[gmx-users] Gromacs Installation on HP problems

[BONINI at ICIL64.CILEA.IT]

Hi,

 I've got some problem installing Gromacs 3.1.3 on our HP SuperDome machine.
 I used configure with --enable-mpi option, then "make" and "make install".
 In this case CFLAGS couldn't be correclty setted, so no CFLAGS at all were
 used. Installation worked, but the program was incredibly slow.
 So I setted CFLAGS="-Ae +O3 +Oall" like in configuration script for HP, in 
 this case make phase showed:

>>> This is the GROMACS code generator for MD & MC inner loops
>>> It will generate single precision C code in file innerc.c
>>> Using gromacs invsqrt code
>>> Inlining gromacs invsqrt and/or reciprocal code
>>> Using normal solvent optimized loops
>>> Prefetching coordinates in loops: none
>>> Prefetching forces in loops: none
>>> Nonthreaded inner loops
>>> Vectorizing invsqrt in loops:none
...
Progress: 100%>>> Generated 42309 lines of code in 156
functions

 so it seems OK. After that, some more alarming messages:

mpicc -Ae +O3 +Oall -G -o grompp topio.o toppush.o topcat.o topshake.o 
convparm.o tomorse.o sorting.o splitter.o dum_parm.o readir.o add_par.o 
topexcl.o toputil.o topdirs.o grompp.o  -L/mcae/fftw2.1.3/lib -L/usr/lib ../
mdlib/.libs/libmd_mpi.a ../gmxlib/.libs/libgmx_mpi.a -lnsl /mcae/fftw2.1.3/
lib/libsrfftw_mpi.a /mcae/fftw2.1.3/lib/libsfftw_mpi.a /mcae/fftw2.1.3/lib/
libsrfftw.a /mcae/fftw2.1.3/lifftw2.1.3/lib/libsfftw_mpi.a /mcae/fftw2.1.3/
lib/libsrfftw.a /mcae/fftw2.1.3/li/libsfftw.a -lm -lXm -lXt -lSM -lICE -
lXext -lXp -lX11
cc: warning 454: Option +O4 overrides previous setting of +O3.
ucomp :
   Warning in procedure put_charge_groups_in_box : Infinite loop detected. 
Check for spinning on non-volatile variable. (6005)
   Warning in procedure put_charge_groups_in_box : Infinite loop detected. 
Check for spinning on non-volatile variable. (6005)
   Warning in procedure put_atoms_in_triclinic_unitcell : Infinite loop 
detected. Check for spinning on non-volatile variable. (6005)
   Warning in procedure put_atoms_in_triclinic_unitcell : Infinite loop 
detected. Check for spinning on non-volatile variable. (6005)


The executable generated doesn't work: or it complains about input data (
Warning: Only triclinic boxes with the first vector parallel to the x-axis 
and the second vector in the xy-plane are supported. ... Can not fix pbc.), 
or it starts nomally and then hang on.

How can I overcome these problems?
Thank you for any advice.

f


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	  Francesca Bonini   E-Mail: BONINI at CILEA.IT	
			       Tel.:	02 26995.257	
	  CILEA 					
	  via R. Sanzio 4				
	  20090 Segrate (MI)				
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