Re: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P

Nope. Need a back trace. Mark On Mar 13, 2014 4:59 AM, "arrow50311" wrote: > Hi, > > Gromacs 4.0.7 is different story, and I did not test it with the same > system > though. > > The job script is as follows > > #@ job_name = job4.6 > #@ comment = "Hello World Job" > #@ error = $(job_name).$(jobi

Re: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P

Hi, Gromacs 4.0.7 is different story, and I did not test it with the same system though. The job script is as follows #@ job_name = job4.6 #@ comment = "Hello World Job" #@ error = $(job_name).$(jobid).err #@ output = $(job_name).$(jobid).out #@ environment = COPY_ALL #@ wall_clock_limit = 10:00

Re: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P

I've run gromacs v4.6.3 on BG/Q without problem and my colleagues have run older versions of gromacs on the BG/L also without problem. (No BG/P experience here, unfortunately). Still, it's worth having you post your job submission script for us to take a look at. Also, is it just gromacs 4.6.2

Re: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P

The real problem cannot be diagnosed without a valid stack trace from the core file. No GROMACS developers have access to such a machine, so any resolution is up to you guys providing the information. Mark On Mar 12, 2014 10:44 PM, "arrow50311" wrote: > Is there any follow-up for this question?

Re: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P

Is there any follow-up for this question? I met with exactly the same problem on Bluegene/P. Could anyone offer a help? Thank you, Prentice Bisbal wrote > Mark, > > Since I was working with 4.6.2, I built 4.6.3 to see if this was the > result of a bug in 4.6.2. It isn't I get the same error

Re: [gmx-users] GPU problem

Hi, As the message says, you need at least one MPI process doing PP per GPU, so you need to arrange your MPI to have more than one process if you want to use both GPUs. Depending on your simulation and hardware, you may do better with any even number of processes, corresponding OpenMP setup, and m

[gmx-users] GPU problem

Hi users, I would like to run my job on gpu. I have compiled gromacs version 4.6.1 with cuda 5 in parallel, have changed cutoff scheme to verlet and generated new *.tpr and finally running: mdrun -v -deffnm md I can see following lines in my output: changing nstlist from 5 to 40, rlist from 1 to

Re: [gmx-users] Dubious results with NPT

On 3/12/14, 7:51 AM, sujithkakkat . wrote: Hello, After a while I got back to the problem posted here. This issue was the large value for average pressure(~25 bar against the reference pressure of 1 bar) in NPT simulations with parrinello rahman barostat. The system studied is cyclohexane-w

Re: [gmx-users] Regarding calculation of torsion angles in DNA

On 3/12/14, 1:37 AM, Sathish Kumar wrote: Hai I am trying to calculate torsional angles in DNA, for that first I made angle.ndx file by using mk_angndx -f prod.tpr -n angle.ndx -type dihedral the out put angle.ndx is looks like as following [ Phi=0.0_3_1.31 ] 12 2 3

Re: [gmx-users] Dubious results with NPT

Hello, After a while I got back to the problem posted here. This issue was the large value for average pressure(~25 bar against the reference pressure of 1 bar) in NPT simulations with parrinello rahman barostat. The system studied is cyclohexane-water system with an interface. The forcefield is

Re: [gmx-users] FW: error after 1ns of md run during production

On Wed, Mar 12, 2014 at 4:05 AM, Sucharita Dey wrote: > I have done the subscription, hope my email will be accepted. > > Sucharita Dey,PhD, Research Fellow, Cancer Science Institute of Singapore, > National University of Singapore. 14, Medical Drive, #12-01, Singapore > 117599. Tel: (65) 903552

Re: [gmx-users] surprising: what's the reason?

Sounds like a normal case of being too rough with a system during equilibration, which can lead to http://www.gromacs.org/Documentation/Terminology/Blowing_Up if you get unlucky. There's general advice there. Mark On Wed, Mar 12, 2014 at 7:05 AM, Chetan Mahajan wrote: > Hi Tsjerk, > > Thanks. I

Re: [gmx-users] Thread affinity error when Running Gromacs 4.6.3 on Bluegene/P

On Wed, Mar 12, 2014 at 9:56 AM, Szilárd Páll wrote: > That's a "normal" side-effect of mdrun trying to set thread affinities > [1] on a platform which does not support this. Also, this is not an > error, mdrun should have continued to run. > Indeed. To find the function in which the actual probl

Re: [gmx-users] Single or Double precision?

True, if it's 4.6. If it's earlier, you will need to run mdrun and inspect the log file. Mark On Wed, Mar 12, 2014 at 9:44 AM, Szilárd Páll wrote: > Check the version header, it contain a "Precision" field (e.g. mdrun > -version). > -- > Szilárd > > > On Wed, Mar 12, 2014 at 9:03 AM, Dario Corr

Re: [gmx-users] Thread affinity error when Running Gromacs 4.6.3 on Bluegene/P

That's a "normal" side-effect of mdrun trying to set thread affinities [1] on a platform which does not support this. Also, this is not an error, mdrun should have continued to run. Note that you would be much better off with upgrading to the latest version, there have been many improvements, espe

Re: [gmx-users] Single or Double precision?

Check the version header, it contain a "Precision" field (e.g. mdrun -version). -- Szilárd On Wed, Mar 12, 2014 at 9:03 AM, Dario Corrada wrote: > How I can check if a packaged version of GROMACS (such as those available > from Fedora or Ubuntu repositories) has been pre-compiled with single or

[gmx-users] Single or Double precision?

How I can check if a packaged version of GROMACS (such as those available from Fedora or Ubuntu repositories) has been pre-compiled with single or double precision? -- Dario CORRADA, PhD Bioinformatics and Computational Chemistry specialist URL..: http://it.linkedin.com/in/dariocorrada/ ma