[gmx-users] parallel question!!!

PeiQuan Chen gromacs at 163.com
Sun Apr 6 07:30:01 CEST 2003

Dear gmx-users:

>Hm... you are getting a LAM error message, but you said you compiled  
>with mpich?

>"LAM" is never mentioned in Gromacs, so somewhere you must have  
>compiled something with LAM or used a lam command - perhaps FFTW?


Thank you for your help!Erik!
Yes I have compiled somthing with LAM or used a lam command of FFTW!
I have solved the problem after I have recompiled the FFTW!
But another problem accur:

I want to test the mdrun(with mpich-iccr),but I find a strange phenomenon:
I use the two -np nodes to test how fast the parallel caculation.so I use the tutor/water to test:

Method 1:
grompp -np 1 -f water.mdp -p water.top -c spc216.gro -o water.tpr
mpirun -echo -np 1 /home/pqchen/gromacs/i686-pc-linux-gnu/bin/mdrun -s water.tpr -o water.trr -c water_out.gro -v -g water.log  

Method 2
grompp -np 8 -f water.mdp -p water.top -c spc216.gro -o water.tpr
mpirun -echo -np 8 /home/pqchen/gromacs/i686-pc-linux-gnu/bin/mdrun -s water.tpr -o water.trr -c water_out.gro -v -g water.log

But the Method 2 consumes more time to caculate.Can anybody tell me why??Can anybody help me??

Thank you in advance!

Sincerely yours
PeiQuan Chen
PeiQuan Chen 	Department of Chemistry, Nankai University
WeiJin Road 94, TianJin, 300071, P.R.China
phone:	(86)2223506728		Mobile Phone: (+86)13920675030
gromacs at 163.com	

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