Can't compile from C code

[Michael Vinsky]

I downloaded the code from this link:

https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/structure_kernel_source.tar.gz

but when I try to compile it there are multiple definition errors like "collect2: error: ld returned 1 exit status" and "make: *** [Makefile:24: structure] Error 1". All I did was run "make clean" and "make" so what am I missing?

Thanks!

[Vikram Chhatre]

What is the output of "uname -a"?

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[Michael Vinsky]

Linux mvinsky-VMware-Virtual-Platform 6.11.0-25-generic #25~24.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 15 17:20:50 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

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[Vikram Chhatre]

The only thing I can think of is that you are running a virtual Linux environment and perhaps some of the libraries needed for Make aren't properly linked. Do you have access to a workstation/server with Linux natively installed? If so, I would try there.

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[Michael Vinsky]

I tried it on a linux workstation (6.8.0-59-generic #61~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 15 17:03:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux). Still got the same messages. Here are the last few lines:

/usr/bin/ld: output.o:(.bss+0x194): multiple definition of `EXTRACOLS'; structure.o:(.bss+0x19c): first defined here
/usr/bin/ld: output.o:(.bss+0x198): multiple definition of `PHENOTYPE'; structure.o:(.bss+0x1a0): first defined here
/usr/bin/ld: output.o:(.bss+0x19c): multiple definition of `POPFLAG'; structure.o:(.bss+0x1a4): first defined here

collect2: error: ld returned 1 exit status

make: *** [Makefile:24: structure] Error 1

Its seems the issue is that there are due to multiple definitions of global variables across C source files. I think its because you need to distinguish between definition and declaration of global variables. Its like in params.c seed needs to be defined as "int SEED;" and in params.h it needs to be declared as "extern int SEED;". Does that make sense?

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[Francisco Pina Martins]

Dear Michael,

Try editing the Makefile, and in the first line, change:

OPT = -O3

to

OPT = -O3 -fcommon

This seems to be an issue with how recent versions of GCC deal with multiple definitions of the same variable.

Best,

Francisco

[Michael Vinsky]

*Note: Vikram also tested this out and it wouldn't compile for him either but I found this discussion 

https://groups.google.com/g/structure-software/c/SsOXY9Y8t8o/m/Kwn0o5SCCwAJ 

and found this person wrote a script to install Structure which did one interesting thing. He included "sed -i 's/OPT = -O3/OPT = -O3 -fcommon/' Makefile". I ran this before using "make" and it looks like it compiled. I will need to test it out but this might be the missing solution.