[gmx-users] mdrun with mpich

Itamar Kass ikass at cc.huji.ac.il
Thu Feb 2 07:12:01 CET 2006

Why not using fortan?
install it using Fink and let lam have it.


| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585194
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Net: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
  ----- Original Message ----- 
  From: Pradeep Kota 
  To: Discussion list for GROMACS users 
  Sent: Thursday, February 02, 2006 4:43 AM
  Subject: [gmx-users] mdrun with mpich

  Dear users,
      I have compiled gromacs on our dual core mac os x G5 cluster, and tried running a simulation on a 540 residue protein for 1 ns on 8 processors. i used mpich as the mpi environment for parallelising gromacs. it worked fine, and the job was split properly and assigned to nodes. now, the cpu usage per processor is not more than 50% on any of the processors. and the total running time for this was 13hrs. though output is written properly onto the specified output file, mdirun doesnot terminate even after running through all the steps. it still shows two mdrun_mpi processes running on the head node, with a 0% cpu usage. was going through gmx-users mailing list and somehow figured out that mpich is not a good idea for running gromacs. so, i wanted to switch over to lam. now when i complie gromacs using lam, it is not able to link the libraries properly. so, i tried reinstalling lam on my cluster. now, lam keeps complaining about not being able to find a fortran compiler. i should not need a fortran compiler unless i'm using SUN or SGI for this purpose..(am i going wrong here?). what flags do i need to compile lam with, in order to compile gromacs successfully? any help is very much appreciated..
  thanks in advance,


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