Trouble with installing on a PC

[bforsbe]

Originally reported by: yjin004 (Bitbucket: yjin004, GitHub: Unknown)

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I am having trouble with installing relion 2.0 on a PC. I have installed relion 2.0 on a workstation without trouble.

It always shows error at this step

[ 52%] Linking CXX shared library ../../lib/librelion_lib.so
/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libfftw3.a: could not read symbols: Bad value
collect2: error: ld returned 1 exit status
make[2]: *** [lib/librelion_lib.so] Error 1
make[1]: *** [src/apps/CMakeFiles/relion_lib.dir/all] Error 2
make: *** [all] Error 2

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• Bitbucket: https://bitbucket.org/tcblab/relion2-beta/issue/17

[bforsbe]

Original comment by Bjoern Forsberg (Bitbucket: bforsbe, GitHub: bforsbe):

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I'll look into this, but in the meantime you could try to simply build the libraries statically by changing the cmake configuration command to

#!bash

cmake -DBUILD_SHARED_LIBS=OFF ..

In general however, you should of course be able to build shared as well. Could you give some details on you system for reference? Like operating system/version etc.

[bforsbe]

Original comment by yjin004 (Bitbucket: yjin004, GitHub: Unknown):

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Hi Bjoern, changing the shared library off let me pass the first stage, but further error occurred (as attached)

I am running CentOS7 with kernel build 3.10.0-327.13.1.el7.x86_64

My system specs are as follows:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 4
On-line CPU(s) list: 0-3
Thread(s) per core: 1
Core(s) per socket: 4
Socket(s): 1
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family: 6
Model: 58
Model name: Intel(R) Core(TM) i5-3450 CPU @ 3.10GHz
Stepping: 9
CPU MHz: 1683.687
BogoMIPS: 6192.51
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 6144K
NUMA node0 CPU(s): 0-3

[bforsbe]

Original comment by yjin004 (Bitbucket: yjin004, GitHub: Unknown):

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I tried to fix by reinstalling fftw fltk but does not seems to fix the problem.
If i try to install by omitting the GUI, the installation completes.

[bforsbe]

Original comment by Bjoern Forsberg (Bitbucket: bforsbe, GitHub: bforsbe):

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If I understood things correctly, cmake finds you system-installed fftw and fltk-libraries. However, these are not compiled as shared libraries, and cannot be used to build a shared relion-library. I think we have good grip on what needs to happen, and there will be a fix for it. If you want the GUI right now, I would suggest using

#!bash

cmake -DFORCE_OWN_FFTW=ON -DFORCE_OWN_FLTK=ON ..

This should build shared fftw- and fltk-libraries which do not cause problems at linktime.

[bforsbe]

Original comment by yjin004 (Bitbucket: yjin004, GitHub: Unknown):

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Hi Bjoern,

I have already tried the command. When I force install both, the fltk fails to install with and error. patch command not found. The problem was fixed by reinstalling patch.

The problem is resolved. Thank you.

[bforsbe]

Original comment by Dari Kimanius (Bitbucket: dkimanius, GitHub: dkimanius):

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The only way I can think of to make sure that cmake can predict whether a static library is built the right way (in this case with the fPIC flag) is to try to do a trial build of a tiny binary that depends on the library. This can be done during build setup using try_compile, but is a rather advanced feature that we don't prioritize right now.

[bforsbe]

Original comment by Bjoern Forsberg (Bitbucket: bforsbe, GitHub: bforsbe):

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Issue #60 was marked as a duplicate of this issue.