[gmx-users] Re: How to install GROMACS in Rocks Cluster 5.4 : ERROR

[Justin A. Lemkul]

Miguel Quiliano Meza wrote:
> Dear community.
> 
> Justin was right.
> 
> I did not want to make the explanation so long, but you're right I have 
> to put those details. As you will see I had to redirect the "outputs" 
> after perform "*./configure*" and "*make*" (these files are attach to 
> this mail).
> 
> I sincerely hope you can give their opinions and help.
> 
> Thanks in advance.
> 
> Miguel Quiliano.
> 
> Here are the general procedure:
> 
> root at bioinfocluster src]# tar xf gromacs-4.5.4.tar.gz 
> [root at bioinfocluster src]# export LDFLAGS="-L/opt/rocks/lib"
> [root at bioinfocluster src]# export CPPFLAGS="-I/opt/rocks/include"
> [root at bioinfocluster gromacs-4.5.4]# ./configure --enable-mpi 
> --prefix=/share/apps/opt/gromacs > output
> [root at bioinfocluster gromacs-4.5.4]# make >output2 
> mempool.c: In function '_gmx_sel_mempool_alloc_group':
> mempool.c:201: warning: dereferencing type-punned pointer will break 
> strict-aliasing rules
> selelem.c: In function '_gmx_selelem_mempool_reserve':
> selelem.c:203: warning: dereferencing type-punned pointer will break 
> strict-aliasing rules
> selelem.c:208: warning: dereferencing type-punned pointer will break 
> strict-aliasing rules
> checkpoint.c: In function 'do_cpt_state':
> checkpoint.c:852: warning: dereferencing type-punned pointer will break 
> strict-aliasing rules
> /usr/bin/ld: /opt/rocks/lib/libfftw3f.a(plan-guru-dft-c2r.o): relocation 
> R_X86_64_32 against `a local symbol' can not be used when making a 
> shared object; recompile with -fPIC

This issue and its resolution are specifically described in the installation 
instructions:

http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites

(Under the "a few tips" heading)

-Justin

> /opt/rocks/lib/libfftw3f.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make[3]: *** [libmd_mpi.la <http://libmd_mpi.la/>] Error 1
> make[2]: *** [all-recursive] Error 1
> make[1]: *** [all] Error 2
> make: *** [all-recursive] Error 1
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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