Is it possible to run PAUP with Open MPI?

More Andrii Tarieiev's questions See All

Is there any alternative to BUSCO for searching orthologues within genomes available?

I have a need to search for single-copy conservative orthologs within several plant genomes and used BUSCO tool for that. However, I found that the results produced by different versions on the...

29 January 2021 7,764 6 View

Can anyone suggest good open access and peer reviewed international journal on optimization processes for underground coal mine?

Question I'm searching for open access and peer reviewed international journal (obviously of high quality and with Impact Factor) to publish research on development and operation for mineral...

24 January 2019 5,626 5 View

There is a probability distribution of a discrete random variable "x", what is the probability that the distribution stay constant during time "t"?

There is a probability distribution of a discrete random variable "x" (is given below), which the probability that the distribution stay constant (with a tolerance of 5%) with the passage of the...

14 October 2016 1,005 3 View

Could you point at research applying deep neural networks in the educational context?

Deep neural networks have recently demonstrated the state of the art and superior performance when applied to common pattern recognition problems, including image and speech recognition. I'm...

25 June 2016 9,758 9 View

How to calculate and plot 3D Fourier transform in Python?

Hello, I am trying to calculate 3D FT in Python of 2D signal that is saved in the 3D matrix where two axes represent spacial dimention and the third one represents time. Could you help me with a...

27 April 2016 831 12 View

How to correctly calculate melting temperature and annealing temperature of primers?

There are many formulas and program applications to compute melting temperature and annealing temperature of PCR primers nowadays, but these tools usually have different results. Would you be so...

28 February 2013 9,056 25 View

What is the best tool for comparing and aligning large sequence fragments?

I need to compare some sequences longer than 10Mb. What kind of software is the best for such work? Can I do this work locally (without internet sources)? If I have sequences in FASTAQ format, I...

24 January 2013 9,459 5 View

Phylogenetic markers selection for distinguishing taxa in plants

We work with one genus Betula on the territory of Ukraine. We try to diverse different taxa in this genus based on molecular markers. But we have a problem, that traditional molecular markers...

10 December 2012 8,132 37 View

PME calculation on a GPU GROMACS?

Hi all I used the following script to run the simulation but for some reason, I was not able to assign GPU to do the PME calculation? How to do that? The size of the system is huge (600.000...

14 January 2021 7,441 1 View

I am getting the following error when I am running the command bellow on 8 core 320 queue cpu?

Command: gmx_mpi mdrun -v -deffnm md_0_10 -plumed plumed3.dat Error: Program: gmx mdrun, version 2018.2 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void...

05 November 2020 9,912 1 View

How to make parrallel inlet boundary UDF work?

Hi everyone, It is quite urgent for me! I am doing 2D rotating detonation engine (RDE) simulation in ANSYS Fluent. For inlet boundary condition, there are three possible cases: 1. Pi > Po,...

02 August 2020 8,443 1 View

How should I initialise the mpirun parameters for running a quantum espresso 'scf' calculation for the best parallel computing performance?

Hi, I am trying to do a Quantum espresso SCF calculation on an Intel Xeon Gold Gold 5120 CPU @ 2.20 GHz (2 Processor). It has 56 cores and a 96 GB RAM. I am trying to do a parallel calculation...

01 July 2020 6,821 3 View

Why is the multicore MPI version of MrBayes running slower than the serial version?

I'm attempting to run a parallel MrBayes analysis using MPI on a Linux machine with 33 processor cores (it's not a cluster, it's just the single multicore machine) but I can't get it to work....

01 February 2020 5,449 1 View

Matrix Multiplication using MPI in Python?

Hello all, I am new to MPI and I'm trying to create a simple Matrix Multiplication program with MPI in Python using multiple cores by generating the random values into matrices. My code works for...

14 January 2020 7,894 5 View

Is there a way to do Time course image analysis using 3D Slicer?

I'm using 3D slicer to run batch analysis of 2D and 3D MPI data (not MRI). I have a time course data set of the same 2D data and want to extract signal quantitation for the whole time course on...

11 December 2019 5,529 0 View

Error while processing metgrid of WRF model "ERROR: Error in ext_pkg_write_field application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0" ?

Hello Everyone I am Trying to run WRF model and incountering with an error while running WPS-metgrid.exe error is as below !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! Successful completion of...

11 December 2019 8,881 2 View

How do we fix badly or non equilibrated configurations in gromacs?

Program: gmx mdrun, version 2019.1 Source file: src/gromacs/mdlib/sim_util.cpp (line 752) MPI rank: 3 (out of 4) Fatal error: Step 700: The total potential energy is nan, which is not finite. The...

10 November 2019 7,165 2 View

How to run mdrun in gpu powered system?

Hello, I am new to MD simulations, Ubuntu and also for GPU powered computing. I had run some basic simulations using gromacs earlier but with a non GPU system. Now I have upgraded my work station...

09 October 2019 9,712 2 View

Kadache Nabil

A trivial solution is to use the following C/C++ function

int system( const char *command ); to run an external command (in your case python program with PAUP module in your case).

#include "mpi.h"

#include

int np=MPI_Comm_size(MPI_COMM_WORLD)

int rank=MPI_Comm_rank(MPI_COMM_WORD)

system("python myprogram.py"); // will be executed by every MPI node.