OK. One thing that I've noticed when compiling with -static is that xleap
won't build. Something about X11 not playing nice with static linking
(because it's a server? I don't know). Therefore, try using the -noX11 when
using the -static flag if you're also using it to build AmberTools (or the
equivalent parts in amber9 and earlier).
Good luck,
Jason
On Fri, Mar 25, 2011 at 10:21 PM, Sergio R Aragon <aragons.sfsu.edu> wrote:
> Hello Jason,
>
> Back with Amber 8 or 9 the amber installation failed when I tried -static.
> It was not a compiler issue - I routinely compile -static for my own
> software with PGI. If things have changed, perhaps it is doable now - I
> haven't tried since. It would be nice to be able to compile that way and
> have portable binaries. When I have some time in the next couple of weeks
> I'll try this and report.
>
> Sergio
>
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: Friday, March 25, 2011 7:21 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] AMD Opteron system - compiling pmemd with intel or
> gfortran?
>
> Why can't you compile with -static? Is it your PGI installation that won't
> let you (i.e. they only have dynamic libs)? Or does the amber installation
> fail?
>
> -static should be supported...
>
> All the best,
> Jason
>
> On Fri, Mar 25, 2011 at 4:42 PM, Sergio R Aragon <aragons.sfsu.edu> wrote:
>
> > Hi Ilyas,
> >
> > On an AMD Opteron system the architecture specific compilers from the
> > Portland Group (PGI) will probably do much better than the generic
> gfortran.
> > You may want to benchmark that option. I use Opteron exclusively with
> PGI
> > compilers and in my systems pmemd runs faster than sander.mpi. The only
> > caveat is that I do not run this comparison across a network, but only
> > within a multicore CPU - I don't have fast network interconnects so I
> avoid
> > that. I use MPICH2. PGI compilers are not free, unfortunately. Since one
> > can't compile amber -static (to load all libraries), I can't send you the
> > compiled pmemd and sander.MPI from my PGI compiled AMBER 10 because it
> won't
> > run on your system w/o the PGI libraries. However, the following should
> be
> > possible to achieve a benchmark. Go to the PGI web site and download
> their
> > software with a trial license. Then you can compile, benchmark and if
> > things are good you can decide to buy.
> >
> > Cheers, Sergio
> >
> > Sergio Aragon
> > Professor of Chemistry
> > SFSU
> >
> >
> > -----Original Message-----
> > From: Ilyas Yildirim [mailto:i-yildirim.northwestern.edu]
> > Sent: Friday, March 25, 2011 1:54 PM
> > To: AMBER Mailing List
> > Subject: [AMBER] AMD Opteron system - compiling pmemd with intel or
> > gfortran?
> >
> > Dear All - I am trying to compile pmemd in an AMD opteron cluster. AMBER
> 9
> > and 10 and pmemd are compiled using gfortran. I benchmarked sander.MPI
> and
> > pmemd using exactly the same conditions (core #, local disk, etc). The
> > test jobs finished in 91 and 118 minutes, respectively, for sander.MPI
> and
> > pmemd. Now, this is a very surprising result because in all the intel
> > based clusters I have worked on, pmemd was almost 1.2-1.3 times faster
> > than sander.MPI.
> >
> > I am not the admin of the cluster and do not have much flexibility on
> what
> > to install to the system. I was planning on compiling the intel
> compilers,
> > openmpi, and amber9 on my local directory to see if intel is going to do
> a
> > better job than gfortran for pmemd. The cluster is a little bit messily
> > organized and all the mpi/lib files are put into local places like
> > /usr/bin. Namely, I am having trouble using - for instance - intel
> > compiled openmpi on pmemd installation.
> >
> > Anyways, my question is if it is worth trying all this hassle in and AMD
> > Opteron system or is pmemd really not efficient in this type of system. I
> > checked out the mailing list but could not find an answer to this
> question
> > (or maybe I missed them). There is quite some discussion between intel vs
> > gfortran on pmemd, but did not see anything connected with AMD Opteron
> > systems. Any idea/suggestion/comment is well appreciated. Thanks in
> > advance.
> >
> > Best regards,
> >
> > Ilyas Yildirim, Ph.D.
> > -----------------------------------------------------------
> > = Department of Chemistry - 2145 Sheridan Road =
> > = Northwestern University - Evanston, IL 60208 =
> > = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
> > = http://www.pas.rochester.edu/~yildirim/ =
> > -----------------------------------------------------------
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Mar 25 2011 - 23:00:02 PDT
