration]
    if (!finite (a[i]))
         ^
admutils.c:540:10: note: include the header <math.h> or explicitly provide a declaration for 'finite'
admutils.c:992:1: warning: non-void function does not return a value [-Wreturn-type]
}
^
admutils.c:1256:31: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
      printf ("(setid2pops): %s not found\n");
                             ~^
2 warnings and 1 error generated.
make: *** [admutils.o] Error 1