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REDMD
02-14-2012, 01:56 PM (This post was last modified: 02-14-2012 01:57 PM by andyng.)
Post: #1
REDMD
Hi,

I am able to run normal DMD using pdmd.linux from a precomplie linux_x86_64 and pdmd from precompile osx on a mac. but when I tried to run REDMD on my mac and this is the error I got

"! Number of replicas is specified (8), but is different from number of MPI tasks 1."

The command I used is repdmd -i start -p param -s state -r rex.input

I have also tried to run this over at a PBS cluster system where I can specify 8 cpus and the job started but there is no output file produced. If I run normal DMD, it runs fine.

By reading the user guide, I thought REPDMD needs to be run on a parallel version pDMD, which needs to be compile from the source code. Am I right? or I just did not run the simulation correctly?

Thanks for any help you can provide.

Andy
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02-15-2012, 05:32 AM
Post: #2
RE: REDMD
Hi Andy,

Replica exchange DMD uses MPI library to start multiple simulations and perform temperature exchange. You must have MPI installed on your system. Then you can start replica exchange simulation using mpirun, e.g.
Code:
mpirun -n 8 repdmd -i start -p param -s state -r rex.input

Number of tasks started by mpirun (8 in the example) must be equal to the number of replicas requested in the task file. Exact command will depend on the queuing system setup. If you have choice, select MPICH-1.2.7 as MPI library. MPICH is the most common MPI implementation, and your current version of repdmd was linked against it.

Currently, the policy of the Molecules In Action does not allow distribution of the source code. However, if you encounter DMD binary incompatibility with your computer platform, we will do our best to prepare the compatible code.
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02-15-2012, 09:59 AM
Post: #3
RE: REDMD
Hi shir,

I run MPI on the repdmd and it encounter an error of "runtime version may be incompatible". The cluster use openMPI 1.4.3. Cluster administrator is reluctant to install MPICH on their cluster. I guess I would not be able to run repdmd after all or is there an alternative solution?

Andy


(02-15-2012 05:32 AM)shir Wrote:  Hi Andy,

Replica exchange DMD uses MPI library to start multiple simulations and perform temperature exchange. You must have MPI installed on your system. Then you can start replica exchange simulation using mpirun, e.g.
Code:
mpirun -n 8 repdmd -i start -p param -s state -r rex.input

Number of tasks started by mpirun (8 in the example) must be equal to the number of replicas requested in the task file. Exact command will depend on the queuing system setup. If you have choice, select MPICH-1.2.7 as MPI library. MPICH is the most common MPI implementation, and your current version of repdmd was linked against it.

Currently, the policy of the Molecules In Action does not allow distribution of the source code. However, if you encounter DMD binary incompatibility with your computer platform, we will do our best to prepare the compatible code.
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02-16-2012, 01:44 AM
Post: #4
RE: REDMD
I have compiled replica-exchange DMD with OpenMPI 1.4.3, both static and dynamic executables. Hopefully, one or another works for you.

Statically linked: [attachment=1]

Dynamically linked: [attachment=2]

--
Best,
David
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02-16-2012, 09:04 AM
Post: #5
RE: REDMD
Hi David,

Thanks for the help. I tried the dynamic executables and the program run and producing output files. However, I could not find rx-rate.pl inside the original pdmd-1.0 package. Can you please provide me the file? Thanks.

Andy

(02-16-2012 01:44 AM)shir Wrote:  I have compiled replica-exchange DMD with OpenMPI 1.4.3, both static and dynamic executables. Hopefully, one or another works for you.

Statically linked:

Dynamically linked:

--
Best,
David
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02-17-2012, 06:03 AM
Post: #6
RE: REDMD
Hi Andy,

Here is the rx-rate.pl script. You need to uncompress the file.


.gz  rx-rate.pl.gz (Size: 552 bytes / Downloads: 5)

usage: rx-rate.pl rx-temp-out

here, rx-temp-out is the "rx-temp.out" file generate by the REX simulations.
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02-17-2012, 10:28 AM
Post: #7
RE: REDMD
Dear David, Feng and Nikolay,

Thank you for providing me with this program and all the helps that you've provided. I am really appreciate it.

Andy
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03-15-2012, 10:47 PM
Post: #8
RE: REDMD
Hello David,
we too are having problems with repdmd: we installed mpich2-1.4.1p1 on a Mac Pro 4.1 (processor Quad-Core Intel Xeon @ 2.66GHz and Mac OS X 10.6.8) and followed your instructions (mpirun -n 8 repdmd -i start -p param -s state -r rex.input) but the error is similar to the error given without mpirun:
! Number of replicas is specified (8), but is different from number of MPI tasks 1.
! Number of replicas is specified (8), but is different from number of MPI tasks 1.
! Number of replicas is specified (8), but is different from number of MPI tasks 1.
! Number of replicas is specified (8), but is different from number of MPI tasks 1.
! Number of replicas is specified (8), but is different from number of MPI tasks 1.
! Number of replicas is specified (8), but is different from number of MPI tasks 1.
! Number of replicas is specified (8), but is different from number of MPI tasks 1.
! Number of replicas is specified (8), but is different from number of MPI tasks 1.
Coul you please help us?
Thanks in advance,
Paolo

Laboratory of Prof. Giuseppe Zanotti
Department of Biomedical Sciences
University of Padova
Padova - ITALY
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03-16-2012, 10:57 AM
Post: #9
RE: REDMD
Hi Paolo,

Current version of repdmd is compiled with mpch 1.2.7. This is why it does not start properly with mpich2 1.4.1, which you have installed.
Version with mpich2 is not available right now, it will take some time to compile and test it. We will make the new version available to you as soon as it is ready.

David
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03-16-2012, 06:47 PM
Post: #10
RE: REDMD
Hi David,
thank you for your answer and for preparing the new version of repdmd: we will try to install mpich 1.2.7 in order to run the old version of repdmd now and when the new version will be available we will switch to mpich2.
Best regards,
Paolo
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