On 11/20/12 3:55 PM, Parisa Rahmani wrote:
Yes, I ran two test simulations , one with 5 cpu and another with 1;
5 cpu simulation :
step 50380, will finish at Wed Nov 21 01:46:25 2012
step 50020, will finish at Wed Nov 21 01:48:36 2012
step 50320, will finish at Wed Nov 21 01:46:49 2012
step 50270, will finish at Wed Nov 21 01:47:07 2012
*Time command :*
*real 153m1.968s*
*user 0m0.472s*
*sys 0m2.072s*
*
*
1 cpu simulation :(started almost 5 minutes later)
step 56000, will finish at Wed Nov 21 02:02:07 2012
*Time command :*
*real 177m25.541s*
*user 177m23.041s*
*sys 0m0.352s*
*
*
It appears to me that mdrun is functioning correctly, but overall performance is
based on how large the system is and how good the hardware is. It just seems to
me that you're not getting particularly great scaling.
-Justin
On Tue, Nov 20, 2012 at 8:06 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/20/12 8:43 AM, Parisa Rahmani wrote:
Thanks for your reply.
I have also tried installing with _mpi suffix
Here is the output of ldd:
gromacs3.3/bin$ ldd mdrun_mpi
linux-vdso.so.1 => (0x00007fff4658c000)
libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.**so.1 (0x00007f7d7afe9000)
libfftw3f.so.3 => /usr/lib/libfftw3f.so.3 (0x00007f7d7ac76000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.**6 (0x00007f7d7a9f3000)
libmpich.so.3 => /usr/lib/libmpich.so.3 (0x00007f7d7a603000)
libopa.so.1 => /usr/lib/libopa.so.1 (0x00007f7d7a402000)
libmpl.so.1 => /usr/lib/libmpl.so.1 (0x00007f7d7a1fd000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.**so.1 (0x00007f7d79ff5000)
libcr.so.0 => /usr/lib/libcr.so.0 (0x00007f7d79deb000)
libpthread.so.0 => /lib/x86_64-linux-gnu/**libpthread.so.0
(0x00007f7d79bce000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.**6 (0x00007f7d79847000)
/lib64/ld-linux-x86-64.so.2 (0x00007f7d7b216000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.**so.2 (0x00007f7d79642000)
------------------------------**------------------------------**
------------------------------**--------------------------
gromacs3.3/bin$ ldd mdrun_mpi | grep mpi
libmpich.so.3 => /usr/lib/libmpich.so.3 (0x00007fc78fb5c000)
It seems that gromacs has been compiled with mpich.
Does this executable still give the error listed below? Performance is
one thing, errors are another. You may not necessarily obtain great
scaling, depending on the contents of the system.
-Justin
On Tue, Nov 20, 2012 at 4:15 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/19/12 12:09 PM, Parisa Rahmani wrote:
Dear gmx users
I have a problem with running parallel jobs on my Debian system(Openmpi
installed on it),
**Linux debian 3.2.0-1-amd64 #1 SMP , UTC 2012 x86_64 GNU/Linux**
I am using gmx 3.3.3, because of the *lambda dynamics* method which is
implemented in it.
AS I know ,in gmx 3.x, the number of processors supplied for the
subsequent
mdrun needed to match the input file. but when i use **grompp -np 6 &
mpirun -np 6 mdrun** the following error appears :
ERROR : run input file md.tpr was made for 6 nodes,
while mdrun expected it to be for 1 nodes.
through search of mailing list i found similar problems, but non of
the solutions worked for my case.
wihtout -np option in grompp the error disappears, and then with each
of these commands
**
1)mpirun -np 6 mdrun -deffnm md
2)mpirun -np 6 mdrun -deffnm md -N 6
3)mpirun -np 6 mdrun -np 6 -deffnm md
4)mdrun -np 6 -s md -N 6
**it uses 6 processors(each one at nearly 100%), but the simulation
time is the same as for 1 processor.
I have no problem with parallel jobs on our cluster(gmx 3.3.3 &
openmpi), with following command:
**
grompp -np 6 -f ...
mpiexec mdrun ...(number of processors is specified in the bash file)
**
,
but i can't run it on my 6 core system.
Also, I have no problem with newer version of gmx (4.5.x), but i
should use this version, and Hope someone can help me.
Have you properly compiled an MPI-enabled mdrun? The default
executable
name should be mdrun_mpi. It should be linked against libmpi, so running
ldd on the mdrun executable should tell you.
-Justin
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Virginia Tech
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