[gmx-developers] PP/ PME splitting in cvs version

[Florian Haberl]

Hi, 

i've mailed with Carsten Kutzner, and he said there is a huge performance 
improvement in cvs version of gromacs, which is reached by PP/ PME node 
splitting. So i want to try it:

Normal calculation: mpirun -np x mdrun -deffnm test -v 
works fine with cvs version

so i tried new flag -npme but i 'm not sure how to use it

mpirun -np 4 mdrun -deffnm test -v -npme 1 (running on two seperate nodes each 
dual cpu, so one seperate for pme)

wont work and produce error

p2_32362:  p4_error: : 8258
2 - MPI_ISEND : Invalid count argument is -724992
[2]  Aborting program !
[2] Aborting program!
rm_l_2_32363: (8.171875) net_send: could not write to fd=5, errno = 32
p2_32362: (8.171875) net_send: could not write to fd=5, errno = 32
starting mdrun '?'
5000 steps,     10.0 ps.

p1_32323:  p4_error: net_recv read:  probable EOF on socket: 1
p3_32401: (5.402344) net_recv failed for fd = 6
p3_32401:  p4_error: net_recv read, errno = : 104
p0_32284:  p4_error: net_recv read:  probable EOF on socket: 1
Killed by signal 2.
Killed by signal 2.
p0_32284: (24.269531) net_send: could not write to fd=4, errno = 32


How can i use this new feature? 
Is it meant with nodes physical cpu/ core or node? 



Something won't compile too (cvs version is from today):

uname -a 
Linux ccc080 2.6.16.21-0.13-smp #1 SMP Mon Jul 17 17:22:44 UTC 2006 x86_64 
x86_64 x86_64 GNU/Linux
mpich version: 1.2.6
fftw: 3.0.1

./configure --enable-mpi --without-x --without-xml --enable-fft=fftw3
make

then mv -f ".deps/gmx_rdf.Tpo" ".deps/gmx_rdf.Plo"; else rm -f 
".deps/gmx_rdf.Tpo"; exit 1; fi
 mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include 
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" 
-I/raid1/haberl/bin/fftw/3.0.1-64/include -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_rama.lo -MD 
-MP -MF .deps/gmx_rama.Tpo -c gmx_rama.c -o gmx_rama.o
 mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include 
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" 
-I/raid1/haberl/bin/fftw/3.0.1-64/include -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_rdf.lo -MD 
-MP -MF .deps/gmx_rdf.Tpo -c gmx_rdf.c -o gmx_rdf.o
if /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I. 
-I../../src  -I../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" 
-I/raid1/haberl/bin/fftw/3.0.1-64/include  -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_rms.lo -MD 
-MP -MF ".deps/gmx_rms.Tpo" -c -o gmx_rms.lo gmx_rms.c; \
then mv -f ".deps/gmx_rms.Tpo" ".deps/gmx_rms.Plo"; else rm -f 
".deps/gmx_rms.Tpo"; exit 1; fi
gmx_rdf.c: In function 'do_sq':
gmx_rdf.c:595: error: 'splinevec' undeclared (first use in this function)
gmx_rdf.c:595: error: (Each undeclared identifier is reported only once
gmx_rdf.c:595: error: for each function it appears in.)
gmx_rdf.c:595: error: 'theta' undeclared (first use in this function)
gmx_rdf.c:653: error: 'ELECTRONMASS_keV' undeclared (first use in this 
function)
gmx_rdf.c:653: error: 'KILO' undeclared (first use in this function)
gmx_rdf.c:653: error: 'ELECTRONVOLT' undeclared (first use in this function)
gmx_rdf.c:658: warning: passing argument 1 of 'calc_grid' from incompatible 
pointer type
gmx_rdf.c:658: error: incompatible type for argument 2 of 'calc_grid'
gmx_rdf.c:658: error: incompatible type for argument 3 of 'calc_grid'
gmx_rdf.c:658: warning: passing argument 6 of 'calc_grid' makes pointer from 
integer without a cast
gmx_rdf.c:658: error: too few arguments to function 'calc_grid'
gmx_rdf.c:665: warning: implicit declaration of function 'init_pme'
gmx_rdf.c:665: warning: assignment makes pointer from integer without a cast
gmx_rdf.c:690: warning: implicit declaration of function 'spread_on_grid'
 mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include 
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" 
-I/raid1/haberl/bin/fftw/3.0.1-64/include -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_rms.lo -MD 
-MP -MF .deps/gmx_rms.Tpo -c gmx_rms.c -o gmx_rms.o
make[3]: *** [gmx_rdf.lo] Error 1
make[3]: *** Waiting for unfinished jobs....
gmx_rms.c: In function 'gmx_rms':
gmx_rms.c:776: warning: ignoring return value of 'fwrite', declared with 
attribute warn_unused_result



Greetings,

Florian

-- 
-------------------------------------------------------------------------------
 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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