OK, renouncing to the MKL libraries, led to a correct (serial)
compilation. Actually, it was my fault not to do that before as I am
not going to use qmmm with Amber8 and MKL libraries give problems (on
my platform, in parallel) for qmmm even in Amber10
Thanks
francesco
On Tue, Jun 24, 2008 at 5:07 PM, Vlad Cojocaru
<Vlad.Cojocaru.eml-r.villa-bosch.de> wrote:
> Dear Francesco ,
>
> Below is a summary of the bugfixes that interfere with the RAMD patch. We
> are studying the problem but for now we can only recommend compiling AMBER8
> with the RAMD patch without these bug fixes. I know this is not ideal. Maybe
> you should also compile the AMBER8 without the MKL libraries since anyhow
> you'll use it just for the RAMD runs.
>
> As for porting RAMD to Amber 10. We definitely consider it. For now, the
> limiting factor is my lack of experience with Fortran and parallel
> computing.
>
> Good Luck,
> Vlad
>
> -------------------------------------------------SUMMARY RAMD and AMBER8
> BUGFIXES (message from our
> administrator)----------------------------------------------------------------------------
> The following patches are towards force.f, sander.f and runmd.f and might
> interfere with the ramd patch:
>
> http://amber.scripps.edu/bugfixes80.html
>
> force.f
> bugfix.33 <http://amber.scripps.edu/bugfixes/8.0/bugfix.33>: The forces for
> "cap" water are not accompanied by a corresponding energy term. /(See also
> bugfixes 40, 43 and 45, below
>
> sander.f
> /bugfix.7 <http://amber.scripps.edu/bugfixes/8.0/bugfix.7>: Using a
> restraintmask or a bellymask that invokes distance comparisons will fail.
> bugfix.13 <http://amber.scripps.edu/bugfixes/8.0/bugfix.13>: Several fixes
> to sander.QMMM
> bugfix.47 <http://amber.scripps.edu/bugfixes/8.0/bugfix.47>: Fixes MPI calls
> in /sander/ when the /noBTREE/ is set during compilation.
> bugfix.52 <http://amber.scripps.edu/bugfixes/8.0/bugfix.52>: Manual setting
> of /lastrst/ needs to be allowed for regular Ewald simulations.
>
> runmd.f
> bugfix.25 <http://amber.scripps.edu/bugfixes/8.0/bugfix.25>: Langevin
> dynamics will fail when the target temperature is changed during the run.
> bugfix.32 <http://amber.scripps.edu/bugfixes/8.0/bugfix.32>: The /mden/ file
> can contain a bad value for pressure when the pressure is not being
> regulated.
> bugfix.54 <http://amber.scripps.edu/bugfixes/8.0/bugfix.54>: The /ntt=2/
> option in sander can result in average temperatures that are too high.
> bugfix.56 <http://amber.scripps.edu/bugfixes/8.0/bugfix.56>: Update to
> bugfix.54, which failed to work properly in parallel.
>
> Some of the above might still be possible to patch together with the ramd
> patch. But this i did not test.
>
> I would recommend to only select the patches from the bugfixes page that are
> needed. If one of the above bugfixes are needed, we need to have a look at
> the differences in the patches?
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
>
>
> Francesco Pietra wrote:
>
> I am trying to compile (serial) amber8 - patched with contributed
> software RAMD - on a UMA type dual opetron machine, Debian Linux lenny
> amd64.
>
> The RAMD patch, which only modifies sander
> (http://projects.eml.org/mcm/software), has to be applied before any
> bugfix is applied to amber8 (although, perhaps, bugfix not related to
> sander might have been applied; not tried; I just tried bugfix.all and
> it prevented the RAMD patch to be applied)
>
> Now
> $ ./configure ifort
> AMBERHOME set to /usr/local/amber8
> Setting up for architecture ifort
> MKL_HOME is set to /opt/intel/mkl/10.0.1.014/
> Using MKL libraries from /opt/intel/mkl/10.0.1.014/lib/32
> Using parallel communication library: none
> config.h created successfully
>
> $ make serial
>
> gave error:
> ifort -o addles lesmain.so addspace.o readprm.o writprm.so readcrd.o
> writcerd.o pick.o rline.o nxt.o intgr.o find.o of.o geti.o unit.o
> getc.o alert.o echo.o get4c.o getd.o wlesprm.o lesprm.o les2prm.o
> checksz.o ../lib/random.o ../lib/mexit.o ../lib/nxtsec.o
> -L/opt/intel/mkl/10.0.1.014//lib/32 -lvml -lmkl_lapack64 -lmkl -lguide
> -lpthread
>
> ld: skipping incompatible
> /opt/intel/mkl/10.0.1.014/lib/32/libmkl_intel.so when searching for
> libmkl_intel.so
>
> ld: cannot find libmkl_intel,so. Actually this is present where it was
> searched. Thus incompatibility?
>
>
> serial error 2
>
>
> Is it known (or imaginable) if the the problem is raised by having
> patched sander with ramd, or these mkl libraries (which I used for
> both amber10 and dock6.2) are too new for amber8 (not bugfixed)
> anyway? In the first case I could try by commenting out MKL_HOME in my
> .bashrc.
>
> I am in contact with the German group for RAMD, too. However,
> presently there is no one capable of adapting RAMD to current times.
>
> It is clear that my only interest with amber8 if to have it running
> patched with RAMD. Otherwise I have both amber10 and amber9 installed.
> In a way, my question is a jump into the past.
>
> Thanks
>
> francesco pietra
> -----------------------------------------------------------------------
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>
>
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
> ----------------------------------------------------------------------------
> EML Research gGmbH
> Amtgericht Mannheim / HRB 337446
> Managing Partner: Dr. h.c. Klaus Tschira
> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
> http://www.eml-r.org
> ----------------------------------------------------------------------------
>
>
--
Dr Francesco Pietra
Professor of Chemistry
Accademia Lucchese di Scienze, Lettere e Arti, founded in 1594
Palazzo Ducale
55100 Lucca (Italy)
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Received on Wed Jun 25 2008 - 06:07:48 PDT
