Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

2013-02-19 Thread Tomek Wlodarski
Hi, Thanks All for help. Now is working! Best! tomek On Tue, Feb 19, 2013 at 2:38 PM, Mark Abraham wrote: > but this I got also with gromacs 4.5.5 which is running ok so I think this > > > is not a problem in my case. > > > > Like Alexey notice the problem is that my nodes have different > >

Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

2013-02-19 Thread Mark Abraham
but this I got also with gromacs 4.5.5 which is running ok so I think this > is not a problem in my case. > > Like Alexey notice the problem is that my nodes have different > architecture.. but this was not a problem with gromacs 4.5.5 > Yes, that is expected. Probably both machines support SSE2,

Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

2013-02-19 Thread Richard Broadbent
Hi Tomek, Gromacs 4.6 uses very different accelerated kernels to 4.5.5. These are hardware specific and you must therefore select acceleration appropriate for your hardware. your login node will automatically use and select AVX-128-FMA acceleration. However, your compute nodes are considerab

Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

2013-02-19 Thread Bogdan Costescu
On Tue, Feb 19, 2013 at 1:32 PM, Tomek Wlodarski wrote: > The problem is that this is only message I got... But that's an important error. GROMACS 4.6 depends a lot on the compiler generated code, as opposed to 4.5 and previous which used hand-written assembler code. The build procedure detects t

Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

2013-02-19 Thread Tomek Wlodarski
Hi All, The problem is that this is only message I got... I also get this Warning: -- WARNING: Open MPI will create a shared memory backing file in a directory that appears to be mounted on a network filesystem. Creating the

Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

2013-02-17 Thread Alexey Shvetsov
Hi! В письме от 16 февраля 2013 23:27:45 пользователь Tomek Wlodarski написал: > Hi! > > I have problem in running gromacs 4.6 in PBS queue... > I end up with error: > > > [n370:03036] [[19430,0],0]-[[19430,1],8] mca_oob_tcp_msg_recv: readv > failed: Connection reset by peer (104) > --

Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

2013-02-17 Thread Mark Abraham
On Sat, Feb 16, 2013 at 11:27 PM, Tomek Wlodarski wrote: > Hi! > > I have problem in running gromacs 4.6 in PBS queue... > I end up with error: > > > [n370:03036] [[19430,0],0]-[[19430,1],8] mca_oob_tcp_msg_recv: readv > failed: Connection reset by peer (104) > ---

[gmx-users] Gromacs 4.6 crushes in PBS queue system

2013-02-16 Thread Tomek Wlodarski
Hi! I have problem in running gromacs 4.6 in PBS queue... I end up with error: [n370:03036] [[19430,0],0]-[[19430,1],8] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) -- mpirun noticed that process rank 1