[gmx-users] compiler warnings on IBM SP

[David L. Bostick]

Ok, thanks.  I have no idea what could be wrong then b/c I get

Reading file alam.tpr, VERSION 3.1 (single precision)
Reading file alam.tpr, VERSION 3.1 (single precision)
 
Back Off! I just backed up extend60A_3dc1.edr to #extend60A_3dc1.edr#
starting mdrun '4 helix bundle of alamethecin in POPC bilayer'
10000 steps,     20.0 ps.
 
ERROR: 0031-250  task 1: Segmentation fault


on standard error.  The job was preprocessed for 10 processors.  There is
one coredump file, but the job keeps going ... slowly it seems.  Any clues?

David

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David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	
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On Thu, 7 Mar 2002, Erik Lindahl wrote:

> Hi David,
> 
> >
> >
> >1)
> >
> >libtool: link: warning: library
> >`/gpfs/dbostick/fftw_IBMSP/lib/libsfftw_mpi.la' was moved.
> >
> >I assume this is okay because I have the compiled libraries in a directory
> >that I move from place to place.  As long as the path can be found for
> >linking I imagine this is fine..
> >
> Yes - this is just a bug in the FFTW configuration that we can't do much 
> about. It's just libtool telling you that the fftw library was installed 
> to a different path in the first place. It won't cause any problems.
> 
> >
> >
> >2)
> >
> >ld: 0711-230 WARNING: Nested archives are not supported.
> >        Archive member ../mdlib/.libs/libmd_mpi.a[libc.a] is being ignored.
> >
> >I suspect this may be causing my problems when running mdrun_mpi.  How do I
> >fix this?   
> >
> I don't see this on my SP system, but I don't think it will cause any 
> problems. In theory, libtool has the capability to link all libraries 
> into the library you are creating (i.e. include the parts of libc we 
> need into libmd), but since I'm pretty sure your linker/compiler will 
> include libc at the link stage it should probably work. This is a 
> libtool bug ;-)
> 
> >
> >
> >Also in the configure script I changed mpcc to the threadsafe mpcc_r.  Is
> >this okay?
> >
> Sure. We're not using multithreading parallelization yet, but when it's 
> working I will be changing the compiler detection part to use the 
> threadsafe ones by default.
> 
> 
> Cheers,
> 
> Erik
>  
> 
> >
> 
> 
>