<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Dear justin<br> Thank you for your previous reply<br>Now i am trying to run the parallel gromacs simulation (gromacs 4.5.5) first of all i have successfully installed debain package of gromacs-openmpi <br>for that i have configured and compiled using the following command <br>./configure --enable-mpi --enable-double --prefix=/usr/local/mpigromacs --program-suffix=_mpi_d<br>then I issued the <br>make <br>make mdrun<br>make install<br>make install-mdrun<br>It compiles nicely and successfully<br>I have few doubt<br>1) should i need to install both rpm of openmpi (coresponding to my OS) and Debain of gromacs-openmpi ? (compatible to my Linux OS) <span style="font-weight: bold;">Now i have both
</span><br> Otherwise <span style="font-weight: bold;">is it enough to install only Debain gromacs-openmpi to install gromacs in paralleel</span><br><br>2) <span style="font-weight: bold;">how to check Wheather Parallel installation of gromacs ? wheater is installed parallely or not? </span><br>I have <span style="font-weight: bold;">installed on single Hyper threading</span> supported intel pentium i5 (dual core processor,four thread)<br>it means i am<span style="font-weight: bold;"> using thread based parallelism not mpi based parallelism </span>(i know the performance may be poor, though later i will extend this to clustering)<br><br>please tell me The Above my understandings is correct or not <br>if ther are any wrong things in the compilation procedure Please give me some tips to rectify error?<br>I am very grateful to your valuable reply<br><br><br>Also if the above procedure is
correct<br>Can i run the gromacs parallel simulation using the following command<br>mdrun_mpi_d -nt 8 -s topol.tpr<br><br>Don't i Need mpirun command ?<br><br><br>Thanks in Advance <br><br>With regards <br>S.vidhyasankar<br><br><br></div></div></body></html>