Dear Giovanni,
we have the same machine configuration here at IDRIS (
http://www.idris.fr).
I can test your job here if you give me the input files and how to run it.
When I compile sander on the IBM Regatta, I add in the file
"src/sander/mexit.f" these lines :
---------------------- cut here -------------------
.
.
.
implicit none
integer ifil,i,ier
#ifdef MPI
# include "mpif.h"
!! NG add include parallel.h
# include "parallel.h"
#endif
!! NG add call flush
#if ibm_aix
call flush_(6)
#endif
.
.
.
-----------------------cut here -------------------
In my case "MACH" is initialized to "ibm_aix" in the MACHINE file:
setenv MACH ibm_aix
I think it is necessary to clear the output buffer by the call "flush_" to
resolve your problem !
Best regards,
Nicolas Grima.
Le Lundi 30 Septembre 2002 17:51, vous avez écrit :
> Monday September 30, 2002
> Dear users,
> we are still struggling to have sander_classic to run on IBM-AIX.
> At first we had a slew of compilation problems, solved with yours and
> Carlos Sosa's help. We implemented all the amber patches, and Carlos
> Sosa's too, and updated the Machine files as well. The XLFR*** setting
> fixed the namelist problem.
>
> Now we would like to ask you about a "runtime" new problem.
>
> I had sander_classic and sander (Amber6) compiled.
> We have been using sander_classic all along, and so we are still
> "migrating" to sander itself.
> Anyway, now, it runs (with the namelist=old environment set), but
> it does a weird thing.
>
> It does NOT "finish" to write the output files... mdcrd and mden.
> For a test run, where the mdcrd should have 108001 lines, it writes only
> 107985 The mden should have 5010 and it has instead 4980.
> In both cases it is not simply cutting short by one iteration, but really
> cutting the write of the coordinates and parameters for the last(s)
> iteration.
>
> For instance, the data in mdcrd for one "iteration" should take 18 lines.
> The file ends with 2 full lines and the first three data for the third
> line, and no 'newline'.
>
> In mden a block of output for an "iteration" is 9 lines, but the file ends
> with one truncated line....
> Moreover this last "output" is two before the last one.
>
> Anyway, if I look at the sizes of the files, mdcrd and mden, they are round
> multiples of 1024, whereas the "correct" one are not.
> So it seems like there is a problem with "flushing the buffer" (I apologize
> for using sometimes imprecise terms) when the run ends.
>
> A couple of people (using the same machine, but not with amber) suggested
> me to try to compile with less aggressive optimization, because
> optimization can shuffle things around, and maybe a file is not closed at
> the right time, or stuff like that.
> I changed -O3 to -O2 in the Machine file.
> Even recompiled with this change, it still suffers from the same problem.
>
> I tried then a "runtime environment option" (one of the XLFR*** settings)
> that from the user's guide sounded appropriate for this problem:
>
> setenv XLFRTEOPTS "namelist=old:buffering=disable_preconn"
>
> The program slows down significantly (+50%), but still when it stops the
> mden and mdcrd files are identical to the previous case, i.e. cut short.
>
> Has anybody encountered the same problem?
> Do you have a fix for this?
>
> We never had any problem with output files on several "flavors" of linux
> boxes, or Sun's, SGI's, Cray...etc...
>
> The machine is a IBM Regatta, running AIX v5.
> Compilers are IBM's xlf* and xlc*, XL fortran v7.
> Program: from amber6, module sander_classic.
>
> Thank you very much.
> Best regards,
>
> Giovanni
>
> ---------------------------------------------------------------------------
>--- Dr. Giovanni Fossati
> +---------------------------+ Dept. of Physics and Astronomy, MS 108
> | Ph : (713)-348-3425 | Rice University
> | Fax : (713)-348-5143 | 6100 Main street, Houston, TX 77005, USA
> | e-mail: gfossati_at_rice.edu |
> -------------------------------------------------+-------------------------
>--+
--
Grima Nicolas
(Support utilisateurs IDRIS)
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Received on Tue Oct 01 2002 - 02:40:07 PDT
