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On 31/05/2012 10:17 PM, vidhya sankar wrote:
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<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>
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<br>
As you will see in the <a
href="http://www.gromacs.org/Documentation/Installation_Instructions">http://www.gromacs.org/Documentation/Installation_Instructions</a>,
there is no need to do both "make mdrun" and "make" because the
former does part of latter. Likewise for "make install-mdrun" and
"make install". However it doesn't hurt.<br>
<br>
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<div>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>
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<br>
You've installed GROMACS from source already. You have no need of a
binary distribution in an .rpm or .deb. However that binary probably
is linked to FFTW3, which your source installation was not, so PME
will likely be much faster. You should probably get rid of the
source installation, and do it again following <a
href="http://www.gromacs.org/Documentation/Installation_Instructions">http://www.gromacs.org/Documentation/Installation_Instructions</a>,
or use the binary distribution.<br>
<br>
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<div> Otherwise <span style="font-weight: bold;">is it enough
to install only Debain gromacs-openmpi to install gromacs
in paralleel</span><br>
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<br>
Probably it is.<br>
<br>
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<div><br>
2) <span style="font-weight: bold;">how to check Wheather
Parallel installation of gromacs ? wheater is installed
parallely or not? </span><br>
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<br>
Something named gromacs-openmpi, or successfully configured
--with-mpi is very likely to run in parallel with MPI. That's the
point of the name!<br>
<br>
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<div>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>
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<br>
No. See <a
href="http://www.gromacs.org/Documentation/Installation_Instructions">http://www.gromacs.org/Documentation/Installation_Instructions</a>.
Hyper-threading is useless for GROMACS, and you have configured with
MPI, which prevents attempting to use threading of any sort.<br>
<br>
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<div><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>
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<br>
mdrun -nt is not available with an MPI-configured mdrun, and likely
exits with an error.<br>
<br>
Mark<br>
<br>
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Don't i Need mpirun command ?<br>
<br>
<br>
Thanks in Advance <br>
<br>
With regards <br>
S.vidhyasankar<br>
<br>
<br>
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