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

[Justin A. Lemkul]

Please make sure to keep all discussion on the list.

Miguel Quiliano Meza wrote:
> Hi Justin.
> 
> Unfortunately, the problem persist. So... for the moment I had to 

Well, unless you can provide exact input (commands) and output (error messages) 
for what you're doing, you're going to stay stuck, unfortunately.

> install GROMACS 4.0.5 (pre-compiled for Rocks 5.4). This is because We 
> want to know the performance of our cluster.
> 
> Could you tell me please one BIG...BIG.. inconvenient for this version? 
> I mean, I know that in the web page of GROMACS, one can notice it 
> (http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.0.x), but 
> for me the majority of updates are unknown, as a product of my few 
> experience with the program. Will this version permit us run "common" 
> calculations (a big range )?
> 

Perhaps you can state exactly what you're trying to do.  I don't know what "a 
big range" of "common calculations" pertains to.  You can run MD with any 
Gromacs version you like.

If you're looking for differences between the 4.0.x series and 4.5.x, you're 
simply looking in the wrong place.  Hundreds of relevant updates are listed here:

http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x

-Justin

> Thanks in advance.
> 
> M.
> 
> 
> --- El *mar, 12/4/11, Justin A. Lemkul /<jalemkul at vt.edu>/* escribió:
> 
> 
>     De: Justin A. Lemkul <jalemkul at vt.edu>
>     Asunto: Re: How to install GROMACS in Rocks Cluster 5.4 : ERROR
>     Para: "Miguel Quiliano Meza" <qilime at yahoo.es>
>     Fecha: martes, 12 de abril, 2011 10:20
> 
> 
>     The complete output from configuration and compilation are
>     unnecessary.  The text you posted below is enough to solve this
>     issue.  See my post to the list.
> 
>     -Justin
> 
>     Miguel Quiliano Meza wrote:
>      > Hi Justin.
>      >
>      > Sorry if I disturb you for this way. But my message to the
>     GROMACS FORUM has to wait for moderator approval (it`s little
>     big...). For the moment, I consult my doubt for these mail:
>      >
>      > I 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
>      > /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
> 
>     ========================================
> 

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

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

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