[3dem] [Ext] Compiling AreTomo3

[Shawn Zheng]

Hi Reza,

This problem can be solved by recompiling the library code in LibSrc. The
following are the steps
1) open a linux terminal and go inside LibSrc/Util
2) run "make clean" followed by "make all"
3) go inside LibSrc/Mrcfile
4) run "make clean" followed by "make all"
5) recompile AreTomo3.

Please let me know if these steps fix the problem.

Best,
Shawn


On Thu, Jul 25, 2024 at 10:12 AM Reza Khayat <rkhayat at ccny.cuny.edu> wrote:

> Hi,
>
> We are getting the following error when compiling AreTomo3. The error
> occurs for a number of  files being compiled.  Any help would be
> appreciated:
>
> /usr/bin/ld:
> /home/rkhayat/Applications/AreTomo3/LibSrc/Lib/libmrcfile.a(CSaveMainHeader.o):
> relocation R_X86_64_32 against symbol __gxx_personality_v0@@CXXABI_1.3'
> can not be used when making a PIE object; recompile with -fPIE /usr/bin/ld:
> /home/rkhayat/Applications/AreTomo3/LibSrc/Lib/libmrcfile.a(CLoadImage.o):
> relocation R_X86_64_32 against symbol __gxx_personality_v0@@CXXABI_1.3'
> can not be used when making a PIE object; recompile with -fPIE
>
> Bes
> Reza Khayat, PhD
> City College of New York
> Associate Professor
> Department of Chemistry and Biochemistry
> Co-Director NIH G-RISE program
>
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> 3dem at ncmir.ucsd.edu
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>
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