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

[Justin A. Lemkul]

Miguel Quiliano Meza wrote:
> 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.
> 

There is no problem, per se, with what you did.  FFTW appears to have been 
installed fine.  However, as noted in the above quote from the Installation 
Instructions, you will need to re-install FFTW using one of the options listed.

-Justin

> 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>
>     <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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
>     ******************************************
> 
> 
> 

-- 
========================================

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

========================================