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

[Miguel Quiliano Meza]

Hi everyone.

I followed the steps in
http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites for
my problem, but I obtained problems at the moment to perform "make".

So, as mention the web page of gromacs...

If you get errors during GROMACS compilation (the "make" step) that suggest
that you "recompile with -fPIC," then you should return to this FFTW stage
and configure with --enable-shared or --with-pic.

By the way, previously I performed "make" with FFTW version 3.2.2 (default
version in rocks cluster 5.4)

I did:

root at bioinfocluster fftw-3.2.2]# ./configure --enable-threads
--prefix=/share/apps/opt/fftw

Without errors, and then:

[root at bioinfocluster fftw-3.2.2]# make

make[3]: Leaving directory `/share/apps/src/fftw-3.2.2/tools'
make[2]: Leaving directory `/share/apps/src/fftw-3.2.2/tools'
Making all in m4
make[2]: Entering directory `/share/apps/src/fftw-3.2.2/m4'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/share/apps/src/fftw-3.2.2/m4'
make[1]: Leaving directory `/share/apps/src/fftw-3.2.2'

What could be the problem? please advices.

Miguel Quiliano.



>
> 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
> >
>
> --
> ========================================
>
> 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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