Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM

From: PRITI ROY <>
Date: Thu, 5 Jul 2018 01:22:43 +0530

Dear All,

At first, David and George,Thank you for your suggestions.
I am using Amber16 with AmberTools17. In my case, the main problem was mpi
because there was many versions of MPI installed and the mpirun was not set
properly. I have to re-install all the required files for amber and amber
itself also. Then another error was appeared which is as follows:
"rism3d.snglpnt.mpi: error while loading shared libraries: cannot open shared object file: no such file or
and it is resolved by setting LD_LIBRARY_PATH as "export

Now I am stuck in memory problem. My system has 5550 atoms, running one
frame of the trajectory with 48 cores and after 3hours its not yet
finished. I have 300ns long trajectory. Is it possible to speed up this
calculation with this system size?

Can I run this 3d-RISM calculation in GPU as I couldn't found any GPU based
executable of rism3d.snglpnt?

Looking forward of your suggestions.


On Fri, Jun 29, 2018 at 7:32 PM, George M. Giambasu <>

> The post you mentioned says that the error you get appears because you
> might be using a different version of MPI to run your program than that
> you used to compile Amber. This happens all the time when using
> computing clusters. Here are few things to try:
> - make sure that the modules that were loaded at the compile time are
> also loaded at the run time. You can list the available modules using
> "module avail". In your batch script explicitly load those modules, eg:
> module load intel/17.0.4 mvapich2/2.2.
> - make sure that the environmental variables such as PATH and
> LD_LIBRARY_PATH are maintained in the batch script. First thing to do is
> to source $AMBERHOME/ file in the batch script. Then add the
> commands "echo $PATH" and "echo $LD_LIBRARY_PATH" in the batch script to
> actually see what the compute nodes actually use and compare the results
> to what you have on the login node where you compiled the code.
> Let us know what you get from doing this. When you get back to us please
> mention what AmberTools version you are using, compilers version and MPI
> distribution and version.
> (I do have doubts that rism3d will need a special MPI setup than what
> one usually gets when using typical supercomputing facilities).
> best,
> George
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Dr. George M. Giambasu, Ph.D.
> Rutgers, The State University of New Jersey
> 174 Frelinghuysen Road, Room 308E Piscataway,
> NJ 08854, USA
> Office: 1-848-445-5223
> Cell: 1-612-644-8285
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Received on Wed Jul 04 2018 - 13:00:02 PDT
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