[gmx-users] low latency

Dear Karsten and gromacs specialists I enabled flow control on hp procurve now I want to know how I can config low latency on the network ?is it required? thank you ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] flow control

hello I followed Karsten instructions for enabling flow control on HP procurve Gigabit switch but the cpu usages are still lower than 50%. do you have some comments for increasing cpu usages ___ gmx-users mailing list

Re: [gmx-users] dear KUTZNER (flow control)

--- On Fri, 1/2/09, Carsten Kutzner ckut...@gwdg.de wrote: From: Carsten Kutzner ckut...@gwdg.de Subject: Re: [gmx-users] dear KUTZNER (flow control) To: greencom...@yahoo.com, Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, January 2, 2009, 5:27 PM Dear Ha Salem

[gmx-users] dear KUTZNER (flow control)

dear Dr kutzner you showed flow control on HP procurve flow control prevents network congestion,I want know is this feature(flow control) is active by default or we must do some configuration on this switch thank you ___ gmx-users mailing list

[gmx-users] parallel run

Hello I want to know suitable speed of network for parallel run I heard 1Giagabit Network is not enough and I havnt good performance at 1Gigabit , thank you ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] quad cpu

I searched the mailing list and I found some reports about low performance of intel core2 quad cpus in parallel mode I have the same problem and I see low cpu usage(intel core2 quad)in parallel run. do you have some solution or comment for this problem of intel quad cpus? thank you

Re: [gmx-users] quad cpu

PM ha salem wrote: I have gromacs 4 and this problem still exist OK, can you be more specific in this case? If you run the benchmark like d.dppc you should get at least 90% scaling I would think. --- On Thu, 12/4/08, David van der Spoel [EMAIL PROTECTED] wrote: From: David van der

[gmx-users] cpu parallel

Dear Users I have 2 computer,each mashine has 1 core2quad cpu. I have installed lamm 7,when I run mdrun -np4 on 1 machine cpu usage of 4 cores is over 90% and its s faster than single mode but when I run mdrun on 2 machines ,cpu usage of cores is about 30% and it doesnt get more speed can you

[gmx-users] (no subject)

Dear Users I have 2 computer,each mashine has 1 core2quad cpu. I have installed lamm 7,when I run mdrun -np4 on 1 machine cpu usage of 4 cores is over 90% and its s faster than single mode but when I run mdrun on 2 machines ,cpu usage of cores is about 30% and it doesnt get more speed can you

[gmx-users] QMMM

hello I want install gromacs with gamess US for QMMM can you guide me for installation procedure thank you ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] low cpu usage

Dear users my gromacs is 3.3.3 my cpus are intel core2quad 2.4 GHz and my mpi is LAM 7.0.6 I can get the cpu usage of 4 cores on one node but when I run on 2 node the cpu usage of cores is low I have installed gromacs with these instructions Compile LAM 7 ./configure

[gmx-users] Low CPU usage multicore

Dear Users my multi-core cpus usage are low in parallel run,when I run on 1 cpu all of core have 90% usage but when I run on 2 nodes (every one has 1 multicore cpu) the cpu usage is low its about 2 month I cant solve this problem thank you ___

[gmx-users] mpirun problem

dear users I have encouneterd a problem with mpirun I have 2 pc (every pc has 1 intel quad core cpu) ,when I run mdrun on 1 machine with  -np 4 option the calculation run on 4 cores and goes faster ,system monitor show all 4 cores of this cpu are working every core has 90%

[gmx-users] run parallel

dear user my molecule is HSA it has about 12 atoms its not small I run the calculation with nbsp;mpirun -np 4 /usr/local/share/gromacs_331/bin/mdrun -f topol.tprnbsp; o md.trr -c md_out.gro -e md.edr -g md.log amp; then I run top and I see 4 cores are working but the time of calculation is