Re: [gmx-users] em mdrun

2011-02-24 Thread Justin A. Lemkul
Nick wrote: Hello Justin, I forgot to say that with 16 nodes I am getting message below. I search the list and used -pd option but it takes much much loner than one processor! Some systems just don't scale particularly well. --- Progr

Re: [gmx-users] em mdrun

2011-02-24 Thread Nick
Hello Justin, I forgot to say that with 16 nodes I am getting message below. I search the list and used -pd option but it takes much much loner than one processor! --- Program mdrun, VERSION 4.5.3 Source code file: domdec.c, line: 6428 Fatal er

Re: [gmx-users] em mdrun

2011-02-24 Thread Nick
Dear Justin, I tried one processor and it worked but with 16 nodes I get no output but the one I posted in previous message. I thought using 16 nodes should speed up calculations ! Another thing I am cusious about is that, in version 4.0.7 I could run my simulations but with the latest version a l

Re: [gmx-users] em mdrun

2011-02-24 Thread Justin A. Lemkul
Nick wrote: Hello all, When I issue mdrun program for EM altough this is not a parallel simulation, 6 nodes are getting involved. I am using 4.5.3 and get the error: Reading file em-l0.5.tpr, VERSION 4.5.3 (single precision) Starting 16 threads Does anyone have idea why is this happening

[gmx-users] em mdrun

2011-02-24 Thread Nick
Hello all, When I issue mdrun program for EM altough this is not a parallel simulation, 6 nodes are getting involved. I am using 4.5.3 and get the error: Reading file em-l0.5.tpr, VERSION 4.5.3 (single precision) Starting 16 threads Does anyone have idea why is this happening? Thanks -- gmx-