I installed AmberTools18 and I installed MPI libraries as well. Everthing is working but when I want to run sander parallel like this:
mpirun -np 32 sander.MPI -O -i min.in -o min.out -p ras-raf_solvated.prmtop -c ras-raf_solvated.inpcrd \
-r min.rst -ref ras-raf_solvated.inpcrd
it didn't work, then I realized sander.MPI doesn't seem in my AmberTools package. So how can I run it? or if I didn't install how can I install it?
Hi Baris,
In $AMBERHOME, try ./configure -mpi gnu, and make install.
Dear Ishikawa ,
EDIT: I found that my computer had a hardware problem. May be this why it didn't work...
Thanks for your answer. I have done it already but it didn't work:
Here is what I have done:
cd /home/myname
tar xvfj AmberTools18.tar.bz2
export AMBERHOME=/home/myname/amber18
sudo apt-get install bc csh flex gfortran g++ xorg-dev \
zlib1g-dev libbz2-dev patch
cd $AMBERHOME
./configure gnu
****************************
for bison:
sudo apt install bison
**************************************
./configure gnu
source /home/bio/amber18/amber.sh
make install
make test
*****************************
FOR PARALLEL:
*****************************
cd $AMBERHOME
./configure -mpi
************
$ ./configure -mpi gnu
export DO_PARALLEL="mpirun -np 2"
make test
make install
Hi again,
You may check the $AMBERHOME/bin directory if there is the sander.MPI executable before making test.
Dear Ishikawa,
thanks for your answer. I succeded in running sander.MPI parallel program, but now I have another problem: when I use more than 8 cpu, The calculation time is increasing dramatically. I am working under windows 10 ubuntu bash terminal. DO you have any idea how to fix it?
Here is calculation times and number of cpu:
1 cpu 2.1 hours.
4 cpu 35.2 minutes.
8 cpu 21.1 minutes. >>>>>THE BEST
12 cpu 28.8 minutes.
16 cpu 23.3 minutes.
20 cpu 57.1 minutes.
24 cpu 1.3 hours.
32 cpu 1.4 hours.
40 cpu 2.9 hours.
Hi again,
This may be due to Windows 10... If so, you should do MDS using a Linux machine.
Dear Ishikawa ,
thanks for your answer. Actually I was thinking the same, but your answer made me more confident. I will test it on a Linux Machine and I will share results here again.
Important question:
Can sander run in parallel and interface with programs like plumed WITHOUT an AMBER license?
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