Re: [gmx-users] mpi run in Gromacs

On 2/03/2011 11:37 PM, Erik Marklund wrote: Selina Nawaz skrev 2011-03-02 11.54: Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman website.

Re: [gmx-users] mpi run in Gromacs

Selina Nawaz skrev 2011-03-02 11.54: Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman website. I have set the system up in an NPT ensemble

[gmx-users] mpi run in Gromacs

Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman website. I have set the system up in an NPT ensemble using a semi-isotropic pressure coupli

RE: [gmx-users] mpi run in Gromacs 4.5.3

users Subject: Re: [gmx-users] mpi run in Gromacs 4.5.3 Te, Jerez A., Ph.D. wrote: > Hi Mark, > > Thank you for your reply. Just to confirm, mdrun_mpi is still being used in > Gromacs 4.5.3? The gromacs manual (Appendix A.5- Running Gromacs in parallel) > suggested using "mdrun -

Re: [gmx-users] mpi run in Gromacs 4.5.3

one, --enable-mpi. Obviously you need a correctly-configured MPI compiler and environment for it to work Mark Thanks, JT -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Mon 12/13/2010 4:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users]

Re: [gmx-users] mpi run in Gromacs 4.5.3

ing support, the -nt option will be printed if you issue mdrun -h. -Justin Thanks, JT -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Mon 12/13/2010 4:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mpi run in Gromacs 4.5.3 O

RE: [gmx-users] mpi run in Gromacs 4.5.3

ROMACS users Subject: Re: [gmx-users] mpi run in Gromacs 4.5.3 On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote: > > Hi, > I have been trying to run Gromacs 4.5.3 parallel simulations using > openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this > version of Gromacs. &g

Re: [gmx-users] mpi run in Gromacs 4.5.3

On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote: Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version of Gromacs. I don't understand what (you think) you mean. You can use thread-based paralleli

[gmx-users] mpi run in Gromacs 4.5.3

Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version of Gromacs. Our system administrator told me that all mpi related options have been turned on while installing Gromacs. With either commands: mdrun -

Re: RE: [gmx-users] mpi run

- Original Message - From: #ZHAO LINA# Date: Thursday, July 8, 2010 18:53 Subject: RE: [gmx-users] mpi run To: Discussion list for GROMACS users P {margin-top:0;margin-bottom:0;} --- | > During your installation, if

RE: [gmx-users] mpi run

: Discussion list for GROMACS users Subject: Re: [gmx-users] mpi run Hi Mahmoud, for anyone to be able to help you, you need to provide a lot more information, at least: - which mpi library are you using? - how did you compile and/or install Gromacs? - what commands do you use to run mdrun and what was the

Re: [gmx-users] mpi run

Hi Mahmoud, for anyone to be able to help you, you need to provide a lot more information, at least: - which mpi library are you using? - how did you compile and/or install Gromacs? - what commands do you use to run mdrun and what was the output of it? Best, Carsten On Jul 8, 2010, at 9:41 AM

[gmx-users] mpi run

Dear GMX Users, I have a PC with 4 CPU, but the Gromacs only use one CPU. the command of mpiru works on linux; however, the command of mdrun_mpi does not work. Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4 Many thanks, Mahmoud -- gmx-users mailing listgmx

Re: [gmx-users] mpi-run

nanogroup wrote: Dear GMX Users, I want to run Gromacs on a multiprocessor PC. The MPI files are correctly installed and the gromacs is also configured. However, at the end of configuration section, an Error appears that the FFTW can not be found! Indeed, the FFTW is already installed but

[gmx-users] mpi-run

Dear GMX Users, I want to run Gromacs on a multiprocessor PC. The MPI files are correctly installed and the gromacs is also configured. However, at the end of configuration section, an Error appears that the FFTW can not be found! Indeed, the FFTW is already installed but the configuration can