Science Cloud Community Group

Help with MMPBSA.py.MPI

2015-11-10T18:58:37Z

All,

I am having problems with the MMPBSA.py.MPI python script to run normal mode analysis on my amber molecular dynamics trajectory. My batch files run fine in serial mode but fail when I try to use the .MPI implementation with this error message;

Traceback (most recent call last):
File "/opt/amber/bin/MMPBSA.py.MPI", line 51, in <module>
raise MMPBSA_Error('Could not import mpi4py package! Use serial version '
MMPBSA_mods.exceptions.MMPBSA_Error: Could not import mpi4py package! Use serial version or install mpi4py.

The same batch file runs fine if I call the serial version of the program.

Below is the actual script. Thoughts appreciated.

Nic out

#!/bin/bash
#SBATCH --job-name="nmode"
#SBATCH --output="nmode.out"
#SBATCH --partition=shared
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --export=ALL
#SBATCH -t 12:00:00

module load amber
module load openmpi_ib
module load mpi4py

cd $PWD

mpirun -np 4 $AMBERHOME/bin/MMPBSA.py.MPI -O -i nmode_mod.in\
-o nmode_6frames.dat\
-sp /home/csteussy/amber/mmpbsa/ref194na/complex-wat.top \
-srp /home/csteussy/amber/mmpbsa/ref194na/protein-wat.top \
-slp /home/csteussy/amber/mmpbsa/ref194na/ligand-wat.top \
-cp /home/csteussy/amber/mmpbsa/ref194na/complex.top \
-rp /home/csteussy/amber/mmpbsa/ref194na/protein.top \
-lp /home/csteussy/amber/mmpbsa/ref194na/ligand.top \
-y /home/csteussy/amber/mmpbsa/ref194na/complex_prodc.mdcrd.gz \
-yr /home/csteussy/amber/mmpbsa/ref194na/protein_prodc.mdcrd.gz \
-yl /home/csteussy/amber/mmpbsa/ref194na/ligand_prodc.mdcrd.gz

RE: Notes from the XSEDE BOF

2012-08-07T15:24:56Z

Thanks, Kate. The XSEDE 12 Science Cloud Birds of a Feather gathering generated a wealth of topics. Perhaps we could pick one juicy topic and start a thread here and invite people to share their experiences and insights on the subject.

Notes from the XSEDE BOF

2012-08-06T21:50:42Z

All,

I have been remiss in not posting the results of the XSEDE BOF until now.

First, here is a link to David Lifka's survey -- if you have cloud infrastructure needs or can describe such needs on behalf of communities you are working with, please fill out the survey:
https://cloudsurvey.cac.cornell.edu/default.aspx

Secondly, I attach a file with my raw notes from our discussion. If there are more challenges that you would like to highlight, please start a discussion here.

Science Cloud Summer School 2012: July 30 - August 3

2012-07-26T17:43:11Z

Science Cloud Summer School 2012

July 30 - August 3, 2012

10 participating sites

#ScienceCloudSummer

The Science Cloud Summer School targets education and training of graduate students and the fostering of a community around a topic that has increasing interest and relevance: the use of cloud computing technologies in science - including infrastructure-as-a-service and platform-as-a-service. Because cloud computing systems and technologies provide a considerable departure from traditional models and evolve at a rapid pace, this event would provide a basis for students to immerse in a focused, intensive curriculum to learn fundamentals and experiment with these technologies in practice. We will cover topics of interest to students with both application and computer science focus.

Science Cloud Summer School will be part of the Virtual School of Computational Science and Engineering’s (VSCSE) 2012 Summer School. VSCSE delivers innovative educational experiences on cutting-edge computational science topics to the next generation of graduate students in science and engineering.

Organizer: Geoffrey Fox, Indiana University
REGISTER NOW: https://hub.vscse.org/

For more information, please visit: http://sciencecloudsummer2012.tumblr.com/

Sponsors: FutureGrid, SalsaHPC, XSEDE, VSCSE

Wed. July 18 5:30pm XSEDE12 BOF: Cloud Computing for Science

2012-07-17T18:45:46Z

XSEDE 12 BOF: Cloud Computing for Science: Challenges and Opportunities

Wednesday July 18, 2012 5:30pm - 6:30pm @ Toledo 5th Floor

Kate Keahey, University of Chicago/Argonne National Laboratory, and Manish Parashar, Rutgers University

Abstract: Outsourcing compute infrastructure and services has many potential benefits to scientific projects: it offers access to sophisticated resources that may be beyond the means of a single institution to acquire, allows for more flexible usage patterns, creates potential for access to economies of scale via consolidation, and eliminates the overhead of system acquisition and operation for an institution allowing it to focus on its scientific mission. Cloud computing recently emerged as a promising paradigm to realize such outsourcing as it offers on-demand, short-term access, which allows users to flexibly manage peaks in demand, pay-as-you-go model, which helps save costs for bursty usage patterns (i.e., helps manage “valleys” in demand), and convenience, as users and institutions no longer have to maintain specialized IT departments. However, cloud computing brings with it also challenges as we seek to understand how to best leverage the paradigm.

Many scientific communities are experimenting with this new model, among others using FutureGrid resources and a testbed for initial exploration. The objective of this BOF is to focus discussion on experiences to date as well as define challenges and priorities in understanding how cloud computing can be best leveraged in the scientific context. We plan to discuss application patterns as well as highlight and discuss the priority of the current challenges and open issues in cloud computing for science. Specifically, we will discuss the following challenges. What types of applications are currently considered suitable for the cloud and what are the obstacles to enlarging that set? What is the state-of-the-art of cloud computing performance relative to scientific applications and how is it likely to change in the future? How would programming models have to change (or what new programming models need to be developed) to support scientific applications in the clouds? Given the current cloud computing offering, what middleware needs to be developed to enable scientific communities to leverage clouds? How does cloud computing change the potential for new attacks and what new security tools and mechanisms will be needed to support it? How can we facilitate transition to this new paradigm for the scientific community; what needs to be done/established first? Depending on the profile of attendance, we expect the last question in particular to form a substantial part of the discussion.

The BOF will be structured as follows. We will begin with a short structured talk session, led by the organizers, that will summarize and update several previous discussions on this topic, notably the MAGIC meetings in September, April and May as well as several parallel developments that took place in the scientific context such as the Magellan report, cloud-related experimentation status on the FutureGrid project, and application activity. The second session of the BOF will be devoted to the discussion, elaboration, and prioritization of the challenges listed above. Finally, we will address the prioritization and shape of concrete transition measures. The time allocated to the last two issues will depend on the structure of the attendance; if we can get feedback from XSEDE users we will emphasize the transition measures, if we attract CS practitioners we will focus on technical challenges.