AMBER Archive (2004)

Subject: Re: AMBER: pmemd config.h request for athlon

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri Aug 13 2004 - 13:40:05 CDT

Madalin -
Try using this as config.h for uniprocessor

Begin -->
#!/bin/csh -f
setenv PREPROCFLAGS
setenv CPP "/lib/cpp -traditional "
setenv OPT_LO "ifort -c -auto -tpp6 -mp1 -O0 "
setenv OPT_MED "ifort -c -auto -tpp6 -mp1 -O2 "
setenv OPT_HI "ifort -c -auto -tpp6 -mp1 -ip -O3 "
setenv LOAD "ifort"
setenv LOADLIB
<-- End

Or this for mpich:
Begin -->
#!/bin/csh -f
setenv MPICH_HOME <whereever your mpich installation is>
setenv MPICH_INCLUDE $MPICH_HOME/include
setenv MPICH_LIBDIR $MPICH_HOME/lib
setenv MPILIB "-L$MPICH_LIBDIR -lmpich"
setenv PREPROCFLAGS "-DMPI -DSLOW_NONBLOCKING_MPI"
setenv CPP "/lib/cpp -traditional -I$MPICH_INCLUDE"
setenv OPT_LO "ifort -c -auto -tpp6 -mp1 -O0"
setenv OPT_MED "ifort -c -auto -tpp6 -mp1 -O2"
setenv OPT_HI "ifort -c -auto -tpp6 -mp1 -ip -O3"
setenv LOAD "ifort"
setenv LOADLIB "$MPILIB"
<-- End

I tested the uniprocessor version out and it works. Like Ross said, you are
probably running afoul of the pentium optimizations if you use the p4 ifort
configuration. Really all that is necessary if changing the optimization
setting to what you see in the ifc7 athlon config files, and ditching all
the load libraries. The change of ifc->ifort prevents warning messages, but
is not necessary. Be sure you have set an unlimited stacksize in your
.login (see notes on amber web site on this issue, if it is a mystery to
you), as this can also be the source of segment violations (with ifort 8,
pmemd uses a lot of stack, which is good from a performance point of view,
but a headache due to users needing to be sure they don't have limits on
stack memory usage).

Regards - Bob Duke

----- Original Message -----
From: "Madalin Giambasu" <giambasu_at_biochim.ro>
To: <amber_at_scripps.edu>
Sent: Friday, August 13, 2004 1:47 PM
Subject: AMBER: pmemd config.h request for athlon

>
> Does anyone have a pmemd config.h for athlon ?
>
>
> I have installed ifort8 from l_fc_pc_8.0.046.tar.gz, compiled pmemd
> but i am still receiving errors:
>
> make test.pmemd
> export TESTsander='../../exe/pmemd'; cd 4096wat; ./Run.pure_wat
> forrtl: severe (168): Program Exception - illegal instruction
> Image PC Routine Line Source
> pmemd 08083C8F Unknown Unknown Unknown
> pmemd 42015574 Unknown Unknown Unknown
> pmemd 0804A391 Unknown Unknown Unknown
> ./Run.pure_wat: Program error
> make: *** [test.pmemd] Error 1
>
> Unfortunately I didnot have a config.h for athlon I have used that from
> the Amber site.
>
>
>
>
> -------------------------------------------------------
> Madalin G. Giambasu
> Junior Research Assistant
> Institute of Biochemistry of Romanian Academy of Science
> Splaiul Independentei 296, 060031, Bucharest 17, Romania
> Phone: (+4)021.223.90.69; FAX: (+4)021.223.90.68
>
> -------------------------------------------------------
>
>
> -----------------------------------------------------------------------
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>

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