RE: [gmx-users] memory requirements
Hi Erik, Many thanks-it would be good to have the capabilities to simulate big systems so will go for 1GB per core. -Syma *** Dr Syma Khalid RCUK Fellow (Chemical Biology) School of Chemistry University of Southampton Highfield Southampton phone: (0)2380-594176 SO17 1BJ email: [EMAIL PROTECTED] U.K. *** -Original Message- From: Erik Lindahl [mailto:[EMAIL PROTECTED] Sent: 20 February 2008 22:51 To: [EMAIL PROTECTED]; Discussion list for GROMACS users Subject: Re: [gmx-users] memory requirements Hi, On Feb 20, 2008, at 10:42 PM, Syma Khalid wrote: > > I am about to buy some compute nodes for a mini-cluster (mainly for > running > gromacs simulations). > I have just been asked: > 'One factor that needs to be considered is how much memory should be > supplied per node, I suspect the choice is between 4GB & 8GB per > node (ie. > 0.5 or 1 GB per processor-core for an 8 processor-core node).' > > by our HPC technicians. Any advice as to which I should go for, the > 4 or 8 > GB version? It depends on the type of molecules you intend to simulate. If it's going to be small systems (tens of thousands of atoms) you should be fine with 512MB per core, but for more general stuff I'd go with 1GB per core (that's what we recently ordered). Since a bit of memory will be used by the OS, file system buffers, and executables I would guess the memory "available" to simulation data would be a factor ~3 higher in the latter case. Cheers, Erik Erik Lindahl <[EMAIL PROTECTED]> Backup: <[EMAIL PROTECTED]> Assistant Professor, Computational Structural Biology Center for Biomembrane Research, Dept. Biochemistry & Biophysics Stockholm University, SE-106 91 Stockholm, Sweden Tel: +46(0)8164675 Mobile: +46(0)704218767 Fax: mail a PDF instead ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] memory requirements
Hi, On Feb 20, 2008, at 10:42 PM, Syma Khalid wrote: I am about to buy some compute nodes for a mini-cluster (mainly for running gromacs simulations). I have just been asked: 'One factor that needs to be considered is how much memory should be supplied per node, I suspect the choice is between 4GB & 8GB per node (ie. 0.5 or 1 GB per processor-core for an 8 processor-core node).' by our HPC technicians. Any advice as to which I should go for, the 4 or 8 GB version? It depends on the type of molecules you intend to simulate. If it's going to be small systems (tens of thousands of atoms) you should be fine with 512MB per core, but for more general stuff I'd go with 1GB per core (that's what we recently ordered). Since a bit of memory will be used by the OS, file system buffers, and executables I would guess the memory "available" to simulation data would be a factor ~3 higher in the latter case. Cheers, Erik Erik Lindahl <[EMAIL PROTECTED]> Backup: <[EMAIL PROTECTED]> Assistant Professor, Computational Structural Biology Center for Biomembrane Research, Dept. Biochemistry & Biophysics Stockholm University, SE-106 91 Stockholm, Sweden Tel: +46(0)8164675 Mobile: +46(0)704218767 Fax: mail a PDF instead ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] memory requirements
Hi, I am about to buy some compute nodes for a mini-cluster (mainly for running gromacs simulations). I have just been asked: 'One factor that needs to be considered is how much memory should be supplied per node, I suspect the choice is between 4GB & 8GB per node (ie. 0.5 or 1 GB per processor-core for an 8 processor-core node).' by our HPC technicians. Any advice as to which I should go for, the 4 or 8 GB version? Any advice would be greatly appreciated. Best wishes, -Syma *** Dr Syma Khalid RCUK Fellow (Chemical Biology) School of Chemistry University of Southampton Highfield Southampton phone: (0)2380-594176 SO17 1BJ email: [EMAIL PROTECTED] U.K. *** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
