Hi Thanasis!

I am getting another segfault. This is on a simulation that has a large number of samples (2592 haplotypes sampled) and my suspicion is that MultiDFE sets a maximum sample or DFE size, and then doesn't check the input. (I note that dfe-alpha also sets an arbitrary compile-time maximum on this, but did screen the input.)

My first guess is that it is caused by

Multi_DFE_est_v1.0.c: int max_sfs_size=2000;

#but then but then worryingly a few lines later

char sfsname[2000]

#looks like it might be assuming the same limit, but not using the max_sfs_size to set it?

My other thought is that it might be caused by

bctmat01.hd: #define maxn 2000
bctmat01.hd: #define maxnd 2*maxn

#but then this same global is defined differently here:

Library_DFE_v1.0.h: #define maxnd 10000

Hello-

I am trying to compile MultiDFE on a server and I'm getting multiple "multiple definition" errors, as shown below:

make gcc -o MultiDFE *.c -g -O3 -lm -lgsl -lgslcblas -w /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'n_t2_evaluated' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 't2_lower' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 't2_evaluated_vec' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'n2_evaluated_vec' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'n_s_evaluated' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 's_evaluated_vec' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'data_path' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 's_evaluated_vec_file' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 's_range_file' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'n_s_evaluated_file' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'n2_evaluated_vec_file' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 't2_evaluated_vec_file' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'phase_1_dir' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'phase_2_dir' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 't2_step' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'n2_lower' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'n_n2_evaluated' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'const_pop_dir' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'neutrals_only_mode' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'verbose_mode' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'gss_n2' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'n_sfs' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'trace_level' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'nranges' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'file_label_str' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'total_density_s0' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 'allele_freq_sampled' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: error: /tmp/ccpetgrl.o: multiple definition of 's_ranges' /accre/arch/easybuild/software/Compiler/GCCcore/10.2.0/binutils/2.35/bin/ld.gold: /tmp/cc9K3ndw.o: previous definition here collect2: error: ld returned 1 exit status make: *** [MultiDFE] Error 1

How do I fix this issue?

Thanks,
Alissa