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

2013-08-12 Thread Mark Abraham
Re-sending to list; original bounced when we had some issues with gmx-users over the weekend. Mark -- Forwarded message -- From: Mark Abraham Date: Sat, Aug 10, 2013 at 11:49 AM Subject: Re: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P To: prentice.bis

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

2013-08-09 Thread Prentice Bisbal
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 with 4.6.3, but that is the version I'll be working with from now on, since it's the latest. Since the problem occurs with both versions, might as well try to fix

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

2013-08-07 Thread Bogdan Costescu
On Wed, Aug 7, 2013 at 5:04 PM, Prentice Bisbal wrote: > I couldn't find anything explicit in the documentation, The compute node > kernel (CNK) is proprietary, but is said to be very Linux-like, so a signal > 6 should be the same as on Linux, which would be an abort signal. There are several cal

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

2013-08-07 Thread Prentice Bisbal
Bogdan, Prentice On 08/07/2013 05:51 AM, Bogdan Costescu wrote: Hi Prentice, The subject and first phrase mention version 4.6.3, but all scripts refer to 4.6.2. Are you sure you are not mixing versions ? Do you have another 4.6.x version working already ? Your correct - I'm working with vers

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

2013-08-07 Thread Prentice Bisbal
On 08/07/2013 10:35 AM, Prentice Bisbal wrote: Bogdan, Prentice On 08/07/2013 05:51 AM, Bogdan Costescu wrote: Hi Prentice, The subject and first phrase mention version 4.6.3, but all scripts refer to 4.6.2. Are you sure you are not mixing versions ? Do you have another 4.6.x version working

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

2013-08-07 Thread Bogdan Costescu
Hi Prentice, The subject and first phrase mention version 4.6.3, but all scripts refer to 4.6.2. Are you sure you are not mixing versions ? Do you have another 4.6.x version working already ? > -DCMAKE_C_FLAGS="-O3 -qarch=450d -qtune=450" \ Could you try with a lower optimization level ? > B

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

2013-08-06 Thread Mark Abraham
That all looks fine so far. The core file processor won't help unless you've compiled with -g. Hopefully cmake -DCMAKE_BUILD_TYPE=Debug will do that, but I haven't actually checked that really works. If not, you might have to hack cmake/Platform/BlueGeneP-static-XL-C.cmake. Anyway, if you can comp

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

2013-08-06 Thread Prentice Bisbal
Dear GMX-users, I need some assistance running Gromacs 4.6.3 on a Blue Gene/P. Although I have a background in Chemistry, I'm an experienced professional HPC admin who's relatively new to supporting Blue Genes and Gromacs. My first Gromacs user is having trouble running Gromacs on our BG/P. H